WorldWideScience

Sample records for hetc-3step included fragmentation

  1. HETC-3STEP included fragmentation process

    Energy Technology Data Exchange (ETDEWEB)

    Shigyo, Nobuhiro; Iga, Kiminori; Ishibashi, Kenji [Kyushu Univ., Fukuoka (Japan). Faculty of Engineering

    1997-03-01

    High Energy Transport Code (HETC) based on the cascade-evaporation model is modified to calculate the fragmentation cross section. For the cascade process, nucleon-nucleon cross sections are used for collision computation; effective in-medium-corrected cross sections are adopted instead of the original free-nucleon collision. The exciton model is adopted for improvement of backward nucleon-emission cross section for low-energy nucleon-incident events. The fragmentation reaction is incorporated into the original HETC as a subroutine set by the use of the systematics of the reaction. The modified HETC (HETC-3STEP/FRG) reproduces experimental fragment yields to a reasonable degree. (author)

  2. Proton induced nuclide production cross section by HETC-3STEP/FRG-R

    Energy Technology Data Exchange (ETDEWEB)

    Shigyo, Nobuhiro; Ishibashi, Kenji [Kyushu Univ., Fukuoka (Japan); Yoshizawa, Nobuaki; Takada, Hiroshi

    1998-03-01

    High Energy Transport Code (HETC) based on the intranuclear-cascade-evaporation model is modified to calculate the fragmentation cross section. The exciton model is adopted for improvement of backward nucleon-emission cross section for low-energy nucleon-incident events. The level density parameter depending on the excitation energy is taken in the evaporation process. The fragmentation reaction is incorporated into HETC as a subroutine set by the use of the systematics of the reaction. The modified HETC (HETC-3STEP/FRG-R) reproduces experimental fragment yields to a reasonable degree. (author)

  3. Fragmentation of positronium in collision with Li ion including ...

    Indian Academy of Sciences (India)

    Abstract. Fragmentation of ground state ortho-positronium (Ps) in collision with Li ion (Li+) is studied in the framework of post-collisional Coulomb distorted eikonal ap- proximation (CDEA), giving special emphasis on the dynamics of the electron loss to the continuum (ELC) that occurs when the electron (e) and the positron ...

  4. The C5 Variant of the Butyrylcholinesterase Tetramer Includes a Noncovalently Bound 60 kDa Lamellipodin Fragment.

    Science.gov (United States)

    Schopfer, Lawrence M; Delacour, Hervé; Masson, Patrick; Leroy, Jacqueline; Krejci, Eric; Lockridge, Oksana

    2017-06-29

    Humans with the C5 genetic variant of butyrylcholinesterase (BChE) have 30-200% higher plasma BChE activity, low body weight, and shorter duration of action of the muscle relaxant succinylcholine. The C5 variant has an extra, slow-moving band of BChE activity on native polyacrylamide gel electrophoresis. This band is about 60 kDa larger than wild-type BChE. Umbilical cord BChE in 100% of newborn babies has a C5-like band. Our goal was to identify the unknown, 60 kDa protein in C5. Both wild-type and C5 BChE are under the genetic control of two independent loci, the BCHE gene on Chr 3q26.1 and the RAPH1 (lamellipodin) gene on Chr 2q33. Wild-type BChE tetramers are assembled around a 3 kDa polyproline peptide from lamellipodin. Western blot of boiled C5 and cord BChE showed a positive response with an antibody to the C-terminus of lamellipodin. The C-terminal exon of lamellipodin is about 60 kDa including an N-terminal polyproline. We propose that the unknown protein in C5 and cord BChE is encoded by the last exon of the RAPH1 gene. In 90% of the population, the 60 kDa fragment is shortened to 3 kDa during maturation to adulthood, leaving only 10% of adults with C5 BChE.

  5. Fragmentation study of iridoid glycosides including epimers by liquid chromatography-diode array detection/electrospray ionization mass spectrometry and its application in metabolic fingerprint analysis of Gardenia jasminoides Ellis.

    Science.gov (United States)

    Zhou, Tingting; Liu, Hua; Wen, Jun; Fan, Guorong; Chai, Yifeng; Wu, Yutian

    2010-09-15

    A high-performance liquid chromatography-diode array detection/electrospray ionization mass spectrometry (HPLC-DAD/ESI-MS) method was applied to the characterization of ten iridoid glycosides in Gardenia jasminoides Ellis, a traditional Chinese medicine. During the process of structural elucidation, two groups of isomers including two epimers were structurally characterized and differentiated according to their distinctive fragmentation patterns which were closely related to their isomeric differentiations. Subsequently, the major compounds were purified by multi-dimensional chromatography and semi-preparative HPLC and the structure identification was confirmed with NMR techniques. The major fragmentation pathways of iridoid glycosides in Gardenia jasminoides Ellis obtained through the MS data were schemed systematically, which provided the best sensitivity and specificity for characterization of the iridoid glycosides especially the isomers so far. Based on the fragmentation patterns of iridoid glycosides concluded, seven major iridoid glycosides were characterized in rat plasma after intravenous administration of Gardenia jasminoides Ellis. Copyright 2010 John Wiley & Sons, Ltd.

  6. Measurement of Fragmentation Products including Angular Distributions for 3, 5, and 10 GeV/A C and Si on several nuclear targets at the AGS

    CERN Document Server

    Pinsky, L; Broggi, F; Brugger, M; Campanella, M; Carboni, M; Cerutti, F; Colleoni, P; Crystl, M; D'Ambrosio, C; Elkhayari, N; Empl, A; Fassó, A; Ferrari, A; Ferrari, A; Gadioli, E; Garzelli, M V; Geutersloh, S; Heilbronn, L; Lantz, M; Lebourgeois, M; Lee, K T; Lukasik, G; Mairani, A; Margiotta, A; Mayes, B; Miller, J; Morone, M C; Mostacci, A; Muraro, S; Parodi, K; Patera, V; Pelliccioni, M; Ranft, J; Reddell, B; Roesler, S; Rollet, S; Sala, P R; Sarchiapone, L; Sioli, M; Smirnov, G; Sommerer, F; Theis, C; Trovati, S; Villari, R; Vinke, H; Vlachoudis, V; Vollaire, J; Wilson, T; Zapp, N; Zeitlin, C

    2010-01-01

    Motivated by differences in the predicted fragmentation of heavy ions at energies around 5 GeV/A as employed in the event generators used by the FLUKA Monte Carlo Code [1], a set of measurements were carried out at the AGS facility at the Brookhaven National Laboratory to determine as much information as possible about the cross sections to allow harmonization of those event generators for these incident lab energies. The FLUKA Code employs the RQMD event generator of Sorge [2] for heavy ion interactions starting at 100 MeV/A and extending into the region around 5 GeV/A. Above those energies the DPMJET code of Ranft and Roesler [3] is typically employed to simulate such interactions. The detailed predictions of these event generators had some disagreement in the vicinity of this crossover energy and in order to tune these codes to be in closer harmony at the transition, and of course to be simulating nature as closely as possible, data were taken at 3, 5 and 10 GeV/A with beams of Fe, Si and C on a variety of...

  7. Process Fragments

    Science.gov (United States)

    Eberle, Hanna; Unger, Tobias; Leymann, Frank

    The concepts presented in this paper are motivated by the assumption that process knowledge is distributed knowledge and not completely known just by one person. Driven by this assumption we deal in this paper with the following questions: How can partial process knowledge be represented? How can this partial knowledge be used to define something more complete? To use higher level artefacts as building blocks to new applications has a long tradition in software engineering to increase flexibility and reduce modeling costs. In this paper we take a first step in applying this concept to processes, by defining process building blocks and operations which compose process building blocks. The building blocks will be referred to as process fragments in the following. The process fragment composition may take place either at design or runtime of the process. The design time approach reduces design costs by reusing artefacts. However the runtime fragment composition approach realizes high flexibility due to the possibility in the dynamic selection of the fragments to be composed. The contribution of this work lies in a fragment definition that enables the fragment modeler to represent his 'local' and fragmentary knowledge in a formal way and which allows fragment models to be composed.

  8. Chameleon fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    Brax, Philippe [Institut de Physique Théorique, CEA, IPhT, CNRS, URA 2306, F-91191Gif/Yvette Cedex (France); Upadhye, Amol, E-mail: philippe.brax@cea.fr, E-mail: aupadhye@anl.gov [Institute for the Early Universe, Ewha University, International Education, Building #601, 11-1, Daehyun-Dong Seodaemun-Gu, Seoul 120-750 (Korea, Republic of)

    2014-02-01

    A scalar field dark energy candidate could couple to ordinary matter and photons, enabling its detection in laboratory experiments. Here we study the quantum properties of the chameleon field, one such dark energy candidate, in an ''afterglow'' experiment designed to produce, trap, and detect chameleon particles. In particular, we investigate the possible fragmentation of a beam of chameleon particles into multiple particle states due to the highly non-linear interaction terms in the chameleon Lagrangian. Fragmentation could weaken the constraints of an afterglow experiment by reducing the energy of the regenerated photons, but this energy reduction also provides a unique signature which could be detected by a properly-designed experiment. We show that constraints from the CHASE experiment are essentially unaffected by fragmentation for φ{sup 4} and 1/φ potentials, but are weakened for steeper potentials, and we discuss possible future afterglow experiments.

  9. Rock fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    Brown, W.S.; Green, S.J.; Hakala, W.W.; Hustrulid, W.A.; Maurer, W.C. (eds.)

    1976-01-01

    Experts in rock mechanics, mining, excavation, drilling, tunneling and use of underground space met to discuss the relative merits of a wide variety of rock fragmentation schemes. Information is presented on novel rock fracturing techniques; tunneling using electron beams, thermocorer, electric spark drills, water jets, and diamond drills; and rock fracturing research needs for mining and underground construction. (LCL)

  10. Bespoke Fragments

    DEFF Research Database (Denmark)

    Kruse Aagaard, Anders

    2017-01-01

    The PhD project Bespoke Fragments is investigating the space emerging in the exploration of the relationship between digital drawing and fabrication, and the field of materials and their properties and capacities. Through a series of different experiments, the project situates itself in a shuttling...... tangible experiments, the project discusses materiality and digitally controlled fabrication tools as a expansion of the architect’s tool box and workflow. Bespoke Fragments considers this expansion as an opportunity to establish a connection between forms of digital drawing and the specificities...... of materials. Through that connection, the project seeks to use the realisation to generate developments and findings and, through an iterative mode of thinking, establish a dialogue between drawing, materials, and fabrication. The use of digital fabrication tools through digital drawing opens up a new...

  11. Architectural fragments

    DEFF Research Database (Denmark)

    Bang, Jacob Sebastian

    2018-01-01

    . I try to invent the ways of drawing the models - that decode and unfold them into architectural fragments- into future buildings or constructions in the landscape. [1] Luigi Moretti: Italian architect, 1907 - 1973 [2] Man Ray: American artist, 1890 - 1976. in 2015, I saw the wonderful exhibition......I have created a large collection of plaster models: a collection of Obstructions, errors and opportunities that may develop into architecture. The models are fragments of different complex shapes as well as more simple circular models with different profiling and diameters. In this contect I have...... been studying Luigi Moretti's [1] plastermodel - "the Model of the inner spaces of the Saint Maria of the Divine Providence" - in which context I see my own models. In 1934, Man Ray [2] photographed mathematical rmodels (in plaster) at the Henri Poincaré Institute in Paris and later used...

  12. Fragmentation based

    Directory of Open Access Journals (Sweden)

    Shashank Srivastava

    2014-01-01

    Gaining the understanding of mobile agent architecture and the security concerns, in this paper, we proposed a security protocol which addresses security with mitigated computational cost. The protocol is a combination of self decryption, co-operation and obfuscation technique. To circumvent the risk of malicious code execution in attacking environment, we have proposed fragmentation based encryption technique. Our encryption technique suits the general mobile agent size and provides hard and thorny obfuscation increasing attacker’s challenge on the same plane providing better performance with respect to computational cost as compared to existing AES encryption.

  13. Bespoke Fragments

    DEFF Research Database (Denmark)

    Kruse Aagaard, Anders

    2016-01-01

    the digital environment with the reality of materials – and use realisation and materialisation to generate architectural developments and findings through an iterative mode of thinking about the dialogue between drawing, materials and fabrication. The control of fabrication tools through digital drawing......The Ph.D. -project Bespoke Fragments seeks to explore and utilise the space emerging between the potentials of digital drawing and fabrication and the field of materials and their properties and capacities. Within this span, the project is situated in a shuttling between the virtual and the actual......, investigating levels of control and uncertainty encountering with these. Through tangible experiments, the project discusses materiality and digitally controlled fabrications tools as direct expansions of the architect's digital drawing and workflow. The project sees this expansion as an opportunity to connect...

  14. Framing Fragmentation

    DEFF Research Database (Denmark)

    Bundgaard, Charlotte

    2009-01-01

    Contemporary industrialized architecture based on advanced information technology and highly technological production processes, implies a radically different approach to architecture than what we have experienced in the past. Works of architecture composed of prefabricated building components......, contain distinctive architectural traits, not only based on rational repetition, but also supporting composition and montage as dynamic concepts. Prefab architecture is an architecture of fragmentation, individualization and changeability, and this sets up new challenges for the architect. This paper...... tries to develop a strategy for the architect dealing with industrially based architecture; a strategy which exploits architectural potentials in industrial building, which recognizes the rules of mass production and which redefines the architect’s position among the agents of building. If recent...

  15. METHOD FOR CONTROLLING FRAGMENTATION OF DRIED FOOD DURING COMPRESSION

    Science.gov (United States)

    readily with little fragmentation to original characteristics. Examination included 15 food types. Measurement of fragmentation is described. Storage stability is reported. A progress flow chart is included.

  16. Fragmentation and Hadronization

    OpenAIRE

    Webber, B.R.

    1999-01-01

    Experimental data, theoretical ideas and models concerning jet fragmentation and the hadronization process are reviewed, concentrating on the following topics: factorization and small-x resummation of fragmentation functions, hadronization models, single-particle yields and spectra in Z decay, comparisons between quark and gluon jets, current and target fragmentation in deep inelastic scattering, heavy quark fragmentation, Bose-Einstein correlations and WW fragmentation.

  17. Fragmentation and Hadronization

    OpenAIRE

    Webber, B.R.

    2000-01-01

    Experimental data, theoretical ideas and models concerning jet fragmentation and the hadronization process are reviewed, concentrating on the following topics: factorization and small-x resummation of fragmentation functions, hadronization models, single-particle yields and spectra in Z decay, comparisons between quark and gluon jets, current and target fragmentation in deep inelastic scattering, heavy quark fragmentation, Bose-Einstein correlations and WW fragmentation.

  18. Mass spectrometry for fragment screening.

    Science.gov (United States)

    Chan, Daniel Shiu-Hin; Whitehouse, Andrew J; Coyne, Anthony G; Abell, Chris

    2017-11-08

    Fragment-based approaches in chemical biology and drug discovery have been widely adopted worldwide in both academia and industry. Fragment hits tend to interact weakly with their targets, necessitating the use of sensitive biophysical techniques to detect their binding. Common fragment screening techniques include differential scanning fluorimetry (DSF) and ligand-observed NMR. Validation and characterization of hits is usually performed using a combination of protein-observed NMR, isothermal titration calorimetry (ITC) and X-ray crystallography. In this context, MS is a relatively underutilized technique in fragment screening for drug discovery. MS-based techniques have the advantage of high sensitivity, low sample consumption and being label-free. This review highlights recent examples of the emerging use of MS-based techniques in fragment screening. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  19. An Archeology of Fragments

    Directory of Open Access Journals (Sweden)

    Gerald L. Bruns

    2014-10-01

    Full Text Available This is a short (fragmentary history of fragmentary writing from the German Romantics (F. W. Schlegel, Friedrich Hölderlin to modern and contemporary concrete or visual poetry. Such writing is (often deliberately a critique of the logic of subsumption that tries to assimilate whatever is singular and irreducible into totalities of various categorical or systematic sorts. Arguably, the fragment (parataxis is the distinctive feature of literary Modernism, which is a rejection, not of what precedes it, but of what Max Weber called “the rationalization of the world” (or Modernity whose aim is to keep everything, including all that is written, under surveillance and control.

  20. Exact Solutions of Fragmentation Equations with General Fragmentation Rates and Separable Particles Distribution Kernels

    Directory of Open Access Journals (Sweden)

    S. C. Oukouomi Noutchie

    2014-01-01

    Full Text Available We make use of Laplace transform techniques and the method of characteristics to solve fragmentation equations explicitly. Our result is a breakthrough in the analysis of pure fragmentation equations as this is the first instance where an exact solution is provided for the fragmentation evolution equation with general fragmentation rates. This paper is the key for resolving most of the open problems in fragmentation theory including “shattering” and the sudden appearance of infinitely many particles in some systems with initial finite particles number.

  1. INTERMITTENCY, A TEST FOR STRING FRAGMENTATION PROCESSES

    NARCIS (Netherlands)

    SCHOLTEN, O

    The Artru-Mennessier and the string fragmentation procedure as implemented in the code VENUS have been compared. The two fragmentation prescriptions predict a similar rapidity spectrum including its energy dependence and event multiplicities, but give rise to very different intermittency results.

  2. Fragmentation trees reloaded.

    Science.gov (United States)

    Böcker, Sebastian; Dührkop, Kai

    2016-01-01

    Untargeted metabolomics commonly uses liquid chromatography mass spectrometry to measure abundances of metabolites; subsequent tandem mass spectrometry is used to derive information about individual compounds. One of the bottlenecks in this experimental setup is the interpretation of fragmentation spectra to accurately and efficiently identify compounds. Fragmentation trees have become a powerful tool for the interpretation of tandem mass spectrometry data of small molecules. These trees are determined from the data using combinatorial optimization, and aim at explaining the experimental data via fragmentation cascades. Fragmentation tree computation does not require spectral or structural databases. To obtain biochemically meaningful trees, one needs an elaborate optimization function (scoring). We present a new scoring for computing fragmentation trees, transforming the combinatorial optimization into a Maximum A Posteriori estimator. We demonstrate the superiority of the new scoring for two tasks: both for the de novo identification of molecular formulas of unknown compounds, and for searching a database for structurally similar compounds, our method SIRIUS 3, performs significantly better than the previous version of our method, as well as other methods for this task. SIRIUS 3 can be a part of an untargeted metabolomics workflow, allowing researchers to investigate unknowns using automated computational methods.Graphical abstractWe present a new scoring for computing fragmentation trees from tandem mass spectrometry data based on Bayesian statistics. The best scoring fragmentation tree most likely explains the molecular formula of the measured parent ion.

  3. Fragmentation of monoclonal antibodies

    Science.gov (United States)

    Vlasak, Josef

    2011-01-01

    Fragmentation is a degradation pathway ubiquitously observed in proteins despite the remarkable stability of peptide bond; proteins differ only by how much and where cleavage occurs. The goal of this review is to summarize reports regarding the non-enzymatic fragmentation of the peptide backbone of monoclonal antibodies (mAbs). The sites in the polypeptide chain susceptible to fragmentation are determined by a multitude of factors. Insights are provided on the intimate chemical mechanisms that can make some bonds prone to cleavage due to the presence of specific side-chains. In addition to primary structure, the secondary, tertiary and quaternary structures have a significant impact in modulating the distribution of cleavage sites by altering local flexibility, accessibility to solvent or bringing in close proximity side chains that are remote in sequence. This review focuses on cleavage sites observed in the constant regions of mAbs, with special emphasis on hinge fragmentation. The mechanisms responsible for backbone cleavage are strongly dependent on pH and can be catalyzed by metals or radicals. The distribution of cleavage sites are different under acidic compared to basic conditions, with fragmentation rates exhibiting a minimum in the pH range 5–6; therefore, the overall fragmentation pattern observed for a mAb is a complex result of structural and solvent conditions. A critical review of the techniques used to monitor fragmentation is also presented; usually a compromise has to be made between a highly sensitive method with good fragment separation and the capability to identify the cleavage site. The effect of fragmentation on the function of a mAb must be evaluated on a case-by-case basis depending on whether cleavage sites are observed in the variable or constant regions, and on the mechanism of action of the molecule. PMID:21487244

  4. Embedded Fragments Registry (EFR)

    Data.gov (United States)

    Department of Veterans Affairs — In 2009, the Department of Defense estimated that approximately 40,000 service members who served in OEF/OIF may have embedded fragment wounds as the result of small...

  5. Fragmentation Main Model

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — The fragmentation model combines patch size and patch continuity with diversity of vegetation types per patch and rarity of vegetation types per patch. A patch was...

  6. DNA fragmentation in spermatozoa

    DEFF Research Database (Denmark)

    Rex, A S; Aagaard, J.; Fedder, J

    2017-01-01

    Sperm DNA Fragmentation has been extensively studied for more than a decade. In the 1940s the uniqueness of the spermatozoa protein complex which stabilizes the DNA was discovered. In the fifties and sixties, the association between unstable chromatin structure and subfertility was investigated....... In the seventies, the impact of induced DNA damage was investigated. In the 1980s the concept of sperm DNA fragmentation as related to infertility was introduced as well as the first DNA fragmentation test: the Sperm Chromatin Structure Assay (SCSA). The terminal deoxynucleotidyl transferase nick end labelling...... (TUNEL) test followed by others was introduced in the nineties. The association between DNA fragmentation in spermatozoa and pregnancy loss has been extensively investigated spurring the need for a therapeutic tool for these patients. This gave rise to an increased interest in the aetiology of DNA damage...

  7. Fragmented Work Stories

    DEFF Research Database (Denmark)

    Humle, Didde Maria; Reff Pedersen, Anne

    2015-01-01

    stories. We argue that meaning by story making is not always created by coherence and causality; meaning is created by different types of fragmentation: discontinuities, tensions and editing. The objective of this article is to develop and advance antenarrative practice analysis of work stories......Following a strand of narrative studies pointing to the living conditions of storytelling and the micro-level implications of working within fragmented narrative perspectives, this article contributes to narrative research on work stories by focusing on how meaning is created from fragmented...... by exploring how different types of fragmentation create meanings. This is done by studying the work stories of job and personnel consultants and by drawing on the results of a narrative, ethnographic study of a consultancy. The analysis demonstrates how work stories are social practices negotiated, retold...

  8. Crystallographic fragment screening.

    Science.gov (United States)

    Badger, John

    2012-01-01

    Crystallographic fragment screening is a technique for initiating drug discovery in which protein crystals are soaked or grown with high concentrations of small molecule compounds (typically MW 110-250 Da) chosen to represent fragments of potential drugs. Specific binding of these compounds to the protein is subsequently visualized in electron density maps obtained from analysis of X-ray diffraction data collected from these crystals. Theoretical and practical experience indicate that a suitably diverse library of fragment compounds containing only a few hundred compounds may be sufficient to provide a comprehensive screen of the protein target. By soaking crystals in mixtures of 3-10 compounds a fragment screen may be completed within ∼100 diffraction data sets. This data collection requirement may be met given reproducible well-diffracting protein crystals and robotic sample handling equipment at a high flux X-ray source. The leading practical issue for most crystallography laboratories that wish to launch a fragment screening project is the design and/or procurement of an appropriate fragment library. Although several off-the-shelf fragment libraries are available from chemical suppliers, the numbers, sizes, and solubility of the compounds in relatively few of these libraries are well-match to the specific needs of the crystallographic screening experiment. Informed consideration of the properties of compounds in the screening library, possibly augmented by additional filtering of available compounds with appropriate search tools, is required to design a successful experiment. The analysis of results from crystallographic fragment screening involves highly repetitive application of routine image data processing and structure refinement calculations from many very similar crystals. Efficient handling of the data applies a high-throughput structure determination methodology that conveniently packages the structure solution calculations into a single process that

  9. Fragment Impact Toolkit (FIT)

    Energy Technology Data Exchange (ETDEWEB)

    Shevitz, Daniel Wolf [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Key, Brian P. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Garcia, Daniel B. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-09-05

    The Fragment Impact Toolkit (FIT) is a software package used for probabilistic consequence evaluation of fragmenting sources. The typical use case for FIT is to simulate an exploding shell and evaluate the consequence on nearby objects. FIT is written in the programming language Python and is designed as a collection of interacting software modules. Each module has a function that interacts with the other modules to produce desired results.

  10. Mass Spectral Fragmentation of VX

    National Research Council Canada - National Science Library

    Rohrbaugh, Dennis K

    2008-01-01

    The objective of this study was to provide structural identification of VX fragment ions formed during mass spectrometric analysis, elucidation of fragmentation pathways, and a compilation of tandem...

  11. Habitat fragmentation in the temperate zone: a perspective for managers

    Science.gov (United States)

    John Faaborg; Margaret Brittingham; Therese Donovan; John Blake

    1993-01-01

    Habitat fragmentation occurs when a large, fairly continuous tract of vegetation is converted to other vegetation types such that only scattered fragments of the original type remain. Problems associated with habitat fragmentation include overall habitat loss, increase in edge habitat and edge effects (particularly higher parasitism and nest predation rates), and...

  12. Fragments of Time

    DEFF Research Database (Denmark)

    Christiansen, Steen Ledet

    Time travel films necessarily fragment linear narratives, as scenes are revisited with differences from the first time we saw it. Popular films such as Back to the Future mine comedy from these visitations, but there are many different approaches. One extreme is Chris Marker's La Jetée - a film...... made almost completely of still images, recounting the end of the world. These stills can be viewed as fragments that have survived the end of the world and now provide the only access to the events that occured. Shane Carruth's Primer has a different approach to time travel, the narrative diegesis...

  13. The Serendipity of Fragmentation

    DEFF Research Database (Denmark)

    Leixnering, Stephan; Meyer, Renate E.

    , it was the central government’s task to coordinate, steer and control the newly emerged decentralized organizations. This raises questions about the overall design of the public sector at present. Our paper engages with the prevalent public governance phenomenon of fragmentation from a design perspective in order...... form of organizing between networks and formal organization: lacking a single center and featuring multiplex and multifaceted relations within the politico-administrative apparatus and between government and PSOs, high fragmentation, local and robust action, but latent structures of significant formal...

  14. Stone fragmentation by ultrasound

    Indian Academy of Sciences (India)

    Some delicate nerves and fibres in the surrounding areas of the stones present in the kidney are also damaged by high ultrasonic intensity used in such systems. In the present work, enhancement of the kidney stone fragmentation by using ultrasound is studied. The cavitation bubbles are found to implode faster, with more ...

  15. Fragments of the Past

    Directory of Open Access Journals (Sweden)

    Peter Szende

    2016-10-01

    Full Text Available With travel being made more accessible throughout the decades, the hospitality industry constantly evolved their practices as society and technology progressed. Hotels looked for news ways up service their customers, which led to the invention of the Servidor in 1918. Once revolutionary innovations have gone extinct, merely becoming fragments of the past.

  16. Wildlife habitat fragmentation.

    Science.gov (United States)

    John. Lehmkuhl

    2005-01-01

    A primary issue in forest wildlife management is habitat fragmentation and its effects on viability, which is the "bottom line" for plant and animal species of conservation concern. Population viability is the likelihood that a population will be able to maintain itself (remain viable) over a long period of time-usually 100 years or more. Though it is true...

  17. Heavy-Quark Fragmentation

    CERN Document Server

    Cacciari, M; Cacciari, Matteo; Gardi, Einan

    2003-01-01

    We study perturbative and non-perturbative aspects of heavy-quark fragmentation into hadrons, emphasizing the large-x region, where x is the energy fraction of the detected hadron. We first prove that when the moment index N and the quark mass m get large simultaneously with the ratio (N Lambda/m) fixed, the fragmentation function depends on this ratio alone. This opens up the way to formulate the non-perturbative contribution to the fragmentation function at large N as a shape function of m(1-x) which is convoluted with the Sudakov-resummed perturbative result. We implement this resummation and the parametrization of the corresponding shape function using Dressed Gluon Exponentiation. The Sudakov exponent is calculated in a process independent way from a generalized splitting function which describes the emission probability of an off-shell gluon off a heavy quark. Non-perturbative corrections are parametrized based on the renormalon structure of the Sudakov exponent. They appear in moment space as an expone...

  18. Fracture, failure, and fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    Dienes, J.K.

    1984-01-01

    Though continuum descriptions of material behavior are useful for many kinds of problems, particularly those involving plastic flow, a more general approach is required when the failure is likely to involve growth and coalescence of a large number of fractures, as in fragmentation. Failures of this kind appear frequently in rapid dynamic processes such as those resulting from impacts and explosions, particularly in the formation of spall fragments. In the first part of this paper an approach to formulating constitutive relations that accounts for the opening, shear and growth of an ensemble of cracks is discussed. The approach also accounts for plastic flow accompanying fragmentation. The resulting constitutive relations have been incorporated into a Lagrangean computer program. In the second part of this paper a theoretical approach to coalescence is described. The simplest formulation makes use of a linear Liouville equation, with crack growth limited by the mean free path of cracks, assumed constant. This approach allows for an anisotropic distribution of cracks. An alternative approach is also described in which the decrease of the mean free path with increasing crack size is accounted for, but the crack distribution is assumed isotropic. A reduction of the governing Liouville equation to an ordinary differential equation of third order is possible, and the result can be used to determine how mean-free-path decreases with increasing crack size.

  19. Ecosystem extent and fragmentation

    Science.gov (United States)

    Sayre, Roger; Hansen, Matt

    2017-01-01

    One of the candidate essential biodiversity variable (EBV) groups described in the seminal paper by Pereira et al. (2014) concerns Ecosystem Structure. This EBV group is distinguished from another EBV group which encompasses aspects of Ecosystem Function. While the Ecosystem Function EBV treats ecosystem processes like nutrient cycling, primary production, trophic interactions, etc., the Ecosystem Structure EBV relates to the set of biophysical properties of ecosystems that create biophysical environmental context, confer biophysical structure, and occur geographically. The Ecosystem Extent and Fragmentation EBV is one of the EBVs in the Ecosystem Structure EBV group.Ecosystems are understood to exist at multiple scales, from very large areas (macro-ecosystems) like the Arctic tundra, for example, to something as small as a tree in an Amazonian rain forest. As such, ecosystems occupy space and therefore can be mapped across any geography of interest, whether that area of interest be a site, a nation, a region, a continent, or the planet. One of the most obvious and seemingly straightforward EBVs is Ecosystem Extent and Fragmentation. Ecosystem extent refers to the location and geographic distribution of ecosystems across landscapes or in the oceans, while ecosystem fragmentation refers to the spatial pattern and connectivity of ecosystem occurrences on the landscape.

  20. CONTROL OF FRAGMENTATION BY BLASTING

    OpenAIRE

    Božić, Branko

    1998-01-01

    The degree of fragmentation influences the economy of the excavation operations. Characteristics of blasted rock such as fragment size, volume and mass are fundamental variables effecting the economics of a mining operation and are in effect the basis for evaluating the quality of a blast. The properties of fragmentation, such as size and shape, are very important information for the optimization of production. Three factors control the fragment size distribution: the rock structure, the q...

  1. SCALING AND 4-QUARK FRAGMENTATION

    NARCIS (Netherlands)

    SCHOLTEN, O; BOSVELD, GD

    1991-01-01

    The conditions for a scaling behaviour from the fragmentation process leading to slow protons are discussed- The scaling referred to implies that the fragmentation functions depend on the light-cone momentum fraction only. It is shown that differences in the fragmentation functions for valence- and

  2. Habitat fragmentation causes rapid genetic differentiation and ...

    African Journals Online (AJOL)

    ... city buildings. These results were supported by multiple statistical analyses including Mantel's test, PCOORDA and AMOVA. Genetic enrichment and epigenetic variation studies can be included in habitat fragmentation analysis and its implications in inducing homogenization and susceptibility in natural plant populations.

  3. Characterizing DebriSat Fragments: So Many Fragments, So Much Data, and So Little Time

    Science.gov (United States)

    Shiotani, B.; Rivero, M.; Carrasquilla, M.; Allen, S.; Fitz-Coy, N.; Liou, J.-C.; Huynh, T.; Sorge, M.; Cowardin, H.; Opiela, J.; hide

    2017-01-01

    To improve prediction accuracy, the DebriSat project was conceived by NASA and DoD to update existing standard break-up models. Updating standard break-up models require detailed fragment characteristics such as physical size, material properties, bulk density, and ballistic coefficient. For the DebriSat project, a representative modern LEO spacecraft was developed and subjected to a laboratory hypervelocity impact test and all generated fragments with at least one dimension greater than 2 mm are collected, characterized and archived. Since the beginning of the characterization phase of the DebriSat project, over 130,000 fragments have been collected and approximately 250,000 fragments are expected to be collected in total, a three-fold increase over the 85,000 fragments predicted by the current break-up model. The challenge throughout the project has been to ensure the integrity and accuracy of the characteristics of each fragment. To this end, the post hypervelocity-impact test activities, which include fragment collection, extraction, and characterization, have been designed to minimize handling of the fragments. The procedures for fragment collection, extraction, and characterization were painstakingly designed and implemented to maintain the post-impact state of the fragments, thus ensuring the integrity and accuracy of the characterization data. Each process is designed to expedite the accumulation of data, however, the need for speed is restrained by the need to protect the fragments. Methods to expedite the process such as parallel processing have been explored and implemented while continuing to maintain the highest integrity and value of the data. To minimize fragment handling, automated systems have been developed and implemented. Errors due to human inputs are also minimized by the use of these automated systems. This paper discusses the processes and challenges involved in the collection, extraction, and characterization of the fragments as well as the

  4. Synthesis of arabinoxylan fragments

    DEFF Research Database (Denmark)

    Underlin, Emilie Nørmølle; Böhm, Maximilian F.; Madsen, Robert

    The cell wall of plants can be termed the skeleton of the plant. One of the parts making up the cell wall is hemicellulose. Hemicellulose is composed of a number of saccharides where one of the most abundant are the arabinoxylan-oligosaccharides. In many instances the biosynthesis and degration...... of arabinoxylan oligosaccharides remain elusive. As a consequence defined arabinoxylan fragments have been chosen as synthetic targets which subsequently will be submitted to enzymatic studies. A better understanding of these processes could lead to e.g. better utilisation of the biomass for biofuel production...

  5. Fragmentation of Chitosan by Acids

    Directory of Open Access Journals (Sweden)

    Mohammad Reza Kasaai

    2013-01-01

    Full Text Available Fragmentation of chitosan in aqueous solution by hydrochloric acid was investigated. The kinetics of fragmentation, the number of chain scissions, and polydispersity of the fragments were followed by viscometry and size exclusion chromatography. The chemical structure and the degree of N-acetylation (DA of the original chitosan and its fragments were examined by 1H NMR spectroscopy and elemental analysis. The kinetic data indicates that the reaction was of first order. The results of polydispersity and the DA suggest that the selected experimental conditions (temperature and concentration of acid were appropriate to obtain the fragments having the polydispersity and the DA similar to or slightly different from those of the original one. A procedure to estimate molecular weight of fragments as well as the number of chain scissions of the fragments under the experimental conditions was also proposed.

  6. Fragment size distribution statistics in dynamic fragmentation of laser shock-loaded tin

    Directory of Open Access Journals (Sweden)

    Weihua He

    2017-06-01

    Full Text Available This work investigates the geometric statistics method to characterize the size distribution of tin fragments produced in the laser shock-loaded dynamic fragmentation process. In the shock experiments, the ejection of the tin sample with etched V-shape groove in the free surface are collected by the soft recovery technique. Subsequently, the produced fragments are automatically detected with the fine post-shot analysis techniques including the X-ray micro-tomography and the improved watershed method. To characterize the size distributions of the fragments, a theoretical random geometric statistics model based on Poisson mixtures is derived for dynamic heterogeneous fragmentation problem, which reveals linear combinational exponential distribution. The experimental data related to fragment size distributions of the laser shock-loaded tin sample are examined with the proposed theoretical model, and its fitting performance is compared with that of other state-of-the-art fragment size distribution models. The comparison results prove that our proposed model can provide far more reasonable fitting result for the laser shock-loaded tin.

  7. Fragmented QRS and Left Ventricular Geometry in Hypertensive Patients

    Directory of Open Access Journals (Sweden)

    Lütfü Bekar

    2013-08-01

    Full Text Available Introduction: Fragmented QRS is a depolarization abnormality detected with routin ECG recording. It is related with conduction defect which occurs after myocardial fibrosis. In the left ventricular hypertrophy, an excessive amount of collagen accumulates in the interstitium when the myocytes became hypertrophied, resulting in myocardial fibrosis. In this study, we aimed to investigate the relationship of fragmented QRS which was detected on ECG recordings of the hypertensive patients with the left ventricular geometry.Patients and Methods: Essential hypertension patients referred to our hospital on outpatient bases were included in the study. 12-lead resting ECG was taken in all the patients. Left ventricular geometry defined using left ventricular mass index and relative wall thickness with transthorasic echocardiography.Results: Sixy seven patients with fragmented QRS and 63 patients without fragmented QRS included the study. We found that patients in the group with fragmented QRS detected have a wider mean left atrium diameter, greater left ventricular mass and left ventricular mass index compared with the group without fragmented QRS. Concentric and eccentric hypertrophy were more common in fragmented QRS group, while normal geometry and concentric remodelling have greater rates in the normal group.Conclusion: Left ventricular hypertrophy is observed more frequently in the patients with fragmented QRS than without fragmented QRS. This may be associated with the increased myocardial fibrosis in the left ventricular hypertrophy. Existence of fragmented QRS can be used for risk stratification in the hypertensive patients.

  8. CONTROL OF FRAGMENTATION BY BLASTING

    Directory of Open Access Journals (Sweden)

    Branko Božić

    1998-12-01

    Full Text Available The degree of fragmentation influences the economy of the excavation operations. Characteristics of blasted rock such as fragment size, volume and mass are fundamental variables effecting the economics of a mining operation and are in effect the basis for evaluating the quality of a blast. The properties of fragmentation, such as size and shape, are very important information for the optimization of production. Three factors control the fragment size distribution: the rock structure, the quantity of explosive and its distribution within the rock mass. Over the last decade there have been considerable advances in our ability to measure and analyze blasting performance. These can now be combined with the continuing growth in computing power to develop a more effective description of rock fragmentation for use by future blasting practitioners. The paper describes a view of the fragmentation problem by blasting and the need for a new generation of engineering tools to guide the design and implementation of blasting operations.

  9. 3D puzzle reconstruction for archeological fragments

    Science.gov (United States)

    Jampy, F.; Hostein, A.; Fauvet, E.; Laligant, O.; Truchetet, F.

    2015-03-01

    The reconstruction of broken artifacts is a common task in archeology domain; it can be supported now by 3D data acquisition device and computer processing. Many works have been dedicated in the past to reconstructing 2D puzzles but very few propose a true 3D approach. We present here a complete solution including a dedicated transportable 3D acquisition set-up and a virtual tool with a graphic interface allowing the archeologists to manipulate the fragments and to, interactively, reconstruct the puzzle. The whole lateral part is acquired by rotating the fragment around an axis chosen within a light sheet thanks to a step-motor synchronized with the camera frame clock. Another camera provides a top view of the fragment under scanning. A scanning accuracy of 100μm is attained. The iterative automatic processing algorithm is based on segmentation into facets of the lateral part of the fragments followed by a 3D matching providing the user with a ranked short list of possible assemblies. The device has been applied to the reconstruction of a set of 1200 fragments from broken tablets supporting a Latin inscription dating from the first century AD.

  10. Vocabularies Clashing: "The Fragmented Generation" Describes Itself

    Science.gov (United States)

    Collins, Daniel

    2011-01-01

    After reading Scott Seider and Howard Gardner's essay "The Fragmented Generation" (2009) in a college freshman writing class, students responded by providing their own labels for their generation. This article includes excerpts from their essays. Following these excerpts is the instructor's theoretical justification for this kind of classroom…

  11. Habitat fragmentation causes rapid genetic differentiation and ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-08-04

    Aug 4, 2009 ... 1Laboratory of Plant Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun. 130024 ... epigenetic variation studies can be included in habitat fragmentation analysis and its implications in inducing ... together with the environment habitat selection pressure.

  12. Care fragmentation, quality, and costs among chronically ill patients.

    Science.gov (United States)

    Frandsen, Brigham R; Joynt, Karen E; Rebitzer, James B; Jha, Ashish K

    2015-05-01

    To assess the relationship between care fragmentation and both quality and costs of care for commercially insured, chronically ill patients. We used claims data from 2004 to 2008 for 506,376 chronically ill, privately insured enrollees of a large commercial insurance company to construct measures of fragmentation. We included patients in the sample if they had chronic conditions in any of the following categories: cardiovascular disease, diabetes, asthma, arthritis, or migraine. We assigned each patient a fragmentation index based on the patterns of care of their primary care provider (PCP), with care patterns spread across a higher number of providers considered to be more fragmented. We used regression analysis to examine the relationship between fragmentation and both quality and cost outcomes. Patients of PCPs in the highest quartile of fragmentation had a higher chance of having a departure from clinical best practice (32.8%, vs 25.9% among patients of PCPs in the lowest quartile of fragmentation; P fragmentation had higher rates of preventable hospitalizations (9.1% in highest quartile vs 7.1% in lowest quartile; P fragmentation was associated with $4542 higher healthcare spending ($10,396 in the highest quartile vs $5854 in the lowest quartile; P < .001). We found similar or larger effects on quality and costs among patients when we examined the most frequently occurring disease groups individually. Chronically ill patients whose primary care providers offer highly fragmented care more often experience lapses in care quality and incur greater healthcare costs.

  13. An Algebra for Program Fragments

    DEFF Research Database (Denmark)

    Kristensen, Bent Bruun; Madsen, Ole Lehrmann; Møller-Pedersen, Birger

    1985-01-01

    Program fragments are described either by strings in the concrete syntax or by constructor applications in the abstract syntax. By defining conversions between these forms, both may be intermixed. Program fragments are constructed by terminal and nonterminal symbols from the grammar and by variab......Program fragments are described either by strings in the concrete syntax or by constructor applications in the abstract syntax. By defining conversions between these forms, both may be intermixed. Program fragments are constructed by terminal and nonterminal symbols from the grammar...

  14. Heterogeneous fragmentation of metallic liquid microsheet with high velocity gradient

    Science.gov (United States)

    An-Min, He; Pei, Wang; Jian-Li, Shao

    2016-01-01

    Large-scale molecular dynamics simulations are performed to study the fragmentation of metallic liquid sheets with high velocity gradient. Dynamic fragmentation of the system involves the formation of a network of fragments due to the growth and coalescence of holes, decomposition of the network into filaments, and further breakup of the filaments into spherical clusters. The final size distribution of the fragmented clusters in the large volume limit is found to obey a bilinear exponential form, which is resulted from the heterogeneous breakup of quasi-cylindrical filaments. The main factors contributing to fragmentation heterogeneity are introduced, including strain rate inhomogeneity and matter distribution nonuniformity of fragments produced during decomposition of the network structure. Project supported by the Science and Technology Development Foundation of China Academy of Engineering Physics (Grant Nos. 2013A0201010 and 2015B0201039) and the National Natural Science Foundation of China (Grant No. 11402032).

  15. arXiv Generalized Fragmentation Functions for Fractal Jet Observables

    CERN Document Server

    Elder, Benjamin T.; Thaler, Jesse; Waalewijn, Wouter J.; Zhou, Kevin

    2017-06-15

    We introduce a broad class of fractal jet observables that recursively probe the collective properties of hadrons produced in jet fragmentation. To describe these collinear-unsafe observables, we generalize the formalism of fragmentation functions, which are important objects in QCD for calculating cross sections involving identified final-state hadrons. Fragmentation functions are fundamentally nonperturbative, but have a calculable renormalization group evolution. Unlike ordinary fragmentation functions, generalized fragmentation functions exhibit nonlinear evolution, since fractal observables involve correlated subsets of hadrons within a jet. Some special cases of generalized fragmentation functions are reviewed, including jet charge and track functions. We then consider fractal jet observables that are based on hierarchical clustering trees, where the nonlinear evolution equations also exhibit tree-like structure at leading order. We develop a numeric code for performing this evolution and study its phen...

  16. Thermodynamical string fragmentation

    Science.gov (United States)

    Fischer, Nadine; Sjöstrand, Torbjörn

    2017-01-01

    The observation of heavy-ion-like behaviour in pp collisions at the LHC suggests that more physics mechanisms are at play than traditionally assumed. The introduction e.g. of quark-gluon plasma or colour rope formation can describe several of the observations, but as of yet there is no established paradigm. In this article we study a few possible modifications to the Pythia event generator, which describes a wealth of data but fails for a number of recent observations. Firstly, we present a new model for generating the transverse momentum of hadrons during the string fragmentation process, inspired by thermodynamics, where heavier hadrons naturally are suppressed in rate but obtain a higher average transverse momentum. Secondly, close-packing of strings is taken into account by making the temperature or string tension environment-dependent. Thirdly, a simple model for hadron rescattering is added. The effect of these modifications is studied, individually and taken together, and compared with data mainly from the LHC. While some improvements can be noted, it turns out to be nontrivial to obtain effects as big as required, and further work is called for.

  17. Fragmentation model for large L/D (Length over Diameter explosive fragmentation warheads

    Directory of Open Access Journals (Sweden)

    Vladimir M. Gold

    2017-08-01

    Full Text Available New advanced numerical computer model enabling accurate simulation of fragmentation parameters of large Length over Diameter (L/D explosively driven metal shells has been developed and validated. The newly developed large L/D multi-region model links three-dimensional axisymmetric high strain high strain-rate hydrocode analyses with the conventional set of Picatinny Arsenal FRAGmentation (PAFRAG simulation routines. The standard PAFRAG modeling technique is based on the Mott's theory of break-up of idealized cylindrical “ring-bombs”, in which the length of the average fragment is a function of the radius and velocity of the shell at the moment of break-up, and the mechanical properties of the metal. In the newly developed multi-region model, each of the shell region, the break-up is assumed to occur instantaneously, whereas the entire shell is modeled to fragment at multiple times, according to the number of the regions considered. According to PAFRAG methodology, the required input for both the natural and the controlled fragmentation models including the geometry and the velocity of the shell at moment of break-up had been provided from the hydrocode analyses and validated with available experimental data. The newly developed large L/D multi-region PAFRAG model has been shown to accurately reproduce available experimental fragmentation data.

  18. Percentile Fragment Size Predictions for Blasted Rock and the Fragmentation-Energy Fan

    Science.gov (United States)

    Ouchterlony, Finn; Sanchidrián, José A.; Moser, Peter

    2017-04-01

    It is shown that blast fragmentation data in the form of sets of percentile fragment sizes, x P, as function of specific charge (powder factor, q) often form a set of straight lines in a log( x P) versus log( q) diagram that tend to converge on a common focal point. This is clear for single-hole shots with normal specific charge values in specimens of virgin material, and the phenomenon is called the fragmentation-energy fan. Field data from bench blasting with several holes in single or multiple rows in rock give data that scatter much more, but examples show that the fragmentation data tend to form such fans. The fan behavior implies that the slopes of the straight size versus specific charge lines in log-log space depend only on the percentile level in a given test setup. It is shown that this property can be derived for size distribution functions of the form P[ln( x max/ x)/ln( x max/ x 50)]. An example is the Swebrec function; for it to comply with the fragmentation-energy fan properties, the undulation parameter b must be constant. The existence of the fragmentation-energy fan contradicts two basic assumptions of the Kuz-Ram model: (1) that the Rosin-Rammler function reproduces the sieving data well and (2) that the uniformity index n is a constant, independent of q. This favors formulating the prediction formulas instead in terms of the percentile fragment size x P for arbitrary P values, parameters that by definition are independent of any size distribution, be it the Rosin-Rammler, Swebrec or other. A generalization of the fan behavior to include non-dimensional fragment sizes and an energy term with explicit size dependence seems possible to make.

  19. Fragmentation of exotic oxygen isotopes

    Energy Technology Data Exchange (ETDEWEB)

    Leistenschneider, A.; Elze, Th.W.; Gruenschloss, A.; Palit, R. [Johann Wolfgang Goethe-Univ., Frankfurt (Germany). Inst. fuer Kernphysik; Aumann, T.; Cortina, D.; Datta Pramanik, U.; Emling, H.; Geissel, H.; Helariutta, K.; Hellstroem, M.; Ilievski, S.; Jones, K.; Muenzenberg, G.; Scheidenberger, C.; Schmidt, K.-H.; Suemmerer, K. [Gesellschaft fuer Schwerionenforschung (GSI), Darmstadt (Germany); Boretzky, K.; Kratz, J.V.; Le Hong, Khiem [Johannes Gutenberg-Univ., Mainz (Germany). Inst. fue Kernchemie; Canto, L.F. [Universidade Federal, Rio de Janeiro, RJ (Brazil). Inst. de Fisica; Carlson, B.V. [Centro Tecnico Aeroespacial (CTA), Sao Jose dos Campos, SP (Brazil). Inst. Tecnologico de Aeronautica (ITA). Dept. de Fisica; Hussein, M.S. [Sao Paulo Univ. (USP), SP (Brazil). Inst. de Fisica; Kulessa, R.; Lubkiewicz, E.; Wajda, E.; Walus, W. [Uniwersytet Jagellonski, Krakow (Poland). Instytut Fizyki; Reiter, P. [Ludwig-Maximilians-Univ., Garching (Germany). Sektion Physik; Simon, H. [Technische Univ., Darmstadt (Germany). Inst. fuer Kernphysik

    2003-06-01

    Abrasion-ablation models and the empirical EPAX parametrization of projectile fragmentation are described. Their cross section predictions are compared to recent data of the fragmentation of secondary beams of neutron-rich, unstable {sup 19,20,21} O isotopes at beam energies near 600 MeV/nucleon as well as data for stable {sup 17,18} O beams. (author)

  20. Polymer fragmentation in extensional flow

    Energy Technology Data Exchange (ETDEWEB)

    Maroja, Armando M.; Oliveira, Fernando A.; Ciesla, Michal; Longa, Lech

    2001-06-01

    In this paper we present an analysis of fragmentation of dilute polymer solutions in extensional flow. The transition rate is investigated both from theoretical and computational approaches, where the existence of a Gaussian distribution for the breaking bonds has been controversial. We give as well an explanation for the low fragmentation frequency found in DNA experiments.

  1. The spectroscopy of fission fragments

    Energy Technology Data Exchange (ETDEWEB)

    Phillips, W.R. [Department of Physics and Astronomy, University of Manchester, Manchester, M13 9PL (United Kingdom); Collaboration: La Direction des Sciences de la Matiere du CEA (FR); Le Fonds National de la Recherche Scientifique de Belgique (BE)

    1998-12-31

    High-resolution measurements on {gamma} rays from fission fragments have provided a rich source of information, unobtainable at the moment in any other way, on the spectroscopy of neutron-rich nuclei. In recent years important data have been obtained on the yrast- and near yrast-structure of neutron-rich fission fragments. We discuss the scope of measurements which can be made on prompt gamma rays from secondary fission fragments, the techniques used in the experiments and some results recently obtained. (author) 24 refs., 8 figs., 1 tab.

  2. Stathmin 1/2-triggered microtubule loss mediates Golgi fragmentation in mutant SOD1 motor neurons

    NARCIS (Netherlands)

    Bellouze, Sarah; Baillat, Gilbert; Buttigieg, Dorothée; de la Grange, Pierre; Rabouille, Catherine; Haase, Georg

    2016-01-01

    BACKGROUND: Pathological Golgi fragmentation represents a constant pre-clinical feature of many neurodegenerative diseases including amyotrophic lateral sclerosis (ALS) but its molecular mechanisms remain hitherto unclear. RESULTS: Here, we show that the severe Golgi fragmentation in transgenic

  3. Postoperative Airway Obstruction by a Bone Fragment

    Directory of Open Access Journals (Sweden)

    Patrick Schober

    2017-01-01

    Full Text Available Postoperative airway obstructions are potentially life-threatening complications. These obstructions may be classified as functional (sagging tongue, laryngospasm, or bronchospasm, pathoanatomical (airway swelling or hematoma within the airways, or foreign body-related. Various cases of airway obstruction by foreign bodies have previously been reported, for example, by broken teeth or damaged airway instruments. Here we present the exceptional case of a postoperative airway obstruction due to a large fragment of the patient’s maxillary bone, left accidentally in situ after transoral surgical tumor resection. Concerning this type of airway obstruction, we discuss possible causes, diagnosis, and treatment options. Although it is an exceptional case after surgery, clinicians should be aware of this potentially life-threatening complication. In summary, this case demonstrates that the differential diagnosis of postoperative airway obstructions should include foreign bodies derived from surgery, including tissue and bone fragments.

  4. Light quark fragmentations into pions

    Science.gov (United States)

    Edemskaya, A. K.; Naumov, D. V.; Samoylov, O. B.

    2011-12-01

    We discuss a process of hadronization of light quarks into charged pions in e + e - annihilations and in deep inelastic scatering of charged leptons and neutrino off nucleons. The corresponding semi-inclusive cross-sections of pions production we write in terms of quark fragmentation functions and fracture functions. We suggest a new method of measurements of fragmentation and fracture functions based on analysis of semiinclusive data.

  5. QGP and Modified Jet Fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Xin-Nian

    2005-04-18

    Recent progresses in the study of jet modification in hotmedium and their consequences in high-energy heavy-ion collisions are reviewed. In particular, I will discuss energy loss for propagating heavy quarks and the resulting modified fragmentation function. Medium modification of the parton fragmentation function due to quark recombination are formulated within finite temperature field theory and their implication on the search for deconfined quark-gluon plasma is also discussed.

  6. Fragmentation and Isolation

    Science.gov (United States)

    Landscapes are being modified by humans at ever-increasing rates worldwide. This landscape level modification has resulted in changes in ecological patterns and processes, including species distributions. The rate at which humans are altering both terrestrial and aquatic habitats...

  7. Aerodynamic characteristics and respiratory deposition of fungal fragments

    Science.gov (United States)

    Cho, Seung-Hyun; Seo, Sung-Chul; Schmechel, Detlef; Grinshpun, Sergey A.; Reponen, Tiina

    The purpose of this study was to investigate the aerodynamic characteristics of fungal fragments and to estimate their respiratory deposition. Fragments and spores of three different fungal species ( Aspergillus versicolor, Penicillium melinii, and Stachybotrys chartarum) were aerosolized by the fungal spore source strength tester (FSSST). An electrical low-pressure impactor (ELPI) measured the size distribution in real-time and collected the aerosolized fungal particles simultaneously onto 12 impactor stages in the size range of 0.3-10 μm utilizing water-soluble ZEF-X10 coating of the impaction stages to prevent spore bounce. For S. chartarum, the average concentration of released fungal fragments was 380 particles cm -3, which was about 514 times higher than that of spores. A. versicolor was found to release comparable amount of spores and fragments. Microscopic analysis confirmed that S. chartarum and A. versicolor did not show any significant spore bounce, whereas the size distribution of P. melinii fragments was masked by spore bounce. Respiratory deposition was calculated using a computer-based model, LUDEP 2.07, for an adult male and a 3-month-old infant utilizing the database on the concentration and size distribution of S. chartarum and A. versicolor aerosols measured by the ELPI. Total deposition fractions for fragments and spores were 27-46% and 84-95%, respectively, showing slightly higher values in an infant than in an adult. For S. chartarum, fragments demonstrated 230-250 fold higher respiratory deposition than spores, while the number of deposited fragments and spores of A. versicolor were comparable. It was revealed that the deposition ratio (the number of deposited fragments divided by that of deposited spores) in the lower airways for an infant was 4-5 times higher than that for an adult. As fungal fragments have been shown to contain mycotoxins and antigens, further exposure assessment should include the measurement of fungal fragments for

  8. Dynamic contributions to symmetric fragmentation processes

    Science.gov (United States)

    Schulte, H.; Jäckel, B.; Esterlund, R. A.; Knaack, M.; Westmeier, W.; Rox, A.; Patzelt, P.

    1989-11-01

    Angular-distribution anisotropies of fission/fissionlike products from the reactions 5.3 and 7.5 MeV/u 40Ar+ 197Au have been determined as a function of exit-channel mass asymmetry α. At sufficiently large α, the angular distributions become asymmetric about 90° in the rest frame, indicating that the symmetric fragmentation component in this system includes contributions from dynamic processes.

  9. Experimental study on fragmental behavior of coals and biomasses during rapid pyrolysis.

    Science.gov (United States)

    Cui, Tongmin; Xu, Jianliang; Fan, Wenke; Chang, Qinghua; Yu, Guangsuo; Wang, Fuchen

    2016-12-01

    In order to study the primary fragmentation behavior of coals and biomasses, experiments of rapid pyrolysis were carried out. This work focused on the devolatilization and fragmentation characteristics including the solid/gas yield, particle density/morphology, particle size and fragmental probability (S f ). The effects of temperature, time and solid property were investigated. The viscous flow model was employed to characterize the pressure difference (ΔP), which was considered as the driving force of diffusion and fragmentation. The Ohm principle was used to establish the linear relation of devolatilization rate and fragmentation rate. The result showed that temperature and time have positive contribution to the fragmentation. The occurrence of fragmentation was observed more apparently with the decreasing of the ash content in the biomass. The pressure difference has a positive correlation with the fragmental rate, which shows the validity of application Ohm principle in the prediction of fragmenting process. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. HDX reveals unique fragment ligands for the vitamin D receptor.

    Science.gov (United States)

    Carson, Matthew W; Zhang, Jun; Chalmers, Michael J; Bocchinfuso, Wayne P; Holifield, Karol D; Masquelin, Thierry; Stites, Ryan E; Stayrook, Keith R; Griffin, Patrick R; Dodge, Jeffery A

    2014-08-01

    Modulation of the vitamin D receptor (VDR) with a ligand has the potential to be useful for the oral treatment of osteoporosis. One component of our lead generation strategy to identify synthetic ligands for VDR included a fragment based drug design approach. Screening of ligands in a VDR fluorescence polarization assay and a RXR/VDR conformation sensing assay resulted in the identification of multiple fragment hits (lean >0.30). These fragment scaffolds were subsequently evaluated for interaction with the VDR ligand binding domain using hydrogen-deuterium exchange (HDX) mass spectrometry. Significant protection of H/D exchange was observed for some fragments in helixes 3, 7, and 8 of the ligand binding domain, regions which are similar to those seen for the natural hormone VD3. The fragments appear to mimic the A-ring of VD3 thereby providing viable starting points for synthetic expansion. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. ACFIS: a web server for fragment-based drug discovery

    Science.gov (United States)

    Hao, Ge-Fei; Jiang, Wen; Ye, Yuan-Nong; Wu, Feng-Xu; Zhu, Xiao-Lei; Guo, Feng-Biao; Yang, Guang-Fu

    2016-01-01

    In order to foster innovation and improve the effectiveness of drug discovery, there is a considerable interest in exploring unknown ‘chemical space’ to identify new bioactive compounds with novel and diverse scaffolds. Hence, fragment-based drug discovery (FBDD) was developed rapidly due to its advanced expansive search for ‘chemical space’, which can lead to a higher hit rate and ligand efficiency (LE). However, computational screening of fragments is always hampered by the promiscuous binding model. In this study, we developed a new web server Auto Core Fragment in silico Screening (ACFIS). It includes three computational modules, PARA_GEN, CORE_GEN and CAND_GEN. ACFIS can generate core fragment structure from the active molecule using fragment deconstruction analysis and perform in silico screening by growing fragments to the junction of core fragment structure. An integrated energy calculation rapidly identifies which fragments fit the binding site of a protein. We constructed a simple interface to enable users to view top-ranking molecules in 2D and the binding mode in 3D for further experimental exploration. This makes the ACFIS a highly valuable tool for drug discovery. The ACFIS web server is free and open to all users at http://chemyang.ccnu.edu.cn/ccb/server/ACFIS/. PMID:27150808

  12. Quantification of habitat fragmentation reveals extinction risk in terrestrial mammals.

    Science.gov (United States)

    Crooks, Kevin R; Burdett, Christopher L; Theobald, David M; King, Sarah R B; Di Marco, Moreno; Rondinini, Carlo; Boitani, Luigi

    2017-07-18

    Although habitat fragmentation is often assumed to be a primary driver of extinction, global patterns of fragmentation and its relationship to extinction risk have not been consistently quantified for any major animal taxon. We developed high-resolution habitat fragmentation models and used phylogenetic comparative methods to quantify the effects of habitat fragmentation on the world's terrestrial mammals, including 4,018 species across 26 taxonomic Orders. Results demonstrate that species with more fragmentation are at greater risk of extinction, even after accounting for the effects of key macroecological predictors, such as body size and geographic range size. Species with higher fragmentation had smaller ranges and a lower proportion of high-suitability habitat within their range, and most high-suitability habitat occurred outside of protected areas, further elevating extinction risk. Our models provide a quantitative evaluation of extinction risk assessments for species, allow for identification of emerging threats in species not classified as threatened, and provide maps of global hotspots of fragmentation for the world's terrestrial mammals. Quantification of habitat fragmentation will help guide threat assessment and strategic priorities for global mammal conservation.

  13. Fragmentation modes and the evolution of life cycles.

    Science.gov (United States)

    Pichugin, Yuriy; Peña, Jorge; Rainey, Paul B; Traulsen, Arne

    2017-11-01

    Reproduction is a defining feature of living systems. To reproduce, aggregates of biological units (e.g., multicellular organisms or colonial bacteria) must fragment into smaller parts. Fragmentation modes in nature range from binary fission in bacteria to collective-level fragmentation and the production of unicellular propagules in multicellular organisms. Despite this apparent ubiquity, the adaptive significance of fragmentation modes has received little attention. Here, we develop a model in which groups arise from the division of single cells that do not separate but stay together until the moment of group fragmentation. We allow for all possible fragmentation patterns and calculate the population growth rate of each associated life cycle. Fragmentation modes that maximise growth rate comprise a restrictive set of patterns that include production of unicellular propagules and division into two similar size groups. Life cycles marked by single-cell bottlenecks maximise population growth rate under a wide range of conditions. This surprising result offers a new evolutionary explanation for the widespread occurrence of this mode of reproduction. All in all, our model provides a framework for exploring the adaptive significance of fragmentation modes and their associated life cycles.

  14. Fragmentation and ablation during entry

    Energy Technology Data Exchange (ETDEWEB)

    Canavan, G.H.

    1997-09-01

    This note discusses objects that both fragment and ablate during entry, using the results of previous reports to describe the velocity, pressure, and fragmentation of entering objects. It shows that the mechanisms used there to describe the breakup of non-ablating objects during deceleration remain valid for most ablating objects. It treats coupled fragmentation and ablation during entry, building on earlier models that separately discuss the entry of objects that are hard, whose high heat of ablation permits little erosion, and those who are strong whose strength prevents fragmentation, which are discussed in ``Radiation from Hard Objects,`` ``Deceleration and Radiation of Strong, Hard, Asteroids During Atmospheric Impact,`` and ``Meteor Signature Interpretation.`` This note provides a more detailed treatment of the further breakup and separation of fragments during descent. It replaces the constraint on mass per unit area used earlier to determine the altitude and magnitude of peak power radiation with a detailed analytic solution of deceleration. Model predictions are shown to be in agreement with the key features of numerical calculations of deceleration. The model equations are solved for the altitudes of maximum radiation, which agree with numerical integrations. The model is inverted analytically to infer object size and speed from measurements of peak power and altitude to provide a complete model for the approximate inversion of meteor data.

  15. A model of posttraumatic epilepsy after penetrating brain injuries: Effect of lesion size and metal fragments

    National Research Council Canada - National Science Library

    Kendirli, M. Tansel; Rose, Dominique T; Bertram, Edward H

    2014-01-01

    ..., and foreign fragments in the brain, including metal, are asso‐ciated with the highest risk (about 60% will develop epilepsy). The risks may increase with more detectable metal fragments, but it is not known if the fragments have a role in epileptogenesis or whether they are markers for a more extensive injury, which is also a risk factor. Identifying ...

  16. Changes in fragmentation of western Washington forest land (Project WC-EM-08-01)

    Science.gov (United States)

    Andrew Gray

    2013-01-01

    Land conversion and forest fragmentation is an important issue across the country. Forest fragmentation is one of the international Montréal criteria and indicators that the Forest Service, U.S. Department of Agriculture, must assess periodically (Riitters and others 2004). Characteristics of increased fragmentation include increases in the amount of forest-nonforest...

  17. HIERARCHICAL FRAGMENTATION OF THE ORION MOLECULAR FILAMENTS

    Energy Technology Data Exchange (ETDEWEB)

    Takahashi, Satoko; Ho, Paul T. P.; Su, Yu-Nung [Academia Sinica Institute of Astronomy and Astrophysics, P.O. Box 23-141, Taipei 10617, Taiwan (China); Teixeira, Paula S. [Institut fuer Astrophysik, Universitaet Wien, Tuerkenschanzstrasse 17, A-1180, Wien (Austria); Zapata, Luis A., E-mail: satoko_t@asiaa.sinica.edu.tw [Centro de Radioastronomia y Astrofisica, Universidad Nacional Autonoma de Mexico, Morelia, Michoacan 58090 (Mexico)

    2013-01-20

    We present a high angular resolution map of the 850 {mu}m continuum emission of the Orion Molecular Cloud-3 (OMC 3) obtained with the Submillimeter Array (SMA); the map is a mosaic of 85 pointings covering an approximate area of 6.'5 Multiplication-Sign 2.'0 (0.88 Multiplication-Sign 0.27 pc). We detect 12 spatially resolved continuum sources, each with an H{sub 2} mass between 0.3-5.7 M {sub Sun} and a projected source size between 1400-8200 AU. All the detected sources are on the filamentary main ridge (n{sub H{sub 2}}{>=}10{sup 6} cm{sup -3}), and analysis based on the Jeans theorem suggests that they are most likely gravitationally unstable. Comparison of multi-wavelength data sets indicates that of the continuum sources, 6/12 (50%) are associated with molecular outflows, 8/12 (67%) are associated with infrared sources, and 3/12 (25%) are associated with ionized jets. The evolutionary status of these sources ranges from prestellar cores to protostar phase, confirming that OMC-3 is an active region with ongoing embedded star formation. We detect quasi-periodical separations between the OMC-3 sources of Almost-Equal-To 17''/0.035 pc. This spatial distribution is part of a large hierarchical structure that also includes fragmentation scales of giant molecular cloud ( Almost-Equal-To 35 pc), large-scale clumps ( Almost-Equal-To 1.3 pc), and small-scale clumps ( Almost-Equal-To 0.3 pc), suggesting that hierarchical fragmentation operates within the Orion A molecular cloud. The fragmentation spacings are roughly consistent with the thermal fragmentation length in large-scale clumps, while for small-scale cores it is smaller than the local fragmentation length. These smaller spacings observed with the SMA can be explained by either a helical magnetic field, cloud rotation, or/and global filament collapse. Finally, possible evidence for sequential fragmentation is suggested in the northern part of the OMC-3 filament.

  18. Extension of moment projection method to the fragmentation process

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Shaohua [Department of Mechanical Engineering, National University of Singapore, Engineering Block EA, Engineering Drive 1, 117576 (Singapore); Yapp, Edward K.Y.; Akroyd, Jethro; Mosbach, Sebastian [Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA (United Kingdom); Xu, Rong [School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 (Singapore); Yang, Wenming [Department of Mechanical Engineering, National University of Singapore, Engineering Block EA, Engineering Drive 1, 117576 (Singapore); Kraft, Markus, E-mail: mk306@cam.ac.uk [Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA (United Kingdom); School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 (Singapore)

    2017-04-15

    The method of moments is a simple but efficient method of solving the population balance equation which describes particle dynamics. Recently, the moment projection method (MPM) was proposed and validated for particle inception, coagulation, growth and, more importantly, shrinkage; here the method is extended to include the fragmentation process. The performance of MPM is tested for 13 different test cases for different fragmentation kernels, fragment distribution functions and initial conditions. Comparisons are made with the quadrature method of moments (QMOM), hybrid method of moments (HMOM) and a high-precision stochastic solution calculated using the established direct simulation algorithm (DSA) and advantages of MPM are drawn.

  19. Amplified-fragment length polymorphism fingerprinting of Mycoplasma species

    DEFF Research Database (Denmark)

    Kokotovic, Branko; Friis, N.F.; Jensen, J.S.

    1999-01-01

    I restriction endonucleases and subsequent ligation of corresponding site-specific adapters. The amplification of AFLP templates with a single set of nonselective primers resulted in reproducible fingerprints of approximately 60 to 80 fragments in the size range of 50 to 500 bp, The method was able......Amplified-fragment length polymorphism (AFLP) is a whole-genome fingerprinting method based on selective amplification of restriction fragments. The potential of the method for the characterization of mycoplasmas was investigated in a total of 50 strains of human and animal origin, including...

  20. A thermodynamic theory of dynamic fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    Yew, Ching H. [Texas Univ., Austin, TX (United States); Taylor, P.A. [Sandia National Labs., Albuquerque, NM (United States)

    1993-08-01

    We present a theory of dynamic fragmentation of brittle materials based on thermodynamic arguments. We recover the expressions for average fragment size and number as originally derived by Grady. We extend the previous work by obtaining descriptions of fragment size distribution and compressibility change due to the fragmentation process. The size distribution is assumed to be proportional to the spectral power of the strain history and a sample distribution is presented for a fragmentation process corresponding to a constant rate strain history. The description of compressibility change should be useful in computational studies of fragmentation. These results should provide insight into the process of fragmentation of brittle materials from hypervelocity impact.

  1. 34 CFR 303.15 - Include; including.

    Science.gov (United States)

    2010-07-01

    ... 34 Education 2 2010-07-01 2010-07-01 false Include; including. 303.15 Section 303.15 Education Regulations of the Offices of the Department of Education (Continued) OFFICE OF SPECIAL EDUCATION AND REHABILITATIVE SERVICES, DEPARTMENT OF EDUCATION EARLY INTERVENTION PROGRAM FOR INFANTS AND TODDLERS WITH...

  2. Population pressure and farm fragmentation:

    African Journals Online (AJOL)

    user

    Small farmers play a dominant role in rural area in Rwanda according to many researchers. These farmers have some particular characteristics: most of them have tiny farms, while purchasing and borrowing of land are frequent. In addition, the size of farms is not only very small but farms are further fragmented into ...

  3. Fragmentation of stretched liquid ligaments

    NARCIS (Netherlands)

    Marmottant, P.G.M.; Villermaux, Emmanuel

    2004-01-01

    The dynamics and fragmentation of stretched liquid ligaments is investigated. The ligaments are produced by the withdrawal of a tube initially dipping at a free surface. Time resolved high speed motion experiments reveal two different elongation behaviors, depending on the nondimensional number t,

  4. Fragmented nature: consequences for biodiversity

    NARCIS (Netherlands)

    Olff, H.; Ritchie, M.E.

    2002-01-01

    We discuss how fragmentation of resources and habitat operate differently on species diversity across spatial scales, ranging from positive effects on local species coexistence to negative effect on intermediate spatial scales, to again positive effects on large spatial and temporal scales. Species

  5. Fragmented nature : consequences for biodiversity

    NARCIS (Netherlands)

    Olff, Han; Ritchie, Mark E.

    2002-01-01

    We discuss how fragmentation of resources and habitat operate differently on species diversity across spatial scales, ranging from positive effects on local species coexistence to negative effect on intermediate spatial scales, to again positive effects on large spatial and temporal scales. Species

  6. The VERDI fission fragment spectrometer

    Directory of Open Access Journals (Sweden)

    Frégeau M.O.

    2013-12-01

    Full Text Available The VERDI time-of-flight spectrometer is dedicated to measurements of fission product yields and of prompt neutron emission data. Pre-neutron fission-fragment masses will be determined by the double time-of-flight (TOF technique. For this purpose an excellent time resolution is required. The time of flight of the fragments will be measured by electrostatic mirrors located near the target and the time signal coming from silicon detectors located at 50 cm on both sides of the target. This configuration, where the stop detector will provide us simultaneously with the kinetic energy of the fragment and timing information, significantly limits energy straggling in comparison to legacy experimental setup where a thin foil was usually used as a stop detector. In order to improve timing resolution, neutron transmutation doped silicon will be used. The high resistivity homogeneity of this material should significantly improve resolution in comparison to standard silicon detectors. Post-neutron fission fragment masses are obtained form the time-of-flight and the energy signal in the silicon detector. As an intermediary step a diamond detector will also be used as start detector located very close to the target. Previous tests have shown that poly-crystalline chemical vapour deposition (pCVD diamonds provides a coincidence time resolution of 150 ps not allowing complete separation between very low-energy fission fragments, alpha particles and noise. New results from using artificial single-crystal diamonds (sCVD show similar time resolution as from pCVD diamonds but also sufficiently good energy resolution.

  7. Fragment Merger: An Online Tool to Merge Overlapping Long Sequence Fragments

    Directory of Open Access Journals (Sweden)

    Anna Kramvis

    2013-03-01

    Full Text Available While PCR amplicons extend to a few thousand bases, the length of sequences from direct Sanger sequencing is limited to 500–800 nucleotides. Therefore, several fragments may be required to cover an amplicon, a gene or an entire genome. These fragments are typically sequenced in an overlapping fashion and assembled by manually sliding and aligning the sequences visually. This is time-consuming, repetitive and error-prone, and further complicated by circular genomes. An online tool merging two to twelve long overlapping sequence fragments was developed. Either chromatograms or FASTA files are submitted to the tool, which trims poor quality ends of chromatograms according to user-specified parameters. Fragments are assembled into a single sequence by repeatedly calling the EMBOSS merger tool in a consecutive manner. Output includes the number of trimmed nucleotides, details of each merge, and an optional alignment to a reference sequence. The final merge sequence is displayed and can be downloaded in FASTA format. All output files can be downloaded as a ZIP archive. This tool allows for easy and automated assembly of overlapping sequences and is aimed at researchers without specialist computer skills. The tool is genome- and organism-agnostic and has been developed using hepatitis B virus sequence data.

  8. Fragmentation

    Science.gov (United States)

    K.H. Riitters

    2009-01-01

    Effective resource management takes into account the administrative and biophysical settings within which natural resources occur. A setting may be described in many ways; for example, by forest land ownership, by reserved and roadless designation, or by the distribution of human populations in relation to forest (chapter 3). The physical arrangement of forest in a...

  9. Relationships between Liquid Atomization and Solid Fragmentation

    Science.gov (United States)

    2016-03-01

    fragment size distributions found in the research literature , including specific examples of Weibull, Gamma, and root normal size distributions. This...bn 1               n m b n n m 1 1 1 The research literature usually considers Weibull size distributions to be the same when mn...approximations based on test or computational data, while those given in the grey cells are exact values derived from theory. As seen in Appendix A, the

  10. Statistical Models of Areal Distribution of Fragmented Land Cover Types

    Science.gov (United States)

    Hlavka, C.; Dungan, J.; DAntoni, Hector

    1997-01-01

    Imagery of coarse resolution, such weather satellite imagery with 1 square kilometer pixels, is increasingly used to monitor dynamic and fragmented types of land surface types, such as scars from recent fires and ponds in wetlands. Accurate estimates of these land cover types at regional to global scales are required to assess the roles of fires and wetlands in global warming, yet difficult to compute when much of the area is accounted for by fragments about the same size as the pixels. In previous research, we found that size distribution of the fragments in several example scenes fit simple two-parameter models and related effects of coarse resolution to errors in area estimates based on pixel counts. We summarize our model based approach to improved area estimations and report on progress to develop accurate areas estimates based on modeling the size distribution of the fragments, including analysis of size distributions on an expanded set of maps developed from digital imagery.

  11. Procedure for assessing the performance of a rockfall fragmentation model

    Science.gov (United States)

    Matas, Gerard; Lantada, Nieves; Corominas, Jordi; Gili, Josep Antoni; Ruiz-Carulla, Roger; Prades, Albert

    2017-04-01

    A Rockfall is a mass instability process frequently observed in road cuts, open pit mines and quarries, steep slopes and cliffs. It is frequently observed that the detached rock mass becomes fragmented when it impacts with the slope surface. The consideration of the fragmentation of the rockfall mass is critical for the calculation of block's trajectories and their impact energies, to further assess their potential to cause damage and design adequate preventive structures. We present here the performance of the RockGIS model. It is a GIS-Based tool that simulates stochastically the fragmentation of the rockfalls, based on a lumped mass approach. In RockGIS, the fragmentation initiates by the disaggregation of the detached rock mass through the pre-existing discontinuities just before the impact with the ground. An energy threshold is defined in order to determine whether the impacting blocks break or not. The distribution of the initial mass between a set of newly generated rock fragments is carried out stochastically following a power law. The trajectories of the new rock fragments are distributed within a cone. The model requires the calibration of both the runout of the resultant blocks and the spatial distribution of the volumes of fragments generated by breakage during their propagation. As this is a coupled process which is controlled by several parameters, a set of performance criteria to be met by the simulation have been defined. The criteria includes: position of the centre of gravity of the whole block distribution, histogram of the runout of the blocks, extent and boundaries of the young debris cover over the slope surface, lateral dispersion of trajectories, total number of blocks generated after fragmentation, volume distribution of the generated fragments, the number of blocks and volume passages past a reference line and the maximum runout distance Since the number of parameters to fit increases significantly when considering fragmentation, the

  12. Fragment separator momentum compression schemes

    Energy Technology Data Exchange (ETDEWEB)

    Bandura, Laura, E-mail: bandura@anl.gov [Facility for Rare Isotope Beams (FRIB), 1 Cyclotron, East Lansing, MI 48824-1321 (United States); National Superconducting Cyclotron Lab, Michigan State University, 1 Cyclotron, East Lansing, MI 48824-1321 (United States); Erdelyi, Bela [Argonne National Laboratory, Argonne, IL 60439 (United States); Northern Illinois University, DeKalb, IL 60115 (United States); Hausmann, Marc [Facility for Rare Isotope Beams (FRIB), 1 Cyclotron, East Lansing, MI 48824-1321 (United States); Kubo, Toshiyuki [RIKEN Nishina Center, RIKEN, Wako (Japan); Nolen, Jerry [Argonne National Laboratory, Argonne, IL 60439 (United States); Portillo, Mauricio [Facility for Rare Isotope Beams (FRIB), 1 Cyclotron, East Lansing, MI 48824-1321 (United States); Sherrill, Bradley M. [National Superconducting Cyclotron Lab, Michigan State University, 1 Cyclotron, East Lansing, MI 48824-1321 (United States)

    2011-07-21

    We present a scheme to use a fragment separator and profiled energy degraders to transfer longitudinal phase space into transverse phase space while maintaining achromatic beam transport. The first order beam optics theory of the method is presented and the consequent enlargement of the transverse phase space is discussed. An interesting consequence of the technique is that the first order mass resolving power of the system is determined by the first dispersive section up to the energy degrader, independent of whether or not momentum compression is used. The fragment separator at the Facility for Rare Isotope Beams is a specific application of this technique and is described along with simulations by the code COSY INFINITY.

  13. Fragment separator momentum compression schemes.

    Energy Technology Data Exchange (ETDEWEB)

    Bandura, L.; Erdelyi, B.; Hausmann, M.; Kubo, T.; Nolen, J.; Portillo, M.; Sherrill, B.M. (Physics); (MSU); (Northern Illinois Univ.); (RIKEN)

    2011-07-21

    We present a scheme to use a fragment separator and profiled energy degraders to transfer longitudinal phase space into transverse phase space while maintaining achromatic beam transport. The first order beam optics theory of the method is presented and the consequent enlargement of the transverse phase space is discussed. An interesting consequence of the technique is that the first order mass resolving power of the system is determined by the first dispersive section up to the energy degrader, independent of whether or not momentum compression is used. The fragment separator at the Facility for Rare Isotope Beams is a specific application of this technique and is described along with simulations by the code COSY INFINITY.

  14. Fragment separator momentum compression schemes

    Science.gov (United States)

    Bandura, Laura; Erdelyi, Bela; Hausmann, Marc; Kubo, Toshiyuki; Nolen, Jerry; Portillo, Mauricio; Sherrill, Bradley M.

    2011-07-01

    We present a scheme to use a fragment separator and profiled energy degraders to transfer longitudinal phase space into transverse phase space while maintaining achromatic beam transport. The first order beam optics theory of the method is presented and the consequent enlargement of the transverse phase space is discussed. An interesting consequence of the technique is that the first order mass resolving power of the system is determined by the first dispersive section up to the energy degrader, independent of whether or not momentum compression is used. The fragment separator at the Facility for Rare Isotope Beams is a specific application of this technique and is described along with simulations by the code COSY INFINITY.

  15. Fragmentering og korridorer i landskabet

    DEFF Research Database (Denmark)

    Hammershøj, M.; Madsen, A. B.

    , at fragmentering af habitater resulterer i en reduktion og isolering af mange plante- og dyrepopulationer. Det er desuden vist, at korridorer har en funktion som habitater, hvilket er medvirkende til, at et område med korridorer kan huse flere arter og individer end et tilsvarende område uden korridorer. Der......Rapporten indeholder en litteraturudredning, der er baseret på en bearbejdning af den tilgængelige nationale og internationale litteratur omhandlende fragmentering og korridorer på det botaniske og zoologiske område. I alt 1.063 titler ligger til grund for udredningen. Udredningen har vist...... mangler dog entydige beviser for, at korridorer kan være af afgørende betydning for rekolonisering af habitater, i hvilke en given art er forsvundet. Afslutningsvis gives en liste med forskningsbehov samt en række anbefalinger....

  16. Fragmentation in the biopharmaceutical industry.

    Science.gov (United States)

    Goldsmith, Andrew D; Varela, Francisco E

    2017-02-01

    The large number of biopharmaceutical mergers and acquisitions (M&A) that occurred over the past decade has generated questions about whether the industry is consolidating around too-few players, negatively impacting both the number of medicines developed and overall innovation. However, closer examination of the level of biopharmaceutical consolidation by prescription sales shows that the industry was more fragmented in 2015 than in 2003. The trend towards increasing fragmentation is also observed across noncommercial and independent metrics over the same time period. The number and size of M&A deals has masked an active and competitive marketplace in which market growth and the number of companies entering the market exceeded the apparent reduction in the number of players caused by acquisitions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Carcinogenesis of Depleted Uranium Fragments.

    Science.gov (United States)

    1996-02-01

    29 of 54 Chinese hamsters injected intravenously with a relatively high dose of Thorotrast (> 0.4 Bq/g) developed fibrosarcomas from perivascular...leakage of some injections (Guilmette et al., 1989). Plutonium fragments have been injected into the footpads of dogs to simulate the plutonium...extensively studied in animals, particularly in rats (Haley, 1982; Haley et al., 1982; Diamond et al., 1987; Morrow et al., 1982) and dogs (Morrow et al

  18. Modeling of Fragmentation of Asteroids

    Science.gov (United States)

    Agrawal, Parul; Prabhu, Dinesh K.; Carlozzi, Alexander; Hart, Kenneth; Bryson, Katie; Sears, Derek

    2015-01-01

    The objective of this study is to understand fragmentation and fracture of a given asteroid and mechanisms of break-up. The focus of the present work is to develop modeling techniques for stony asteroids in 10m-100m range to answer two questions: 1) What is the role of material makeup of an asteroid in the stress distribution? 2)How is stress distribution altered in the presence of pre-existing defects?

  19. Structure, fragmentation and fracture functions

    CERN Document Server

    Canal-Garcia, C A

    2000-01-01

    We address the partonic description of the proton, the photon and the "color singlet, " as seen in inclusive and semi-inclusive DIS, in e /sup +/e/sup $/collisions, and in diffractive processes, respectively. Their formal treatment using structure, fragmentation, and fracture functions is outlined giving an insight into the perturbative QCD framework for these functions. Examples and comparisons with experimental data from LEP, HERA, and Tevatron are also covered. (52 refs).

  20. Fibril fragmentation enhances amyloid cytotoxicity.

    Science.gov (United States)

    Xue, Wei-Feng; Hellewell, Andrew L; Gosal, Walraj S; Homans, Steve W; Hewitt, Eric W; Radford, Sheena E

    2009-12-04

    Fibrils associated with amyloid disease are molecular assemblies of key biological importance, yet how cells respond to the presence of amyloid remains unclear. Cellular responses may not only depend on the chemical composition or molecular properties of the amyloid fibrils, but their physical attributes such as length, width, or surface area may also play important roles. Here, we report a systematic investigation of the effect of fragmentation on the structural and biological properties of amyloid fibrils. In addition to the expected relationship between fragmentation and the ability to seed, we show a striking finding that fibril length correlates with the ability to disrupt membranes and to reduce cell viability. Thus, despite otherwise unchanged molecular architecture, shorter fibrillar samples show enhanced cytotoxic potential than their longer counterparts. The results highlight the importance of fibril length in amyloid disease, with fragmentation not only providing a mechanism by which fibril load can be rapidly increased but also creating fibrillar species of different dimensions that can endow new or enhanced biological properties such as amyloid cytotoxicity.

  1. Residual Fragments after Percutaneous Nephrolithotomy

    Directory of Open Access Journals (Sweden)

    Kaan Özdedeli

    2012-09-01

    Full Text Available Clinically insignificant residual fragments (CIRFs are described as asymptomatic, noninfectious and nonobstructive stone fragments (≤4 mm remaining in the urinary system after the last session of any intervention (ESWL, URS or PCNL for urinary stones. Their insignificance is questionable since CIRFs could eventually become significant, as their presence may result in recurrent stone growth and they may cause pain and infection due to urinary obstruction. They may become the source of persistent infections and a significant portion of the patients will have a stone-related event, requiring auxilliary interventions. CT seems to be the ultimate choice of assessment. Although there is no concensus about the timing, recent data suggests that it may be performed one month after the procedure. However, imaging can be done in the immediate postoperative period, if there are no tubes blurring the assessment. There is some evidence indicating that selective medical therapy may have an impact on decreasing stone formation rates. Retrograde intrarenal surgery, with its minimally invasive nature, seems to be the best way to deal with residual fragments.

  2. A Method for Predicting Fragmentation Characteristics of Natural and Performed Explosive Fragmentation Munitions

    National Research Council Canada - National Science Library

    Gold, Vladimir

    2001-01-01

    New methodology for simulating performance of explosive fragmentation munitions presented in this work integrates three-dimensional axisymmetric hydrocode analyses with analytical fragmentation modeling...

  3. Fragmentation of small carbon clusters, a review

    Energy Technology Data Exchange (ETDEWEB)

    Beroff, K. [Laboratoire des Collisions Atomiques et Moleculaires, CNRS and Universite Paris-Sud, batiment 351, 91405 Orsay Cedex (France)], E-mail: karine.beroff@u-psud.fr; Chabot, M. [Institut de Physique Nucleaire, CNRS-IN2P3 and Universite Paris-Sud, 91405 Orsay Cedex (France); Mezdari, F. [Laboratoire des Collisions Atomiques et Moleculaires, CNRS and Universite Paris-Sud, batiment 351, 91405 Orsay Cedex (France); Martinet, G.; Tuna, T. [Institut de Physique Nucleaire, CNRS-IN2P3 and Universite Paris-Sud, 91405 Orsay Cedex (France); Desesquelles, P. [Centre de Spectrometrie Nucleaire et Spectrometrie de Masse, Universite Paris-Sud and CNRS-IN2P3, batiment 104, 91405 Orsay Cedex (France); LePadellec, A. [Institut de Recherche sur les Systemes Atomiques et Moleculaires Complexes, Universite Paul Sabatier and CNRS, batiment 3R1B4, 31062 Toulouse Cedex 9 (France); Barat, M. [Laboratoire des Collisions Atomiques et Moleculaires, CNRS and Universite Paris-Sud, batiment 351, 91405 Orsay Cedex (France)

    2009-03-15

    An overview of the works devoted to fragmentation of small carbon clusters is given in a first part. Fragmentation of swift neutral and (multi) charged carbon clusters studied with the AGAT spectrometer is presented and discussed in a second part.

  4. Fragmentation of small carbon clusters, a review

    OpenAIRE

    Béroff, K.; Chabot, M.; Mezdari, F.; Martinet, G.; Tuna, T.; Désesquelles, P.; Le Padellec, Arnaud; Barat, M.

    2008-01-01

    An overview of the works devoted to fragmentation of small carbon clusters is given in a first part. Fragmentation of swift neutral and (multi) charged carbon clusters studied with the AGAT spectrometer is presented and discussed in a second part.

  5. Identification of amplified fragment length polymorphism (AFLP ...

    African Journals Online (AJOL)

    Identification of amplified fragment length polymorphism (AFLP) fragments linked to soybean mosaic virus resistance gene in Glycine soja and conversion to a sequence characterized amplified regions (SCAR) marker for rapid selection.

  6. Neo-Epitopes—Fragments of Cartilage and Connective Tissue Degradation in Early Rheumatoid Arthritis and Unclassified Arthritis

    DEFF Research Database (Denmark)

    Maijer, Karen I; Gudmann, Natasja Stæhr; Karsdal, Morten Asser

    2016-01-01

    Objective: Tissue destruction in rheumatoid arthritis (RA) is predominantly mediated by matrix metalloproteinases (MMPs), thereby generating protein fragments. Previous studies have revealed that these fragments include MMP-mediated collagen type I, II, and III degradation, citrullinated and MMP...

  7. Fragment Kinetic Energies and Modes of Fragment Formation

    Science.gov (United States)

    Odeh, T.; Bassini, R.; Begemann-Blaich, M.; Fritz, S.; Gaff-Ejakov, S. J.; Gourio, D.; Groß, C.; Immé, G.; Iori, I.; Kleinevoß, U.; Kunde, G. J.; Kunze, W. D.; Lynen, U.; Maddalena, V.; Mahi, M.; Möhlenkamp, T.; Moroni, A.; Müller, W. F.; Nociforo, C.; Ocker, B.; Petruzzelli, F.; Pochodzalla, J.; Raciti, G.; Riccobene, G.; Romano, F. P.; Saija, A.; Schnittker, M.; Schüttauf, A.; Schwarz, C.; Seidel, W.; Serfling, V.; Sfienti, C.; Trautmann, W.; Trzcinski, A.; Verde, G.; Wörner, A.; Xi, Hongfei; Zwieglinski, B.

    2000-05-01

    Kinetic energies of light fragments ( A<=10) from the decay of target spectators in 197Au+197Au collisions at 1000 MeV per nucleon have been measured with high-resolution telescopes at backward angles. Except for protons and apart from the observed evaporation components, the kinetic-energy spectra exhibit slope temperatures of about 17 MeV, independent of the particle species, but not corresponding to the thermal or chemical degrees of freedom at breakup. It is suggested that these slope temperatures may reflect the intrinsic Fermi motion and thus the bulk density of the spectator system at the instant of becoming unstable.

  8. Optimal Economic Landscapes with Habitat Fragmentation Effects

    OpenAIRE

    Lewis, David J.; Wu, JunJie

    2005-01-01

    Habitat fragmentation is widely considered a primary threat to biodiversity. This paper develops a theoretical model of land use to analyze the optimal conservation of landscapes when land quality is spatially heterogeneous and wildlife habitat is fragmented and socially valuable. When agriculture is the primary cause of fragmentation, we show that reforestation efforts should be targeted to the most fragmented landscapes with an aggregate share of forest equal to a threshold, defined by the ...

  9. Injuries caused by fragmenting rifle ammunition.

    Science.gov (United States)

    Jorgensen, Jorgen Joakim; Naess, Paal Aksel; Gaarder, Christine

    2016-09-01

    Although penetrating injuries are encountered on a regular basis in high volume trauma centres, most civilian trauma teams will be unfamiliar with the treatment of patients with injuries caused by fragmenting ammunition. The terrorist attacks in Norway on July 22, 2011 included a shooting spree causing 69 deaths and 60 injured. One of the weapons used was a semi-automatic rifle, calibre 5.56mm, with soft tip, short stop ammunition. The aim of the present study was to describe the characteristic injury patterns and lessons learned from the treatment of multiple patients admitted at the regional trauma centre with injuries from this type of ammunition. We undertook an observational study of patients admitted at Oslo University Hospital, Ulleval after the shooting spree at Utoya on July 22, 2011. Data on demographics, injuries, injury severity, surgical procedures and outcome were collected prospectively. Of the 21 patients admitted after the shooting incident, 18 were identified with injuries caused by fragmenting ammunition and included in the study. Median age was 17 years (IQR 16, 19), median ISS 21 (IQR 12, 30) and 12 patients were female. They had been hit by a total of 38 projectiles, of which 32 were fragmenting bullets. Of the seven patients who sustained injuries to the head, neck and face, one patient required a craniotomy and one patient had a non-survivable head injury. Of the 11 patients with torso injuries, six of the eight patients with chest injuries had intra-thoracic injuries that could be treated with chest tubes only. One patient had cardiac tamponade, requiring thoracotomy. Six patients underwent laparotomy, four of them more than one. Of the 10 patients with extremity injuries, two had nerve injuries and six patients had fractures. Five amputations were performed within the first nine days. A total of 101 operations were required within the first four weeks. The majority of these were repeated soft tissue debridements due to progressive necrosis

  10. Characterization of hypervelocity metal fragments for explosive initiation

    Science.gov (United States)

    Yeager, John D.; Bowden, Patrick R.; Guildenbecher, Daniel R.; Olles, Joseph D.

    2017-07-01

    The fragment impact response of two plastic-bonded explosive (PBX) formulations was studied using explosively driven aluminum fragments. A generic aluminum-capped detonator generated sub-mm aluminum particles moving at hypersonic velocities. The ability of these fragments to initiate reaction or otherwise damage two PBX materials was assessed using go/no-go experiments at standoff distances of up to 160 mm. Lower density PBX 9407 (RDX-based) was initiable at up to 115 mm, while higher density PBX 9501 (HMX-based) was only initiable at up to 6 mm. Several techniques were used to characterize the size, distribution, and velocity of the particles. Witness plate materials, including copper and polycarbonate, and backlit high speed video were used to characterize the distribution of particles, finding that the aluminum cap did not fragment homogeneously but rather with larger particles in a ring surrounding finer particles. Finally, precise digital holography experiments were conducted to measure the three-dimensional shape and size of the fastest-moving fragments, which ranged between 100 and 700 μm and traveled between 2.2 and 3.2 km/s. Crucially, these experiments showed variability in the fragmentation in terms of the number of fragments at the leading edge of the fragment field, indicating that both single and multiple shock impacts could be imparted to the target material. These types of data are critical for safety experiments and hydrocode simulations to quantify shock-to-detonation transition mechanisms and the associated risk-margins for these materials.

  11. Validation of Geant4 fragmentation for Heavy Ion Therapy

    Science.gov (United States)

    Bolst, David; Cirrone, Giuseppe A. P.; Cuttone, Giacomo; Folger, Gunter; Incerti, Sebastien; Ivanchenko, Vladimir; Koi, Tatsumi; Mancusi, Davide; Pandola, Luciano; Romano, Francesco; Rosenfeld, Anatoly B.; Guatelli, Susanna

    2017-10-01

    12C ion therapy has had growing interest in recent years for its excellent dose conformity. However at therapeutic energies, which can be as high as 400 MeV/u, carbon ions produce secondary fragments. For an incident 400 MeV/u 12C ion beam, ∼ 70 % of the beam will undergo fragmentation before the Bragg Peak. The dosimetric and radiobiological impact of these fragments must be accurately characterised, as it can result in increasing the risk of secondary cancer for the patient as well as altering the relative biological effectiveness. This work investigates the accuracy of three different nuclear fragmentation models available in the Monte Carlo Toolkit Geant4, the Binary Intranuclear Cascade (BIC), the Quantum Molecular Dynamics (QMD) and the Liege Intranuclear Cascade (INCL++). The models were benchmarked against experimental data for a pristine 400 MeV/u 12C beam incident upon a water phantom, including fragment yield, angular and energy distribution. For fragment yields the three alternative models agreed between ∼ 5 and ∼ 35 % with experimental measurements, the QMD using the ;Frag; option gave the best agreement for lighter fragments but had reduced agreement for larger fragments. For angular distributions INCL++ was seen to provide the best agreement among the models for all elements with the exception of Hydrogen, while BIC and QMD was seen to produce broader distributions compared to experiment. BIC and QMD performed similar to one another for kinetic energy distributions while INCL++ suffered from producing lower energy distributions compared to the other models and experiment.

  12. The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds

    Science.gov (United States)

    Steinmann, Casper; Fedorov, Dmitri G.; Jensen, Jan H.

    2012-01-01

    We extend the effective fragment molecular orbital method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including proteins. Errors in energy for RHF and MP2 are within 2 kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides similar to FMO but obtained two to five times faster. For proteins, the errors are also within a few kcal/mol of the FMO results. We developed both the RHF and MP2 gradient for EFMO. Compared to ab initio, the EFMO optimized structures had an RMSD of 0.40 and 0.44 Å for RHF and MP2, respectively. PMID:22844433

  13. The effective fragment molecular orbital method for fragments connected by covalent bonds.

    Directory of Open Access Journals (Sweden)

    Casper Steinmann

    Full Text Available We extend the effective fragment molecular orbital method (EFMO into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including proteins. Errors in energy for RHF and MP2 are within 2 kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides similar to FMO but obtained two to five times faster. For proteins, the errors are also within a few kcal/mol of the FMO results. We developed both the RHF and MP2 gradient for EFMO. Compared to ab initio, the EFMO optimized structures had an RMSD of 0.40 and 0.44 Å for RHF and MP2, respectively.

  14. Self-organized criticality in fragmenting

    DEFF Research Database (Denmark)

    Oddershede, L.; Dimon, P.; Bohr, J.

    1993-01-01

    The measured mass distributions of fragments from 26 fractured objects of gypsum, soap, stearic paraffin, and potato show evidence of obeying scaling laws; this suggests the possibility of self-organized criticality in fragmenting. The probability of finding a fragment scales inversely to a power...

  15. Scaling and four-quark fragmentation

    NARCIS (Netherlands)

    Scholten, O.; Bosveld, G. D.

    1991-01-01

    The conditions for a scaling behaviour from the fragmentation process leading to slow protons are discussed. The scaling referred to implies that the fragmentation functions depend on the light-cone momentum fraction only. It is shown that differences in the fragmentation functions for valence- and

  16. Population pressure and farm fragmentation: Challenges facing ...

    African Journals Online (AJOL)

    In addition, the size of farms is not only very small but farms are further fragmented into diminutive size fields due to increasing population pressure. The magnitude of fragmentation has increased overtime. Effects of population pressure and farm fragmentation are studied based on a survey of 200 households from Rusatira ...

  17. Micro-Satellite Impact Tests to Investigate Multi-Layer Insulation Fragments

    Science.gov (United States)

    Murakami, Junko; Hanada, Toshiya; Liou, J.-C.; Stansbery, Eugene

    2009-03-01

    This paper summarizes two satellite impact experiments completed in 2008. The objective of the experiments is to investigate the physical properties of satellite fragments, including those originated from Multi-Layer Insulation and a solar panel. One test generated approximately 1,800 fragments while the other produced only 1,000 fragments. This difference came from the number of needle-like fragments from carbon fiber reinforced plastics. All collected fragments were analyzed using the same method as described in the NASA standard breakup model and compared with the breakup model. This paper will present: (1) the area-to-mass ratio, size, and mass distributions of the fragments, and (2) the differences in fragment properties between the two tests.

  18. Fragmentation in massive star formation.

    Science.gov (United States)

    Beuther, Henrik; Schilke, Peter

    2004-02-20

    Studies of evolved massive stars indicate that they form in a clustered mode. During the earliest evolutionary stages, these regions are embedded within their natal cores. Here we present high-spatial-resolution interferometric dust continuum observations disentangling the cluster-like structure of a young massive star-forming region. The derived protocluster mass distribution is consistent with the stellar initial mass function. Thus, fragmentation of the initial massive cores may determine the initial mass function and the masses of the final stars. This implies that stars of all masses can form via accretion processes, and coalescence of intermediate-mass protostars appears not to be necessary.

  19. DRAG COEFFICIENTS FOR IRREGULAR FRAGMENTS

    Science.gov (United States)

    1986-08-01

    regular fragments.were studied In the report, I.e., a sphere, a c-ibe and a bar. Th.a bar length, 1530) 77= pp. P width and thickness were. in the ratio...measurements for the 96 fragmento are contained in Tables A-1, A-2 and A-3 of Appendix A. The esiential aspects of the vertical wind tunnel are shown...THICKNESS L’ MAXIMUM LENGTH P ..UPS AVERAGE LENGTH W’ M AXIMUM WIDTH PLUS AVERAGE WIDTH T’ M I’XIX1MUM THICKNESS PLUS AVERAIE THICKNESS i -- STANDARO DEVIATION

  20. Dihadron fragmentation functions for large invariant mass.

    Science.gov (United States)

    Zhou, J; Metz, A

    2011-04-29

    Using perturbative quantum chromodynamics, we compute dihadron fragmentation functions for a large invariant mass of the dihadron pair. The main focus is on the interference fragmentation function H(1)(∢), which plays an important role in spin physics of the nucleon. Our calculation also reveals that H(1)(∢) and the Collins fragmentation function have closely related underlying dynamics. By considering semi-inclusive deep-inelastic scattering, we further show that collinear factorization in terms of dihadron fragmentation functions and collinear factorization in terms of single-hadron fragmentation functions provide the same result in the region of intermediate invariant mass.

  1. Reframing landscape fragmentation's effects on ecosystem services.

    Science.gov (United States)

    Mitchell, Matthew G E; Suarez-Castro, Andrés F; Martinez-Harms, Maria; Maron, Martine; McAlpine, Clive; Gaston, Kevin J; Johansen, Kasper; Rhodes, Jonathan R

    2015-04-01

    Landscape structure and fragmentation have important effects on ecosystem services, with a common assumption being that fragmentation reduces service provision. This is based on fragmentation's expected effects on ecosystem service supply, but ignores how fragmentation influences the flow of services to people. Here we develop a new conceptual framework that explicitly considers the links between landscape fragmentation, the supply of services, and the flow of services to people. We argue that fragmentation's effects on ecosystem service flow can be positive or negative, and use our framework to construct testable hypotheses about the effects of fragmentation on final ecosystem service provision. Empirical efforts to apply and test this framework are critical to improving landscape management for multiple ecosystem services. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. The formation of planets by disc fragmentation

    Directory of Open Access Journals (Sweden)

    Stamatellos Dimitris

    2013-04-01

    Full Text Available I discuss the role that disc fragmentation plays in the formation of gas giant and terrestrial planets, and how this relates to the formation of brown dwarfs and low-mass stars, and ultimately to the process of star formation. Protostellar discs may fragment, if they are massive enough and can cool fast enough, but most of the objects that form by fragmentation are brown dwarfs. It may be possible that planets also form, if the mass growth of a proto-fragment is stopped (e.g. if this fragment is ejected from the disc, or suppressed and even reversed (e.g by tidal stripping. I will discuss if it is possible to distinguish whether a planet has formed by disc fragmentation or core accretion, and mention of a few examples of observed exoplanets that are suggestive of formation by disc fragmentation.

  3. Sleep fragmentation in canine narcolepsy.

    Science.gov (United States)

    Kaitin, K I; Kilduff, T S; Dement, W C

    1986-01-01

    Genetically narcoleptic dogs were recorded continuously for 24 h to examine their sleep-wake patterns and to evaluate the extent of sleep fragmentation. Three narcoleptic and three control dogs from each of two affected breeds (Labrador retrievers and Doberman pinschers) were surgically implanted with electrodes for recording standard sleep parameters. Recordings were scored in 30-s epochs for the states of active waking, drowsiness, light sleep, deep slow wave sleep, REM sleep, and cataplexy. All affected dogs displayed marked fragmentation and disruption of the sleep-wake cycle characterized by repeated awakenings, frequent shifts in sleep stages, numerous attacks of cataplexy occurring from active waking, and a disturbance of the normal REM-NREM periodicity. This sleep disruption was reflected in significantly greater numbers of episodes of each behavioral state as well as in a 38% increase in the total number of all states. These results demonstrate a severe disturbance of the normal sleep pattern in canine narcoleptics. The possibility of a general dysfunction of circadian organization is discussed.

  4. Binding-site assessment by virtual fragment screening.

    Directory of Open Access Journals (Sweden)

    Niu Huang

    Full Text Available The accurate prediction of protein druggability (propensity to bind high-affinity drug-like small molecules would greatly benefit the fields of chemical genomics and drug discovery. We have developed a novel approach to quantitatively assess protein druggability by computationally screening a fragment-like compound library. In analogy to NMR-based fragment screening, we dock approximately 11,000 fragments against a given binding site and compute a computational hit rate based on the fraction of molecules that exceed an empirically chosen score cutoff. We perform a large-scale evaluation of the approach on four datasets, totaling 152 binding sites. We demonstrate that computed hit rates correlate with hit rates measured experimentally in a previously published NMR-based screening method. Secondly, we show that the in silico fragment screening method can be used to distinguish known druggable and non-druggable targets, including both enzymes and protein-protein interaction sites. Finally, we explore the sensitivity of the results to different receptor conformations, including flexible protein-protein interaction sites. Besides its original aim to assess druggability of different protein targets, this method could be used to identifying druggable conformations of flexible binding site for lead discovery, and suggesting strategies for growing or joining initial fragment hits to obtain more potent inhibitors.

  5. A Comminution Model for Secondary Fragmentation Assessment for Block Caving

    Science.gov (United States)

    Gómez, René; Castro, Raúl L.; Casali, Aldo; Palma, Sergio; Hekmat, Asieh

    2017-11-01

    Predicting the rock fragmentation obtained in drawpoints or secondary fragmentation is crucial in Block caving application since many engineering decisions are based on this key variable. These can include drawpoints size and spacing, equipment selection; draw control procedures, production rates, dilution entry and operational blasting requirements. Secondary fragmentation depends on several variables including structures, rock mass strength, the vertical pressure acting on the column, the rate of draw, and the height of the ore column. In order to study these variables, 18 experiments on gravity flow under confinement were run to quantify the fragmentation occurring in a draw column. Based on these experiments, a mathematical model was developed the basis of which considers a modified comminution model fitted using the experimental data. Finally, the fitted model was scaled up to represent what is expected to occur in practice compared to field data with an estimated accuracy of around 1.5% of size distributions. An approximation of the secondary fragmentation expected as a function of draw height and vertical pressure, for example for 400 m of ore column (mean vertical pressure of 4.2 MPa), the mean size, d 50, could decrease from 0.82 to 0.47 m and the large size, d 80, from 1.08 to 0.62 m.

  6. Is forest fragmentation driven by the spatial configuration of land quality? The case of western Oregon.

    Science.gov (United States)

    Ralph J. Alig; David J. Lewis; Jennifer J. Swenson

    2005-01-01

    We investigated spatial configuration of economic returns, to enhance models of forest fragmentation for western Oregon and western Washington. Drawing from spatial land rent theory, economic drivers of forest fragmentation at the landscape level include land quality comprised of attributes such as soil fertility or the distance of urban plots to amenities. We included...

  7. A linear relationship between crystal size and fragment binding time observed crystallographically: implications for fragment library screening using acoustic droplet ejection.

    Directory of Open Access Journals (Sweden)

    Krystal Cole

    Full Text Available High throughput screening technologies such as acoustic droplet ejection (ADE greatly increase the rate at which X-ray diffraction data can be acquired from crystals. One promising high throughput screening application of ADE is to rapidly combine protein crystals with fragment libraries. In this approach, each fragment soaks into a protein crystal either directly on data collection media or on a moving conveyor belt which then delivers the crystals to the X-ray beam. By simultaneously handling multiple crystals combined with fragment specimens, these techniques relax the automounter duty-cycle bottleneck that currently prevents optimal exploitation of third generation synchrotrons. Two factors limit the speed and scope of projects that are suitable for fragment screening using techniques such as ADE. Firstly, in applications where the high throughput screening apparatus is located inside the X-ray station (such as the conveyor belt system described above, the speed of data acquisition is limited by the time required for each fragment to soak into its protein crystal. Secondly, in applications where crystals are combined with fragments directly on data acquisition media (including both of the ADE methods described above, the maximum time that fragments have to soak into crystals is limited by evaporative dehydration of the protein crystals during the fragment soak. Here we demonstrate that both of these problems can be minimized by using small crystals, because the soak time required for a fragment hit to attain high occupancy depends approximately linearly on crystal size.

  8. A linear relationship between crystal size and fragment binding time observed crystallographically: implications for fragment library screening using acoustic droplet ejection.

    Science.gov (United States)

    Cole, Krystal; Roessler, Christian G; Mulé, Elizabeth A; Benson-Xu, Emma J; Mullen, Jeffrey D; Le, Benjamin A; Tieman, Alanna M; Birone, Claire; Brown, Maria; Hernandez, Jesus; Neff, Sherry; Williams, Daniel; Allaire, Marc; Orville, Allen M; Sweet, Robert M; Soares, Alexei S

    2014-01-01

    High throughput screening technologies such as acoustic droplet ejection (ADE) greatly increase the rate at which X-ray diffraction data can be acquired from crystals. One promising high throughput screening application of ADE is to rapidly combine protein crystals with fragment libraries. In this approach, each fragment soaks into a protein crystal either directly on data collection media or on a moving conveyor belt which then delivers the crystals to the X-ray beam. By simultaneously handling multiple crystals combined with fragment specimens, these techniques relax the automounter duty-cycle bottleneck that currently prevents optimal exploitation of third generation synchrotrons. Two factors limit the speed and scope of projects that are suitable for fragment screening using techniques such as ADE. Firstly, in applications where the high throughput screening apparatus is located inside the X-ray station (such as the conveyor belt system described above), the speed of data acquisition is limited by the time required for each fragment to soak into its protein crystal. Secondly, in applications where crystals are combined with fragments directly on data acquisition media (including both of the ADE methods described above), the maximum time that fragments have to soak into crystals is limited by evaporative dehydration of the protein crystals during the fragment soak. Here we demonstrate that both of these problems can be minimized by using small crystals, because the soak time required for a fragment hit to attain high occupancy depends approximately linearly on crystal size.

  9. Single chain Fab (scFab fragment

    Directory of Open Access Journals (Sweden)

    Brenneis Mariam

    2007-03-01

    Full Text Available Abstract Background The connection of the variable part of the heavy chain (VH and and the variable part of the light chain (VL by a peptide linker to form a consecutive polypeptide chain (single chain antibody, scFv was a breakthrough for the functional production of antibody fragments in Escherichia coli. Being double the size of fragment variable (Fv fragments and requiring assembly of two independent polypeptide chains, functional Fab fragments are usually produced with significantly lower yields in E. coli. An antibody design combining stability and assay compatibility of the fragment antigen binding (Fab with high level bacterial expression of single chain Fv fragments would be desirable. The desired antibody fragment should be both suitable for expression as soluble antibody in E. coli and antibody phage display. Results Here, we demonstrate that the introduction of a polypeptide linker between the fragment difficult (Fd and the light chain (LC, resulting in the formation of a single chain Fab fragment (scFab, can lead to improved production of functional molecules. We tested the impact of various linker designs and modifications of the constant regions on both phage display efficiency and the yield of soluble antibody fragments. A scFab variant without cysteins (scFabΔC connecting the constant part 1 of the heavy chain (CH1 and the constant part of the light chain (CL were best suited for phage display and production of soluble antibody fragments. Beside the expression system E. coli, the new antibody format was also expressed in Pichia pastoris. Monovalent and divalent fragments (DiFabodies as well as multimers were characterised. Conclusion A new antibody design offers the generation of bivalent Fab derivates for antibody phage display and production of soluble antibody fragments. This antibody format is of particular value for high throughput proteome binder generation projects, due to the avidity effect and the possible use of

  10. Fragmentation in Carbon Therapy Beams

    CERN Document Server

    Charara, Y M

    2010-01-01

    The state of the art Monte Carlo code HETC-HEDS was used to simulate spallation products, secondary neutron, and secondary proton production in A-150 Tissue Equivalent Plastic phantoms to investigate fragmentation of carbon therapy beams. For a 356 MeV/Nucleon carbon ion beam, production of charged particles heavier than protons was 0.24 spallation products per incident carbon ion with atomic numbers ranging from 1 through 5 (hydrogen to boron). In addition, there were 4.73 neutrons and 2.95 protons produced per incident carbon ion. Furthermore, as the incident energy increases, the neutron production rate increases at a rate of 20% per 10 MeV/nucleon. Secondary protons were created at a rate between 2.62-2.87 per carbon ion, while spallation products were created at a rate between 0.20-0.24 per carbon ion.

  11. Fluid fragmentation from hospital toilets

    CERN Document Server

    Traverso, G; Lu, C -C; Maa, R; Langer, R; Bourouiba, L

    2013-01-01

    Hospital-acquired infections represent significant health and financial burdens to society. Clostridium difficile (C. difficile) is a particularly challenging bacteria with the potential to cause severe diarrhea and death. One mode of transmission for C. difficile, as well as other pathogens, which has received little attention is the potential air contamination by pathogen-bearing droplets emanating from toilets. In the fluid dynamics video submitted to the APS DFD Gallery of Fluid Motion 2013, we present flow visualizations via high-speed recordings showing the capture of the product of the fluid fragmentation generated by hospital toilet high-pressure flushes. Important quantities of both large and small droplets are observed. We illustrate how high-pressure flushes and cleaning products currently used in hospital toilets result in aggravating, rather than alleviating, the suspension and recirculation of tenacious airborne pathogen-bearing droplets.

  12. High yield DNA fragmentation using cyclical hydrodynamic shearing

    NARCIS (Netherlands)

    Shui, Lingling; Sparreboom, Wouter; Spang, Peter; Roeser, Tina; Nieto, Benjamin; Guasch, Francesc; Corbera, Antoni Homs; van den Berg, Albert; Carlen, Edwin

    2013-01-01

    We report a new DNA fragmentation technique that significantly simplifies conventional hydrodynamic shearing fragmentation by eliminating the need for sample recirculation while maintaining high fragmentation yield and low fragment length variation, and therefore, reduces instrument complexity and

  13. Use of amplified fragment length polymorphism analysis to identify medically important Candida spp., including C. dubliniensis.

    NARCIS (Netherlands)

    Borst, A; Theelen, B; Reinders, E; Boekhout, T; Fluit, AC; Savelkoul, P.H.M.

    2003-01-01

    Non-Candida albicans Candida species are increasingly being isolated. These species show differences in levels of resistance to antimycotic agents and mortality. Therefore, it is important to be able to correctly identify the causative organism to the species level. Identification of C. dubliniensis

  14. Optical modulator including grapene

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Ming; Yin, Xiaobo; Zhang, Xiang

    2016-06-07

    The present invention provides for a one or more layer graphene optical modulator. In a first exemplary embodiment the optical modulator includes an optical waveguide, a nanoscale oxide spacer adjacent to a working region of the waveguide, and a monolayer graphene sheet adjacent to the spacer. In a second exemplary embodiment, the optical modulator includes at least one pair of active media, where the pair includes an oxide spacer, a first monolayer graphene sheet adjacent to a first side of the spacer, and a second monolayer graphene sheet adjacent to a second side of the spacer, and at least one optical waveguide adjacent to the pair.

  15. The chemistry of protoplanetary fragments formed via gravitational instabilities

    Science.gov (United States)

    Ilee, J. D.; Forgan, D. H.; Evans, M. G.; Hall, C.; Booth, R.; Clarke, C. J.; Rice, W. K. M.; Boley, A. C.; Caselli, P.; Hartquist, T. W.; Rawlings, J. M. C.

    2017-11-01

    In this paper, we model the chemical evolution of a 0.25 M⊙ protoplanetary disc surrounding a 1 M⊙ star that undergoes fragmentation due to self-gravity. We use smoothed particle hydrodynamics including a radiative transfer scheme, along with a time-dependent chemical evolution code to follow the composition of the disc and resulting fragments over approximately 4000 yr. Initially, four quasi-stable fragments are formed, of which two are eventually disrupted by tidal torques in the disc. From the results of our chemical modelling, we identify species that are abundant in the fragments (e.g. H2O, H2S, HNO, N2, NH3, OCS, SO), species that are abundant in the spiral shocks within the disc (e.g. CO, CH4, CN, CS, H2CO) and species that are abundant in the circumfragmentary material (e.g. HCO+). Our models suggest that in some fragments it is plausible for grains to sediment to the core before releasing their volatiles into the planetary envelope, leading to changes in, e.g., the C/O ratio of the gas and ice components. We would therefore predict that the atmospheric composition of planets generated by gravitational instability should not necessarily follow the bulk chemical composition of the local disc material.

  16. Hadronic and electromagnetic fragmentation of ultrarelativistic heavy ions at LHC

    Directory of Open Access Journals (Sweden)

    H. H. Braun

    2014-02-01

    Full Text Available Reliable predictions of yields of nuclear fragments produced in electromagnetic dissociation and hadronic fragmentation of ion beams are of great practical importance in analyzing beam losses and interactions with the beam environment at the Large Hadron Collider (LHC at CERN as well as for estimating radiation effects of galactic cosmic rays on the spacecraft crew and electronic equipment. The model for predicting the fragmentation of relativistic heavy ions is briefly described, and then applied to problems of relevance for LHC. The results are based on the fluka code, which includes electromagnetic dissociation physics and dpmjet-iii as hadronic event generator. We consider the interaction of fully stripped lead ions with nuclei in the energy range from about one hundred MeV to ultrarelativistic energies. The yields of fragments close in the mass and charge to initial ions are calculated. The approach under discussion provides a good overall description of Pb fragmentation data at 30 and 158A  GeV as well as recent LHC data for sqrt[s_{NN}]=2.76  TeV Pb-Pb interactions. Good agreement with the calculations in the framework of different models is found. This justifies application of the developed simulation technique both at the LHC injection energy of 177A  GeV and at its collision energies of 1.38, 1.58, and 2.75A  TeV, and gives confidence in the results obtained.

  17. Session A6 Rangelands as dynamic systems — Fragmentation of ...

    African Journals Online (AJOL)

    In this symposium, we consider the effects of fragmentation of rangelands and ensuing loss of biological complexity for a variety of processes including behaviour and performance of large herbivores, responses of plant communities to herbivory, and functioning of human social and economic systems. We invite posters that ...

  18. Urinary collagen fragments are significantly altered in diabetes

    DEFF Research Database (Denmark)

    2010-01-01

    ) with 85% (95% CI: 81-88%) accuracy. Specific collagen fragments were associated with diabetes and type of diabetes indicating changes in collagen turnover and extracellular matrix as one hallmark of the molecular pathophysiology of diabetes. Additional biomarkers including inflammatory processes and pro...

  19. Visual Impairment, Including Blindness

    Science.gov (United States)

    ... Who Knows What? (log-in required) Select Page Visual Impairment, Including Blindness Mar 31, 2017 Links updated, ... doesn’t wear his glasses. Back to top Visual Impairments in Children Vision is one of our ...

  20. Impact of Fragmentation Issue in Construction Industry: An Overview

    Directory of Open Access Journals (Sweden)

    Mohd Nawi Mohd Nasrun

    2014-01-01

    Full Text Available In general, fragmentation within the construction industry arises from two areas within the traditional construction process; the construction work process where the most significant division is in the separation of the design and construction phase, and the construction structure itself. The fragmentation process in traditional contracting practice further hinders the integration of construction knowledge among contractors, diminishing the opportunity for them to influence design decisions. When design professionals fail to consider as to how a contractor would construct the designed project results in scheduling problems, delays, and disputes during the construction process. Moving towards team integration is considered a significant strategy for overcoming the issue. Accordingly, this paper discusses the fragmentation issue in more detail including its definition, and causes and effects to the construction projects. It also explores that the team integration strategy alleviates scheduling problems, and helps avoid delays and disputes during the construction process, preventing harm to overall project performance.

  1. Filter for interpretation of fragmentation during entry

    Energy Technology Data Exchange (ETDEWEB)

    Canavan, G.H.

    1997-10-01

    Objects that fragment cascade and decelerate abruptly, producing short, bright, signatures which can be used to estimate object diameter and speed. Other objects can be incorporated into a generalized fragmentation filter. This note summarizes the results of previous reports on the prediction and inversion of signatures from objects that radiate, ablate, and fragment during entry and uses them to produce models for the parameters of entering objects.

  2. Interaction of three fission fragments and yields of various ternary fragments

    Science.gov (United States)

    Denisov, V. Yu.; Pilipenko, N. A.; Sedykh, I. Yu.

    2017-01-01

    The interaction potential energy of the three deformed fragments formed in fission of 252Cf is studied for various combinations of three-fragment fission. The lowest height of the potential energy ridge between three touching and separated deformed fragments is sought. The excitation energies of various three-deformed-fragment configurations, at the lowest barrier heights related to the yield of the corresponding configuration, are considered in detail. The most probable three-fragment fission configurations are discussed. The yields of various ternary fragments in fission of 250Cf agree well with available experimental data.

  3. Electronic Predetermination of Ethylene Fragmentation Dynamics

    Directory of Open Access Journals (Sweden)

    Xinhua Xie

    2014-04-01

    Full Text Available We experimentally investigate the dependence of the fragmentation behavior of the ethylene dication on the intensity and duration of the laser pulses that initiate the fragmentation dynamics by strong-field double ionization. Using coincidence momentum imaging for the detection of ionic fragments, we disentangle the different contributions of ionization from lower-valence orbitals and field-driven excitation dynamics to the population of certain dissociative excited ionic states that are connected to one of several possible fragmentation pathways towards a given set of fragment ions. We find that the excitation probability to a particular excited state and therewith the outcome of the fragmentation reaction strongly depend on the parameters of the laser pulse. This, in turn, opens up new possibilities for controlling the outcome of fragmentation reactions of polyatomic molecules in that it may allow one to selectively enhance or suppress individual fragmentation channels, which was not possible in previous attempts of controlling fragmentation processes of polyatomic molecules with strong laser fields.

  4. Molecular energies from an incremental fragmentation method

    Science.gov (United States)

    Meitei, Oinam Romesh; Heßelmann, Andreas

    2016-02-01

    The systematic molecular fragmentation method by Collins and Deev [J. Chem. Phys. 125, 104104 (2006)] has been used to calculate total energies and relative conformational energies for a number of small and extended molecular systems. In contrast to the original approach by Collins, we have tested the accuracy of the fragmentation method by utilising an incremental scheme in which the energies at the lowest level of the fragmentation are calculated on an accurate quantum chemistry level while lower-cost methods are used to correct the low-level energies through a high-level fragmentation. In this work, the fragment energies at the lowest level of fragmentation were calculated using the random-phase approximation (RPA) and two recently developed extensions to the RPA while the incremental corrections at higher levels of the fragmentation were calculated using standard density functional theory (DFT) methods. The complete incremental fragmentation method has been shown to reproduce the supermolecule results with a very good accuracy, almost independent on the molecular type, size, or type of decomposition. The fragmentation method has also been used in conjunction with the DFT-SAPT (symmetry-adapted perturbation theory) method which enables a breakdown of the total nonbonding energy contributions into individual interaction energy terms. Finally, the potential problems of the method connected with the use of capping hydrogen atoms are analysed and two possible solutions are supplied.

  5. Next-generation fragment separators for exotic beams

    Science.gov (United States)

    Bandura, Laura Leigh

    The next generation of nuclear physics research will require advanced exotic beam facilities based on heavy-ion drivers. Exotic beams of rare nuclei will be produced via fragmentation and fission reactions resulting from a high-energy heavy-ion beam hitting a target. A large aperture fragment separator with superconducting magnets is needed for capture, selection, and transport of rare isotopes for experiments. The code COSY INFINTIY uses powerful differential algebra (DA) methods for computing the dynamics of the beam in the fragment separator. A hybrid map-Monte Carlo code has been developed and added to COSY to calculate beam-material interactions. This code tracks the fragmentation and fission of the beam in target and absorber material while computing energy loss and energy and angular straggling as well as charge state evolution of the beam by implementing auxiliary codes such as ATIMA and GLOBAL. EPAX has been utilized to return the cross-sections of fragmentation products. The special case of fission has been treated by integrating the code MCNPX to accurately predict cross-sections and dynamics of exotic beams produced by a 238U beam incident on a Li or C target. Fragment separator designs based on optical symmetries and optimized to be aberration-free are presented. For isotope separation, the Brho-DeltaE-Brho method is used, requiring the addition of an energy absorber. Shaped surfaces are used in order to reduce optical aberrations, resulting in a high-purity rare isotope beam. Beam purity is investigated for four rare isotope production mechanisms, namely light and heavy nuclear fragmentation and light and heavy nuclear fission. Each of these presents unique challenges due to the dynamics of the beam and background contamination produced. Optimized fragment separator settings are presented for each production reaction mechanism and purity results are shown after each selection stage. These include a first- and second-stage achromatic selection and gas

  6. Modelling rock fragmentation of Extremely Energetic Rockfalls

    Science.gov (United States)

    De Blasio, Fabio; Dattola, Giuseppe; Battista Crosta, Giovanni

    2017-04-01

    Extremely energetic rockfalls (EER) are phenomena for which the combination of a large volume (at least some thousands of m ) and a free fall height of hundreds of metres, results in a large released energy. We fix a threshold value of around 1/50 of kilotons to define such a type of events. Documented examples include several events with dif-ferent size in the Alps (Dru, 2005, 2011, 265,000, 59,200 m3; val Fiscalina - Cima Una, 2007, 40,000 m3; Thurwieser 2004, ca 2 Mm3; Cengalo, 2011, 1.5*105 m3 in 2016, in Switzerland; Civetta, 2013, ca 50,000 m3;), in the Apennines (Gran Sasso, 2006, 30,000 m3), Rocky Mountains (Yosemite, Happy Isles, 38,000 m3), and Himalaya. EERs may become more frequent on steep and sharp mountain peaks as a consequence of permafrost thawing at higher altitudes. In contrast to low energy rockfalls where block disintegration is limited, in EERs the impact after free fall causes an immediate and efficient release of energy much like an explosion. The severe disintegration of the rock and the corresponding air blast are capable of snapping trees many hundreds of metres ahead of the fall area. Pulverized rock at high speed can abrade tree logs, and the resulting suspension flow may travel much further the impact zone, blanketing vast surrounding areas. Using both published accounts of some of these events and collecting direct data for some of them, we present some basic models to describe the involved processes based on analogies with explosions and explosive fragmentation. Of the initial energy, one part is used up in the rock disintegration, and the rest is shared between the shock wave and air blast. The fragmentation energy is calculated based on the fitting of the dust size spectrum by using different proba-bilistic distribution laws and the definition of a surface energy and by considering the involved strain rate. We find the fragmentation is around one third of the initial boulder energy. Finally, we evaluate the velocity of the

  7. Quark to Λ-hyperon spin transfers in the current-fragmentation region

    Science.gov (United States)

    Chi, Yujie; Ma, Bo-Qiang

    2013-11-01

    We perform a study on the struck quark to the Λ-hyperon fragmentation processes by taking into account the anti-quark fragmentations and intermediate decays from other hyperons. We concentrate on how the longitudinally polarized quark fragments to the longitudinally polarized Λ, how unpolarized quark and anti-quark fragment to the unpolarized Λ, and how quark and anti-quark fragment to the Λ through the intermediate decay processes. We calculate the effective fragmentation functions in the light-cone SU(6) quark-spectator-diquark model via the Gribov-Lipatov relation, with the Melosh-Wigner rotation effect also included. The calculated results are in reasonable agreement with the HERMES semi-inclusive ep experimental data and the OPAL and ALEPH e+e- annihilation experimental data.

  8. Applications of 19F-NMR in Fragment-Based Drug Discovery

    Directory of Open Access Journals (Sweden)

    Raymond S. Norton

    2016-07-01

    Full Text Available 19F-NMR has proved to be a valuable tool in fragment-based drug discovery. Its applications include screening libraries of fluorinated fragments, assessing competition among elaborated fragments and identifying the binding poses of promising hits. By observing fluorine in both the ligand and the target protein, useful information can be obtained on not only the binding pose but also the dynamics of ligand-protein interactions. These applications of 19F-NMR will be illustrated in this review with studies from our fragment-based drug discovery campaigns against protein targets in parasitic and infectious diseases.

  9. Listening to Include

    Science.gov (United States)

    Veck, Wayne

    2009-01-01

    This paper attempts to make important connections between listening and inclusive education and the refusal to listen and exclusion. Two lines of argument are advanced. First, if educators and learners are to include each other within their educational institutions as unique individuals, then they will need to listen attentively to each other.…

  10. Decoupling habitat fragmentation from habitat loss: butterfly species mobility obscures fragmentation effects in a naturally fragmented landscape of lake islands.

    Science.gov (United States)

    MacDonald, Zachary G; Anderson, Iraleigh D; Acorn, John H; Nielsen, Scott E

    2018-01-01

    Since the publication of the theory of island biogeography, ecologists have postulated that fragmentation of continuous habitat presents a prominent threat to species diversity. However, negative fragmentation effects may be artifacts; the result of species diversity declining with habitat loss, and habitat loss correlating positively with degree of fragmentation. In this study, we used butterfly assemblages on islands of Lake of the Woods, Ontario, Canada to decouple habitat fragmentation from habitat loss and test two competing hypotheses: (1) the island effect hypothesis, which predicts that decreasing fragment size and increasing fragment isolation reduces species diversity beyond the effects of habitat loss, and (2) the habitat amount hypothesis, which negates fragmentation effects and predicts that only total habitat area determines the diversity of species persisting on fragmented landscapes. Using eight independent size classes of islands (ranging from 0.1 to 8.0 ha) that varied in number of islands while holding total area constant, species diversity comparisons, species accumulation curves, and species-area relationship extrapolations demonstrated that smaller insular habitats contained at least as many butterfly species as continuous habitat. However, when highly mobile species occurring on islands without their larval food plants were excluded from analyses, island effects on potentially reproducing species became apparent. Similarily, generalized linear models suggested that effects of island isolation and vascular plant richness on insular butterfly richness were confounded by species of high mobility. We conclude that inter-fragment movements of highly mobile species may obscure important fragmentation effects on potentially reproducing populations, questioning support for the habitat amount hypothesis.

  11. Analytic device including nanostructures

    KAUST Repository

    Di Fabrizio, Enzo M.

    2015-07-02

    A device for detecting an analyte in a sample comprising: an array including a plurality of pixels, each pixel including a nanochain comprising: a first nanostructure, a second nanostructure, and a third nanostructure, wherein size of the first nanostructure is larger than that of the second nanostructure, and size of the second nanostructure is larger than that of the third nanostructure, and wherein the first nanostructure, the second nanostructure, and the third nanostructure are positioned on a substrate such that when the nanochain is excited by an energy, an optical field between the second nanostructure and the third nanostructure is stronger than an optical field between the first nanostructure and the second nanostructure, wherein the array is configured to receive a sample; and a detector arranged to collect spectral data from a plurality of pixels of the array.

  12. FRAGMENTATION OF CONTINENTAL UNITES STATES FORESTS

    Science.gov (United States)

    We report a multiple-scale analysis of forest fragmentation based on 30-m land-cover maps for the conterminous United States. Each 0.09-ha unit of forest was classified according to fragmentation indices measured within the surrounding landscape, for five landscape sizes from 2....

  13. Generalized Fragmentation Functions for Fractal Jet Observables

    NARCIS (Netherlands)

    Elder, B.T.; Procura, M.; Thaler, J.; Waalewijn, W.J.; Zhou, K.

    We introduce a broad class of fractal jet observables that recursively probe the collective properties of hadrons produced in jet fragmentation. To describe these collinear-unsafe observables, we generalize the formalism of fragmentation functions, which are important objects in QCD for calculating

  14. Fragmentation of eastern United States forest types

    Science.gov (United States)

    Kurt H. Riitters; John W. Coulston

    2013-01-01

    Fragmentation is a continuing threat to the sustainability of forests in the Eastern United States, where land use changes supporting a growing human population are the primary driver of forest fragmentation (Stein and others 2009). While once mostly forested, approximately 40 percent of the original forest area has been converted to other land uses, and most of the...

  15. Pollen and gene flow in fragmented habitats

    NARCIS (Netherlands)

    Kwak, Manja M.; Velterop, Odilia; van Andel, Jelte

    . Habitat fragmentation affects both plants and pollinators. Habitat fragmentation leads to changes in species richness, population number and size, density, and shape, thus to changes in the spatial arrangement of flowers. These changes influence the amount of food for flower-visiting insects and

  16. A Multi-Scale Perspective of the Effects of Forest Fragmentation on Birds in Eastern Forests

    Science.gov (United States)

    Frank R. Thompson; Therese M. Donovan; Richard M. DeGraff; John Faaborg; Scott K. Robinson

    2002-01-01

    We propose a model that considers forest fragmentation within a spatial hierarchy that includes regional or biogeographic effects, landscape-level fragmentation effects, and local habitat effects. We hypothesize that effects operate "top down" in that larger scale effects provide constraints or context for smaller scale effects. Bird species' abundance...

  17. Habitat fragmentation and interspecific competition: Implications for lynx conservation [Chapter 4

    Science.gov (United States)

    Steven W. Buskirk

    2000-01-01

    Habitat fragmentation and interspecific competition are two important forces that potentially affect lynx populations. Fragmentation operates by various mechanisms, including direct habitat loss, vehicle collisions and behavioral disturbance from roads, and changes in landscape features such as edges. Competition takes two forms: Exploitation competition involves...

  18. Long-term effects of fragmentation and fragment properties on bird species richness in Hawaiian forests

    Science.gov (United States)

    David J. Flaspohler; Christian P. Giardina; Gregory P. Asner; Patrick Hart; Jonathan Price; Cassie Ka’apu Lyons; Xeronimo. Castaneda

    2010-01-01

    Forest fragmentation is a common disturbance affecting biological diversity, yet the impacts of fragmentation on many forest processes remain poorly understood. Forest restoration is likely to be more successful when it proceeds with an understanding of how native and exotic vertebrates utilize forest patches of different size. We used a system of forest fragments...

  19. Simulation analysis of effects of single fragment size on air-blast wave and fragment propagation

    Directory of Open Access Journals (Sweden)

    ZHENG Hongwei

    2017-12-01

    Full Text Available [Objectives] This paper involves the propagation and attenuation of the velocity and energy of air-blast waves and high-velocity fragments while taking their combined effects into account.[Methods] With ANSYS/LS-DYNA software, a simulation model of a columnar TNT air blast is built with prefabricated fragments affixed to its end. When the total quality of fragments is constant, the effects of a single fragment's size on the propagation of the air-blast wave and fragments are studied by changing the size of the single fragment.[Results] The results show that fragments greatly reduce the intensity and velocity of a shockwave, and block the air-blast waves behind them. When the total quality of the fragments remains constant, the effects of single fragment size on blast shockwave propagation characteristics show little difference. The smaller the single fragment, the more kinetic energy the fragments will have and the faster that energy will dissipate.[Conclusions] As a result, more attention should be paid to the combined effects of air-blast waves and high-velocity fragments. Such research can provide reference points for the deeper study of blast loads and their interaction.

  20. Fragmentation alters stream fish community structure in dendritic ecological networks.

    Science.gov (United States)

    Perkin, Joshuah S; Gido, Keith B

    2012-12-01

    Effects of fragmentation on the ecology of organisms occupying dendritic ecological networks (DENs) have recently been described through both conceptual and mathematical models, but few hypotheses have been tested in complex, real-world ecosystems. Stream fishes provide a model system for assessing effects of fragmentation on the structure of communities occurring within DENs, including how fragmentation alters metacommunity dynamics and biodiversity. A recently developed habitat-availability measure, the "dendritic connectivity index" (DCI), allows for assigning quantitative measures of connectivity in DENs regardless of network extent or complexity, and might be used to predict fish community response to fragmentation. We characterized stream fish community structure in 12 DENs in the Great Plains, USA, during periods of dynamic (summer) and muted (fall) discharge regimes to test the DCI as a predictive model of fish community response to fragmentation imposed by road crossings. Results indicated that fish communities in stream segments isolated by road crossings had reduced species richness (alpha diversity) relative to communities that maintained connectivity with the surrounding DEN during summer and fall. Furthermore, isolated communities had greater dissimilarity (beta diversity) to downstream sites notisolated by road crossings during summer and fall. Finally, dissimilarity among communities within DENs decreased as a function of increased habitat connectivity (measured using the DCI) for summer and fall, suggesting that communities within highly connected DENs tend to be more homogeneous. Our results indicate that the DCI is sensitive to community effects of fragmentation in riverscapes and might be used by managers to predict ecological responses to changes in habitat connectivity. Moreover, our findings illustrate that relating structural connectivity of riverscapes to functional connectivity among communities might aid in maintaining metacommunity

  1. Biogeographical and taxonomic biases in tropical forest fragmentation research.

    Science.gov (United States)

    Deikumah, Justus P; McAlpine, Clive A; Maron, Martine

    2014-12-01

    Despite several decades of research on the effects of fragmentation and habitat change on biodiversity, there remain strong biases in the geographical regions and taxonomic species studied. The knowledge gaps resulting from these biases are of particular concern if the forests most threatened with modification are also those for which the effects of such change are most poorly understood. To quantify the nature and magnitude of such biases, we conducted a systematic review of the published literature on forest fragmentation in the tropics for the period 1980-2012. Studies included focused on any type of response of single species, communities, or assemblages of any taxonomic group to tropical forest fragmentation and on fragmentation-related changes to forests. Of the 853 studies we found in the SCOPUS database, 64% were conducted in the Neotropics, 13% in Asia, 10% in the Afrotropics, and 5% in Australasia. Thus, although the Afrotropics is subject to the highest rates of deforestation globally, it was the most disproportionately poorly studied biome. Significant taxonomic biases were identified. Of the taxonomic groups considered, herpetofauna was the least studied in the tropics, particularly in Africa. Research examining patterns of species distribution was by far the most common type (72%), and work focused on ecological processes (28%) was rare in all biomes, but particularly in the Afrotropics and for fauna. We suggest research efforts be directed toward less-studied biogeographic regions, particularly where the threat of forest fragmentation continues to be high. Increased research investment in the Afrotropics will be important to build knowledge of threats and inform responses in a region where almost no efforts to restore its fragmented landscapes have yet begun and forest protection is arguably most tenuous. © 2014 Society for Conservation Biology.

  2. Diquark Fragmentation Contribution in Λ b Production

    Science.gov (United States)

    Osati, T.; Movlanaei, M.

    2017-05-01

    In the framework of the quark-diquark model of baryons, Λ b can be considered as b constituent quark an ud constituent diquark. In this study, we investigate the effect ud scalar diquark fragmentation into Λ b , therefor we calculate frgmentation functions of b quark and ud diquark into Λ b baryon through the use of perturbative QCD. In the next stage, throuth the use of the obtained fragmentation functions, we calculate the total fragmentation probabilities and average fragmentation parameters for b→Λ b and u d→Λ b . Finally, the inclusive cross section of Λ b baryon in electron-positron annihilation in ALEPH experiment is calculated with regard to ud diquark fragmentation contribution.

  3. Synergistic impacts of habitat loss and fragmentation on model ecosystems.

    Science.gov (United States)

    Bartlett, Lewis J; Newbold, Tim; Purves, Drew W; Tittensor, Derek P; Harfoot, Michael B J

    2016-09-28

    Habitat loss and fragmentation are major threats to biodiversity, yet separating their effects is challenging. We use a multi-trophic, trait-based, and spatially explicit general ecosystem model to examine the independent and synergistic effects of these processes on ecosystem structure. We manipulated habitat by removing plant biomass in varying spatial extents, intensities, and configurations. We found that emergent synergistic interactions of loss and fragmentation are major determinants of ecosystem response, including population declines and trophic pyramid shifts. Furthermore, trait-mediated interactions, such as a disproportionate sensitivity of large-sized organisms to fragmentation, produce significant effects in shaping responses. We also show that top-down regulation mitigates the effects of land use on plant biomass loss, suggesting that models lacking these interactions-including most carbon stock models-may not adequately capture land-use change impacts. Our results have important implications for understanding ecosystem responses to environmental change, and assessing the impacts of habitat fragmentation. © 2016 The Authors.

  4. Being Included and Excluded

    DEFF Research Database (Denmark)

    Korzenevica, Marina

    2016-01-01

    Following the civil war of 1996–2006, there was a dramatic increase in the labor mobility of young men and the inclusion of young women in formal education, which led to the transformation of the political landscape of rural Nepal. Mobility and schooling represent a level of prestige that rural...... politics. It analyzes how formal education and mobility either challenge or reinforce traditional gendered norms which dictate a lowly position for young married women in the household and their absence from community politics. The article concludes that women are simultaneously excluded and included from...... people regard as a prerequisite for participating in local community politics. Based on a fieldwork in two villages of Panchthar district in eastern Nepal, this article explores how these changes strengthen or weaken women’s political agency and how this is reflected in their participation in community...

  5. Posterior epidural migration of herniated lumbar disc fragment.

    Science.gov (United States)

    Sengoz, Ahmet; Kotil, Kadir; Tasdemiroglu, Erol

    2011-03-01

    Posterior epidural migration of a free disc fragment in the lumbar region is a very rare condition that has only been reported in isolated cases to date. Patients with this condition present with radiculopathy or major neurological deficits. Difficulties in diagnosis and the choice and timing of surgical treatment are important in these cases. In this clinical case series, features of cases with posterior epidural migration of free lumbar disc fragments accompanied by cauda equina syndrome are discussed. Eight cases (0.27%) of posterior epidural migration of disc fragments were detected among 2880 patients surgically treated for lumbar disc herniation between 1995 and 2008. Seven of these patients had cauda equina syndrome. The mean duration of symptoms in the 8 cases was 4.2 days (range 1-10 days). The group included 6 men and 2 women, with a mean age of 48 years (range 34-72 years). The sequestered disc fragments were at the L3-4 level in 6 patients (75%) and the L4-5 level in 2 (25%). Magnetic resonance imaging showed tumor-like ring contrast enhancement around sequestered fragments in 5 patients. The patients' motor, sensory, sexual, and urological functions were evaluated postoperatively, and modified Odom criteria and a visual analog scale were used in the assessment of postoperative outcomes. A microsurgical approach was used in all cases. Sequestrectomy with minimal hemilaminotomy and removal of the free segments were performed. The patients were followed up for a mean period of 28.5 months. Three patients (37.5%) had excellent results, 3 (37.5%) had good results, 1 patient (12.5%) had fair results, and only 1 patient had poor results according to the Odom criteria. The main factors affecting the long-term outcomes were the presence of cauda equina syndrome and the time period between onset of symptoms and surgery. Patients with posterior migration of a disc fragment present with severe neurological deficits such as cauda equina syndrome. Because the

  6. Indirect Immunodetection of Fungal Fragments by Field Emission Scanning Electron Microscopy.

    Science.gov (United States)

    Afanou, Komlavi Anani; Straumfors, Anne; Skogstad, Asbjørn; Nayak, Ajay P; Skaar, Ida; Hjeljord, Linda; Tronsmo, Arne; Eduard, Wijnand; Green, Brett James

    2015-09-01

    Submicronic fungal fragments have been observed in in vitro aerosolization experiments. The occurrence of these particles has therefore been suggested to contribute to respiratory health problems observed in mold-contaminated indoor environments. However, the role of submicronic fragments in exacerbating adverse health effects has remained unclear due to limitations associated with detection methods. In the present study, we report the development of an indirect immunodetection assay that utilizes chicken polyclonal antibodies developed against spores from Aspergillus versicolor and high-resolution field emission scanning electron microscopy (FESEM). Immunolabeling was performed with A. versicolor fragments immobilized and fixed onto poly-l-lysine-coated polycarbonate filters. Ninety percent of submicronic fragments and 1- to 2-μm fragments, compared to 100% of >2-μm fragments generated from pure freeze-dried mycelial fragments of A. versicolor, were positively labeled. In proof-of-concept experiments, air samples collected from moldy indoor environments were evaluated using the immunolabeling technique. Our results indicated that 13% of the total collected particles were derived from fungi. This fraction comprises 79% of the fragments that were detected by immunolabeling and 21% of the spore particles that were morphologically identified. The methods reported in this study enable the enumeration of fungal particles, including submicronic fragments, in a complex heterogeneous environmental sample. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  7. Quantifying the dynamic of OSA brain using multifractal formalism: A novel measure for sleep fragmentation.

    Science.gov (United States)

    Raiesdana, Somayeh

    2017-01-01

    It is thought that the critical brain dynamics in sleep is modulated during frequent periods of wakefulness. This paper utilizes the capacity of EEG based scaling analysis to quantify sleep fragmentation in patients with obstructive sleep apnea. The scale-free (fractal) behavior refers to a state where no characteristic scale dominates the dynamics of the underlying process which is evident as long range correlations in a time series. Here, Multiscaling (multifractal) spectrum is utilized to quantify the disturbed dynamic of an OSA brain with fragmented sleep. The whole night multichannel sleep EEG recordings of 18 subjects were employed to compute and quantify variable power-law long-range correlations and singularity spectra. Based on this characteristic, a new marker for sleep fragmentation named ``scaling based sleep fragmentation'' was introduced. This measure takes into account the sleep run length and stage transition quality within a fuzzy inference system to improve decisions made on sleep fragmentation. The proposed index was implemented, validated with sleepiness parameters and compared to some common indexes including sleep fragmentation index, arousal index, sleep diversity index, and sleep efficiency index. Correlations were almost significant suggesting that the sleep characterizing measure, based on singularity spectra range, could properly detect fragmentations and quantify their rate. This method can be an alternative for quantifying the sleep fragmentation in clinical practice after being approved experimentally. Control of sleep fragmentation and, subsequently, suppression of excessive daytime sleepiness will be a promising outlook of this kind of researches.

  8. Improved chemical shift based fragment selection for CS-Rosetta using Rosetta3 fragment picker

    Energy Technology Data Exchange (ETDEWEB)

    Vernon, Robert [Hospital for Sick Children, Program in Molecular Structure and Function (Canada); Shen, Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Baker, David [University of Washington, Department of Biochemistry (United States); Lange, Oliver F., E-mail: oliver.lange@tum.de [Technische Universitaet Muenchen, Department Chemie, Biomolecular NMR and Munich Center for Integrated Protein Science (Germany)

    2013-10-15

    A new fragment picker has been developed for CS-Rosetta that combines beneficial features of the original fragment picker, MFR, used with CS-Rosetta, and the fragment picker, NNMake, that was used for purely sequence based fragment selection in the context of ROSETTA de-novo structure prediction. Additionally, the new fragment picker has reduced sensitivity to outliers and other difficult to match data points rendering the protocol more robust and less likely to introduce bias towards wrong conformations in cases where data is bad, missing or inconclusive. The fragment picker protocol gives significant improvements on 6 of 23 CS-Rosetta targets. An independent benchmark on 39 protein targets, whose NMR data sets were published only after protocol optimization had been finished, also show significantly improved performance for the new fragment picker (van der Schot et al. in J Biomol NMR, 2013)

  9. Dual Fragment Impact of PBX Charges

    Science.gov (United States)

    Haskins, Peter; Briggs, Richard; Leeming, David; White, Nathan; Cheese, Philip; DE&S MoD UK Team; Ordnance Test Solutions Ltd Team

    2017-06-01

    Fragment impact can pose a significant hazard to many systems containing explosives or propellants. Testing for this threat is most commonly carried out using a single fragment. However, it can be argued that an initial fragment strike (or strikes) could sensitise the energetic material to subsequent impacts, which may then lead to a more violent reaction than would have been predicted based upon single fragment studies. To explore this potential hazard we have developed the capability to launch 2 fragments from the same gun at a range of velocities, and achieve impacts on an acceptor charge with good control over the spatial and temporal separation of the strikes. In this paper we will describe in detail the experimental techniques we have used, both to achieve the dual fragment launch and observe the acceptor charge response. In addition, we will describe the results obtained against PBX filled explosive targets; discuss the mechanisms controlling the target response and their significance for vulnerability assessment. Results of these tests have clearly indicated the potential for detonation upon the second strike, at velocities well below those needed for shock initiation by a single fragment.

  10. On Disciplinary Fragmentation and Scientific Progress

    Science.gov (United States)

    Balietti, Stefano; Mäs, Michael; Helbing, Dirk

    2015-01-01

    Why are some scientific disciplines, such as sociology and psychology, more fragmented into conflicting schools of thought than other fields, such as physics and biology? Furthermore, why does high fragmentation tend to coincide with limited scientific progress? We analyzed a formal model where scientists seek to identify the correct answer to a research question. Each scientist is influenced by three forces: (i) signals received from the correct answer to the question; (ii) peer influence; and (iii) noise. We observed the emergence of different macroscopic patterns of collective exploration, and studied how the three forces affect the degree to which disciplines fall apart into divergent fragments, or so-called “schools of thought”. We conducted two simulation experiments where we tested (A) whether the three forces foster or hamper progress, and (B) whether disciplinary fragmentation causally affects scientific progress and vice versa. We found that fragmentation critically limits scientific progress. Strikingly, there is no effect in the opposite causal direction. What is more, our results shows that at the heart of the mechanisms driving scientific progress we find (i) social interactions, and (ii) peer disagreement. In fact, fragmentation is increased and progress limited if the simulated scientists are open to influence only by peers with very similar views, or when within-school diversity is lost. Finally, disciplines where the scientists received strong signals from the correct answer were less fragmented and experienced faster progress. We discuss model’s implications for the design of social institutions fostering interdisciplinarity and participation in science. PMID:25790025

  11. Augmented generation of protein fragments during wakefulness as the molecular cause of sleep: a hypothesis

    Science.gov (United States)

    Varshavsky, Alexander

    2012-01-01

    Despite extensive understanding of sleep regulation, the molecular-level cause and function of sleep are unknown. I suggest that they originate in individual neurons and stem from increased production of protein fragments during wakefulness. These fragments are transient parts of protein complexes in which the fragments were generated. Neuronal Ca2+ fluxes are higher during wakefulness than during sleep. Subunits of transmembrane channels and other proteins are cleaved by Ca2+-activated calpains and by other nonprocessive proteases, including caspases and secretases. In the proposed concept, termed the fragment generation (FG) hypothesis, sleep is a state during which the production of fragments is decreased (owing to lower Ca2+ transients) while fragment-destroying pathways are upregulated. These changes facilitate the elimination of fragments and the remodeling of protein complexes in which the fragments resided. The FG hypothesis posits that a proteolytic cleavage, which produces two fragments, can have both deleterious effects and fitness-increasing functions. This (previously not considered) dichotomy can explain both the conservation of cleavage sites in proteins and the evolutionary persistence of sleep, because sleep would counteract deleterious aspects of protein fragments. The FG hypothesis leads to new explanations of sleep phenomena, including a longer sleep after sleep deprivation. Studies in the 1970s showed that ethanol-induced sleep in mice can be strikingly prolonged by intracerebroventricular injections of either Ca2+ alone or Ca2+ and its ionophore (Erickson et al., Science 1978;199:1219–1221; Harris, Pharmacol Biochem Behav 1979;10:527–534; Erickson et al., Pharmacol Biochem Behav 1980;12:651–656). These results, which were never interpreted in connection to protein fragments or the function of sleep, may be accounted for by the FG hypothesis about molecular causation of sleep. PMID:22930402

  12. Delivery of gene-expressing fragments using quantum dot

    Science.gov (United States)

    Hoshino, Akiyoshi; Manabe, Noriyoshi; Hanada, Sanshiro; Fujioka, Kouki; Yasuhara, Masato; Kondo, Akihiko; Yamamoto, Kenji

    2009-02-01

    Gene therapy is an attractive approach to supplement a deficient gene function. Although there has been some success with specific gene delivery using various methods including viral vectors and liposomes, most of these methods have a limited efficiency or also carry a risk for oncogenesis. Fluorescent nanoparticles, such as nanocrystal quantum dots (QDs), have potential to be applied to molecular biology and bioimaging, since some nanocrystals emit higher and longer lasting fluorescence than conventional organic probes do. We herein report that quantum dots (QDs) conjugated with nuclear localizing signal peptides (NLSP) successfully introduced the gene-fragments with promoter elements, which promoted the expression of the enhanced green fluorescent protein (eGFP) gene in mammalian cells. The expression of eGFP protein was observed when the QD/geneconstruct was added to the culture media. The gene-expression efficiency varied depending on multiple factors around QDs, such as 1) the reading direction of gene fragments, 2) the quantity of gene fragments attached on the surface of QD-constructs, 3) the surface electronic charges varied according to the structure of QD/gene-constructs, and 4) the particle size of QD/gene complex varied according to the structure and amounts of gene fragments. Using this QD/geneconstruct system, eGFP protein could be detected 28 days after the gene-introduction whereas the fluorescence of QDs was disappeared. This system therefore provides another method for the intracellular delivery of gene-fragments without using either viral vectors or specific liposomes. These results suggest that inappropriate treatment and disposal of QDs may still have risks to the environmental pollution including human health under certain conditions. Here we propose the further research for the immune and physiological responses in not only immune cells but also other cells, in order to clear the effect of all other nanoscale products as well as nanocrystal

  13. Heart Rate Fragmentation: A Symbolic Dynamical Approach

    Directory of Open Access Journals (Sweden)

    Madalena D. Costa

    2017-11-01

    Full Text Available Background: We recently introduced the concept of heart rate fragmentation along with a set of metrics for its quantification. The term was coined to refer to an increase in the percentage of changes in heart rate acceleration sign, a dynamical marker of a type of anomalous variability. The effort was motivated by the observation that fragmentation, which is consistent with the breakdown of the neuroautonomic-electrophysiologic control system of the sino-atrial node, could confound traditional short-term analysis of heart rate variability.Objective: The objectives of this study were to: (1 introduce a symbolic dynamical approach to the problem of quantifying heart rate fragmentation; (2 evaluate how the distribution of the different dynamical patterns (“words” varied with the participants' age in a group of healthy subjects and patients with coronary artery disease (CAD; and (3 quantify the differences in the fragmentation patterns between the two sample populations.Methods: The symbolic dynamical method employed here was based on a ternary map of the increment NN interval time series and on the analysis of the relative frequency of symbolic sequences (words with a pre-defined set of features. We analyzed annotated, open-access Holter databases of healthy subjects and patients with CAD, provided by the University of Rochester Telemetric and Holter ECG Warehouse (THEW.Results: The degree of fragmentation was significantly higher in older individuals than in their younger counterparts. However, the fragmentation patterns were different in the two sample populations. In healthy subjects, older age was significantly associated with a higher percentage of transitions from acceleration/deceleration to zero acceleration and vice versa (termed “soft” inflection points. In patients with CAD, older age was also significantly associated with higher percentages of frank reversals in heart rate acceleration (transitions from acceleration to

  14. Heart Rate Fragmentation: A Symbolic Dynamical Approach.

    Science.gov (United States)

    Costa, Madalena D; Davis, Roger B; Goldberger, Ary L

    2017-01-01

    Background: We recently introduced the concept of heart rate fragmentation along with a set of metrics for its quantification. The term was coined to refer to an increase in the percentage of changes in heart rate acceleration sign, a dynamical marker of a type of anomalous variability. The effort was motivated by the observation that fragmentation, which is consistent with the breakdown of the neuroautonomic-electrophysiologic control system of the sino-atrial node, could confound traditional short-term analysis of heart rate variability. Objective: The objectives of this study were to: (1) introduce a symbolic dynamical approach to the problem of quantifying heart rate fragmentation; (2) evaluate how the distribution of the different dynamical patterns ("words") varied with the participants' age in a group of healthy subjects and patients with coronary artery disease (CAD); and (3) quantify the differences in the fragmentation patterns between the two sample populations. Methods: The symbolic dynamical method employed here was based on a ternary map of the increment NN interval time series and on the analysis of the relative frequency of symbolic sequences (words) with a pre-defined set of features. We analyzed annotated, open-access Holter databases of healthy subjects and patients with CAD, provided by the University of Rochester Telemetric and Holter ECG Warehouse (THEW). Results: The degree of fragmentation was significantly higher in older individuals than in their younger counterparts. However, the fragmentation patterns were different in the two sample populations. In healthy subjects, older age was significantly associated with a higher percentage of transitions from acceleration/deceleration to zero acceleration and vice versa (termed "soft" inflection points). In patients with CAD, older age was also significantly associated with higher percentages of frank reversals in heart rate acceleration (transitions from acceleration to deceleration and vice

  15. Composite Overwrap Fragmentation Observations, Concerns, and Recommendations

    Science.gov (United States)

    Bangham, Mike; Hovater, Mary

    2017-01-01

    A series of test activities has raised some concerns about the generation of orbital debris caused by failures of composite overwrapped pressure vessels (COPVs). These tests have indicated that a large number of composite fragments can be produced by either pressure burst failures or by high-speed impacts. A review of prior high-speed tests with COPV indicates that other tests have produced large numbers of composite fragments. As was the case with the test referenced here, the tests tended to produce a large number of small composite fragments with relatively low velocities induced by the impact and or gas expansion.

  16. Bone fragments a body can make

    Energy Technology Data Exchange (ETDEWEB)

    Stout, S.D.; Ross, L.M. Jr. (Department of Anthropology, University of Missouri, Columbia (USA))

    1991-05-01

    Data obtained from various analytical techniques applied to a number of small bone fragments recovered from a crime scene were used to provide evidence for the occurrence of a fatality. Microscopic and histomorphometric analyses confirmed that the fragments were from a human skull. X-ray microanalysis of darkened areas on the bone fragments revealed a chemical signature that matched the chemical signature of a shotgun pellet recovered at the scene of the crime. The above findings supported the deoxyribonucleic acid (DNA) fingerprint evidence which, along with other evidence, was used to convict a man for the murder of his wife, even though her body was never recovered.

  17. The late effect of grenade fragments.

    Science.gov (United States)

    Symonds, R P; Mackay, C; Morley, P

    1985-06-01

    Following the explosion of a grenade or shell, the victim may be peppered with literally hundreds of pieces of metal. Troublesome fragments which perforate a major viscus may be removed but others are often left behind, as it is felt (usually correctly) that these fragments will cause no harm. We describe a case in which a grenade fragment received 16 years previously pierced the large bowel. A psoas abscess developed which was located by ultrasound. Pus was aspirated under ultrasound control and the lesion was successfully treated by antibiotics.

  18. Extraction of 16th Century Calender Fragments

    DEFF Research Database (Denmark)

    Holck, Jakob Povl; Etheridge, Christian

    at the Cultural Heritage & Archaeometric Research Team, SDU. Upon finding medieval manuscript fragments in the university library’s special collections, scholars at the Centre for Medieval Literature are consulted. In most cases, digital pictures of the finds will circulate in the international community...... of medieval scholars. Thousands of 16th and 17th Century books are stored in the University Library of Southern Denmark. One out of five of these books is expected to contain medieval manuscript fragments or fragments of rare prints, e.g. incunabula....

  19. The effect of coupling on bubble fragmentation acoustics.

    Science.gov (United States)

    Czerski, Helen; Deane, Grant B

    2011-01-01

    Understanding the formation and evolution of bubble populations is important in a wide range of situations, including industrial processes, medical applications, and ocean science. Passive acoustical techniques can be used to track changes in the population, since each bubble formation or fragmentation event is likely to produce sound. This sound potentially contains a wealth of information about the fragmentation process and the products, but to fully exploit these data it is necessary to understand the physical processes that determine its characteristics. The focus of this paper is binary fragmentation, when turbulence causes one bubble to split into two. Specifically, the effect that bubble-bubble coupling has on the sound produced is examined. A numerical simulation of the acoustical excitation of fragmenting bubbles is used to generate model acoustic signals, which are compared with experimental data. A frequency range with a suppressed acoustic output which is observed in the experimental data can be explained when coupling is taken into account. In addition, although the driving mechanism of neck collapse is always consistent with the data for the larger bubble of the newly formed pair, a different mechanism must be driving the smaller bubble in some situations.

  20. Inner-shell excitation and ionic fragmentation of molecules

    Energy Technology Data Exchange (ETDEWEB)

    Hitchcock, A.P.; Tyliszczak, T. [McMaster Univ., Hamilton, Ontario (Canada); Cavell, R.G. [Univ. of Alberta, Edmonton (Canada)] [and others

    1997-04-01

    Inner-shell excitation and associated decay spectroscopies are site specific probes of electronic and geometrical structure and photoionization dynamics. X-ray absorption probes the geometric and electronic structure, while time-of-flight mass spectrometry with multi-coincidence detection provides information on the photofragmentation dynamics of the initially produced inner-shell state. Auger decay of inner-shell excited and ionised states is an efficient source of multiply charged ions. The charge separation and fragmentation of these species, studied by photoelectron-photoion-photoion coincidence (also called charge separation mass spectrometry) gives insights into bonding and electronic structure. In molecules, the dependence of the fragmentation process on the X-ray energy can reveal cases of site and/or state selective fragmentation. At the ALS the authors have examined the soft X-ray spectroscopy and ionic fragmentation of a number of molecules, including carboranes, silylenes, phosphorus halides, SF{sub 6} and CO{sub 2}. Their work is illustrated using results from the carborane and PF{sub 3} studies.

  1. Embedded Fragments from U.S. Military Personnel—Chemical Analysis and Potential Health Implications

    Directory of Open Access Journals (Sweden)

    José A. Centeno

    2014-01-01

    Full Text Available Background: The majority of modern war wounds are characterized by high-energy blast injuries containing a wide range of retained foreign materials of a metallic or composite nature. Health effects of retained fragments range from local or systemic toxicities to foreign body reactions or malignancies, and dependent on the chemical composition and corrosiveness of the fragments in vivo. Information obtained by chemical analysis of excised fragments can be used to guide clinical decisions regarding the need for fragment removal, to develop therapeutic interventions, and to better anticipate future medical problems from retained fragment related injuries. In response to this need, a new U.S Department of Defense (DoD directive has been issued requiring characterization of all removed fragments to provide a database of fragment types occurring in combat injuries. Objectives: The objective of this study is to determine the chemical composition of retained embedded fragments removed from injured military personnel, and to relate results to histological findings in tissue adjacent to fragment material. Methods: We describe an approach for the chemical analysis and characterization of retained fragments and adjacent tissues, and include case examples describing fragments containing depleted uranium (DU, tungsten (W, lead (Pb, and non-metal foreign bodies composed of natural and composite materials. Fragments obtained from four patients with penetrating blast wounds to the limbs were studied employing a wide range of chemical and microscopy techniques. Available adjacent tissues from three of the cases were histologically, microscopically, and chemically examined. The physical and compositional properties of the removed foreign material surfaces were examined with energy dispersive x-ray fluorescence spectrometry (EDXRF, scanning electron microscopy (SEM, laser ablation inductively-coupled plasma mass-spectrometry (LA-ICP-MS, and confocal laser Raman

  2. Anthropogenic Fragmentation in the western United States

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — We evaluated the fragmentation of the western United States by anthropogenic features. The addition of roads, railroads, and power lines to wildlands, and the...

  3. The Fragmentation of the College Mathematics Curriculum

    Science.gov (United States)

    Singleton, Cynthia

    2008-01-01

    The purpose of this paper examines to what extent and asking reason the fragmentation of college mathematics have attained the present development in the course of looking at the history of mathematics education. (Contains 1 table.)

  4. The NJL Model for Quark Fragmentation Functions

    Energy Technology Data Exchange (ETDEWEB)

    T. Ito, W. Bentz, I. Cloet, A W Thomas, K. Yazaki

    2009-10-01

    A description of fragmentation functions which satisfy the momentum and isospin sum rules is presented in an effective quark theory. Concentrating on the pion fragmentation function, we first explain the reason why the elementary (lowest order) fragmentation process q → qπ is completely inadequate to describe the empirical data, although the “crossed” process π → qq describes the quark distribution functions in the pion reasonably well. Then, taking into account cascade-like processes in a modified jet-model approach, we show that the momentum and isospin sum rules can be satisfied naturally without introducing any ad-hoc parameters. We present numerical results for the Nambu-Jona-Lasinio model in the invariant mass regularization scheme, and compare the results with the empirical parametrizations. We argue that this NJL-jet model provides a very useful framework to calculate the fragmentation functions in an effective chiral quark theory.

  5. New Methodology for Simulating Fragmentation Munitions

    National Research Council Canada - National Science Library

    Gold, V

    2001-01-01

    This document on New Methodology for Simulating Fragmentation Munitions consists of the 17 presentation slides that were presented at the Proceedings of the 36th Annual Gun and Ammunition Symposium...

  6. Fragmentation of Care in Ectopic Pregnancy.

    Science.gov (United States)

    Stulberg, Debra B; Dahlquist, Irma; Jarosch, Christina; Lindau, Stacy T

    2016-05-01

    Ectopic pregnancy is an important cause of maternal morbidity and mortality. Women who experience fragmented care may undergo unnecessary delays to diagnosis and treatment. Based on ectopic pregnancy cases observed in clinical practice that raised our concern about fragmentation of care, we designed an exploratory study to describe the number, characteristics, and outcomes of fragmented care among patients with ectopic pregnancy at one urban academic hospital. Chart review with descriptive statistics. Fragmented care was defined as a patient being evaluated at an outside facility for possible ectopic pregnancy and transferred, referred, or discharged before receiving care at the study institution. Of 191 women seen for possible or definite ectopic pregnancy during the study period, 42 (22 %) met the study definition of fragmented care. The study was under-powered to observe statistically significant differences across groups, but we found concerning, non-significant trends: patients with fragmented care were more likely to be Medicaid recipients (65.9 vs. 58.8 %) and to experience a complication (23.8 vs. 18.1 %) compared to those with non-fragmented care. Most patients (n = 37) received no identifiable treatment prior to transfer and arrived to the study hospital with no communication to the receiving hospital from the outside provider (n = 34). Nine patients (21 %) presented with ruptured ectopic pregnancies. The fragmentation we observed in our study may contribute to previously identified socio-economic disparities in ectopic pregnancy outcomes. If future research confirms these findings, health information exchanges and regional coordination of care may be important strategies for reducing maternal mortality.

  7. Studies of Shell Fragment Mass Distribution

    Science.gov (United States)

    1946-01-05

    E-i C) C 5a- 3 HljI 4----- oI ’H+ COC -4 E- I yh E0 O . ’-0 - - 38 Tho,:s2- data arm fairly consitEACnt ý,eith the ecec ption of Shot :,,42 forTPT hs...fragments. In addition, fragment retardation at the New Mexico range is significantly smaller because of the higher altitude. 0 Lo to C𔃻 00 t t fLd 4

  8. Observations of Titan IIIC Transtage Fragmentation Debris

    Science.gov (United States)

    Cowardin, Heather; Seitzer, P.; Abercromby, K.; Barker, E.; Buckalew, B.; Cardona, T.; Krisko, P.; Lederer, S.

    2013-01-01

    The fragmentation of a Titan IIIC Transtage (1968-081) on 21 February 1992 is one of only two known break-ups in or near geosynchronous orbit. The original rocket body and 24 pieces of debris are currently being tracked by the U. S. Space Surveillance Network (SSN). The rocket body (SSN# 3432) and several of the original fragments (SSN# 25000, 25001, 30000, and 33511) were observed in survey mode during 2004-2010 using the 0.6-m Michigan Orbital DEbris Survey Telescope (MODEST) in Chile using a broad R filter. This paper presents a size distribution for all calibrated magnitude data acquired on MODEST. Size distribution plots are also shown using historical models for small fragmentation debris (down to 10 cm) thought to be associated with the Titan Transtage break-up. In November 2010, visible broadband photometry (Johnson/Kron-Cousins BVRI) was acquired with the 0.9-m Small and Moderate Aperture Research Telescope System (SMARTS) at the Cerro Tololo Inter-American Observatory (CTIO) in Chile on several Titan fragments (SSN 25001, 33509, and 33510) and the parent rocket body (SSN 3432). Color index data are used to determine the fragment brightness distribution and how the data compares to spacecraft materials measured in the laboratory using similar photometric measurement techniques. In order to better characterize the break-up fragments, spectral measurements were acquired on three Titan fragments (one fragment observed over two different time periods) using the 6.5-m Magellan telescopes at Las Campanas Observatory in Chile. The telescopic spectra of SSN 25000 (May 2012 and January 2013), SSN 38690, and SSN 38699 are compared with laboratory acquired spectra of materials (e.g., aluminum and various paints) to determine the surface material.

  9. Design Tools for FRIB Fragment Separators

    Science.gov (United States)

    Bandura, Laura

    2009-10-01

    A key component of the Facility for Rare Isotope Beams, FRIB will be the in-flight fragment separator used to select and purify the isotope of interest for experiments. In order to simulate this process, we have developed a hybrid map-Monte Carlo code based on the ion optics code COSY INFINITY that accurately models fragment production and atomic processes. The code COSY INFINTIY uses powerful differential algebraic methods for computing the dynamics of the beam in the fragment separator. Ion production and atomic processes have been added to COSY to calculate beam-material interactions. The code tracks the fragmentation and fission of the beam in target and absorber material while computing energy loss and energy and angular straggling as well as charge state evolution of the beam by implementing auxiliary codes such as ATIMA and GLOBAL. EPAX has been utilized to return the cross sections of fragmentation products. The hybrid map-Monte Carlo code extensions added to COSY provide an integrated beam dynamics-nuclear processes design optimization and simulation framework that is efficient and accurate. The code may be used to optimize any fragment separator system for the selection of any rare isotope.

  10. Spermatozoal cell death-inducing DNA fragmentation factor-α-like effector A (CIDEA) gene expression and DNA fragmentation in infertile men with metabolic syndrome and normal seminogram.

    Science.gov (United States)

    Elsamanoudy, Ayman Z; Abdalla, Hussein Abdelaziz; Hassanien, Mohammed; Gaballah, Mohammad A

    2016-01-01

    This is the first study to investigate spermatozoal cell death-inducing DNA fragmentation factor-α-like effector A (CIDEA) gene expression and DNA fragmentations in the spermatozoa of men diagnosed with metabolic syndrome (MS) who have normal seminograms with unexplained infertility, and to correlate these parameters with seminal glucose concentration. This study included 120 participants: 75 male subjects with MS (38 fertile and 37 infertile), and a control group of 45 fertile males without MS. HOMA-IR, semen analysis, and biochemical measurement of seminal plasma insulin and glucose levels were carried out. Spermatozoal insulin gene and CIDEA gene expressions were performed by the RT-PCR method. The percentage of spermatozoal DNA fragmentation was also estimated. The spermatozoal insulin and CIDEA gene expression, as well as the DNA fragmentation, were significantly higher in the infertile MS group than in the fertile MS group, and significantly higher in both the MS groups than in the control group. Seminal glucose concentration showed significant positive correlations with seminal insulin level, spermatozoa insulin, CIDEA gene expression, and DNA fragmentation. Moreover, there was a positive correlation between spermatozoa CIDEA gene expression and DNA fragmentation. It can be concluded that MS may affect male fertility at the molecular level, through its possible inducing effect of spermatozoa CIDEA and insulin gene expression, DNA fragmentation, and increased seminal glucose.

  11. Fragment-based drug discovery and protein–protein interactions

    Directory of Open Access Journals (Sweden)

    Turnbull AP

    2014-09-01

    -dimensional character. These physiochemical properties can potentially be exploited in the rational design of PPI-specific fragment libraries and correlate well with optimized PPI inhibitors, which tend to have properties outside currently accepted guidelines for drug-likeness. Several examples of small-molecule PPI inhibitors derived from fragment-based drug discovery now exist and are described in this review, including navitoclax, a novel Bcl-2 family inhibitor which has entered Phase II clinical trials in patients with small-cell lung cancer and chronic lymphocytic leukemia.Keywords: hot spot, druggability, ligandability

  12. RESTseq - Efficient Benchtop Population Genomics with RESTriction Fragment SEQuencing

    OpenAIRE

    Eckart Stolle; Moritz, Robin F.A.

    2013-01-01

    We present RESTseq, an improved approach for a cost efficient, highly flexible and repeatable enrichment of DNA fragments from digested genomic DNA using Next Generation Sequencing platforms including small scale Personal Genome sequencers. Easy adjustments make it suitable for a wide range of studies requiring SNP detection or SNP genotyping from fine-scale linkage mapping to population genomics and population genetics also in non-model organisms. We demonstrate the validity of our approach ...

  13. Fragment library design: using cheminformatics and expert chemists to fill gaps in existing fragment libraries.

    Science.gov (United States)

    Kutchukian, Peter S; So, Sung-Sau; Fischer, Christian; Waller, Chris L

    2015-01-01

    Fragment based screening (FBS) has emerged as a mainstream lead discovery strategy in academia, biotechnology start-ups, and large pharma. As a prerequisite of FBS, a structurally diverse library of fragments is desirable in order to identify chemical matter that will interact with the range of diverse target classes that are prosecuted in contemporary screening campaigns. In addition, it is also desirable to offer synthetically amenable starting points to increase the probability of a successful fragment evolution through medicinal chemistry. Herein we describe a method to identify biologically relevant chemical substructures that are missing from an existing fragment library (chemical gaps), and organize these chemical gaps hierarchically so that medicinal chemists can efficiently navigate the prioritized chemical space and subsequently select purchasable fragments for inclusion in an enhanced fragment library.

  14. Process of Fragment-Based Lead Discovery—A Perspective from NMR

    Directory of Open Access Journals (Sweden)

    Rongsheng Ma

    2016-07-01

    Full Text Available Fragment-based lead discovery (FBLD has proven fruitful during the past two decades for a variety of targets, even challenging protein–protein interaction (PPI systems. Nuclear magnetic resonance (NMR spectroscopy plays a vital role, from initial fragment-based screening to lead generation, because of its power to probe the intrinsically weak interactions between targets and low-molecular-weight fragments. Here, we review the NMR FBLD process from initial library construction to lead generation. We describe technical aspects regarding fragment library design, ligand- and protein-observed screening, and protein–ligand structure model generation. For weak binders, the initial hit-to-lead evolution can be guided by structural information retrieved from NMR spectroscopy, including chemical shift perturbation, transferred pseudocontact shifts, and paramagnetic relaxation enhancement. This perspective examines structure-guided optimization from weak fragment screening hits to potent leads for challenging PPI targets.

  15. DNA restriction fragment length polymorphisms in differential diagnosis of genetic disease: application in neuromuscular diseases

    NARCIS (Netherlands)

    Defesche, J. C.; de Vissar, M.; Bakker, E.; Bouwsma, G.; de Vijlder, J. J.; Bolhuis, P. A.

    1989-01-01

    Three families, in which several male individuals suffer from a hereditary neuromuscular disease, were examined by analysis of naturally occurring restriction fragment length polymorphisms (RFLPs) and by screening for deletions. Originally, differential diagnosis included spinal muscular atrophy

  16. Bullet fragments in Belding's ground squirrels in Oregon and California in 2014-2015

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The dataset includes specifics on fragments of bullets recovered from shot Belding's ground squirrels from Oregon and California. Ground squirrels were radiographed...

  17. Modeling the Effects of Ecosystem Fragmentation and Restoration: Management Models for Mobile Animals

    National Research Council Canada - National Science Library

    Sisk, Thomas

    1998-01-01

    .... Key questions include: What are the life history characteristics that determine the type and magnitude of a species' sensitivity to fragmentation and, more specifically, habitat edges and landscape boundaries...

  18. WHAT IS CONTROLLING THE FRAGMENTATION IN THE INFRARED DARK CLOUD G14.225–0.506?: DIFFERENT LEVELS OF FRAGMENTATION IN TWIN HUBS

    Energy Technology Data Exchange (ETDEWEB)

    Busquet, Gemma; Girart, Josep Miquel [Institut de Ciències de l’Espai (CSIC-IEEC), Campus UAB, Carrer de Can Magrans, S/N, E-08193, Cerdanyola del Vallès, Catalunya (Spain); Estalella, Robert [Departament d’Astronomia i Meteorologia, Institut de Ciències del Cosmos (ICC), Universitat de Barcelona (IEEC-UB), Martí i Franquès, 1, E-08028 Barcelona, Catalunya (Spain); Palau, Aina [Instituto de Radioastronomía y Astrofísica, Universidad Nacional Autónoma de México, P.O. Box 3-72, 58090 Morelia, Michoacán, México (Mexico); Liu, Hauyu Baobab; Ho, Paul T. P. [Academia Sinica Institute of Astronomy and Astrophysics, Taipei, Taiwan (China); Zhang, Qizhou [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); De Gregorio-Monsalvo, Itziar [European Southern Observatory (ESO), Karl-Schwarzschild-Str. 2, D-85748 Garching (Germany); Pillai, Thushara [Max Planck Institut für Radioastronomie, Auf dem Hügel 69, D-53121 Bonn (Germany); Anglada, Guillem, E-mail: busquet@ice.cat [Instituto de Astrofísica de Andalucía, CSIC, Glorieta de la Astronomía, s/n, E-18008, Granada (Spain)

    2016-03-20

    We present observations of the 1.3 mm continuum emission toward hub-N and hub-S of the infrared dark cloud G14.225–0.506 carried out with the Submillimeter Array, together with observations of the dust emission at 870 and 350 μm obtained with APEX and CSO telescopes. The large-scale dust emission of both hubs consists of a single peaked clump elongated in the direction of the associated filament. At small scales, the SMA images reveal that both hubs fragment into several dust condensations. The fragmentation level was assessed under the same conditions and we found that hub-N presents 4 fragments while hub-S is more fragmented, with 13 fragments identified. We studied the density structure by means of a simultaneous fit of the radial intensity profile at 870 and 350 μm and the spectral energy distribution adopting a Plummer-like function to describe the density structure. The parameters inferred from the model are remarkably similar in both hubs, suggesting that density structure could not be responsible for determining the fragmentation level. We estimated several physical parameters, such as the level of turbulence and the magnetic field strength, and we found no significant differences between these hubs. The Jeans analysis indicates that the observed fragmentation is more consistent with thermal Jeans fragmentation compared with a scenario in which turbulent support is included. The lower fragmentation level observed in hub-N could be explained in terms of stronger UV radiation effects from a nearby H ii region, evolutionary effects, and/or stronger magnetic fields at small scales, a scenario that should be further investigated.

  19. Meteorite Falls and the Fragmentation of Meteorites

    Science.gov (United States)

    Momeni, Daniel

    2016-01-01

    In order to understand the fragmentation of objects entering the atmosphere and why some produce more fragments than others, I have searched the Meteoritical Society database for meteorites greater than 20 kilograms that fell in the USA, China, and India. I also studied the video and film records of 21 fireballs that produced meteorites. A spreadsheet was prepared that noted smell, fireball, explosion, whistling, rumbling, the number of fragments, light, and impact sounds. Falls with large numbers of fragments were examined to look for common traits. These were: the Norton County aubrite, explosion and a flare greater than 100 fragments; the Forest City H5 chondrite explosion, a flare, a dust trail, 505 specimens; the Richardton H5 chondrite explosion and light, 71 specimens; the Juancheng H5 chondrite explosion, a rumbling, a flare, a dust trail,1000 specimens; the Tagish Lake C2 chondrite explosion, flare, dust trail, 500 specimens. I conclude that fragmentation is governed by the following: (1) Bigger meteors undergo more stress which results in more specimens; (2) Harder meteorites also require more force to break them up which will cause greater fragmentation; (3) Force and pressure are directly proportional during falls. General observations made were; (1) Meteorites produce fireballs sooner due to high friction; (2) Meteors tend to explode as well because of high stress; (3) Softer meteorites tend to cause dust trails; (4) Some falls produce light as they fall at high velocity. I am grateful to NASA Ames for this opportunity and Derek Sears, Katie Bryson, and Dan Ostrowski for discussions.

  20. DNA fragmentation in spermatozoa: a historical review.

    Science.gov (United States)

    Rex, A S; Aagaard, J; Fedder, J

    2017-07-01

    Sperm DNA Fragmentation has been extensively studied for more than a decade. In the 1940s the uniqueness of the spermatozoa protein complex which stabilizes the DNA was discovered. In the fifties and sixties, the association between unstable chromatin structure and subfertility was investigated. In the seventies, the impact of induced DNA damage was investigated. In the 1980s the concept of sperm DNA fragmentation as related to infertility was introduced as well as the first DNA fragmentation test: the Sperm Chromatin Structure Assay (SCSA). The terminal deoxynucleotidyl transferase nick end labelling (TUNEL) test followed by others was introduced in the nineties. The association between DNA fragmentation in spermatozoa and pregnancy loss has been extensively investigated spurring the need for a therapeutic tool for these patients. This gave rise to an increased interest in the aetiology of DNA damage. The present decade continues within this research area. Some of the more novel methods recently submerging are sorting of cells with increased DNA fragmentation and hyaluronic acid (HA) binding techniques. The clinical value of these tests remains to be elucidated. In spite of half a century of research within the area, this analysis is not routinely implemented into the fertility clinics. The underlying causes are multiple. The abundance of methods has impeded the need for a clinical significant threshold. One of the most promising methods was commercialized in 2005 and has been reserved for larger licensed laboratories. Myriads of reviews and meta-analyses on studies using different assays for analysis of DNA fragmentation, different clinical Artificial Reproductive Treatments (ART), different definitions of successful ART outcome and small patient cohorts have been published. Although the area of DNA fragmentation in spermatozoa is highly relevant in the fertility clinics, the need for further studies focusing on standardization of the methods and clinical

  1. Bacterial natural transformation by highly fragmented and damaged DNA.

    Science.gov (United States)

    Overballe-Petersen, Søren; Harms, Klaus; Orlando, Ludovic A A; Mayar, J Victor Moreno; Rasmussen, Simon; Dahl, Tais W; Rosing, Minik T; Poole, Anthony M; Sicheritz-Ponten, Thomas; Brunak, Søren; Inselmann, Sabrina; de Vries, Johann; Wackernagel, Wilfried; Pybus, Oliver G; Nielsen, Rasmus; Johnsen, Pål Jarle; Nielsen, Kaare Magne; Willerslev, Eske

    2013-12-03

    DNA molecules are continuously released through decomposition of organic matter and are ubiquitous in most environments. Such DNA becomes fragmented and damaged (often bacterial evolution. Here, we show that fragmented DNA molecules (≥ 20 bp) that additionally may contain abasic sites, cross-links, or miscoding lesions are acquired by the environmental bacterium Acinetobacter baylyi through natural transformation. With uptake of DNA from a 43,000-y-old woolly mammoth bone, we further demonstrate that such natural transformation events include ancient DNA molecules. We find that the DNA recombination is RecA recombinase independent and is directly linked to DNA replication. We show that the adjacent nucleotide variations generated by uptake of short DNA fragments escape mismatch repair. Moreover, double-nucleotide polymorphisms appear more common among genomes of transformable than nontransformable bacteria. Our findings reveal that short and damaged, including truly ancient, DNA molecules, which are present in large quantities in the environment, can be acquired by bacteria through natural transformation. Our findings open for the possibility that natural genetic exchange can occur with DNA up to several hundreds of thousands years old.

  2. Production of Energetic Light Fragments in Spallation Reactions

    Directory of Open Access Journals (Sweden)

    Mashnik Stepan G.

    2014-03-01

    Full Text Available Different reaction mechanisms contribute to the production of light fragments (LF from nuclear reactions. Available models cannot accurately predict emission of LF from arbitrary reactions. However, the emission of LF is important formany applications, such as cosmic-ray-induced single event upsets, radiation protection, and cancer therapy with proton and heavy-ion beams, to name just a few. The cascade-exciton model (CEM and the Los Alamos version of the quark-gluon string model (LAQGSM, as implemented in the CEM03.03 and LAQGSM03.03 event generators used in the Los Alamos Monte Carlo transport code MCNP6, describe quite well the spectra of fragments with sizes up to 4He across a broad range of target masses and incident energies. However, they do not predict high-energy tails for LF heavier than 4He. The standard versions of CEM and LAQGSM do not account for preequilibrium emission of LF larger than 4He. The aim of our work is to extend the preequilibrium model to include such processes. We do this by including the emission of fragments heavier than 4He at the preequilibrium stage, and using an improved version of the Fermi Break-up model, providing improved agreement with various experimental data.

  3. Jet axes and universal transverse-momentum- dependent fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    Neill, Duff [Theoretical Division, MS B283, Los Alamos National Laboratory,Los Alamos, NM 87545 (United States); Scimemi, Ignazio [Departamento de Física Teórica II, Universidad Complutense de Madrid,Ciudad Universitaria, 28040 Madrid (Spain); Waalewijn, Wouter J. [Institute for Theoretical Physics Amsterdam and Delta Institute for Theoretical Physics,University of Amsterdam,Science Park 904, 1098 XH Amsterdam (Netherlands); Nikhef, Theory Group,Science Park 105, 1098 XG, Amsterdam (Netherlands)

    2017-04-04

    We study the transverse momentum spectrum of hadrons in jets. By measuring the transverse momentum with respect to a judiciously chosen axis, we find that this observable is insensitive to (the recoil of) soft radiation. Furthermore, for small transverse momenta we show that the effects of the jet boundary factorize, leading to a new transverse-momentum-dependent (TMD) fragmentation function. In contrast to the usual TMD fragmentation functions, it does not involve rapidity divergences and is universal in the sense that it is independent of the type of process and number of jets. These results directly apply to sub-jets instead of hadrons. We discuss potential applications, which include studying nuclear modification effects in heavy-ion collisions and identifying boosted heavy resonances.

  4. Global-Scale Patterns of Forest Fragmentation

    Directory of Open Access Journals (Sweden)

    Kurt Riitters

    2000-12-01

    Full Text Available We report an analysis of forest fragmentation based on 1-km resolution land-cover maps for the globe. Measurements in analysis windows from 81 km 2 (9 x 9 pixels, "small" scale to 59,049 km 2 (243 x 243 pixels, "large" scale were used to characterize the fragmentation around each forested pixel. We identified six categories of fragmentation (interior, perforated, edge, transitional, patch, and undetermined from the amount of forest and its occurrence as adjacent forest pixels. Interior forest exists only at relatively small scales; at larger scales, forests are dominated by edge and patch conditions. At the smallest scale, there were significant differences in fragmentation among continents; within continents, there were significant differences among individual forest types. Tropical rain forest fragmentation was most severe in North America and least severe in Europe-Asia. Forest types with a high percentage of perforated conditions were mainly in North America (five types and Europe-Asia (four types, in both temperate and subtropical regions. Transitional and patch conditions were most common in 11 forest types, of which only a few would be considered as "naturally patchy" (e.g., dry woodland. The five forest types with the highest percentage of interior conditions were in North America; in decreasing order, they were cool rain forest, coniferous, conifer boreal, cool mixed, and cool broadleaf.

  5. Stream hydrological fragmentation drives bacterioplankton community composition.

    Directory of Open Access Journals (Sweden)

    Stefano Fazi

    Full Text Available In Mediterranean intermittent streams, the hydrological fragmentation in summer and the successive water flow re-convergence in autumn allow exploring how local processes shape the microbial community within the same habitat. The objectives of this study were to determine how bacterial community composition responded to hydrological fragmentation in summer, and to evaluate whether the seasonal shifts in community composition predominate over the effects of episodic habitat fragmentation. The bacterial community was assessed along the intermittent stream Fuirosos (Spain, at different levels of phylogenetic resolution by in situ hybridization, fingerprinting, and 16S rRNA gene sequencing. The hydrological fragmentation of the stream network strongly altered the biogeochemical conditions with the depletion of oxidized solutes and caused changes in dissolved organic carbon characteristics. In the isolated ponds, beta-Proteobacteria and Actinobacteria increased their abundance with a gradual reduction of the alpha-diversity as pond isolation time increased. Moreover, fingerprinting analysis clearly showed a shift in community composition between summer and autumn. In the context of a seasonal shift, the temporary stream fragmentation simultaneously reduced the microbial dispersion and affected local environmental conditions (shift in redox regime and quality of the dissolved organic matter tightly shaping the bacterioplankton community composition.

  6. Correlation measurements of fission-fragment properties

    Directory of Open Access Journals (Sweden)

    Oberstedt A.

    2010-10-01

    Full Text Available For the development of future nuclear fission applications and for a responsible handling of nuclear waste the a-priori assessment of the fission-fragments’ heat production and toxicity is a fundamental necessity. The success of an indispensable modelling of the fission process strongly depends on a good understanding of the particular mechanism of scission, the mass fragmentation and partition of excitation energy. Experimental observables are fission-fragment properties like mass- and energy-distributions, and the prompt neutron as well as γ-ray multiplicities and emission spectra. The latter quantities should preferably be known as a function of fragment mass and excitation energy. Those data are highly demanded as published by the OECD-NEA in its high priority data request list. With the construction of the double (v, E spectrometer VERDI we aim at measuring pre- and post-neutron masses directly and simultaneously to avoid prompt neutron corrections. From the simultaneous measurement of pre- and post-neutron fission-fragment data the prompt neutron multiplicity may then be inferred fully correlated with fragment mass yield and total kinetic energy. Using an ultra-fast fission event trigger spectral prompt fission γ-ray measurements may be performed. For that purpose recently developed lanthanum-halide detectors, with excellent timing characteristics, were coupled to the VERDI spectrometer allowing for a very good discrimination of fission γ-rays and prompt neutrons due to their different time-of-flight.

  7. Dendrite fragmentation: an experiment-driven simulation.

    Science.gov (United States)

    Cool, T; Voorhees, P W

    2018-02-28

    The processes leading to the fragmentation of secondary dendrite arms are studied using a three-dimensional Sn dendritic structure that was measured experimentally as an initial condition in a phase-field simulation. The phase-field model replicates the kinetics of the coarsening process seen experimentally. Consistent with the experiment, the simulations of the Sn-rich dendrite show that secondary dendrite arm coalescence is prevalent and that fragmentation is not. The lack of fragmentation is due to the non-axisymmetric morphology and comparatively small spacing of the dendrite arms. A model for the coalescence process is proposed, and, consistent with the model, the radius of the contact region following coalescence increases as t1/3 We find that small changes in the width and spacing of the dendrite arms can lead to a very different fragmentation-dominated coarsening process. Thus, the alloy system and growth conditions of the dendrite can have a major impact on the fragmentation process.This article is part of the theme issue 'From atomistic interfaces to dendritic patterns'. © 2018 The Author(s).

  8. Dendrite fragmentation: an experiment-driven simulation

    Science.gov (United States)

    Cool, T.; Voorhees, P. W.

    2018-01-01

    The processes leading to the fragmentation of secondary dendrite arms are studied using a three-dimensional Sn dendritic structure that was measured experimentally as an initial condition in a phase-field simulation. The phase-field model replicates the kinetics of the coarsening process seen experimentally. Consistent with the experiment, the simulations of the Sn-rich dendrite show that secondary dendrite arm coalescence is prevalent and that fragmentation is not. The lack of fragmentation is due to the non-axisymmetric morphology and comparatively small spacing of the dendrite arms. A model for the coalescence process is proposed, and, consistent with the model, the radius of the contact region following coalescence increases as t1/3. We find that small changes in the width and spacing of the dendrite arms can lead to a very different fragmentation-dominated coarsening process. Thus, the alloy system and growth conditions of the dendrite can have a major impact on the fragmentation process. This article is part of the theme issue `From atomistic interfaces to dendritic patterns'.

  9. Assessment of Fragmentation Performance of Blast-enhanced Explosive Fragmentation Munitions

    Science.gov (United States)

    2010-10-01

    weighing the individual fragments with precision electronic scales and measuring their average projected areas using the icosahedron gage technique...The icosahedron gage is an electro-optical devise that throws a shadow of a fragment on an electronic sensing surface resulting in an automated

  10. Distal border fragments of the equine navicular bone: association between magnetic resonance imaging characteristics and clinical lameness

    Science.gov (United States)

    Yorke, Elizabeth H.; Judy, Carter E.; Saveraid, Travis C.; McGowan, Conor P.; Caldwell, Fred J.

    2014-01-01

    Distal border fragments of the navicular bone are increasingly being detected due to the improved capabilities of magnetic resonance imaging (MRI), but their clinical significance remains unclear. The purpose of this retrospective study was to describe the location, size, and frequency of fragments in a cohort of horses presented for MRI of the foot and to compare MRI findings with severity of lameness. Archived MRI studies and medical records were searched from March 2006 to June 2008. Horses were included if a distal border fragment of the navicular bone was visible in MRI scans. Confidence interval comparisons and linear regression analyses were used to test hypotheses that fragments were associated with lameness and lameness severity was positively correlated with fragment volume and biaxial location. A total of 453 horses (874 limbs) were included. Fragments were identified in 60 horses (13.25%) and 90 limbs (10.3%). Fifty percent of the horses had unilateral fragments and 50% had bilateral fragments. Fragments were located at the lateral (62.2%), medial (8.89%), or medial and lateral (28.9%) angles of the distal border of the navicular bone. There was no increased probability of being categorized as lame if a fragment was present. There was no significant difference in fragment volume across lameness severity categorizations. Confidence intervals indicated a slightly increased probability of being classified as lame if both medial and lateral fragments were present. Findings indicated that distal border fragments of the navicular bone in equine MRI studies are unlikely to be related to existing lameness.

  11. Antiproton Induced Fission and Fragmentation of Nuclei

    CERN Multimedia

    2002-01-01

    The annihilation of slow antiprotons with nuclei results in a large highly localized energy deposition primarily on the nuclear surface. \\\\ \\\\ The study of antiproton induced fission and fragmentation processes is expected to yield new information on special nuclear matter states, unexplored fission modes, multifragmentation of nuclei, and intranuclear cascades.\\\\ \\\\ In order to investigate the antiproton-nucleus interaction and the processes following the antiproton annihilation at the nucleus, we propose the following experiments: \\item A)~Measurement of several fragments from fission and from multifragmentation in coincidence with particle spectra, especially neutrons and kaons. \\item B)~Precise spectra of $\\pi$, K, n, p, d and t with time-of-flight techniques. \\item C)~Installation of the Berlin 4$\\pi$ neutron detector with a 4$\\pi$ Si detector placed inside for fragments and charged particles. This yields neutron multiplicity distributions and consequently distributions of thermal excitation energies and...

  12. Crystallographic fragment-based drug discovery: use of a brominated fragment library targeting HIV protease.

    Science.gov (United States)

    Tiefenbrunn, Theresa; Forli, Stefano; Happer, Meaghan; Gonzalez, Ana; Tsai, Yingssu; Soltis, Michael; Elder, John H; Olson, Arthur J; Stout, Charles D

    2014-02-01

    A library of 68 brominated fragments was screened against a new crystal form of inhibited HIV-1 protease in order to probe surface sites in soaking experiments. Often, fragments are weak binders with partial occupancy, resulting in weak, difficult-to-fit electron density. The use of a brominated fragment library addresses this challenge, as bromine can be located unequivocally via anomalous scattering. Data collection was carried out in an automated fashion using AutoDrug at SSRL. Novel hits were identified in the known surface sites: 3-bromo-2,6-dimethoxybenzoic acid (Br6) in the flap site and 1-bromo-2-naphthoic acid (Br27) in the exosite, expanding the chemistry of known fragments for development of higher affinity potential allosteric inhibitors. At the same time, mapping the binding sites of a number of weaker binding Br-fragments provides further insight into the nature of these surface pockets. © 2013 John Wiley & Sons A/S.

  13. Forming spectroscopic massive protobinaries by disc fragmentation

    Science.gov (United States)

    Meyer, D. M.-A.; Kuiper, R.; Kley, W.; Johnston, K. G.; Vorobyov, E.

    2018-01-01

    The surroundings of massive protostars constitute an accretion disc which has numerically been shown to be subject to fragmentation and responsible for luminous accretion-driven outbursts. Moreover, it is suspected to produce close binary companions which will later strongly influence the star's future evolution in the Hertzsprung-Russel diagram. We present three-dimensional gravitation-radiation-hydrodynamic numerical simulations of 100 M⊙ pre-stellar cores. We find that accretion discs of young massive stars violently fragment without preventing the (highly variable) accretion of gaseous clumps on to the protostars. While acquiring the characteristics of a nascent low-mass companion, some disc fragments migrate on to the central massive protostar with dynamical properties showing that its final Keplerian orbit is close enough to constitute a close massive protobinary system, having a young high- and a low-mass components. We conclude on the viability of the disc fragmentation channel for the formation of such short-period binaries, and that both processes - close massive binary formation and accretion bursts - may happen at the same time. FU-Orionis-type bursts, such as observed in the young high-mass star S255IR-NIRS3, may not only indicate ongoing disc fragmentation, but also be considered as a tracer for the formation of close massive binaries - progenitors of the subsequent massive spectroscopic binaries - once the high-mass component of the system will enter the main-sequence phase of its evolution. Finally, we investigate the Atacama Large (sub-)Millimeter Array observability of the disc fragments.

  14. Geospatial analysis of forest fragmentation in Uttara Kannada District, India

    Directory of Open Access Journals (Sweden)

    Ramachandra T V

    2016-04-01

    Full Text Available Background: Landscapes consist of heterogeneous interacting dynamic elements with complex ecological, economic and cultural attributes. These complex interactions help in the sustenance of natural resources through bio-geochemical and hydrological cycling. The ecosystem functions are altered with changes in the landscape structure. Fragmentation of large contiguous forests to small and isolated forest patches either by natural phenomena or anthropogenic activities leads to drastic changes in forest patch sizes, shape, connectivity and internal heterogeneity, which restrict the movement leading to inbreeding among Meta populations with extirpation of species. Methods: Landscape dynamics are assessed through land use analysis by way of remote sensing data acquired at different time periods. Forest fragmentation is assessed at the pixel level through computation of two indicators, i.e., Pf (the ratio of pixels that are forested to the total non-water pixels in the window and Pff (the proportion of all adjacent (cardinal directions only pixel pairs that include at least one forest pixel, for which both pixels are forested. Results: Uttara Kannada District has the distinction of having the highest forest cover in Karnataka State, India. This region has been experiencing changes in its forest cover and consequent alterations in functional abilities of its ecosystem. Temporal land use analyses show the trend of deforestation, evident from the reduction of evergreen - semi evergreen forest cover from 57.31 % (1979 to 32.08 % (2013 Forest fragmentation at the landscape level shows a decline of interior forests 64.42 % (1979 to 25.62 % (2013 and transition of non-forest categories such as crop land, plantations and built-up areas, amounting now to 47.29 %. PCA prioritized geophysical and socio variables responsible for changes in the landscape structure at local levels. Conclusion: Terrestrial forest ecosystems in Uttara Kannada District of Central

  15. Dissipative fragmentation in a phase space approach

    Energy Technology Data Exchange (ETDEWEB)

    Adorno, A.; Di Toro, M.; Bonasera, A.; Gregoire, C.; Gulminelli, F.

    Semi-classical approaches have evidenced the role of one and two-body dissipation in nucleus-nucleus collisions. On the other hand, a substantial energy dissipation and some angular momentum transfer have been observed at moderate energy where a fragmentation process is the dominant reaction mechanism. In order to analyse main features of these reactions, we developed a phenomenological model taking into account phase space constraints. The transition between deep inelastic collisions and abrasion-like fragmentation is described and a general agreement with available data is found.

  16. Parton Propagation and Fragmentation in QCD Matter

    Energy Technology Data Exchange (ETDEWEB)

    Alberto Accardi, Francois Arleo, William Brooks, David D' Enterria, Valeria Muccifora

    2009-12-01

    We review recent progress in the study of parton propagation, interaction and fragmentation in both cold and hot strongly interacting matter. Experimental highlights on high-energy hadron production in deep inelastic lepton-nucleus scattering, proton-nucleus and heavy-ion collisions, as well as Drell-Yan processes in hadron-nucleus collisions are presented. The existing theoretical frameworks for describing the in-medium interaction of energetic partons and the space-time evolution of their fragmentation into hadrons are discussed and confronted to experimental data. We conclude with a list of theoretical and experimental open issues, and a brief description of future relevant experiments and facilities.

  17. Computer Model Of Fragmentation Of Atomic Nuclei

    Science.gov (United States)

    Wilson, John W.; Townsend, Lawrence W.; Tripathi, Ram K.; Norbury, John W.; KHAN FERDOUS; Badavi, Francis F.

    1995-01-01

    High Charge and Energy Semiempirical Nuclear Fragmentation Model (HZEFRG1) computer program developed to be computationally efficient, user-friendly, physics-based program for generating data bases on fragmentation of atomic nuclei. Data bases generated used in calculations pertaining to such radiation-transport applications as shielding against radiation in outer space, radiation dosimetry in outer space, cancer therapy in laboratories with beams of heavy ions, and simulation studies for designing detectors for experiments in nuclear physics. Provides cross sections for production of individual elements and isotopes in breakups of high-energy heavy ions by combined nuclear and Coulomb fields of interacting nuclei. Written in ANSI FORTRAN 77.

  18. Globalisation vs. fragmentation of space

    Directory of Open Access Journals (Sweden)

    Prošić Slobodan

    2015-01-01

    Full Text Available The author does not argue in the present paper with rival theories; instead he links them in a rhizomatic fashion provoking thereby a cartography of the landscape we are facing while the Cartesian tradition of reduction of complexities to simples is shifting towards the irreducible fold (Deleuze. The virtual and the real is not discernible. Entities isolated in the past are now part and parcel of the hybrid and rhizomatic network expanding and flowing throughout the intensive space. They form the hybrid spatium which includes everything: social networks, media, fora, wars, the national and the supranational, global and local, marginal and trivial. Disseminating itself, it invades social spaces, and finally encompasses the whole horizon. Fluidity (Bauman is another expression for emptied social spaces and the shift to the societies of control anticipated by Michel Foucault. Through constant reiteration of the difference, the fold shifts to its alternative - envolution. This very frontier has constantly evaded us, in spite of the effort to overcome it. It is conceived, not according to the linear model, but as an 'intensity' (Deleuze and matrix which constantly reproduces itself and becomes, by the same token, the fate of the postmodern civilization, his own trademark and destiny.

  19. QRS fragmentation is superior to QRS duration in predicting mortality in adults with tetralogy of Fallot.

    Science.gov (United States)

    Bokma, Jouke P; Winter, Michiel M; Vehmeijer, Jim T; Vliegen, Hubert W; van Dijk, Arie P; van Melle, Joost P; Meijboom, Folkert J; Post, Martijn C; Zwinderman, Aeilko H; Mulder, Barbara J M; Bouma, Berto J

    2017-05-01

    Although QRS duration >180 ms has prognostic value in adults with tetralogy of Fallot (TOF), its sensitivity to predict mortality is low. Fragmented QRS complexes, a simple measurement on ECG, are related to myocardial fibrosis and dysfunction in patients with TOF. Our objective was to determine whether QRS fragmentation predicts major outcomes in TOF. This multicentre study included adult patients with TOF from a prospective registry. Notches in the QRS complex in ≥2 contiguous leads on a 12-lead ECG, not related to bundle branch block, were defined as QRS fragmentation, which was classified as none, moderate (≤4 leads) or severe (≥5 leads). The primary and secondary outcomes were all-cause mortality and clinical ventricular arrhythmia, respectively. A total of 794 adult patients with TOF (median age 27 years, 55% male; 52% no QRS fragmentation, 32% moderate, 16% severe) were included. During long-term (median 10.4 years) follow-up, 46 (6%) patients died and 35 (4%) patients had ventricular arrhythmias. Overall, 10-year survival was 98% in patients without fragmented QRS complexes, 93% in patients with moderate QRS fragmentation and 81% in patients with severe QRS fragmentation. In multivariable Cox hazards regression analysis, extent of QRS fragmentation (HR: 2.24/class, 95% CI 1.48 to 3.40, pfragmentation was also independently predictive for ventricular arrhythmia (HR: 2.00/class, 95% CI 1.26 to 3.16, p=0.003). The extent of QRS fragmentation is superior to QRS duration in predicting mortality in adult patients with TOF and may be used in risk stratification. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  20. Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics

    Science.gov (United States)

    Vaniya, Arpana

    2015-01-01

    Identification of unknown metabolites is the bottleneck in advancing metabolomics, leaving interpretation of metabolomics results ambiguous. The chemical diversity of metabolism is vast, making structure identification arduous and time consuming. Currently, comprehensive analysis of mass spectra in metabolomics is limited to library matching, but tandem mass spectral libraries are small compared to the large number of compounds found in the biosphere, including xenobiotics. Resolving this bottleneck requires richer data acquisition and better computational tools. Multi-stage mass spectrometry (MSn) trees show promise to aid in this regard. Fragmentation trees explore the fragmentation process, generate fragmentation rules and aid in sub-structure identification, while mass spectral trees delineate the dependencies in multi-stage MS of collision-induced dissociations. This review covers advancements over the past 10 years as a tool for metabolite identification, including algorithms, software and databases used to build and to implement fragmentation trees and mass spectral annotations. PMID:26213431

  1. Limiting Accretion onto Massive Stars by Fragmentation-Induced Starvation

    Energy Technology Data Exchange (ETDEWEB)

    Peters, Thomas; /ZAH, Heidelberg; Klessen, Ralf S.; /ZAH, Heidelberg /KIPAC, Menlo Park; Mac Low, Mordecai-Mark; /Amer. Museum Natural Hist.; Banerjee, Robi; /ZAH, Heidelberg

    2010-08-25

    Massive stars influence their surroundings through radiation, winds, and supernova explosions far out of proportion to their small numbers. However, the physical processes that initiate and govern the birth of massive stars remain poorly understood. Two widely discussed models are monolithic collapse of molecular cloud cores and competitive accretion. To learn more about massive star formation, we perform simulations of the collapse of rotating, massive, cloud cores including radiative heating by both non-ionizing and ionizing radiation using the FLASH adaptive mesh refinement code. These simulations show fragmentation from gravitational instability in the enormously dense accretion flows required to build up massive stars. Secondary stars form rapidly in these flows and accrete mass that would have otherwise been consumed by the massive star in the center, in a process that we term fragmentation-induced starvation. This explains why massive stars are usually found as members of high-order stellar systems that themselves belong to large clusters containing stars of all masses. The radiative heating does not prevent fragmentation, but does lead to a higher Jeans mass, resulting in fewer and more massive stars than would form without the heating. This mechanism reproduces the observed relation between the total stellar mass in the cluster and the mass of the largest star. It predicts strong clumping and filamentary structure in the center of collapsing cores, as has recently been observed. We speculate that a similar mechanism will act during primordial star formation.

  2. Efficient Expression of Antibody Fragments with the Brevibacillus Expression System

    Directory of Open Access Journals (Sweden)

    Hiroshi Hanagata

    2014-05-01

    Full Text Available Antibodies, owing to their capability to bind specifically to a target molecule, have been and will continue to be applied in various areas, including research, diagnosis and therapy. In particular, antibody fragments, which are size-reduced antibodies comprising functional variable domains, are suited for production in bacteria. They also are useful in applications requiring intracellular delivery and for further engineering toward molecules possessing multiple custom functions. An expression system based on Brevibacillus is characterized by high efficiency and simple genetic recombination for secretory production. The Brevibacillus expression system has been successfully utilized for the efficient production of antibody fragments, e.g., scFvs (single-chain antibody fragments comprising heavy-chain and light-chain variable domains, linked by a spacer sequence. Expression in fusion with a Halobacterium-derived secretory protein was shown to confer enhanced productivity. In the case of Fabs, productivity as high as 100 mg/L was accomplished in a simple system, i.e., shake flask cultures. The Brevibacillus expression system offers several advantages, shared by other bacterial systems, such as E. coli, in particular, for the ease in genetic engineering and culture production.

  3. Tropical forest fragmentation affects floral visitors but not the structure of individual-based palm-pollinator networks.

    Directory of Open Access Journals (Sweden)

    Wesley Dáttilo

    Full Text Available Despite increasing knowledge about the effects of habitat loss on pollinators in natural landscapes, information is very limited regarding the underlying mechanisms of forest fragmentation affecting plant-pollinator interactions in such landscapes. Here, we used a network approach to describe the effects of forest fragmentation on the patterns of interactions involving the understory dominant palm Astrocaryum mexicanum (Arecaceae and its floral visitors (including both effective and non-effective pollinators at the individual level in a Mexican tropical rainforest landscape. Specifically, we asked: (i Does fragment size affect the structure of individual-based plant-pollinator networks? (ii Does the core of highly interacting visitor species change along the fragmentation size gradient? (iii Does forest fragment size influence the abundance of effective pollinators of A. mexicanum? We found that fragment size did not affect the topological structure of the individual-based palm-pollinator network. Furthermore, while the composition of peripheral non-effective pollinators changed depending on fragment size, effective core generalist species of pollinators remained stable. We also observed that both abundance and variance of effective pollinators of male and female flowers of A. mexicanum increased with forest fragment size. These findings indicate that the presence of effective pollinators in the core of all forest fragments could keep the network structure stable along the gradient of forest fragmentation. In addition, pollination of A. mexicanum could be more effective in larger fragments, since the greater abundance of pollinators in these fragments may increase the amount of pollen and diversity of pollen donors between flowers of individual plants. Given the prevalence of fragmentation in tropical ecosystems, our results indicate that the current patterns of land use will have consequences on the underlying mechanisms of pollination in

  4. Tropical forest fragmentation affects floral visitors but not the structure of individual-based palm-pollinator networks.

    Science.gov (United States)

    Dáttilo, Wesley; Aguirre, Armando; Quesada, Mauricio; Dirzo, Rodolfo

    2015-01-01

    Despite increasing knowledge about the effects of habitat loss on pollinators in natural landscapes, information is very limited regarding the underlying mechanisms of forest fragmentation affecting plant-pollinator interactions in such landscapes. Here, we used a network approach to describe the effects of forest fragmentation on the patterns of interactions involving the understory dominant palm Astrocaryum mexicanum (Arecaceae) and its floral visitors (including both effective and non-effective pollinators) at the individual level in a Mexican tropical rainforest landscape. Specifically, we asked: (i) Does fragment size affect the structure of individual-based plant-pollinator networks? (ii) Does the core of highly interacting visitor species change along the fragmentation size gradient? (iii) Does forest fragment size influence the abundance of effective pollinators of A. mexicanum? We found that fragment size did not affect the topological structure of the individual-based palm-pollinator network. Furthermore, while the composition of peripheral non-effective pollinators changed depending on fragment size, effective core generalist species of pollinators remained stable. We also observed that both abundance and variance of effective pollinators of male and female flowers of A. mexicanum increased with forest fragment size. These findings indicate that the presence of effective pollinators in the core of all forest fragments could keep the network structure stable along the gradient of forest fragmentation. In addition, pollination of A. mexicanum could be more effective in larger fragments, since the greater abundance of pollinators in these fragments may increase the amount of pollen and diversity of pollen donors between flowers of individual plants. Given the prevalence of fragmentation in tropical ecosystems, our results indicate that the current patterns of land use will have consequences on the underlying mechanisms of pollination in remnant forests.

  5. Fragments on teachers' reflective practicum

    Directory of Open Access Journals (Sweden)

    Živković Predrag Ž.

    2013-01-01

    Full Text Available in many historical and comparative overviews of the works, in which there is an analytical discussion of the dominant pedagogical theories in the twentieth century, John Dewey (Dewey, 1933 is referred to as the founder and creator of the concept of reflection (reflective thought and knowledge in practice. Reflection as a concept is understood as the forms and the form of problem solving, as well as continuously thinking about the causes of problems in situations in situ, including active and systematically and consistently changing connecting ideas with solutions to the problems and situations that preceded them (Hatton & Smith, 1995. Reflective thinking is the most general level to tackle practical problems, allowing the ''recommended'' doubts and confusion before proposing possible solutions to the problem. Dewey wrote about a reflective action which refers to the use of solutions to the problem and to thinking through the course of the action. in later works of the authors who have dealt with this problem, an unambiguous link can be observed between the so-called ''professional'' action and the reflection on action which, in this cyclical relationship, leads to visible changes (Zeichner & Gore, 1984. Already at first glance, this implies a connection with experiential learning and adult position of observation and reflection in various models of experiential learning, which will be discussed later. it would be useful to compare this method with a cyclic action of routine as an expression of impulse, tradition and authority. Reflective action, as opposed to the routine, is a consistently and carefully thought-out action (practice reflection, which is an ''awakened'' knowledge and belief, and that is an expression of openness, accountability and commitment. We are ready for reflection, says Schon, when the ''knowledge-in-action'' - a kind of knowledge that professionals notice when it is acted spontaneously - occurs suddenly and unintentionally

  6. Explaining fragmented and fluid mobilization in gold mining concessions in eastern Democratic Republic of the Congo

    OpenAIRE

    Geenen, Sara; Verweijen, Judith

    2017-01-01

    Abstract: The expansion of industrial mining in the eastern Democratic Republic of the Congo has sparked social mobilization in gold mining concessions, most of which are important sites for artisanal mining. Congruent with observations on the nature of social movements in Africa, such mobilization is hyper-fragmented and fluid. We ascribe this high degree of fluidity and fragmentation both to factors internal to the social mobilization effort, including limited organizational potential and t...

  7. Concise and stereoselective synthesis of the N7-C25 fragment of psymberin.

    Science.gov (United States)

    Rech, Jason C; Floreancig, Paul E

    2005-11-10

    [reaction: see text] The N7-C25 fragment of the potent and selective cytotoxic agent psymberin has been prepared through a short (12 linear steps, 15 total steps) and stereoselective sequence. Highlights of this route include a very rapid construction of the pentasubstituted arene, a substrate-controlled diastereoselective fragment coupling using a Mukaiyama aldol reaction, and an efficient entry into a key tetrahydropyranyl cyanide.

  8. Habitat Loss, Not Fragmentation, Drives Occurrence Patterns of Canada Lynx at the Southern Range Periphery

    OpenAIRE

    Hornseth, Megan L.; Walpole, Aaron A.; Walton, Lyle R.; Bowman, Jeff; Ray, Justina C.; Fortin, Marie-Josée; Murray, Dennis L.

    2014-01-01

    Peripheral populations often experience more extreme environmental conditions than those in the centre of a species' range. Such extreme conditions include habitat loss, defined as a reduction in the amount of suitable habitat, as well as habitat fragmentation, which involves the breaking apart of habitat independent of habitat loss. The 'threshold hypothesis' predicts that organisms will be more affected by habitat fragmentation when the amount of habitat on the landscape is scarce (i.e., le...

  9. Molecular markers. Amplified fragment length polymorphism

    Directory of Open Access Journals (Sweden)

    Pržulj Novo

    2005-01-01

    Full Text Available Amplified Fragment Length Polymorphism molecular markers (AFLPs has been developed combining procedures of RFLPs and RAPDs molekular markers, i.e. the first step is restriction digestion of the genomic DNA that is followed by selective amplification of the restricted fragments. The advantage of the AFLP technique is that it allows rapid generation of a large number of reproducible markers. The reproducibility of AFLPs markers is assured by the use of restriction site-specific adapters and adapter-specific primers for PCR reaction. Only fragments containing the restriction site sequence plus the additional nucleotides will be amplified and the more selected nucleotides added on the primer sequence the fewer the number of fragments amplified by PCR. The amplified products are normally separated on a sequencing gel and visualized after exposure to X-ray film or by using fluorescent labeled primers. AFLP shave proven to be extremely proficient in revealing diversity at below the species level. A disadvantage of AFLP technique is that AFLPs are essentially a dominant marker system and not able to identify heterozygotes.

  10. Decentralized Development Planning and Fragmentation of ...

    African Journals Online (AJOL)

    of intense research and debate, especially in the developed world (Lewis, .... ple and lower units of government, leading to the fragmentation of government in a polity. In ... public services for the citizenry through competition, and improved political ..... Within the challenges of weak urban planning, poor management of land ...

  11. (DAD1) gene fragment of Chinese kale

    African Journals Online (AJOL)

    To clone the defective in anther dehiscence1 (DAD1) gene fragment of Chinese kale, about 700 bp product was obtained by PCR amplification using Chinese kale genomic DNA as the template and a pair of specific primers designed according to the conserved sequence of DAD1 genes of Arabidopsis thaliana and ...

  12. A note on convex renorming and fragmentability

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    A note on convex renorming and fragmentability. A K MIRMOSTAFAEE. Department of Mathematics, Damghan University of Sciences, P.O. 36715/364,. Damghan, Iran. E-mail: kmirmostafaee@dubs.ac.ir ... general, the domain of sn+1 consists of partial plays of the type. (A1,... ,Ai,Bi,Ai+1,... ,An+1), where, for every i ≤ n, (A1 ...

  13. The paradox of forest fragmentation genetics

    Science.gov (United States)

    Andrea T. Kramer; Jennifer L. Ison; Mary V. Ashley; Henry F. Howe

    2008-01-01

    Theory predicts widespread loss of genetic diversity from drift and inbreeding in trees subjected to habitat fragmentation, yet empirical support of this theory is scarce. We argue that population genetics theory may be misapplied in light of ecological realities that, when recognized, require scrutiny of underlying evolutionary assumptions. One ecological reality is...

  14. Fluorescent amplified fragment length polymorphism (AFLP ...

    African Journals Online (AJOL)

    Rosa rugosa is an excellent ornamental plant with important ecological, economical and medicinal values in China. Polymorphism amplifications of the genomic DNA of 5 wild R. rugosa accessions and 25 cultivars that originated from China with fluorescent amplified fragment length polymorphism molecular markers were ...

  15. Probabilistic Role Models and the Guarded Fragment

    DEFF Research Database (Denmark)

    Jaeger, Manfred

    2004-01-01

    We propose a uniform semantic framework for interpreting probabilistic concept subsumption and probabilistic role quantification through statistical sampling distributions. This general semantic principle serves as the foundation for the development of a probabilistic version of the guarded fragm...... fragment of first-order logic. A characterization of equivalence in that logic in terms of bisimulations is given....

  16. Probabilistic role models and the guarded fragment

    DEFF Research Database (Denmark)

    Jaeger, Manfred

    2006-01-01

    We propose a uniform semantic framework for interpreting probabilistic concept subsumption and probabilistic role quantification through statistical sampling distributions. This general semantic principle serves as the foundation for the development of a probabilistic version of the guarded fragm...... fragment of first-order logic. A characterization of equivalence in that logic in terms of bisimulations is given....

  17. Relationship between morphological and amplified fragment length ...

    African Journals Online (AJOL)

    ... morphological and amplified fragment length polymorphism (AFLP) marker based genetic diversity, to estimate mid parent heterosis and to correlate the estimated parental genetic diversity with heterosis chilli. Five CMS B - lines and 30 testers were used for morphological and AFLP marker genetic divergence analysis.

  18. Modified Fragmentation Function from Quark Recombination

    Energy Technology Data Exchange (ETDEWEB)

    Majumder, A.; Wang, Enke; Wang, Xin-Nian

    2005-07-26

    Within the framework of the constituent quark model, it isshown that the single hadron fragmentation function of a parton can beexpressed as a convolution of shower diquark or triquark distributionfunction and quark recombination probability, if the interference betweenamplitudes of quark recombination with different momenta is neglected.Therecombination probability is determined by the hadron's wavefunction inthe constituent quark model. The shower diquark or triquark distributionfunctions of a fragmenting jet are defined in terms of overlappingmatrices of constituent quarks and parton field operators. They aresimilar in form to dihadron or trihadron fragmentation functions in termsof parton operator and hadron states. Extending the formalism to thefield theory at finite temperature, we automatically derive contributionsto the effective single hadron fragmentation function from therecombination of shower and thermal constituent quarks. Suchcontributions involve single or diquark distribution functions which inturn can be related to diquark or triquark distribution functions via sumrules. We also derive QCD evolution equations for quark distributionfunctions that in turn determine the evolution of the effective jetfragmentation functions in a thermal medium.

  19. Targeting incentives to reduce habitat fragmentation

    Science.gov (United States)

    David Lewis; Andrew Plantinga; Junjie Wu

    2009-01-01

    This article develops a theoretical model to analyze the spatial targeting of incentives for the restoration of forested landscapes when wildlife habitat can be enhanced by reducing fragmentation. The key theoretical result is that the marginal net benefits of increasing forest can be convex, in which case corner solutions--converting either none or all of the...

  20. Metagenome Fragment Classification Using -Mer Frequency Profiles

    Directory of Open Access Journals (Sweden)

    Gail Rosen

    2008-01-01

    Full Text Available A vast amount of microbial sequencing data is being generated through large-scale projects in ecology, agriculture, and human health. Efficient high-throughput methods are needed to analyze the mass amounts of metagenomic data, all DNA present in an environmental sample. A major obstacle in metagenomics is the inability to obtain accuracy using technology that yields short reads. We construct the unique -mer frequency profiles of 635 microbial genomes publicly available as of February 2008. These profiles are used to train a naive Bayes classifier (NBC that can be used to identify the genome of any fragment. We show that our method is comparable to BLAST for small 25 bp fragments but does not have the ambiguity of BLAST's tied top scores. We demonstrate that this approach is scalable to identify any fragment from hundreds of genomes. It also performs quite well at the strain, species, and genera levels and achieves strain resolution despite classifying ubiquitous genomic fragments (gene and nongene regions. Cross-validation analysis demonstrates that species-accuracy achieves 90% for highly-represented species containing an average of 8 strains. We demonstrate that such a tool can be used on the Sargasso Sea dataset, and our analysis shows that NBC can be further enhanced.

  1. RESPONSE TO "THE OPTIMAL FRAGMENTATION PRINCIPLE".

    Science.gov (United States)

    Response to "The Optimal Fragmentation Principle"To follow up on my comment to Dale Johnson and to respond to his entertaining and provocative letter, I confess to some frustration in seeing a show-and-tell of a sophisticated tool for data mining and exploration, without ...

  2. Distribution and Causes of Global Forest Fragmentation

    Directory of Open Access Journals (Sweden)

    Timothy G. Wade

    2003-12-01

    Full Text Available Because human land uses tend to expand over time, forests that share a high proportion of their borders with anthropogenic uses are at higher risk of further degradation than forests that share a high proportion of their borders with non-forest, natural land cover (e.g., wetland. Using 1-km advanced very high resolution radiometer (AVHRR satellite-based land cover, we present a method to separate forest fragmentation into natural and anthropogenic components, and report results for all inhabited continents summarized by World Wildlife Fund biomes. Globally, over half of the temperate broadleaf and mixed forest biome and nearly one quarter of the tropical rainforest biome have been fragmented or removed by humans, as opposed to only 4% of the boreal forest. Overall, Europe had the most human-caused fragmentation and South America the least. This method may allow for improved risk assessments and better targeting for protection and remediation by identifying areas with high amounts of human-caused fragmentation.

  3. Ligament Mediated Fragmentation of Viscoelastic Liquids

    Science.gov (United States)

    Keshavarz, Bavand; Houze, Eric C.; Moore, John R.; Koerner, Michael R.; McKinley, Gareth H.

    2016-10-01

    The breakup and atomization of complex fluids can be markedly different than the analogous processes in a simple Newtonian fluid. Atomization of paint, combustion of fuels containing antimisting agents, as well as physiological processes such as sneezing are common examples in which the atomized liquid contains synthetic or biological macromolecules that result in viscoelastic fluid characteristics. Here, we investigate the ligament-mediated fragmentation dynamics of viscoelastic fluids in three different canonical flows. The size distributions measured in each viscoelastic fragmentation process show a systematic broadening from the Newtonian solvent. In each case, the droplet sizes are well described by Gamma distributions which correspond to a fragmentation-coalescence scenario. We use a prototypical axial step strain experiment together with high-speed video imaging to show that this broadening results from the pronounced change in the corrugated shape of viscoelastic ligaments as they separate from the liquid core. These corrugations saturate in amplitude and the measured distributions for viscoelastic liquids in each process are given by a universal probability density function, corresponding to a Gamma distribution with nmin=4 . The breadth of this size distribution for viscoelastic filaments is shown to be constrained by a geometrical limit which can not be exceeded in ligament-mediated fragmentation phenomena.

  4. The St Marys fragmentation grenade explosion.

    Science.gov (United States)

    Nocera, A

    1997-05-19

    The accidental explosion of a fragmentation grenade in a munitions factory at St Marys injured four workers, two critically. The prompt response by ambulances and physician-staffed helicopter emergency medical service prevented deaths, but the incident suggests lessons for the future handling of urban explosions.

  5. Fragmentation of forest, grassland, and shrubland

    Science.gov (United States)

    Kurt H. Riitters

    2013-01-01

    As humans introduce competing land uses into natural landscapes, the public concerns regarding landcover patterns are expressed through headline issues such as urban sprawl, forest fragmentation, water quality, and wilderness preservation. The spatial arrangement of an environment affects all human perceptions and ecological processes within that environment, but this...

  6. Element Distribution and Multiplicity of Heavy Fragments

    CERN Multimedia

    2002-01-01

    This experiment will measure the energy and angular distribution of heavy fragments produced in the reactions of |1|2C on several targets between |2|7Al and |2|3|8U at 86~MeV/u. The systematic investigation of a highly excited interaction region (fireball) by means of a clean N and Z identification of heavy tar fragments, may result in a better understanding of temperature concept and of the degree of equilibration of the local interaction region with respect to the total system. For this investigation a large-area position sensitive ionization chamber of 50~msr solid angle in conjunction with a time-of-flight telescope consisting of parallel-plate detectors will be used. \\\\ \\\\ In order to get information on the transverse momentum transfer and the inelasticity of the collision, the energy of the PROJECTILE-FRAGMENTS will be measured at forward angles with a plastic scintillator hodoscope. In addition to this inclusive measurement correlations between heavy fragments will be investigated by means of three pos...

  7. Effects of soil, altitude, rainfall, and distance on the floristic similarity of Atlantic Forest fragments in the east-Northeast

    Directory of Open Access Journals (Sweden)

    Flávia de Barros Prado Moura

    2013-09-01

    Full Text Available This paper presents the results of a floristic survey conducted on an Atlantic Forest fragment in the state of Alagoas, Brazil. Besides, the results of a similarity analysis between ten rainforest fragments from the Brazilian east-Northeast are presented. The floristic comparison was based on binary data with regard to the presence/ absence criterion for tree species identified in the ten fragments by means of Sørensen’s similarity index. A dendrogram was prepared using cluster analysis (Jaccard’s index and canonical correspondence analysis (CCA to test the abiotic factors, which can differently influence the similarity of fragments. The fragments showed low similarity indices. The variations were due to the fact that each fragment is a patch of what once was a continuous and heterogeneous region. However, the diversity loss, including the disappearance of more demanding species, can lead, in large-scale, to homogeneity and simplification of the northeastern Atlantic Forest.

  8. Patch size, functional isolation, visibility and matrix permeability influences neotropical primate occurrence within highly fragmented landscapes.

    Directory of Open Access Journals (Sweden)

    Lucas Goulart da Silva

    Full Text Available Forest fragmentation and habitat loss are among the major current extinction causes. Remaining fragments are mostly small, isolated and showing poor quality. Being primarily arboreal, Neotropical primates are generally sensitive to fragmentation effects. Furthermore, primates are involved in complex ecological process. Thus, landscape changes that negatively interfere with primate population dynamic affect the structure, composition, and ultimately the viability of the whole community. We evaluated if fragment size, isolation and visibility and matrix permeability are important for explaining the occurrence of three Neotropical primate species. Employing playback, we verified the presence of Callicebus nigrifrons, Callithrix aurita and Sapajus nigritus at 45 forest fragments around the municipality of Alfenas, Brazil. We classified the landscape and evaluated the metrics through predictive models of occurrence. We selected the best models through Akaike Selection Criterion. Aiming at validating our results, we applied the plausible models to another region (20 fragments at the neighboring municipality of Poço Fundo, Brazil. Twelve models were plausible, and three were validated, two for Sapajus nigritus (Area and Area+Visibility and one for Callicebus nigrifrons (Area+Matrix. Our results reinforce the contribution of fragment size to maintain biodiversity within highly degraded habitats. At the same time, they stress the importance of including novel, biologically relevant metrics in landscape studies, such as visibility and matrix permeability, which can provide invaluable help for similar studies in the future and on conservation practices in the long run.

  9. Patch size, functional isolation, visibility and matrix permeability influences neotropical primate occurrence within highly fragmented landscapes.

    Science.gov (United States)

    da Silva, Lucas Goulart; Ribeiro, Milton Cezar; Hasui, Érica; da Costa, Carla Aparecida; da Cunha, Rogério Grassetto Teixeira

    2015-01-01

    Forest fragmentation and habitat loss are among the major current extinction causes. Remaining fragments are mostly small, isolated and showing poor quality. Being primarily arboreal, Neotropical primates are generally sensitive to fragmentation effects. Furthermore, primates are involved in complex ecological process. Thus, landscape changes that negatively interfere with primate population dynamic affect the structure, composition, and ultimately the viability of the whole community. We evaluated if fragment size, isolation and visibility and matrix permeability are important for explaining the occurrence of three Neotropical primate species. Employing playback, we verified the presence of Callicebus nigrifrons, Callithrix aurita and Sapajus nigritus at 45 forest fragments around the municipality of Alfenas, Brazil. We classified the landscape and evaluated the metrics through predictive models of occurrence. We selected the best models through Akaike Selection Criterion. Aiming at validating our results, we applied the plausible models to another region (20 fragments at the neighboring municipality of Poço Fundo, Brazil). Twelve models were plausible, and three were validated, two for Sapajus nigritus (Area and Area+Visibility) and one for Callicebus nigrifrons (Area+Matrix). Our results reinforce the contribution of fragment size to maintain biodiversity within highly degraded habitats. At the same time, they stress the importance of including novel, biologically relevant metrics in landscape studies, such as visibility and matrix permeability, which can provide invaluable help for similar studies in the future and on conservation practices in the long run.

  10. Analysis of Fragmentation and Resulting Shrapnel Penetration of Naturally Fragmenting Cylindrical Bombs

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, S.E.

    2000-08-01

    Fragmentation of exploding cylinders and penetration mechanics of surrounding vessel walls were examined and a qualitative understanding was achieved. This understanding provided a basis for making simplifying approximations and assumptions that aided in creating a shrapnel penetration model. Several mathematical models were discussed, and results from 6 cylinder tests were analyzed in order to select a model that best represented the data. It was determined that the overall best mathematical model to predict shrapnel penetration uses the modified Gurney equation to calculate fragment velocity, the Mott equation to calculate largest fragment weight, and the Christman/Gehring equation to calculate penetration depth.

  11. Habitat fragmentation impacts mobility in a common and widespread woodland butterfly: do sexes respond differently?

    Directory of Open Access Journals (Sweden)

    Bergerot Benjamin

    2012-04-01

    Full Text Available Abstract Background Theory predicts a nonlinear response of dispersal evolution to habitat fragmentation. First, dispersal will be favoured in line with both decreasing area of habitat patches and increasing inter-patch distances. Next, once these inter-patch distances exceed a critical threshold, dispersal will be counter-selected, unless essential resources no longer co-occur in compact patches but are differently scattered; colonization of empty habitat patches or rescue of declining populations are then increasingly overruled by dispersal costs like mortality risks and loss of time and energy. However, to date, most empirical studies mainly document an increase of dispersal associated with habitat fragmentation. We analyzed dispersal kernels for males and females of the common, widespread woodland butterfly Pararge aegeria in highly fragmented landscape, and for males in landscapes that differed in their degree of habitat fragmentation. Results The male and female probabilities of moving were considerably lower in the highly fragmented landscapes compared to the male probability of moving in fragmented agricultural and deciduous oak woodland landscapes. We also investigated whether, and to what extent, daily dispersal distance in the highly fragmented landscape was influenced by a set of landscape variables for both males and females, including distance to the nearest woodland, area of the nearest woodland, patch area and abundance of individuals in the patch. We found that daily movement distance decreased with increasing distance to the nearest woodland in both males and females. Daily distances flown by males were related to the area of the woodland capture site, whereas no such effect was observed for females. Conclusion Overall, mobility was strongly reduced in the highly fragmented landscape, and varied considerably among landscapes with different spatial resource distributions. We interpret the results relative to different cost

  12. Habitat fragmentation impacts mobility in a common and widespread woodland butterfly: do sexes respond differently?

    Science.gov (United States)

    Bergerot, Benjamin; Merckx, Thomas; Van Dyck, Hans; Baguette, Michel

    2012-04-27

    Theory predicts a nonlinear response of dispersal evolution to habitat fragmentation. First, dispersal will be favoured in line with both decreasing area of habitat patches and increasing inter-patch distances. Next, once these inter-patch distances exceed a critical threshold, dispersal will be counter-selected, unless essential resources no longer co-occur in compact patches but are differently scattered; colonization of empty habitat patches or rescue of declining populations are then increasingly overruled by dispersal costs like mortality risks and loss of time and energy. However, to date, most empirical studies mainly document an increase of dispersal associated with habitat fragmentation. We analyzed dispersal kernels for males and females of the common, widespread woodland butterfly Pararge aegeria in highly fragmented landscape, and for males in landscapes that differed in their degree of habitat fragmentation. The male and female probabilities of moving were considerably lower in the highly fragmented landscapes compared to the male probability of moving in fragmented agricultural and deciduous oak woodland landscapes. We also investigated whether, and to what extent, daily dispersal distance in the highly fragmented landscape was influenced by a set of landscape variables for both males and females, including distance to the nearest woodland, area of the nearest woodland, patch area and abundance of individuals in the patch. We found that daily movement distance decreased with increasing distance to the nearest woodland in both males and females. Daily distances flown by males were related to the area of the woodland capture site, whereas no such effect was observed for females. Overall, mobility was strongly reduced in the highly fragmented landscape, and varied considerably among landscapes with different spatial resource distributions. We interpret the results relative to different cost-benefit ratios of movements in fragmented landscapes.

  13. DFT Conformation and Energies of Amylose Fragments at Atomic Resolution Part I: Syn Forms of Alpha-Maltotetraose

    Science.gov (United States)

    DFT optimization studies of ninety syn '-maltotetraose (DP-4) amylose fragments have been carried out at the B3LYP/6-311++G** level of theory. The DP-4 fragments studied include V-helix, tightly bent conformations, a boat, and a 1C4 conformer. The standard hydroxymethyl rotamers (gg, gt, tg) were ...

  14. Fragment quantum mechanical calculation of proteins and its applications.

    Science.gov (United States)

    He, Xiao; Zhu, Tong; Wang, Xianwei; Liu, Jinfeng; Zhang, John Z H

    2014-09-16

    Conspectus The desire to study molecular systems that are much larger than what the current state-of-the-art ab initio or density functional theory methods could handle has naturally led to the development of novel approximate methods, including semiempirical approaches, reduced-scaling methods, and fragmentation methods. The major computational limitation of ab initio methods is the scaling problem, because the cost of ab initio calculation scales nth power or worse with system size. In the past decade, the fragmentation approach based on chemical locality has opened a new door for developing linear-scaling quantum mechanical (QM) methods for large systems and for applications to large molecular systems such as biomolecules. The fragmentation approach is highly attractive from a computational standpoint. First, the ab initio calculation of individual fragments can be conducted almost independently, which makes it suitable for massively parallel computations. Second, the electron properties, such as density and energy, are typically combined in a linear fashion to reproduce those for the entire molecular system, which makes the overall computation scale linearly with the size of the system. In this Account, two fragmentation methods and their applications to macromolecules are described. They are the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method and the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach. The EE-GMFCC method is developed from the MFCC approach, which was initially used to obtain accurate protein-ligand QM interaction energies. The main idea of the MFCC approach is that a pair of conjugate caps (concaps) is inserted at the location where the subsystem is divided by cutting the chemical bond. In addition, the pair of concaps is fused to form molecular species such that the overcounted effect from added concaps can be properly removed. By introducing the electrostatic

  15. Fragmentation of massive dense cores down to ≲ 1000 AU: Relation between fragmentation and density structure

    Energy Technology Data Exchange (ETDEWEB)

    Palau, Aina; Girart, Josep M. [Institut de Ciències de l' Espai (CSIC-IEEC), Campus UAB-Facultat de Ciències, Torre C5-parell 2, E-08193 Bellaterra, Catalunya (Spain); Estalella, Robert [Departament d' Astronomia i Meteorologia (IEEC-UB), Institut de Ciències del Cosmos, Universitat de Barcelona, Martí i Franquès, 1, E-08028 Barcelona (Spain); Fuente, Asunción [Observatorio Astronómico Nacional, P.O. Box 112, E-28803 Alcalá de Henares, Madrid (Spain); Fontani, Francesco; Sánchez-Monge, Álvaro [Osservatorio Astrofisico di Arcetri, INAF, Lago E. Fermi 5, I-50125 Firenze (Italy); Commerçon, Benoit; Hennebelle, Patrick [Laboratoire de Radioastronomie, UMR CNRS 8112, École Normale Supérieure et Observatoire de Paris, 24 rue Lhomond, F-75231 Paris Cedex 05 (France); Busquet, Gemma [INAF-Istituto di Astrofisica e Planetologia Spaziali, Area di Recerca di Tor Vergata, Via Fosso Cavaliere 100, I-00133 Roma (Italy); Bontemps, Sylvain [Université de Bordeaux, LAB, UMR 5804, F-33270 Floirac (France); Zapata, Luis A. [Centro de Radioastronomía y Astrofísica, Universidad Nacional Autónoma de México, P.O. Box 3-72, 58090 Morelia, Michoacán (Mexico); Zhang, Qizhou [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Di Francesco, James, E-mail: palau@ieec.uab.es [Department of Physics and Astronomy, University of Victoria, P.O. Box 355, STN CSC, Victoria, BC, V8W 3P6 (Canada)

    2014-04-10

    In order to shed light on the main physical processes controlling fragmentation of massive dense cores, we present a uniform study of the density structure of 19 massive dense cores, selected to be at similar evolutionary stages, for which their relative fragmentation level was assessed in a previous work. We inferred the density structure of the 19 cores through a simultaneous fit of the radial intensity profiles at 450 and 850 μm (or 1.2 mm in two cases) and the spectral energy distribution, assuming spherical symmetry and that the density and temperature of the cores decrease with radius following power-laws. Even though the estimated fragmentation level is strictly speaking a lower limit, its relative value is significant and several trends could be explored with our data. We find a weak (inverse) trend of fragmentation level and density power-law index, with steeper density profiles tending to show lower fragmentation, and vice versa. In addition, we find a trend of fragmentation increasing with density within a given radius, which arises from a combination of flat density profile and high central density and is consistent with Jeans fragmentation. We considered the effects of rotational-to-gravitational energy ratio, non-thermal velocity dispersion, and turbulence mode on the density structure of the cores, and found that compressive turbulence seems to yield higher central densities. Finally, a possible explanation for the origin of cores with concentrated density profiles, which are the cores showing no fragmentation, could be related with a strong magnetic field, consistent with the outcome of radiation magnetohydrodynamic simulations.

  16. RESTseq--efficient benchtop population genomics with RESTriction Fragment SEQuencing.

    Directory of Open Access Journals (Sweden)

    Eckart Stolle

    Full Text Available We present RESTseq, an improved approach for a cost efficient, highly flexible and repeatable enrichment of DNA fragments from digested genomic DNA using Next Generation Sequencing platforms including small scale Personal Genome sequencers. Easy adjustments make it suitable for a wide range of studies requiring SNP detection or SNP genotyping from fine-scale linkage mapping to population genomics and population genetics also in non-model organisms. We demonstrate the validity of our approach by comparing two honeybee and several stingless bee samples.

  17. Understanding the impacts of forest fragmentation in the Southern Appalachian Mountains

    Energy Technology Data Exchange (ETDEWEB)

    Pearson, S.M.

    1993-06-01

    Southern Appalachian forests are rich in biological diversity. These forests contain many species adapted to conditions ranging from mesic coves to xeric ridges. The major plant communities include wetlands and balds as well as hardwood and coniferous forests. To understand the impacts of habitat fragmentation, the sensitivity of ecosystems, communities, and species to fragmentation must be determined. Recognizing the natural patterns of heterogeneity in these forest and the importance of this heterogeneity to ecological processes will promote our understanding of fragmentation. The impact of a specific forest use (economic development, forest harvesting, recreation) depends on the type of habitat modification.and the spatial extent and pattern of this use. Information on ecological processes, maps of natural communities, and projections about activities that modify forests are needed in order to implement management strategies that will minimize forest fragmentation.

  18. Golgi Fragmentation in Amyotrophic Lateral Sclerosis, an Overview of Possible Triggers and Consequences

    Directory of Open Access Journals (Sweden)

    Vinod eSundaramoorthy

    2015-10-01

    Full Text Available Amyotrophic Lateral Sclerosis (ALS is an invariably fatal neurodegenerative disorder, which specifically targets motor neurons in the brain, brain stem and spinal cord. Whilst the etiology of ALS remains unknown, fragmentation of the Golgi apparatus is detected in ALS patient motor neurons and in animal/cellular disease models. The Golgi is a highly dynamic organelle that acts as a dispatching station for the vesicular transport of secretory/transmembrane proteins. It also mediates autophagy and maintains endoplasmic reticulum (ER and axonal homeostasis. Both the trigger for Golgi fragmentation and the functional consequences of a fragmented Golgi apparatus in ALS remain unclear. However recent evidence has highlighted defects in vesicular trafficking as a pathogenic mechanism in ALS. This review summarises the evidence describing Golgi fragmentation in ALS, with possible links to other disease processes including cellular trafficking, ER stress, defective autophagy and axonal degeneration.

  19. Habitat fragmentation effects on biodiversity patterns

    Science.gov (United States)

    Conceição, Katiane S.; de Oliveira, Viviane M.

    2010-09-01

    We study the effects of habitat fragmentation on biodiversity patterns by means of a simple spatial model which considers selective geographic colonization, diffusion and mutation. In our model, regions of the lattice are characterized by the amount of resources available to populations of species which are going to colonize that regions. We simulate the fragmentation of the habitat by assuming that a proportion p of the sites is not available for colonization, that is, there is no resource availability in those sites. We analyse the patterns of the species-area relationship and the abundance distribution considering two sample methods, in order to simulate the cases in which the habitats are distributed in islands and continents. We have observed that the pattern of the species-area curve is changed when different sample methods are considered. We have also verified that the abundance distribution is bimodal when small mutation probabilities are considered.

  20. Fission fragment distributions within dynamical approach

    Science.gov (United States)

    Mazurek, K.; Nadtochy, P. N.; Ryabov, E. G.; Adeev, G. D.

    2017-04-01

    The review covers recent developments and achievements in the dynamical description of fission process at high excitation energy. It is shown that the dynamical approach based on multidimensional Langevin equations combined with the statistical description of nuclear decay by particles evaporation is capable of fairly well describing the formation of fission fragment mass-energy, charge, and angular distributions of fission fragments in coincidence with the pre- and post-scission particle emission. The final yields of fission and evaporation residues channels products could be obtained. The detailed description of fission dynamics allows studying different stages of fission process, indicating the most important ingredients governing fission process and studying in detail such fundamental nuclear properties as nuclear viscosity and fission timescale. The tasks and perspectives of multidimensional dynamical approach are also discussed.

  1. Anatomy of a cluster IDP. Part 2: Noble gas abundances, trace element geochemistry, isotopic abundances, and trace organic chemistry of several fragments from L2008#5

    Science.gov (United States)

    Thomas, K. L.; Clemett, S. J.; Flynn, G. J.; Keller, L. P.; Mckay, David S.; Messenger, S.; Nier, A. O.; Schlutter, D. J.; Sutton, S. R.; Walker, R. M.

    1994-01-01

    The topics discussed include the following: noble gas content and release temperatures; trace element abundances; heating summary of cluster fragments; isotopic measurements; and trace organic chemistry.

  2. Fragmentation of very high energy heavy ions

    CERN Document Server

    Giorgini, M

    2001-01-01

    A stack of CR39 (C12H18O7)n nuclear track detectors with a Cu target was exposed to a 158 A GeV lead ion beam at the CERN-SPS, in order to study the fragmentation properties of lead nuclei. Measurements of the total, break-up and pick-up charge-changing cross sections of ultrarelativistic Pb ions on Cu and CR39 targets are presented and discussed.

  3. Intentional Information Fragmentation in Email Management

    OpenAIRE

    Shanahan, Daniel Patrick

    2012-01-01

    Personal Information Management (PIM) studies the practice of storing, organizing, and retrieving information by an individual in support of their roles and tasks (Bergman, et al., 2004). One important problem in PIM is information fragmentation (IF) â the condition of having data in different formats, distributed across multiple locations, manipulated by different applications, and residing in a generally disconnected manner (Tungare, 2007). IF can conflict with the PIM ideal that users sh...

  4. N/z Dependence of Projectile Fragmentation

    Science.gov (United States)

    Trautmann, W.; Adrich, P.; Aumann, T.; Bacri, C. O.; Barczyk, T.; Bassini, R.; Bianchin, S.; Boiano, C.; Botvina, A. S.; Boudard, A.; Brzychczyk, J.; Chbihi, A.; Cibor, J.; Czech, B.; de Napoli, M.; Ducret, J.-É.; Emling, H.; Frankland, J. D.; Hellström, M.; Henzlova, D.; Immè, G.; Iori, I.; Johansson, H.; Kezzar, K.; Lafriakh, A.; Le Fèvre, A.; Le Gentil, E.; Leifels, Y.; Lühning, J.; Łukasik, J.; Lynch, W. G.; Lynen, U.; Majka, Z.; Mocko, M.; Müller, W. F. J.; Mykulyak, A.; Orth, H.; Otte, A. N.; Palit, R.; Pawłowski, P.; Pullia, A.; Raciti, G.; Rapisarda, E.; Sann, H.; Schwarz, C.; Sfienti, C.; Simon, H.; Sümmerer, K.; Tsang, M. B.; Verde, G.; Volant, C.; Wallace, M.; Weick, H.; Wiechula, J.; Wieloch, A.; Zwiegliński, B.

    The N/Z dependence of projectile fragmentation at relativistic energies has been studied in a recent experiment at the GSI laboratory with the ALADiN forward spectrometer coupled to the LAND neutron detector. Besides a primary beam of 124Sn, also secondary beams of 124La and 107Sn delivered by the FRS fragment separator have been used in order to extend the range of isotopic compositions of the produced spectator sources. With the achieved mass resolution of ΔA/A ≈ 1.5%, lighter isotopes with atomic numbers Z ≤ 10 are individually resolved. The presently ongoing analyses of the measured isotope yields focus on isoscaling and its relation to the properties of hot fragments at freeze-out and on the derivation of chemical freeze-out temperatures which are found to be independent of the isotopic composition of the studied systems. The latter result is at variance with the predictions for limiting temperatures as obtained with finite-temperature Hartree-Fock calculations.

  5. Gluon fragmentation into P wave heavy quarkonium

    Energy Technology Data Exchange (ETDEWEB)

    Braaten, Eric; Yuan, Tzu Chiang

    1994-03-01

    The fragmentation functions for gluons to split into P-wave heavy quarkonium states are calculated to leading order in the QCD coupling constant. Long-distance effects are factored into two nonperturbative parameters: the derivative of the radial wavefunction at the origin and a second parameter related to the probability for a heavy-quark-antiquark pair that is produced in a color-octet S-wave state to form a color-singlet P-wave bound state. The fragmentation probabilities for a high transverse momentum gluon to split into the P-wave charmonium states \\chi_{c0}, \\chi_{c1}, and \\chi_{c2} are estimated to be 0.4 \\times 10^{-4}, 1.8 \\times 10^{-4}, and 2.4 \\times 10^{-4}, respectively. This fragmentation process may account for a significant fraction of the rate for the inclusive production of \\chi_{cJ} at large transverse momentum in p \\bar p colliders.

  6. Commissioning the A1900 projectile fragment separator

    CERN Document Server

    Morrissey, D J; Steiner, M; Stolz, A; Wiedenhöver, I

    2003-01-01

    An important part of the recent upgrade of the NSCL facility is the replacement of the A1200 fragment separator with a new high acceptance device called the A1900. The design of the A1900 device represents a third generation projectile fragment separator (relative to the early work at LBL) as it is situated immediately after the primary accelerator, has a very large acceptance, a bending power significantly larger than that of the cyclotron and is constructed from large superconducting magnets (quadrupoles with 20 and 40 cm diameter warm bores). The A1900 can accept over 90% of a large range of projectile fragmentation products produced at the NSCL, leading to large gains in the intensity of the secondary beams. The results of initial tests of the system with a restricted momentum acceptance (+-0.5%) indicate that the A1900 is performing up to specifications. Further large gains in the intensities of primary beams, typically two or three orders of magnitude, will be possible as the many facets of high current...

  7. In silico fragment-based drug design.

    Science.gov (United States)

    Konteatis, Zenon D

    2010-11-01

    In silico fragment-based drug design (FBDD) is a relatively new approach inspired by the success of the biophysical fragment-based drug discovery field. Here, we review the progress made by this approach in the last decade and showcase how it complements and expands the capabilities of biophysical FBDD and structure-based drug design to generate diverse, efficient drug candidates. Advancements in several areas of research that have enabled the development of in silico FBDD and some applications in drug discovery projects are reviewed. The reader is introduced to various computational methods that are used for in silico FBDD, the fragment library composition for this technique, special applications used to identify binding sites on the surface of proteins and how to assess the druggability of these sites. In addition, the reader will gain insight into the proper application of this approach from examples of successful programs. In silico FBDD captures a much larger chemical space than high-throughput screening and biophysical FBDD increasing the probability of developing more diverse, patentable and efficient molecules that can become oral drugs. The application of in silico FBDD holds great promise for historically challenging targets such as protein-protein interactions. Future advances in force fields, scoring functions and automated methods for determining synthetic accessibility will all aid in delivering more successes with in silico FBDD.

  8. Cationized Carbohydrate Gas-Phase Fragmentation Chemistry

    Science.gov (United States)

    Bythell, Benjamin J.; Abutokaikah, Maha T.; Wagoner, Ashley R.; Guan, Shanshan; Rabus, Jordan M.

    2017-04-01

    We investigate the fragmentation chemistry of cationized carbohydrates using a combination of tandem mass spectrometry, regioselective labeling, and computational methods. Our model system is D-lactose. Barriers to the fundamental glyosidic bond cleavage reactions, neutral loss pathways, and structurally informative cross-ring cleavages are investigated. The most energetically favorable conformations of cationized D-lactose were found to be similar. In agreement with the literature, larger group I cations result in structures with increased cation coordination number which require greater collision energy to dissociate. In contrast with earlier proposals, the B n -Y m fragmentation pathways of both protonated and sodium-cationized analytes proceed via protonation of the glycosidic oxygen with concerted glycosidic bond cleavage. Additionally, for the sodiated congeners our calculations support sodiated 1,6-anhydrogalactose B n ion structures, unlike the preceding literature. This affects the subsequent propensity of formation and prediction of B n /Y m branching ratio. The nature of the anomeric center (α/β) affects the relative energies of these processes, but not the overall ranking. Low-energy cross-ring cleavages are observed for the metal-cationized analytes with a retro-aldol mechanism producing the 0,2 A 2 ion from the sodiated forms . Theory and experiment support the importance of consecutive fragmentation processes, particularly for the protonated congeners at higher collision energies.

  9. Fibril Fragmentation Enhances Amyloid Cytotoxicity*♦

    Science.gov (United States)

    Xue, Wei-Feng; Hellewell, Andrew L.; Gosal, Walraj S.; Homans, Steve W.; Hewitt, Eric W.; Radford, Sheena E.

    2009-01-01

    Fibrils associated with amyloid disease are molecular assemblies of key biological importance, yet how cells respond to the presence of amyloid remains unclear. Cellular responses may not only depend on the chemical composition or molecular properties of the amyloid fibrils, but their physical attributes such as length, width, or surface area may also play important roles. Here, we report a systematic investigation of the effect of fragmentation on the structural and biological properties of amyloid fibrils. In addition to the expected relationship between fragmentation and the ability to seed, we show a striking finding that fibril length correlates with the ability to disrupt membranes and to reduce cell viability. Thus, despite otherwise unchanged molecular architecture, shorter fibrillar samples show enhanced cytotoxic potential than their longer counterparts. The results highlight the importance of fibril length in amyloid disease, with fragmentation not only providing a mechanism by which fibril load can be rapidly increased but also creating fibrillar species of different dimensions that can endow new or enhanced biological properties such as amyloid cytotoxicity. PMID:19808677

  10. Intermittency in {sup 197}Au fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    Dabrowska, A.; Holynski, R.; Olszewski, A.; Szarska, M.; Wilczynska, B.; Wolter, W.; Wosiek, B. [Institute of Nuclear Physics, Cracow (Poland); Cherry, M.L.; Deines-Jones, P.; Jones, W.V.; Sengupta, K.; Wefel, B. [Louisiana State Univ., Baton Rouge, LA (United States). Dept. of Physics and Astronomy; Waddington, C.J. [Minnesota Univ., Minneapolis, MN (United States). School of Physics and Astronomy; Pozharova, E.A.; Skorodko, T.Yu. [Inst. of Theoretical and Experimental Physics, Moscow (Russian Federation); KLMM Collaboration

    1995-07-01

    The concept of factorial moments was applied to an analysis of the dynamical fluctuations in the charge distributions of the fragments emitted from gold nuclei with energies 10.6 and < 1.0 GeV/n interacting with emulsion nuclei. Clear evidence for intermittent fluctuations has been found in an analysis using all the particles released from the gold projectile, with a stronger effect observed below 1 GeV/n than at 10.6 GeV/n. For the full data sets, however, the intermittency effect was found to be very sensitive to the singly charged particles, and neglecting these particles strongly reduces the intermittency signal. When the analysis is restricted to the multiply charged fragments, an intermittency effect is revealed only for multifragmentation events, although one that is enhanced as compared to the analysis of all, singly and multiply charged, particles. The properties of the anomalous fractal dimensions suggest a sequential decay mechanism, rather than the existence of possible critical behaviour in the process of nuclear fragmentation. The likely influence of the charge conservation effects and the finite size of decaying systems on the observed intermittency signals was pointed out. (author). 37 refs, 9 figs, 5 tabs.

  11. Mining for viral fragments in methylation enriched sequencing data

    Directory of Open Access Journals (Sweden)

    Klaas eMensaert

    2015-02-01

    Full Text Available Most next generation sequencing experiments generate more data than is required for the experimental set up. For example, methyl-CpG binding domain (MBD affinity purification based sequencing is often used for DNA-methylation profiling, but up to 30% of the sequenced fragments cannot be mapped uniquely to the reference genome. Here we present and evaluate a methodology for the identification of viruses in these otherwise unused paired-end MBD-seq data. Viral detection is accomplished by mapping non-reference alignable reads to a comprehensive set of viral genomes. As viruses play an important role in epigenetics and cancer development, 92 (premalignant and benign samples, originating from two different collections of cervical samples and related cell lines, were used in this study. These samples include primary carcinomas (n=22, low- & high-grade cervical intrapeithelial neoplasia (CIN1 & CIN2/3 - n=2/n=30 and normal tissue (n=20, as well as control samples (n=17. Viruses that were detected include phages, adenoviruses, herpesviridae and HPV. HPV, which causes virtually all cervical cancers, was identified in 95% of the carcinomas, 100% of the CIN2/3 samples, both CIN1 samples and in 55% of the normal samples. Comparing the amount of mapped fragments on HPV for each HPV-infected sample yielded a significant difference between normal samples and carcinomas or CIN2/3 samples (adjusted p-values resp. < 10^-5, < 10^-5, reflecting different viral loads and/or methylation degrees in non-normal samples. Fragments originating from different HPV types could be distinguished and were independently validated by PCR-based assays with a specificity of 98% and a sensitivitity of 66%. In conclusion, although limited by the a priori knowledge of viral reference genome sequences, the proposed methodology can provide a first but substantial insight into the presence, concentration and types of methylated viral sequences in MBD-seq data without additional costs.

  12. Investigation of Explosively Driven Fragmentation of Metals - Two Dimensional Fracture and Fragmentation of Metal Shells: Progress Report II

    Energy Technology Data Exchange (ETDEWEB)

    Grady, D

    2003-02-01

    High explosive enclosed by a metal case qualitatively describes an essential component of high energy systems of importance to the Department of Energy. Detonation of the high explosive causes intense transient pressure loading of the metal following arrival of normal or obliquely incident explosive detonation wave. Subsequent expansion and deformation of the metal case leads to eventual rupture and the opening of fractures and fissures. Details of the rupture process are critical to performance of the system. Consequently, it is essential that the material and kinematic issues governing the processes of dynamic loading and subsequent failure of an explosive-metal case component within a functioning system be adequately understood. Among the reasons are to quantify existing performance, characterize potential degradation of performance resulting from system aging, and optimizing or maintaining system performance through implementation of structural or material changes. The physical and engineering issues underlying this dynamic response and failure phenomena are not adequately understood. The purpose of the present program is to identify the key issues and develop theoretical, computational and experimental models needed to achieve a satisfactory theoretical and analysis framework for analysis of metal case failure in the explosive environment. Specific tasks within the present program include: (1) Models and theories currently being pursued based on physical principles of both the statistical fragmentation concepts of Mott and the energy-based concept of others show promise of providing the analytic and computational methodology capable of predicting explosion-induced fracture and fragmentation of metal components. Experimental studies initiated in the earlier effort offer promise to provide critical test data for validation. The present task shall involve the further refinement and development of the dynamic failure and fragmentation models and theories, and the

  13. Dissertation: Precompound Emission of Energetic Light Fragments in Spallation Reactions

    Energy Technology Data Exchange (ETDEWEB)

    Kerby, Leslie Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-08-04

    Emission of light fragments (LF) from nuclear reactions is an open question. Different reaction mechanisms contribute to their production; the relative roles of each, and how they change with incident energy, mass number of the target, and the type and emission energy of the fragments is not completely understood. None of the available models are able to accurately predict emission of LF from arbitrary reactions. However, the ability to describe production of LF (especially at energies ≳ 30 MeV) from many reactions is important for different applications, such as cosmic-ray-induced Single Event Upsets (SEUs), radiation protection, and cancer therapy with proton and heavy-ion beams, to name just a few. The Cascade-Exciton Model (CEM) version 03.03 and the Los Alamos version of the Quark-Gluon String Model (LAQGSM) version 03.03 event generators in Monte Carlo N-Particle Transport Code version 6 (MCNP6) describe quite well the spectra of fragments with sizes up to ⁴He across a broad range of target masses and incident energies (up to ~ 5 GeV for CEM and up to ~ 1 TeV/A for LAQGSM). However, they do not predict the high energy tails of LF spectra heavier than ⁴He well. Most LF with energies above several tens of MeV are emitted during the precompound stage of a reaction. The current versions of the CEM and LAQGSM event generators do not account for precompound emission of LF larger than ⁴He. The aim of our work is to extend the precompound model in them to include such processes, leading to an increase of predictive power of LF-production in MCNP6. This entails upgrading the Modified Exciton Model currently used at the preequilibrium stage in CEM and LAQGSM. It also includes expansion and examination of the coalescence and Fermi break-up models used in the precompound stages of spallation reactions within CEM and LAQGSM. Extending our models to include emission of fragments heavier than ⁴He at the precompound stage has indeed provided results that have much

  14. Fish responses to experimental fragmentation of seagrass habitat.

    Science.gov (United States)

    Macreadie, Peter I; Hindell, Jeremy S; Jenkins, Gregory P; Connolly, Rod M; Keough, Michael J

    2009-06-01

    Understanding the consequences of habitat fragmentation has come mostly from comparisons of patchy and continuous habitats. Because fragmentation is a process, it is most accurately studied by actively fragmenting large patches into multiple smaller patches. We fragmented artificial seagrass habitats and evaluated the impacts of fragmentation on fish abundance and species richness over time (1 day, 1 week, 1 month). Fish assemblages were compared among 4 treatments: control (single, continuous 9-m(2) patches); fragmented (single, continuous 9-m(2) patches fragmented to 4 discrete 1-m(2) patches); prefragmented/patchy (4 discrete 1-m(2) patches with the same arrangement as fragmented); and disturbance control (fragmented then immediately restored to continuous 9-m(2) patches). Patchy seagrass had lower species richness than actively fragmented seagrass (up to 39% fewer species after 1 week), but species richness in fragmented treatments was similar to controls. Total fish abundance did not vary among treatments and therefore was unaffected by fragmentation, patchiness, or disturbance caused during fragmentation. Patterns in species richness and abundance were consistent 1 day, 1 week, and 1 month after fragmentation. The expected decrease in fish abundance from reduced total seagrass area in fragmented and patchy seagrass appeared to be offset by greater fish density per unit area of seagrass. If fish prefer to live at edges, then the effects of seagrass habitat loss on fish abundance may have been offset by the increase (25%) in seagrass perimeter in fragmented and patchy treatments. Possibly there is some threshold of seagrass patch connectivity below which fish abundances cannot be maintained. The immediate responses of fish to experimental habitat fragmentation provided insights beyond those possible from comparisons of continuous and historically patchy habitat. ©2009 Society for Conservation Biology.

  15. Colorado Plateau Rapid Ecoregion Assessment Indicators: Natural Vegetation Fragmentation

    Data.gov (United States)

    Bureau of Land Management, Department of the Interior — This dataset presents measures of landscape fragmentation calculated by FRAGSTATS at 4KM and HUC5 reporting unit levels. Fragmentation integrates the influence of...

  16. Fragmentation Point Detection of JPEG Images at DHT Using Validator

    Science.gov (United States)

    Mohamad, Kamaruddin Malik; Deris, Mustafa Mat

    File carving is an important, practical technique for data recovery in digital forensics investigation and is particularly useful when filesystem metadata is unavailable or damaged. The research on reassembly of JPEG files with RST markers, fragmented within the scan area have been done before. However, fragmentation within Define Huffman Table (DHT) segment is yet to be resolved. This paper analyzes the fragmentation within the DHT area and list out all the fragmentation possibilities. Two main contributions are made in this paper. Firstly, three fragmentation points within DHT area are listed. Secondly, few novel validators are proposed to detect these fragmentations. The result obtained from tests done on manually fragmented JPEG files, showed that all three fragmentation points within DHT are successfully detected using validators.

  17. Global patterns of fragmentation and connectivity of mammalian carnivore habitat

    OpenAIRE

    Crooks, Kevin R.; Burdett, Christopher L.; Theobald, David M.; Rondinini, Carlo; Boitani, Luigi

    2011-01-01

    Although mammalian carnivores are vulnerable to habitat fragmentation and require landscape connectivity, their global patterns of fragmentation and connectivity have not been examined. We use recently developed high-resolution habitat suitability models to conduct comparative analyses and to identify global hotspots of fragmentation and connectivity for the world's terrestrial carnivores. Species with less fragmentation (i.e. more interior high-quality habitat) had larger geographical ranges...

  18. Cross sections and kinematics of proton induced fragmentation of carbon

    Energy Technology Data Exchange (ETDEWEB)

    Streibel, T.; Roecher, H.; Huentrup, G.; Heinrich, W. [Siegen Univ. (Germany). Dept. of Physics

    1997-09-01

    Charge changing fragmentation cross sections for C at a proton energy of about 70 MeV were measured. The discrepancies between measurement and model predictions indicate the necessity of further investigations. We have also measured distributions of fragment emission angles which can be described using a model with a momentum transfer to the fragmenting nucleus. The developed model leads to predictions for momentum distributions of proton induced target fragments of C at small energies. (orig.)

  19. The relationship between sperm viability and DNA fragmentation rates.

    Science.gov (United States)

    Samplaski, Mary K; Dimitromanolakis, Apostolos; Lo, Kirk C; Grober, Ethan D; Mullen, Brendan; Garbens, Alaina; Jarvi, Keith A

    2015-05-14

    In humans, sperm DNA fragmentation rates have been correlated with sperm viability rates. Reduced sperm viability is associated with high sperm DNA fragmentation, while conversely high sperm viability is associated with low rates of sperm DNA fragmentation. Both elevated DNA fragmentation rates and poor viability are correlated with impaired male fertility, with a DNA fragmentation rate of >30% indicating subfertility. We postulated that in some men, the sperm viability assay could predict the sperm DNA fragmentation rates. This in turn could reduce the need for sperm DNA fragmentation assay testing, simplifying the infertility investigation and saving money for infertile couples. All men having semen analyses with both viability and DNA fragmentation testing were identified via a prospectively collected database. Viability was measured by eosin-nigrosin assay. DNA fragmentation was measured using the sperm chromosome structure assay. The relationship between DNA fragmentation and viability was assessed using Pearson's correlation coefficient. From 2008-2013, 3049 semen analyses had both viability and DNA fragmentation testing. A strong inverse relationship was seen between sperm viability and DNA fragmentation rates, with r=-0.83. If viability was ≤50% (n=301) then DNA fragmentation was ≥ 30% for 95% of the samples. If viability was ≥75% (n=1736), then the DNA fragmentation was ≤30% for 95% of the patients. Sperm viability correlates strongly with DNA fragmentation rates. In men with high levels of sperm viability≥75%, or low levels of sperm viability≤ 30%, DFI testing may be not be routinely necessary. Given that DNA fragmentation testing is substantially more expensive than vitality testing, this may represent a valuable cost-saving measure for couples undergoing a fertility evaluation.

  20. Implications of Fine-Grained Habitat Fragmentation and Road Mortality for Jaguar Conservation in the Atlantic Forest, Brazil.

    Directory of Open Access Journals (Sweden)

    Laury Cullen

    Full Text Available Jaguar (Panthera onca populations in the Upper Paraná River, in the Brazilian Atlantic Forest region, live in a landscape that includes highly fragmented areas as well as relatively intact ones. We developed a model of jaguar habitat suitability in this region, and based on this habitat model, we developed a spatially structured metapopulation model of the jaguar populations in this area to analyze their viability, the potential impact of road mortality on the populations' persistence, and the interaction between road mortality and habitat fragmentation. In more highly fragmented populations, density of jaguars per unit area is lower and density of roads per jaguar is higher. The populations with the most fragmented habitat were predicted to have much lower persistence in the next 100 years when the model included no dispersal, indicating that the persistence of these populations are dependent to a large extent on dispersal from other populations. This, in turn, indicates that the interaction between road mortality and habitat fragmentation may lead to source-sink dynamics, whereby populations with highly fragmented habitat are maintained only by dispersal from populations with less fragmented habitat. This study demonstrates the utility of linking habitat and demographic models in assessing impacts on species living in fragmented landscapes.

  1. Implications of Fine-Grained Habitat Fragmentation and Road Mortality for Jaguar Conservation in the Atlantic Forest, Brazil.

    Science.gov (United States)

    Cullen, Laury; Stanton, Jessica C; Lima, Fernando; Uezu, Alexandre; Perilli, Miriam L L; Akçakaya, H Reşit

    2016-01-01

    Jaguar (Panthera onca) populations in the Upper Paraná River, in the Brazilian Atlantic Forest region, live in a landscape that includes highly fragmented areas as well as relatively intact ones. We developed a model of jaguar habitat suitability in this region, and based on this habitat model, we developed a spatially structured metapopulation model of the jaguar populations in this area to analyze their viability, the potential impact of road mortality on the populations' persistence, and the interaction between road mortality and habitat fragmentation. In more highly fragmented populations, density of jaguars per unit area is lower and density of roads per jaguar is higher. The populations with the most fragmented habitat were predicted to have much lower persistence in the next 100 years when the model included no dispersal, indicating that the persistence of these populations are dependent to a large extent on dispersal from other populations. This, in turn, indicates that the interaction between road mortality and habitat fragmentation may lead to source-sink dynamics, whereby populations with highly fragmented habitat are maintained only by dispersal from populations with less fragmented habitat. This study demonstrates the utility of linking habitat and demographic models in assessing impacts on species living in fragmented landscapes.

  2. Identification of screwworm species by polymerase chain reaction-restriction fragment length polymorphism.

    Science.gov (United States)

    Taylor, D B; Szalanski, A L; Peterson, R D

    1996-01-01

    Restriction fragment length polymorphisms in polymerase chain reaction amplified fragments (PCR-RFLP) of mitochondrial DNA were used to differentiate species of New World screwworms (Diptera: Calliphoridae). Twenty-seven restriction enzymes were screened on five regions of mtDNA. Eleven restriction fragment length patterns differentiated New World screwworm, Cochliomyia hominivorax (Coquerel), from secondary screwworm, Cochliomyia macellaria (F.). Five restriction fragment length patterns were polymorphic in C.hominivorax while all fragment patterns were fixed in C.macellaria. Diagnostic restriction fragment length patterns were used for species diagnosis, whereas intraspecific variable patterns were used to characterize field samples and laboratory strains. The PCR-RFLP technique is flexible with regard to developmental stage of the sample and method of preservation. We were able to characterize specimens of all life stages from egg to adult including larvae preserved in alcohol and pinned adults. PCR-RFLP is rapid and inexpensive, enabling specimens to be characterized within 24 h for less than $2.50.

  3. Sperm DNA fragmentation abnormalities in men from couples with a history of recurrent miscarriage.

    Science.gov (United States)

    Leach, Mikaela; Aitken, Robert J; Sacks, Gavin

    2015-08-01

    Previous studies have described an association between sperm with DNA damage and a history of recurrent miscarriage (RM), although it is not clear whether there is benefit in screening for sperm DNA fragmentation and to what extent DNA fragmentation impacts upon RM. To identify what proportion of couples experiencing RM are affected by DNA fragmentation abnormalities. In this retrospective study, between 2008 and 2013, couples with a history of recurrent miscarriage (≥3 first trimester miscarriages) were investigated comprehensively for known causes (karyotype, uterine, antiphospholipid syndrome, thrombophilia) and also by semen analysis, including DNA fragmentation [sperm chromatin structure analysis (SCSA)]. Statistical analysis was performed on SPSS software with significance taken as P fragmentation index (DFI) of 9.50%. Normal levels were found in 70.5% of men (DFI 30%). Couples with otherwise unexplained recurrent miscarriage had significantly higher DFI than those with other causes identified on routine screening (P = 0.012). In couples experiencing RM, 30% (32/108) of men had sperm with high levels of DNA fragmentation (DFI > 15%). This may be a contributing factor to the clinical syndrome of RM, and future clinical trials of therapies for these couples are warranted. © 2015 The Royal Australian and New Zealand College of Obstetricians and Gynaecologists.

  4. Sperm DNA fragmentation as a result of ultra-endurance exercise training in male athletes.

    Science.gov (United States)

    Vaamonde, D; Algar-Santacruz, C; Abbasi, A; García-Manso, J M

    2018-02-01

    Intensive sports practice seems to exert negative effects on semen parameters; in order to assess these effects, the objective of this study was to assess semen, including DNA fragmentation, and hormone parameters in elite triathletes. Twelve high-level triathletes preparing for a National Triathlon Championship participated in the study. The qualitative sperm parameters analysed were volume, sperm count, motility, morphology and DNA fragmentation; when needed, additional testing was performed. Assessed hormones were testosterone (T), cortisol (C) and testosterone-cortisol ratio (T/C). Maximum oxygen consumption and training characteristics were also assessed. Hormonal values and physical semen parameters were within normal ranges. DNA fragmentation showed high values (20.4 ± 6.1%). Round cells in semen were higher than normal (2.8 ± 1.5 million/ml), with the presence of macrophages. Correlations were found for several parameters: concentration of round cells positively correlated with progressive sperm motility (p = .01) and sperm morphology (p = .02); contrarily, the correlation found with DNA fragmentation was negative (p = .04). Sperm DNA fragmentation and the T/C ratio, however, were correlated in a positive manner (p = .03). As evidenced by the observed results, sperm DNA fragmentation is affected by high-level sports practice; therefore, high loads of endurance training could potentially interfere with the athlete's fertility potential. © 2017 Blackwell Verlag GmbH.

  5. Habitat loss, not fragmentation, drives occurrence patterns of Canada lynx at the southern range periphery.

    Directory of Open Access Journals (Sweden)

    Megan L Hornseth

    Full Text Available Peripheral populations often experience more extreme environmental conditions than those in the centre of a species' range. Such extreme conditions include habitat loss, defined as a reduction in the amount of suitable habitat, as well as habitat fragmentation, which involves the breaking apart of habitat independent of habitat loss. The 'threshold hypothesis' predicts that organisms will be more affected by habitat fragmentation when the amount of habitat on the landscape is scarce (i.e., less than 30% than when habitat is abundant, implying that habitat fragmentation may compound habitat loss through changes in patch size and configuration. Alternatively, the 'flexibility hypothesis' predicts that individuals may respond to increased habitat disturbance by altering their selection patterns and thereby reducing sensitivity to habitat loss and fragmentation. While the range of Canada lynx (Lynx canadensis has contracted during recent decades, the relative importance of habitat loss and habitat fragmentation on this phenomenon is poorly understood. We used a habitat suitability model for lynx to identify suitable land cover in Ontario, and contrasted occupancy patterns across landscapes differing in cover, to test the 'threshold hypothesis' and 'flexibility hypothesis'. When suitable land cover was widely available, lynx avoided areas with less than 30% habitat and were unaffected by habitat fragmentation. However, on landscapes with minimal suitable land cover, lynx occurrence was not related to either habitat loss or habitat fragmentation, indicating support for the 'flexibility hypothesis'. We conclude that lynx are broadly affected by habitat loss, and not specifically by habitat fragmentation, although occurrence patterns are flexible and dependent on landscape condition. We suggest that lynx may alter their habitat selection patterns depending on local conditions, thereby reducing their sensitivity to anthropogenically-driven habitat

  6. One abstinence day decreases sperm DNA fragmentation in 90 % of selected patients.

    Science.gov (United States)

    Pons, Isabel; Cercas, Rosa; Villas, Celia; Braña, Cristina; Fernández-Shaw, Sylvia

    2013-09-01

    The aim of this prospective descriptive study was to evaluate the efficacy of reducing sexual abstinence as a strategy to decrease sperm DNA fragmentation. Men with one or more of the following characteristics were included in the study: older than 44, smoking more than 10 cigarettes per day, with a body mass index over 25, diabetes mellitus, varicocele, a previous chemotherapy treatment, severe oligozoospermia, prostatitis, cryptorchidism, having a partner with recurrent miscarriage and/or implantation failure, poor embryo morphology and/or fertilization failure. Patients were asked to produce a semen sample after 3 to 7 abstinence days which was subjected to a sperm DNA fragmentation test. When DNA fragmentation was above or equal to 30 %, it was considered to be altered. Patients with increased DNA fragmentation were asked to produce another semen sample following a "one abstinence day protocol". This protocol required producing up to three semen samples with 1 day of abstinence and measuring sperm DNA fragmentation. Four hundred and sixteen patients produced a first semen sample after a sexual abstinence of 3 to 7 days. Sperm DNA fragmentation was altered in 46 samples (11.1 %). Thirty five patients with increased DNA fragmentation samples completed the "one abstinence day protocol". DNA fragmentation decreased to normal values in one of the three attempts in 91.4 % of the patients: 81.3 % in the first attempt, 12.5 % in the second try and 6.3 % in the third. This approach could be a simple, low-cost and effective way to decrease sperm DNA damage to normal values.

  7. Particle Size Reduction in Geophysical Granular Flows: The Role of Rock Fragmentation

    Science.gov (United States)

    Bianchi, G.; Sklar, L. S.

    2016-12-01

    Particle size reduction in geophysical granular flows is caused by abrasion and fragmentation, and can affect transport dynamics by altering the particle size distribution. While the Sternberg equation is commonly used to predict the mean abrasion rate in the fluvial environment, and can also be applied to geophysical granular flows, predicting the evolution of the particle size distribution requires a better understanding the controls on the rate of fragmentation and the size distribution of resulting particle fragments. To address this knowledge gap we are using single-particle free-fall experiments to test for the influence of particle size, impact velocity, and rock properties on fragmentation and abrasion rates. Rock types tested include granodiorite, basalt, and serpentinite. Initial particle masses and drop heights range from 20 to 1000 grams and 0.1 to 3.0 meters respectively. Preliminary results of free-fall experiments suggest that the probability of fragmentation varies as a power function of kinetic energy on impact. The resulting size distributions of rock fragments can be collapsed by normalizing by initial particle mass, and can be fit with a generalized Pareto distribution. We apply the free-fall results to understand the evolution of granodiorite particle-size distributions in granular flow experiments using rotating drums ranging in diameter from 0.2 to 4.0 meters. In the drums, we find that the rates of silt production by abrasion and gravel production by fragmentation scale with drum size. To compare these rates with free-fall results we estimate the particle impact frequency and velocity. We then use population balance equations to model the evolution of particle size distributions due to the combined effects of abrasion and fragmentation. Finally, we use the free-fall and drum experimental results to model particle size evolution in Inyo Creek, a steep, debris-flow dominated catchment, and compare model results to field measurements.

  8. Habitat loss, not fragmentation, drives occurrence patterns of Canada lynx at the southern range periphery.

    Science.gov (United States)

    Hornseth, Megan L; Walpole, Aaron A; Walton, Lyle R; Bowman, Jeff; Ray, Justina C; Fortin, Marie-Josée; Murray, Dennis L

    2014-01-01

    Peripheral populations often experience more extreme environmental conditions than those in the centre of a species' range. Such extreme conditions include habitat loss, defined as a reduction in the amount of suitable habitat, as well as habitat fragmentation, which involves the breaking apart of habitat independent of habitat loss. The 'threshold hypothesis' predicts that organisms will be more affected by habitat fragmentation when the amount of habitat on the landscape is scarce (i.e., less than 30%) than when habitat is abundant, implying that habitat fragmentation may compound habitat loss through changes in patch size and configuration. Alternatively, the 'flexibility hypothesis' predicts that individuals may respond to increased habitat disturbance by altering their selection patterns and thereby reducing sensitivity to habitat loss and fragmentation. While the range of Canada lynx (Lynx canadensis) has contracted during recent decades, the relative importance of habitat loss and habitat fragmentation on this phenomenon is poorly understood. We used a habitat suitability model for lynx to identify suitable land cover in Ontario, and contrasted occupancy patterns across landscapes differing in cover, to test the 'threshold hypothesis' and 'flexibility hypothesis'. When suitable land cover was widely available, lynx avoided areas with less than 30% habitat and were unaffected by habitat fragmentation. However, on landscapes with minimal suitable land cover, lynx occurrence was not related to either habitat loss or habitat fragmentation, indicating support for the 'flexibility hypothesis'. We conclude that lynx are broadly affected by habitat loss, and not specifically by habitat fragmentation, although occurrence patterns are flexible and dependent on landscape condition. We suggest that lynx may alter their habitat selection patterns depending on local conditions, thereby reducing their sensitivity to anthropogenically-driven habitat alteration.

  9. Adverse Effect of Post-Discharge Care Fragmentation on Outcomes after Readmissions after Liver Transplantation.

    Science.gov (United States)

    Kothari, Anai N; Loy, Veronica M; Brownlee, Sarah A; Ezure, Yoshiki; Schaidle-Blackburn, Colleen; Cotler, Scott J; di Sabato, Diego; Kuo, Paul C; Lu, Amy D

    2017-07-01

    Post-discharge surgical care fragmentation is defined as readmission to any hospital other than the hospital at which surgery was performed. The objective of this study was to assess the impact of fragmented readmissions within the first year after orthotopic liver transplantation (OLT). The Healthcare Cost and Utilization Project State Inpatient Databases for Florida and California from 2006 to 2011 were used to identify OLT patients. Post-discharge fragmentation was defined as any readmission to a non-index hospital, including readmitted patients transferred to the index hospital after 24 hours. Outcomes included adverse events, defined as 30-day mortality and 30-day readmission after a fragmented readmission. All statistical analyses considered a hierarchical data structure and were performed with multilevel, mixed-effects models. We analyzed 2,996 patients with 7,485 readmission encounters at 299 hospitals; 1,236 (16.5%) readmissions were fragmented. After adjustment for age, sex, readmission reason, index liver transplantation cost, readmission length of stay, number of previous readmissions, and time from transplantation, post-discharge fragmentation increased the odds of both 30-day mortality (odds ratio [OR] = 1.75; 95% CI 1.16 to 2.65) and 30-day readmission (OR = 2.14; 95% CI 1.83 to 2.49). Predictors of adverse events after a fragmented readmission included increased number of previous readmissions (OR = 1.07; 95% CI 1.01 to 1.14) and readmission within 90 days of OLT (OR = 2.19; 95% CI 1.61 to 2.98). Post-discharge fragmentation significantly increases the risk of both 30-day mortality and subsequent readmission after a readmission in the first year after OLT. More inpatient visits before a readmission and less time elapsed from index surgery increase the odds of an adverse event after discharge from a fragmented readmission. These parameters could guide transfer decisions for patients with post-discharge fragmentation. Copyright © 2017 American

  10. Fragment and particle size distribution of impacted ceramic tiles

    NARCIS (Netherlands)

    Carton, E.P.; Weerheijm, J.; Ditzhuijzen, C.; Tuinman, I.

    2014-01-01

    The fragmentation of ceramic tiles under ballistic impact has been studied. Fragments and aerosol (respirable) particles were collected and analyzed to determine the total surface area generated by fracturing (macro-cracking and comminution) of armor grade ceramics. The larger fragments were

  11. Regional Forest Fragmentation and the Nesting Success of Migratory Birds

    Science.gov (United States)

    Scott K. Robinson; Frank R. Thompson III; Therese M. Donovan; Donald R. Whitehead; John Faaborg

    1995-01-01

    Forest fragmentation, the disruption in the continuity of forest habitat, is hypothesized to be a major cause of population decline for, some species of forest birds because fragmentation reduces nesting (reproductive) success. Nest predation and parasitism by cowbirds increased with forest fragmentation in nine midwestern (United States)landscapes that varied from 6...

  12. Temporal change in fragmentation of continental US forests

    Science.gov (United States)

    James D. Wickham; Kurt H. Riitters; Timothy G. Wade; Collin Homer

    2008-01-01

    Changes in forest ecosystem function and condition arise from changes in forest fragmentation. Previous studies estimated forest fragmentation for the continental United States (US). In this study, new temporal land-cover data from the National Land Cover Database (NLCD) were used to estimate changes in forest fragmentation at multiple scales for the continental US....

  13. Scaling properties of crack branching and brittle fragmentation

    Directory of Open Access Journals (Sweden)

    Uvarov S.

    2011-01-01

    Full Text Available The present study is focused on the correlation of scaling properties of crack branching and brittle fragmentation with damage accumulation and a change in the fracture mechanism. The experimental results obtained from the glass fragmentation tests indicate that the size distribution of fragments has a fractal character and is described by a power law.

  14. Fragment library design: efficiently hunting drugs in chemical space

    NARCIS (Netherlands)

    Boyd, S.M.; de Kloe, G.E.

    2010-01-01

    With the growth in fragment-based drug discovery, numerous strategies have been described for the design of fragment libraries. Key choices need to be made on both the selection criteria to be applied and the source of the fragments in the library. Here we review some of the key trends and recent

  15. High-throughput on-chip DNA fragmentation

    NARCIS (Netherlands)

    Shui, Lingling; Jin, Mingliang; Bomer, Johan G.; Carlen, Edwin; van den Berg, Albert; Abelmann, Leon; Abelmann, L.; Groenland, J.P.J.; van Honschoten, J.W.

    2010-01-01

    free microfluidic deoxyribonucleic acid (DNA) fragmentation chip that is based on hydrodynamic shearing. Genomic DNA has been reproducibly fragmented with 2-10 kbp fragment lengths by applying hydraulic pressure ΔP across micromachined constrictions in the microfluidic channels. The utilization of a

  16. Neisseria gonorrhoeae Crippled Its Peptidoglycan Fragment Permease To Facilitate Toxic Peptidoglycan Monomer Release.

    Science.gov (United States)

    Chan, Jia Mun; Dillard, Joseph P

    2016-11-01

    Neisseria gonorrhoeae (gonococci) and Neisseria meningitidis (meningococci) are human pathogens that cause gonorrhea and meningococcal meningitis, respectively. Both N. gonorrhoeae and N. meningitidis release a number of small peptidoglycan (PG) fragments, including proinflammatory PG monomers, although N. meningitidis releases fewer PG monomers. The PG fragments released by N. gonorrhoeae and N. meningitidis are generated in the periplasm during cell wall remodeling, and a majority of these fragments are transported into the cytoplasm by an inner membrane permease, AmpG; however, a portion of the PG fragments are released into the extracellular environment through unknown mechanisms. We previously reported that the expression of meningococcal ampG in N. gonorrhoeae reduced PG monomer release by gonococci. This finding suggested that the efficiency of AmpG-mediated PG fragment recycling regulates the amount of PG fragments released into the extracellular milieu. We determined that three AmpG residues near the C-terminal end of the protein modulate AmpG's efficiency. We also investigated the association between PG fragment recycling and release in two species of human-associated nonpathogenic Neisseria: N. sicca and N. mucosa Both N. sicca and N. mucosa release lower levels of PG fragments and are more efficient at recycling PG fragments than N. gonorrhoeae Our results suggest that N. gonorrhoeae has evolved to increase the amounts of toxic PG fragments released by reducing its PG recycling efficiency. Neisseria gonorrhoeae and Neisseria meningitidis are human pathogens that cause highly inflammatory diseases, although N. meningitidis is also frequently found as a normal member of the nasopharyngeal microbiota. Nonpathogenic Neisseria, such as N. sicca and N. mucosa, also colonize the nasopharynx without causing disease. Although all four species release peptidoglycan fragments, N. gonorrhoeae is the least efficient at recycling and releases the largest amount of

  17. Sustained Sleep Fragmentation Induces Sleep Homeostasis in Mice

    Science.gov (United States)

    Baud, Maxime O.; Magistretti, Pierre J.; Petit, Jean-Marie

    2015-01-01

    Study Objectives: Sleep fragmentation (SF) is an integral feature of sleep apnea and other prevalent sleep disorders. Although the effect of repetitive arousals on cognitive performance is well documented, the effects of long-term SF on electroencephalography (EEG) and molecular markers of sleep homeostasis remain poorly investigated. To address this question, we developed a mouse model of chronic SF and characterized its effect on EEG spectral frequencies and the expression of genes previously linked to sleep homeostasis including clock genes, heat shock proteins, and plasticity-related genes. Design: N/A. Setting: Animal sleep research laboratory. Participants : Sixty-six C57BL6/J adult mice. Interventions: Instrumental sleep disruption at a rate of 60/h during 14 days Measurements and Results: Locomotor activity and EEG were recorded during 14 days of SF followed by recovery for 2 days. Despite a dramatic number of arousals and decreased sleep bout duration, SF minimally reduced total quantity of sleep and did not significantly alter its circadian distribution. Spectral analysis during SF revealed a homeostatic drive for slow wave activity (SWA; 1–4 Hz) and other frequencies as well (4–40 Hz). Recordings during recovery revealed slow wave sleep consolidation and a transient rebound in SWA, and paradoxical sleep duration. The expression of selected genes was not induced following chronic SF. Conclusions: Chronic sleep fragmentation (SF) increased sleep pressure confirming that altered quality with preserved quantity triggers core sleep homeostasis mechanisms. However, it did not induce the expression of genes induced by sleep loss, suggesting that these molecular pathways are not sustainably activated in chronic diseases involving SF. Citation: Baud MO, Magistretti PJ, Petit JM. Sustained sleep fragmentation induces sleep homeostasis in mice. SLEEP 2015;38(4):567–579. PMID:25325477

  18. N-Terminal Fragments of Huntingtin Longer than Residue 170 form Visible Aggregates Independently to Polyglutamine Expansion.

    Science.gov (United States)

    Chen, Moore Z; Mok, Sue-Ann; Ormsby, Angelique R; Muchowski, Paul J; Hatters, Danny M

    2017-01-01

    A hallmark of Huntington's disease is the progressive aggregation of full length and N-terminal fragments of polyglutamine (polyQ)-expanded Huntingtin (Htt) into intracellular inclusions. The production of N-terminal fragments appears important for enabling pathology and aggregation; and hence the direct expression of a variety of N-terminal fragments are commonly used to model HD in animal and cellular models. It remains unclear how the length of the N-terminal fragments relates to polyQ - mediated aggregation. We investigated the fundamental intracellular aggregation process of eight different-length N-terminal fragments of Htt in both short (25Q) and long polyQ (97Q). N-terminal fragments were fused to fluorescent proteins and transiently expressed in mammalian cell culture models. These included the classic exon 1 fragment (90 amino acids) and longer forms of 105, 117, 171, 513, 536, 552, and 586 amino acids based on wild-type Htt (of 23Q) sequence length nomenclature. N-terminal fragments of less than 171 amino acids only formed inclusions in polyQ-expanded form. By contrast the longer fragments formed inclusions irrespective of Q-length, with Q-length playing a negligible role in extent of aggregation. The inclusions could be classified into 3 distinct morphological categories. One type (Type A) was universally associated with polyQ expansions whereas the other two types (Types B and C) formed independently of polyQ length expansion. PolyQ-expansion was only required for fragments of less than 171 amino acids to aggregate. Longer fragments aggregated predominately through a non-polyQ mechanism, involving at least one, and probably more distinct clustering mechanisms.

  19. Inferring Resilience to Fragmentation-Induced Changes in Plant Communities in a Semi-Arid Mediterranean Ecosystem

    Science.gov (United States)

    de Frutos, Ángel; Navarro, Teresa; Pueyo, Yolanda; Alados, Concepción L.

    2015-01-01

    Predicting the capacity of ecosystems to absorb impacts from disturbance events (resilience), including land-use intensification and landscape fragmentation, is challenging in the face of global change. Little is known about the impacts of fragmentation on ecosystem functioning from a multi-dimensional perspective (multiple traits). This study used 58 500-m linear transects to quantify changes in the functional composition and resilience of vascular plant communities in response to an increase in landscape fragmentation in 18 natural scrubland fragments embedded within a matrix of abandoned crop fields in Cabo de Gata-Níjar Natural Park, Almería, Spain. Changes in functional community composition were measured using functional diversity indices (functional richness and functional dispersion) that were based on 12 plant traits. Resilience was evaluated using the functional redundancy and response diversity from the perspective of plant dispersal, which is important, particularly, in fragmented landscapes. Scrubland fragmentation was measured using the Integral Index of Connectivity (IIC). The functional richness of the plant communities was higher in the most fragmented scrubland. Conversely, the functional dispersion (i.e., spread) of trait values among species in the functional trait space was lower at the most fragmented sites; consequently, the ecological tolerance of the vegetation to scrubland fragmentation decreased. Classifying the plant species into four functional groups indicated that fragmentation favoured an increase in functional redundancy in the ‘short basal annual forbs and perennial forbs’ group, most of which are species adapted to degraded soils. An assessment based on the traits associated with plant dispersal indicated that the resilience of ‘woody plants’, an important component in the Mediterranean scrubland, and habitat fragmentation were negatively correlated; however, the correlation was positive in the ‘short basal annual

  20. Deciding Security for a Fragment of ASLan

    DEFF Research Database (Denmark)

    Mödersheim, Sebastian Alexander

    2012-01-01

    situations in security such as the interaction between the workflow of a system with its access control policies. While even the transition relation is undecidable for ASLan in general, we show the security problem is decidable for a large and useful fragment that we call TASLan, as long as we bound...... the number of steps of honest participants. The restriction of TASLan is that all messages and predicates must be in a certain sense unambiguous in their interpretation, excluding “type-confusions” similar to some tagging results for security protocols....

  1. Fragmentation pathways of nanofractal structures on surfaces

    DEFF Research Database (Denmark)

    Dick, Veronika V.; Solov'yov, Ilia; Solov'yov, Andrey V.

    2011-01-01

    We present a theoretical analysis of the post-growth processes occurring in nanofractals grown on a surface. For this study we have developed a method that accounts for the internal dynamics of particles in a fractal. We demonstrate that the detachment of particles from the fractal...... and their diffusion within the fractal and over the surface determines the shape of the islands remaining on a surface after the fractal fragmentation. We consider different scenarios of fractal post-growth relaxation and analyze the time evolution of the island's morphology. The results of our calculations...

  2. Projectile fragmentation wall for CHICSi detector

    CERN Document Server

    Budzanowski, A; Siwek, A; Skwirczynska, I; Staszel, P

    2002-01-01

    The Forward Wall Detector (FWD) is designed to identify projectile-like fragments from heavy-ion reactions at the CELSIUS storage ring in Uppsala, Sweden. FWD covers the polar angle from 3.9 deg. to 11.7 deg. with geometrical efficiency of 81%. The single-detection module can be either of phoswich type (10 mm fast plastic+80 mm CsI(Tl)) or DELTA E-E telescope (750 mu m Si + 80 mm CsI(Tl)). It is expected to have charge identification up to Z=18 and mass resolution for H and He isotopes.

  3. Disruption of lactogenesis by retained placental fragments.

    Science.gov (United States)

    Anderson, A M

    2001-05-01

    This case report describes a situation in which lack of milk production led the mother to seek help from a lactation consultant in private practice. Despite extensive breast stimulation with the baby at breast and mechanical breast expression, no milk was produced. Retained placenta was suspected by the lactation consultant. The mother was later diagnosed with placenta increta. Only when this condition was diagnosed and resolved did milk onset occur. It is important to evaluate for retained placental fragments when lactation appears to be delayed.

  4. Fragmentation and clustering in star matter

    Directory of Open Access Journals (Sweden)

    Gulminelli F.

    2012-07-01

    Full Text Available The specificity of the crust-core phase transition in neutron star at zero and finite temperature will be discussed. It will be shown that, as a consequence of the presence of long range Coulomb interactions, the equivalence of statistical ensembles is violated and a clusterised phase is expected which is not accessible in the grancanonical ensemble. A specific analytical Nuclear Statistical Equilibrium model will be presented and some new quantitative results relevant for the supernova dynamics will be shown. Finally, the analogies and differences with the phenomenon of nuclear fragmentation will be highlighted.

  5. TRANSVERSE POLARIZATION DISTRIBUTION AND FRAGMENTATION FUNCTIONS

    Energy Technology Data Exchange (ETDEWEB)

    BOER,D.

    2000-04-11

    The authors discuss transverse polarization distribution and fragmentation functions, in particular, T-odd functions with transverse momentum dependence, which might be relevant for the description of single transverse spin asymmetries. The role of intrinsic transverse momentum in the expansion in inverse powers of the hard scale is elaborated upon. The sin {phi} single spin asymmetry in the process e {rvec p} {r_arrow} e{prime} {pi}{sup +} X as recently reported by the HERMES Collaboration is investigated, in particular, by using the bag model.

  6. The effects of Ethernet LANs' fragmentation

    Directory of Open Access Journals (Sweden)

    Ion Bolun

    2006-09-01

    Full Text Available Three configurations of Ethernet networks that operate in duplex mode at relatively low load of transmission media are investigated. Configurations differ by number of collision domains and switches used in the network. To investigate the dependences among basic parameters, analytic models of the functioning of such networks are elaborated. Calculations made for a relatively large set of values of initial data confirm the necessity of case dependent special investigations on the physical configuration of concrete Ethernet networks. It has been determined, for example, that the fragmentation doesn't necessarily permit to increase the number of stations in the network; it may be even vice versa.

  7. Predation on artificial bird nests in chaparral fragments.

    Science.gov (United States)

    Langen, Tom A; Bolger, Douglas T; Case, Ted J

    1991-05-01

    The predation rate of artificial bird nests was measured in disturbed chaparral habitat fragments and at an unfragmented site in coastal San Diego County, California USA. Local extinctions of chaparral birds has been previously shown to occur in these fragments. The predation rate was highest at the unfragmented site. Among fragments, predation was higher at moderately disturbed than at highly disturbed sites. These results suggest that nest predator species diversity or density is reduced in disturbed chaparral fragments. Nest predation is probably not the most important cause of the observed loss of chaparral breeding bird diversity in these fragments.

  8. Habitat fragmentation has some impacts on aspects of ecosystem functioning in a sub-tropical seagrass bed.

    Science.gov (United States)

    Sweatman, Jennifer L; Layman, Craig A; Fourqurean, James W

    2017-05-01

    Habitat fragmentation impacts ecosystem functioning in many ways, including reducing the availability of suitable habitat for animals and altering resource dynamics. Fragmentation in seagrass ecosystems caused by propeller scarring is a major source of habitat loss, but little is known about how scars impact ecosystem functioning. Propeller scars were simulated in seagrass beds of Abaco, Bahamas, to explore potential impacts. To determine if plant-herbivore interactions were altered by fragmentation, amphipod grazers were excluded from half the experimental plots, and epiphyte biomass and community composition were compared between grazer control and exclusion plots. We found a shift from light limitation to phosphorus limitation at seagrass patch edges. Fragmentation did not impact top-down control on epiphyte biomass or community composition, despite reduced amphipod density in fragmented habitats. Seagrass and amphipod responses to propeller scarring suggest that severely scarred seagrass beds could be subject to changes in internal nutrient stores and amphipod distribution. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. The pivotal role of the intermediate fragment in initial operative treatment of olecranon fractures

    Directory of Open Access Journals (Sweden)

    Hierholzer Christian

    2011-02-01

    Full Text Available Abstract Background In order to improve initial operative treatment of complex olecranon fractures we searched for new determining details. We assumed that the intermediate fragment plays a decisive role for anatomic restoration of the trochlear notch and consecutive outcome of initial operative treatment. Methods 80 patients operated with diagnosis of complex olecranon fracture were identified in an 8-year-period from trauma unit files at two European Level 1 Trauma Centers. Retrospective review of all operative reports and radiographs/computer-tomography scans identified patients with concomitance of an intermediate fragment. The Patient-Rated Elbow Evaluation Score was calculated for 45 of 80 patients at a minimum of 8 months postoperatively (range 8-84 months. Results 29 patients were treated with stable internal fixation with figure-of-eight tension band wire fixation and 51 patients with posterior plate osteosynthesis with/without intramedullary screw. An intermediate fragment was seen in 52 patients. In 29 of these 52 patients, the intermediate fragment was described in operative report. 24 of these 29 patients were treated with posterior plate osteosynthesis, and 5 patients with figure-of-eight tension band wiring. Complications included superficial infection (2 patients, secondary dislocation (3 patients and heterotopic ossifications (1 patient. Functional outcome demonstrated a total PREE score of 9 points on average in 45 of 80 patients. Conclusion An extraordinary amount of patients showed an intermediate fragment. Consideration, desimpaction and anatomic reduction of the intermediate fragment are necessary preconditions for anatomic restoration of the trochlear notch. There is no clear benefit for plating versus tension band wiring according to our data. In the operative report precise description of the fracture pattern including presence of an intermediate fragment is recommended.

  10. SCEDS: protein fragments for molecular replacement in Phaser

    Energy Technology Data Exchange (ETDEWEB)

    McCoy, Airlie J., E-mail: ajm201@cam.ac.uk [University of Cambridge, Hills Road, Cambridge CB2 0XY (United Kingdom); Nicholls, Robert A. [MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH (United Kingdom); Schneider, Thomas R. [Hamburg Unit c/o DESY, Notkestrasse 85, 22603 Hamburg (Germany); University of Cambridge, Hills Road, Cambridge CB2 0XY (United Kingdom)

    2013-11-01

    Protein fragments suitable for use in molecular replacement can be generated by normal-mode perturbation, analysis of the difference distance matrix of the original versus normal-mode perturbed structures, and SCEDS, a score that measures the sphericity, continuity, equality and density of the resulting fragments. A method is described for generating protein fragments suitable for use as molecular-replacement (MR) template models. The template model for a protein suspected to undergo a conformational change is perturbed along combinations of low-frequency normal modes of the elastic network model. The unperturbed structure is then compared with each perturbed structure in turn and the structurally invariant regions are identified by analysing the difference distance matrix. These fragments are scored with SCEDS, which is a combined measure of the sphericity of the fragments, the continuity of the fragments with respect to the polypeptide chain, the equality in number of atoms in the fragments and the density of C{sup α} atoms in the triaxial ellipsoid of the fragment extents. The fragment divisions with the highest SCEDS are then used as separate template models for MR. Test cases show that where the protein contains fragments that undergo a change in juxtaposition between template model and target, SCEDS can identify fragments that lead to a lower R factor after ten cycles of all-atom refinement with REFMAC5 than the original template structure. The method has been implemented in the software Phaser.

  11. DNA fragment sizing and sorting by laser-induced fluorescence

    Energy Technology Data Exchange (ETDEWEB)

    Jett, J.H.; Hammond, M.L.; Keller, R.A.; Marrone, B.L.; Martin, J.C.

    1992-12-31

    A method is provided for obtaining DNA fingerprints using high speed detection systems, such as flow cytometry to determine unique characteristics of DNA pieces from a selected sample. In one characterization the DNA piece is fragmented at preselected sites to produce a plurality of DNA fragments. The DNA piece or the resulting DNA fragments are treated with a dye effective to stain stoichiometrically the DNA fragments. The fluorescence from the dye in the stained fragments is then examined to generate an output functionally related to the number of nucleotides in each one of the DNA fragments. In one embodiment, the intensity of the fluorescence emissions from each fragment is directly proportional to the fragment length. Additional dyes can be bound to the DNA piece and DNA fragments to provide information additional to length information. Oligonucleotide specific dyes and/or hybridization probes can be bound to the DNA fragments to provide information on oligonucleotide distribution or probe hybridization to DNA fragments of different sizes.

  12. Ion Optics Simulation for Fragment Separator

    Science.gov (United States)

    Kawada, Yosuke; Nakamura, Takashi; Kubo, Toshiyuki; Takeda, Hiroyuki; Sumikama, Toshiyuki

    2009-10-01

    We have developed a Monte-Carlo simulation code for unstable-nuclear beam experiments using a fragment-separator. This code primarily aims at calculating beam traces in the fragment separator BigRIPS and ZeroDegree Spectrometer (ZDS) at RIBF(RIKEN RI-Beam Factory). This code uses externally given transfer-matrices of ion optics such as an output of COSY Infinity[1]. We have applied this code to recent campaign of experiments using ^48Ca at 345MeV/u as primary beam. In the experiments, two modes of ion optical settings , namely ``Standard'' and ``High Brho'' modes were used. The former is an ordinary used starndard setteing, which has a limit in the maximum rigidity (BρHigh Brho'' setting has been developed for a secondary beam with higher rigidity, such as for very neutron rich nuclei ^22C (A/Z=3.67). In this talk, we compare properties of these two optics settings and evaluate beam traces, emittances, and transmissions.[4pt] [1] K. Makino, M. Berz Nucl. Instr. Meth. A 558 (2005)

  13. What is needed to implement a fragmentation capability at RIA

    Science.gov (United States)

    Morrissey, David J.

    2000-10-01

    Examples of the experimental equipment needed to impliment the range of nuclear physics opportunities with fast ion beams, discussed earlier in the workshop, will be presented. In broad brush, a high-energy experimental program will require a separate experimental area with its own high-resolution fragment separator (6% in momentum, 8 Tm bending power, and a large solid angle). The performance of the separator could be enhanced with a Wien filter system before the experimental vaults. Important end-stations would include a high-resolution magnetic spectrograph ( ~6 Tm, ~20 msr, Δp/p ~10,000)for direct nuclear reaction studies; a sweeper magnet system and high efficiency neutron ToF detector for studies of weakly bound nuclei; a position sensitive gamma-ray detector optimized for coincidence studies with high velocity fragments (β ~0.2--0.6) a 4π charged particle detector with a broad dynamic range and low energy threshold such as a TPC. An example floor plan and very rough estimates of the costs will be presented.

  14. QRS-fragmentation: Case report and review of the literature.

    Science.gov (United States)

    Illescas-González, Edgar; Araiza-Garaygordobil, Diego; Sierra Lara, Jorge Daniel; Ramirez-Salazar, Aristoteles; Sierra-Fernández, Carlos; Alexanderson-Rosas, Erick

    2017-01-24

    Fragmentation of QRS complex (QRSf) is an easily evaluable, non-invasive electrocardiographic parameter that represents depolarisation anomalies and has been associated with several adverse outcomes, such as sudden death, fibrosis, arrhythmic burden, and a worse prognosis in different conditions, including coronary artery disease (CAD). The case is presented of a 69-year old male referred due to symptoms of chronic stable angina. His electrocardiogram showed sinus rhythm, absence of Q waves, but the presence of QRSf in the inferior leads and V4-V6. A Tc-99 myocardial perfusion SPECT scan revealed a fixed perfusion defect in the inferolateral region, corresponding to the finding of QRSf. QRSf is an easily valuable electrocardiographic marker with relative sensitivity, but poor specificity. Its routine clinical application could contribute to an increase in the suspicion of coronary artery disease. The presence of fragmented QRS represents distortion of signal conduction and depolarisation, which is related to myocardial scar or myocardial fibrosis. Copyright © 2016 Instituto Nacional de Cardiología Ignacio Chávez. Publicado por Masson Doyma México S.A. All rights reserved.

  15. Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.

    Science.gov (United States)

    Liu, Jinfeng; Zhu, Tong; Wang, Xianwei; He, Xiao; Zhang, John Z H

    2015-12-08

    Developing ab initio molecular dynamics (AIMD) methods for practical application in protein dynamics is of significant interest. Due to the large size of biomolecules, applying standard quantum chemical methods to compute energies for dynamic simulation is computationally prohibitive. In this work, a fragment based ab initio molecular dynamics approach is presented for practical application in protein dynamics study. In this approach, the energy and forces of the protein are calculated by a recently developed electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. For simulation in explicit solvent, mechanical embedding is introduced to treat protein interaction with explicit water molecules. This AIMD approach has been applied to MD simulations of a small benchmark protein Trpcage (with 20 residues and 304 atoms) in both the gas phase and in solution. Comparison to the simulation result using the AMBER force field shows that the AIMD gives a more stable protein structure in the simulation, indicating that quantum chemical energy is more reliable. Importantly, the present fragment-based AIMD simulation captures quantum effects including electrostatic polarization and charge transfer that are missing in standard classical MD simulations. The current approach is linear-scaling, trivially parallel, and applicable to performing the AIMD simulation of proteins with a large size.

  16. Ternary-fragmentation-driving potential energies of 252Cf

    Science.gov (United States)

    Karthikraj, C.; Ren, Zhongzhou

    2017-12-01

    Within the framework of a simple macroscopic model, the ternary-fragmentation-driving potential energies of 252Cf are studied. In this work, all possible ternary-fragment combinations of 252Cf are generated by the use of atomic mass evaluation-2016 (AME2016) data and these combinations are minimized by using a two-dimensional minimization approach. This minimization process can be done in two ways: (i) with respect to proton numbers (Z1, Z2, Z3) and (ii) with respect to neutron numbers (N1, N2, N3) of the ternary fragments. In this paper, the driving potential energies for the ternary breakup of 252Cf are presented for both the spherical and deformed as well as the proton-minimized and neutron-minimized ternary fragments. From the proton-minimized spherical ternary fragments, we have obtained different possible ternary configurations with a minimum driving potential, in particular, the experimental expectation of Sn + Ni + Ca ternary fragmentation. However, the neutron-minimized ternary fragments exhibit a driving potential minimum in the true-ternary-fission (TTF) region as well. Further, the Q -value energy systematics of the neutron-minimized ternary fragments show larger values for the TTF fragments. From this, we have concluded that the TTF region fragments with the least driving potential and high Q values have a strong possibility in the ternary fragmentation of 252Cf. Further, the role of ground-state deformations (β2, β3, β4, and β6) in the ternary breakup of 252Cf is also studied. The deformed ternary fragmentation, which involves Z3=12 -19 fragments, possesses the driving potential minimum due to the larger oblate deformations. We also found that the ground-state deformations, particularly β2, strongly influence the driving potential energies and play a major role in determining the most probable fragment combinations in the ternary breakup of 252Cf.

  17. Prevalence of osteochondral fragments, osteochondrosis dissecans and palmar/plantar osteochondral fragments in Hanoverian Warmblood horses.

    Science.gov (United States)

    Hilla, Dorothea; Distl, Ottmar

    2013-01-01

    In this study, the prevalences of osteochondral fragments in the distal (DUI) and proximal interphalangeal joints (PIJ) as well as in the fetlock, hock and stifle joints, of palmar/plantar osteochondral fragments in the fetlock joints (POFs) and of osteochondrosis dissecans (OCD) in fetlock, hock and stifle joints were estimated in a large sample of Hanoverian Warmblood horses. For this purpose, radiographic findings of 9478 Hanoverian Warmblood horses collected from 2005 to 2011 were analyzed. Overall 31.9% of the horses showed one or more osteochondral fragments in at least one joint. The fetlocks were predominantly affected with a prevalence of 19.7%, followed by the hocks with 8.2% and the stifles with 2.7%. For OCD, an overall prevalence of 14.3% was determined. In fetlock joints, 5.4% of the horses had OCD, in the hock joints 6.9% and in the stifle joints 2.6%, with bilateral occurrence in 25.8% of the hock, 24.9% of the stifle and 12.6% of the fetlock joints. POFs were observed in 6.8% of the horses. With a prevalence of 6.3%, the hindlimbs were significantly more frequently affected than the forelimbs with 0.6%. Of the horses with POFs, 16.5% were also affected with OCD. The high prevalences for osteochondral fragments determined in this study show their great importance with regard to economics and animal welfare.

  18. On the fragmentation of biomolecules: fragmentation of alanine dipeptide along the polypeptide chain

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Yakubovich, Alexander; Solov'yov, Andrey

    2006-01-01

    The interaction potential between amino acids in alanine dipeptide has been studied for the first time taking into account exact molecular geometry. Ab initio calculation has been performed in the framework of density functional theory taking into account all electrons in the system. The fragment...

  19. MaRaCluster: A Fragment Rarity Metric for Clustering Fragment Spectra in Shotgun Proteomics.

    Science.gov (United States)

    The, Matthew; Käll, Lukas

    2016-03-04

    Shotgun proteomics experiments generate large amounts of fragment spectra as primary data, normally with high redundancy between and within experiments. Here, we have devised a clustering technique to identify fragment spectra stemming from the same species of peptide. This is a powerful alternative method to traditional search engines for analyzing spectra, specifically useful for larger scale mass spectrometry studies. As an aid in this process, we propose a distance calculation relying on the rarity of experimental fragment peaks, following the intuition that peaks shared by only a few spectra offer more evidence than peaks shared by a large number of spectra. We used this distance calculation and a complete-linkage scheme to cluster data from a recent large-scale mass spectrometry-based study. The clusterings produced by our method have up to 40% more identified peptides for their consensus spectra compared to those produced by the previous state-of-the-art method. We see that our method would advance the construction of spectral libraries as well as serve as a tool for mining large sets of fragment spectra. The source code and Ubuntu binary packages are available at https://github.com/statisticalbiotechnology/maracluster (under an Apache 2.0 license).

  20. Applying characteristic fragment filtering for rapid detection and identification of ingredients in rhubarb by HPLC coupled with linear ion trap-Orbitrap mass spectrometry.

    Science.gov (United States)

    Wang, Qing; Lu, Zhiwei; Zhang, Li; Zhang, Qingqing; Wang, Meiling; Zhao, Huizhen; Liu, Yuehong; Fu, Shuang; Huang, Zhenghai; Xie, Ziye; Yu, Honghong; Zhang, Zhixin; Gao, Xiaoyan

    2017-07-01

    Chemical characteristic fragment filtering in MSn chromatograms was proposed to detect and identify the components in rhubarb rapidly using high-performance liquid chromatography coupled with linear ion trap-Orbitrap mass spectrometry. Characteristic fragments consist of diagnostic ions and neutral loss fragments. Characteristic fragment filtering is a postacquisition data mining method for the targeted screening of groups with specific structures, including three steps: first, in order to comprehensively summarize characteristic fragments for global identification of the ingredients in rhubarb, representative authentic standards of dominant chemical categories contained in rhubarb were chosen, from which fragmentation rules and a characteristic fragments schedule were proposed; second, characteristic fragment filtering was used to rapidly recognize analogous skeletons; finally, combined with retention time, accurate mass, characteristic fragments, and previous literature, the structures of the filtered compounds were identified or tentatively characterized. As a result, a total of 271 compounds were detected and identified in rhubarb, including 34 anthraquinones, 83 anthrones, 46 tannins, 17 stilbenes, 24 phenylbutanones, 26 acylglucosides, 26 chromones, and 15 other compounds, 69 of which are potentially new compounds. The proposed characteristic fragment filtering strategy would be a reference for the large-scale detection and identification of the ingredients of herbal medicines. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Forest Fragments Surrounded by Sugar Cane Are More Inhospitable to Terrestrial Amphibian Abundance Than Fragments Surrounded by Pasture

    Directory of Open Access Journals (Sweden)

    Paula Eveline Ribeiro D’Anunciação

    2013-01-01

    Full Text Available In recent years, there has been increasing interest in matrix-type influence on forest fragments. Terrestrial amphibians are good bioindicators for this kind of research because of low vagility and high philopatry. This study compared richness, abundance, and species composition of terrestrial amphibians through pitfall traps in two sets of semideciduous seasonal forest fragments in southeastern Brazil, according to the predominant surrounding matrix (sugar cane and pasture. There were no differences in richness, but fragments surrounded by sugar cane had the lowest abundance of amphibians, whereas fragments surrounded by pastures had greater abundance. The most abundant species, Rhinella ornata, showed no biometric differences between fragment groups but like many other amphibians sampled showed very low numbers of individuals in fragments dominated by sugar cane fields. Our data indicate that the sugar cane matrix negatively influences the community of amphibians present in fragments surrounded by this type of land use.

  2. Third prize: the impact of fluid environment manipulation on shockwave lithotripsy artificial calculi fragmentation rates.

    Science.gov (United States)

    Méndez-Probst, Carlos E; Fernadez, Alfonso; Erdeljan, Petar; Vanjecek, Maaike; Cadieux, Peter A; Razvi, Hassan

    2011-03-01

    Studies have suggested that shockwave lithotripsy (SWL) stone fragmentation rates can be affected by characteristics of the fluid media surrounding the stone, although evidence to implicate the impact of urine specific gravity (SG) is limited and inconclusive. Our aim is to further explore the impact fluid media and SGs have on stone fragmentation using a variable focus lithotripter. Artificial stones were presoaked for 24 hours in urine and then shocked in various fluid media including artificial urine (SG 1.010 control, 1.020, and 1.07), human pooled urine (HPU), degassed HPU, Pentastarch, 100% and 30% contrast, degassed 30% contrast, 100% ethanol, deionized water (dH(2)O), degassed dH(2)O, 5% glucose, Ringer lactate, 0.9% saline, glycerol, whole blood, and lubricating gel. After soaking, SWL using the Modulith SLX-F2 electromagnetic lithotripter was performed. Fragments were dried and sieved using a 4-mm diameter opening grid. Fragments >4 mm were weighed and fragmentation coefficients (FCs) calculated (pre-SWL weight - post-SWL weight)/(pre-SWL weight) × 100. Fifteen stones were shocked for each fluid group. Fluid type, viscosity, and degassing all significantly impacted stone fragmentation. While the solutions' SG, per se, did not appear to affect stone fragmentation, the use of degassed 30% contrast significantly improved stone destruction over the SG 1.010 artificial urine control (95.3% vs 71.4, P < 0.01). Furthermore, degassing improved comminution rates by increasing the number of completely fragmented stones (FC = 100%). Using degassed 30% contrast, 12/15 stones were completely fragmented, compared with only 2/15 in the control group (P = 0.007). Among the whole blood, glycerol, and lubricating gel groups, only 1/15, 0/15, and 1/15 stones reached 100% FC respectively in the narrow focus, possibly because of the detrimental impact of increased viscosity. Different fluid media can significantly affect FC in vitro. Among the various fluids tested, degassed

  3. Micro-Satellite Impact Tests to Investigate Multi-Layer Insulation Fragments

    Science.gov (United States)

    Liou, J.C.; Murakami, Junko; Hanaha, Toshiya

    2009-01-01

    This paper summarizes two satellite impact experiments completed in 2008. The objective of the experiments is to investigate the physical properties of satellite fragments, including those originated from Multi-Layer Insulation (MLI) and solar panels. The ultimate goal is to use the results to improve the NASA Standard Breakup Model. The targets were two cubic micro-satellites, 20 cm by 20 cm by 20 cm in size, and approximately 1,500 g in mass. The main structure of each micro-satellite was composed of five layers; the top and bottom layers and three internal layers parallel to the top and bottom layers, plus four side panels. The top layer was equipped with solar cells that was mounted to an aluminum honeycomb sandwich panel with CFRP face sheets. The four side panels and the bottom layer are all covered with MLI. The two satellite impact experiments were conducted using the two-stage light gas gun at the Kyushu Institute of Technology in Kitakyusyu, Japan. For the first experiment (labeled Shot F), the satellite was oriented in such a way that the solar panel was facing the incoming projectile, a 39.3 g aluminum alloy solid sphere. For the second experiment (labeled Shot R), the satellite was oriented so that the solar panel was on the opposite side of the impact surface. The projectile used in the second shot was a 39.2 g aluminum alloy solid sphere. The impact speeds of Shot F and Shot R were 1.74 km/s and 1.78 km/s, respectively. The ratio of the impact kinetic energy to satellite mass for the two experiments was about 40 J/g. Both target satellites were completely fragmented, although there were noticeable differences in the characteristics of the fragments. Approximately 1,800 fragments were collected from Shot F but only 1,000 fragments were collected from Shot R. This difference primarily comes from the number of needle-like CFRP and MLI fragments. The difference in CFRP pieces depends on how the CFRP panels were fragmented. Regarding the MLI pieces, a

  4. Use of amplified fragment length polymorphism analysis to identify medically important Candida spp., including C-dubliniensis

    NARCIS (Netherlands)

    Borst, A; Theelen, B; Reinders, E; Boekhout, T; Fluit, AC; Savelkoul, PHM

    Non-Candida albicans Candida species are increasingly being isolated. These species show differences in levels of resistance to antimycotic agents and mortality. Therefore, it is important to be able to correctly identify the causative organism to the species level. Identification of C. dubliniensis

  5. Fractal Fragmentation triggered by meteor impact: The Ries Crater (Germany)

    Science.gov (United States)

    Paredes Marino, Joali; Perugini, Diego; Rossi, Stefano; Kueppers, Ulrich

    2015-04-01

    FRACTAL FRAGMENTATION TRIGGERED BY METEOR IMPACT: THE RIES CRATER (GERMANY) Joali Paredes (1), Stefano Rossi (1), Diego Perugini (1), Ulrich Kueppers (2) 1. Department of Physics and Geology, University of Perugia, Italy 2. Department of Earth and Environmental Sciences, University of Munich, Germany The Nördlinger Ries is a large circular depression in western Bavaria, Germany. The depression was caused by a meteor impact, which occurred about 14.3 million-14.5 million years ago. The original crater rim had an estimated diameter of 24 kilometers. Computer modeling of the impact event indicates that the impact or probably had diameters of about 1.5 kilometers and impacted the target area at an angle around 30 to 50 degrees from the surface in a west- southwest to east-northeast direction. The impact velocity is thought to have been about 20 km/s. The meteor impact generated extensive fragmentation of preexisting rocks. In addition, melting of these rocks also occurred. The impact melt was ejected at high speed provoking its extensive fragmentation. Quenched melt fragments are ubiquitous in the outcrops. Here we study melt fragment size distributions with the aim of understanding the style of melt fragmentation during ejection and to constrain the rheological properties of such melts. Digital images of suevite (i.e. the rock generated after deposition and diagenesis of ash and fragments produced by the meteor impact) were obtained using a high-resolution optical scanner. Successively, melt fragments were traced by image analysis and the images segmented in order to obtain binary images on which impact melt fragments are in black color, embedded on a white background. Hence, the size of fragments was determined by image analysis. Fractal fragmentation theory has been applied to fragment size distributions of melt fragments in the Ries crater. Results indicate that melt fragments follow fractal distributions indicating that fragmentation of melt generated by the

  6. Microbial platform technology for recombinant antibody fragment production: A review.

    Science.gov (United States)

    Gupta, Sanjeev Kumar; Shukla, Pratyoosh

    2017-02-01

    Recombinant antibody fragments are being used for the last few years as an important therapeutic protein to cure various critical and life threatening human diseases. Several expression platforms now days employed for the production of these recombinant fragments, out of which bacterial system has emerged a promising host for higher expression. Since, a small antibody fragment unlike full antibody does not require human-like post-translational modification therefore it is potentially expressed in prokaryotic production system. Recently, small antibody fragments such as scFvs (single-chain variable fragments) and Fabs (antibody fragments) which does not require glycosylation are successfully produced in bacteria and have commercially launched for therapeutic use as these fragments shows better tissue penetration and less immunogenic to human body compared to full-size antibody. Recently developed Wacker's ESETEC secretion technology is an efficient technology for the expression and secretion of the antibody fragment (Fab) exceeded up to 4.0 g/L while scFv up to 3.5 g/L into the fermentation broth. The Pfenex system and pOP prokaryotic expression vector are another platform used for the considerably good amount of antibody fragment production successfully. In this review, we summarize the recent progress on various expression platforms and cloning approaches for the production of different forms of antibody fragments in E. coli.

  7. Would protecting tropical forest fragments provide carbon and biodiversity cobenefits under REDD+?

    Science.gov (United States)

    Magnago, Luiz Fernando S; Magrach, Ainhoa; Laurance, William F; Martins, Sebastião V; Meira-Neto, João Augusto A; Simonelli, Marcelo; Edwards, David P

    2015-09-01

    Tropical forests store vast amounts of carbon and are the most biodiverse terrestrial habitats, yet they are being converted and degraded at alarming rates. Given global shortfalls in the budgets required to prevent carbon and biodiversity loss, we need to seek solutions that simultaneously address both issues. Of particular interest are carbon-based payments under the Reducing Emissions from Deforestation and Forest Degradation (REDD+) mechanism to also conserve biodiversity at no additional cost. One potential is for REDD+ to protect forest fragments, especially within biomes where contiguous forest cover has diminished dramatically, but we require empirical tests of the strength of any carbon and biodiversity cobenefits in such fragmented systems. Using the globally threatened Atlantic Forest landscape, we measured above-ground carbon stocks within forest fragments spanning 13 to 23 442 ha in area and with different degrees of isolation. We related these stocks to tree community structure and to the richness and abundance of endemic and IUCN Red-listed species. We found that increasing fragment size has a positive relationship with above-ground carbon stock and with abundance of IUCN Red-listed species and tree community structure. We also found negative relationships between distance from large forest block and tree community structure, endemic species richness and abundance, and IUCN Red-listed species abundance. These resulted in positive congruence between carbon stocks and Red-listed species, and the abundance and richness of endemic species, demonstrating vital cobenefits. As such, protecting forest fragments in hotspots of biodiversity, particularly larger fragments and those closest to sources, offers important carbon and biodiversity cobenefits. More generally, our results suggest that macroscale models of cobenefits under REDD+ have likely overlooked key benefits at small scales, indicating the necessity to apply models that include finer

  8. Incorporating fragmentation and non-native species into distribution models to inform fluvial fish conservation.

    Science.gov (United States)

    Taylor, Andrew T; Papeş, Monica; Long, James M

    2018-02-01

    Fluvial fishes face increased imperilment from anthropogenic activities, but the specific factors contributing most to range declines are often poorly understood. For example, the range of the fluvial-specialist shoal bass (Micropterus cataractae) continues to decrease, yet how perceived threats have contributed to range loss is largely unknown. We used species distribution models to determine which factors contributed most to shoal bass range loss. We estimated a potential distribution based on natural abiotic factors and a series of currently occupied distributions that incorporated variables characterizing land cover, non-native species, and river fragmentation intensity (no fragmentation, dams only, and dams and large impoundments). We allowed interspecific relationships between non-native congeners and shoal bass to vary across fragmentation intensities. Results from the potential distribution model estimated shoal bass presence throughout much of their native basin, whereas models of currently occupied distribution showed that range loss increased as fragmentation intensified. Response curves from models of currently occupied distribution indicated a potential interaction between fragmentation intensity and the relationship between shoal bass and non-native congeners, wherein non-natives may be favored at the highest fragmentation intensity. Response curves also suggested that >100 km of interconnected, free-flowing stream fragments were necessary to support shoal bass presence. Model evaluation, including an independent validation, suggested that models had favorable predictive and discriminative abilities. Similar approaches that use readily available, diverse, geospatial data sets may deliver insights into the biology and conservation needs of other fluvial species facing similar threats. © 2017 Society for Conservation Biology.

  9. Muscle fragments on a scaffold in rats

    DEFF Research Database (Denmark)

    Jangö, Hanna; Gräs, Søren; Christensen, Lise

    2015-01-01

    with autologous muscle fiber fragments (MFF), as an adjunct to native tissue POP repair, is a potential new alternative. METHODS: A rat abdominal wall model of native repair was used with six animals in each of three groups: native repair, native repair + MPEG-PLGA, and native repair + MPEG-PLGA + MFF. MFF were...... labeled with PKH26-fluorescence dye. After 8 weeks labeled cells were identified in tissue samples and histopathological and immunohistochemical analyses of connective tissue organization and desmin reactivity of muscle cells were performed. Fresh tissue samples were subjected to uniaxial biomechanical......-PLGA scaffolds seeded with autologous MFF affected some histological and biomechanical properties of native tissue repair in an abdominal wall defect model in rats. The method thus appears to be a simple tissue engineering concept with potential relevance for native tissue repair of POP....

  10. Spontaneously disappearing large herniated lumbar disc fragment

    Directory of Open Access Journals (Sweden)

    Umamaheswara V. Reddy

    2014-01-01

    Full Text Available There are reports of spontaneous regression of large extruded disc; however, the exact underlying mechanism and management of such cases remains controversial. We report a 40-year-old female who opted for conservative management for a large extruded lumbar disc. Follow-up magnetic resonance imaging (MRI showed complete disappearance of the disc fragment; however, there were degenerative changes in the upper and lower adjacent margins of the vertebral body. Spine surgeons should be aware of spontaneous regression of the disc phenomenon as a patient with a large extruded disc who opted for the conservative management initially can have persistence pain, but there may not be an underlying protruded disc.

  11. Fragmentation modeling of a resin bonded sand

    Directory of Open Access Journals (Sweden)

    Hilth William

    2017-01-01

    The calibration procedure, using standard laboratory tests, is complemented by the study of an uniaxial compression test observed by tomography. Using finite elements simulations, this test is simulated considering a non-homogeneous 3D media. The tomography of compression sample gives access to 3D displacement fields by using image correlation techniques. Unfortunately these fields have missing experimental data because of the low resolution of correlations for low displacement magnitudes. We propose a recovery method that reconstructs 3D full displacement fields and 2D boundary displacement fields. These fields are mandatory for the calibration of the constitutive parameters by using 3D finite element simulations. The proposed recovery technique is based on a singular value decomposition of available experimental data. This calibration protocol enables an accurate prediction of the fragmentation of the specimen.

  12. Nonperturbative fragmentation of the top quark

    Energy Technology Data Exchange (ETDEWEB)

    Dobado, A. (Departamento de Fisica Teorica and Instituto de Fisica Fundamental, Universidad Complutense de Madrid, 28040 Madrid (Spain)); Urdiales, M. (Departamento de Fisica Teorica, Universidad Autonoma de Madrid, 28049 Madrid (Spain))

    1991-11-01

    By the use of a simple phenomenological string model, the energy lost by the top quark through nonperturbative fragmentation effects before its weak decay is computed. This energy lost is in first approximation proportional to the rate between the decay time and the hadronization time of the top as measured in the center-of-mass frame of the top and its color partner. Precise computations of the energy lost by the top in terms of its mass when produced in colliders such as the Fermilab Tevatron, CERN Large Hadron Collider, Superconducting Super Collider, and CERN Linear Collider are presented. As expected, this effect decreases quickly with the top mass but it could be relevant for a top mass below 100 GeV.

  13. Magnetic-Moment Fragmentation and Monopole Crystallization

    Directory of Open Access Journals (Sweden)

    M. E. Brooks-Bartlett

    2014-01-01

    Full Text Available The Coulomb phase, with its dipolar correlations and pinch-point–scattering patterns, is central to discussions of geometrically frustrated systems, from water ice to binary and mixed-valence alloys, as well as numerous examples of frustrated magnets. The emergent Coulomb phase of lattice-based systems has been associated with divergence-free fields and the absence of long-range order. Here, we go beyond this paradigm, demonstrating that a Coulomb phase can emerge naturally as a persistent fluctuating background in an otherwise ordered system. To explain this behavior, we introduce the concept of the fragmentation of the field of magnetic moments into two parts, one giving rise to a magnetic monopole crystal, the other a magnetic fluid with all the characteristics of an emergent Coulomb phase. Our theory is backed up by numerical simulations, and we discuss its importance with regard to the interpretation of a number of experimental results.

  14. Communication: Embedded fragment stochastic density functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Neuhauser, Daniel, E-mail: dxn@chem.ucla.edu [Department of Chemistry, University of California at Los Angeles, Los Angeles, California 90095 (United States); Baer, Roi, E-mail: roi.baer@huji.ac.il [Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904 (Israel); Rabani, Eran, E-mail: eran.rabani@gmail.com [School of Chemistry, The Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978 (Israel)

    2014-07-28

    We develop a method in which the electronic densities of small fragments determined by Kohn-Sham density functional theory (DFT) are embedded using stochastic DFT to form the exact density of the full system. The new method preserves the scaling and the simplicity of the stochastic DFT but cures the slow convergence that occurs when weakly coupled subsystems are treated. It overcomes the spurious charge fluctuations that impair the applications of the original stochastic DFT approach. We demonstrate the new approach on a fullerene dimer and on clusters of water molecules and show that the density of states and the total energy can be accurately described with a relatively small number of stochastic orbitals.

  15. QCD at the Tevatron: Jets and fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    V. Daniel Elvira

    2001-09-27

    At the Fermilab Tevatron energies, ({radical} s=1800 GeV and {radical} s = 630 GeV), jet production is the dominant process. During the period 1992-1996, the D0 and CDF experiments accumulated almost 100 pb{sup -1} of data and performed the most accurate jet production measurements up to this date. These measurements and the NLO-QCD theoretical predictions calculated during the last decade, have improved our understanding of QCD, our knowledge of the proton structure, and pushed the limit to the scale associated with quark compositeness to 2.4-2.7 TeV. In this paper, we present the most recent published and preliminary measurements on jet production and fragmentation by the D0 and CDF collaborations.

  16. Isolator fragmentation and explosive initiation tests

    Energy Technology Data Exchange (ETDEWEB)

    Dickson, Peter [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Rae, Philip John [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Timothy J. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Novak, Alan M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Armstrong, Christopher Lee [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Baca, Eva V. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Gunderson, Jake Alfred [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-09-19

    Three tests were conducted to evaluate the effects of firing an isolator in proximity to a barrier or explosive charge. The tests with explosive were conducted without a barrier, on the basis that since any barrier will reduce the shock transmitted to the explosive, bare explosive represents the worst-case from an inadvertent initiation perspective. No reaction was observed. The shock caused by the impact of a representative plastic material on both bare and cased PBX 9501 is calculated in the worst-case, 1-D limit, and the known shock response of the HE is used to estimate minimum run-to-detonation lengths. The estimates demonstrate that even 1-D impacts would not be of concern and that, accordingly, the divergent shocks due to isolator fragment impact are of no concern as initiating stimuli.

  17. The genesis of a fragmented profession

    Directory of Open Access Journals (Sweden)

    Ana Waleska Pollo Mendonça

    2012-02-01

    Full Text Available This text is the first product of a subproject, which intends to study the impact of the Pombal’s Reforms of the minor studies in the process of teacher professionalization, which could be considered as a decisive moment in the history of the teaching profession in the Portuguese-Brazilian world. These reforms express State intervention in the constitution of a selected group of teachers, chosen, paid and controlled by the State, characterizing a process of making the teaching profession a function of the State. The text emphasizes one of the dimensions of this State activity, which constitutes the fragmentation of studies, with long lasting consequences for the way in which the profession organizes itself up to the present day.

  18. DRAGON: Monte Carlo generator of particle production from a fragmented fireball in ultrarelativistic nuclear collisions

    Science.gov (United States)

    Tomášik, Boris

    2009-09-01

    A Monte Carlo generator of the final state of hadrons emitted from an ultrarelativistic nuclear collision is introduced. An important feature of the generator is a possible fragmentation of the fireball and emission of the hadrons from fragments. Phase space distribution of the fragments is based on the blast wave model extended to azimuthally non-symmetric fireballs. Parameters of the model can be tuned and this allows to generate final states from various kinds of fireballs. A facultative output in the OSCAR1999A format allows for a comprehensive analysis of phase-space distributions and/or use as an input for an afterburner. Program summaryProgram title: DRAGON Catalogue identifier: AEDK_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDK_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 6383 No. of bytes in distributed program, including test data, etc.: 32 756 Distribution format: tar.gz Programming language: C++ Computer: PC Pentium 4, though no particular tuning for this machine was performed Operating system: Linux; the program has been successfully run on Gentoo Linux 2.6, RedHat Linux 9, Debian Linux 4.0, all with g++ compiler. It also ran successfully on MS Windows under Microsoft Visual C++ 2008 Express Edition as well as under cygwin/g++ RAM: 100 Mbytes Supplementary material: Sample output files from the test run, provided in the distribution, are available. Classification: 11.2 Nature of problem: Deconfined matter produced in ultrarelativistic nuclear collisions expands and cools down and eventually returns into the confined phase. If the expansion is fast, the fireball could fragment either due to spinodal decomposition or due to suddenly arising bulk viscous force. Particle abundances are reasonably well described with just a few parameters

  19. Assortative mating and fragmentation within dog breeds

    Directory of Open Access Journals (Sweden)

    Hailer Frank

    2008-01-01

    Full Text Available Abstract Background There are around 400 internationally recognized dog breeds in the world today, with a remarkable diversity in size, shape, color and behavior. Breeds are considered to be uniform groups with similar physical characteristics, shaped by selection rooted in human preferences. This has led to a large genetic difference between breeds and a large extent of linkage disequilibrium within breeds. These characteristics are important for association mapping of candidate genes for diseases and therefore make dogs ideal models for gene mapping of human disorders. However, genetic uniformity within breeds may not always be the case. We studied patterns of genetic diversity within 164 poodles and compared it to 133 dogs from eight other breeds. Results Our analyses revealed strong population structure within poodles, with differences among some poodle groups as pronounced as those among other well-recognized breeds. Pedigree analysis going three generations back in time confirmed that subgroups within poodles result from assortative mating imposed by breed standards as well as breeder preferences. Matings have not taken place at random or within traditionally identified size classes in poodles. Instead, a novel set of five poodle groups was identified, defined by combinations of size and color, which is not officially recognized by the kennel clubs. Patterns of genetic diversity in other breeds suggest that assortative mating leading to fragmentation may be a common feature within many dog breeds. Conclusion The genetic structure observed in poodles is the result of local mating patterns, implying that breed fragmentation may be different in different countries. Such pronounced structuring within dog breeds can increase the power of association mapping studies, but also represents a serious problem if ignored. In dog breeding, individuals are selected on the basis of morphology, behaviour, working or show purposes, as well as geographic

  20. Quantum Correlated Multi-Fragment Reaction Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Feagin, James M. [California State Univ., Fullerton, CA (United States)

    2017-06-30

    This grant supported research in basic atomic, molecular and optical physics related to the interactions of atoms with particles and fields. This report will focus on the 12 year period from 2004 to 2017, although the DOE–BES has supported my research every year since 1986. All of the support from the grant was used to pay summer salaries of the PI and students and travel to conferences and meetings. The results were in the form of publications in peer reviewed journals as well as conference invited talks and colloquiums. There were 12 peer reviewed publications in these 12+ years. Innovations in few-body science at molecular and nano levels are a critical component of on- going efforts to establish sustainable environmental and energy resources. The varied research paths taken will require the development of basic science on broad fronts with increasing flexi- bility to crossover technologies. We thus worked to extract understanding and quantum control of few-body microscopic systems based on our long-time experience with more conventional studies of correlated electrons and ions. Given the enormous advances over the past 20 years to our understanding of quantum cor- relations with photon interferometry, AMO collision science generally is ready to move beyond the one-particle, single-port momentum detection that has dominated collision physics since Rutherford. Nevertheless, our familiar theoretical tools for collision theory need to be up- graded to incorporate these more generalized measurement formalisms and ultimately to give incentive for a new generation of experiments. Our interest in these topics remains motivated by the recent surge in and success of exper- iments involving few-body atomic and molecular fragmentation and the detection of all the fragments. The research described here thus involved two parallel efforts with (i) emphasis on reaction imaging while (ii) pursuing longtime work on quantum correlated collective excitations.

  1. A set of primers conserved in genus Parnassius (Lepidoptera, Papilionidae) for amplification and sequencing of 1016 bp fragment of cytochrome oxidase subunit I from museum specimens.

    Science.gov (United States)

    Konopinski, Maciej K

    2008-05-01

    Four short, overlapping amplicons covering a 1016 bp fragment of mitochondrial cytochrome oxidase subunit I were developed. All four fragments were successfully amplified and sequenced in eight species of butterflies belonging to the genus Parnassius including over 100-year-old DNA from pinned museum specimens. The fragment contains sufficient variation for both inter- and intraspecific analyses. A total of 105 sites were polymorphic within 52 haplotypes found in 186 samples from Parnassius mnemosyne. © 2007 The Authors.

  2. Patterns and processes of shell fragmentation in modern and ancient marine environments

    Science.gov (United States)

    Zuschin, Martin; Stachowitsch, Michael; Stanton, Robert J.

    2003-10-01

    Shell fragments are important components of many Recent and fossil marine benthic ecosystems and can provide crucial information on past and present environmental conditions. Interpreting such fragments requires integrated knowledge in various fields and the information potential is therefore rarely optimally utilized. This paper uses the definition of a fragment as being a piece of shell having less than 90% of its original form. It then outlines the potential characteristics, pathways, and fates that shells and their fragments can have. Fragmentation is a key factor shaping the shelly part of death assemblages, but it is difficult to interpret because it can be broadly caused by ecological, biostratinomic or diagenetic processes and also depends on shell strength. Strength, in turn, reflects multifunctionality during ontogeny and depends on a complex set of skeletal and taphonomic factors. Therefore, no particular shell parameter clearly determines strength, but thickness, microstructure type and degree of organic matrix have the strongest influence on pre- and post-mortality strength. Size measurements are usually less important for shell strength than thickness, although ecologically complex size refuges from predation do exist. Similarly, shell shape, sculptural features and specific aperture types (in gastropods) provide various defence strategies rather than increasing strength per se. Key ecological factors of fragmentation include predation due to crushing, peeling, along with mistaken predation, self-inflicted damage during predation and burrowing, and more physical aspects such as impacts by stones. Modern studies must consider damage by benthic commercial fisheries or dredging by scientific vessels. Key biostratinomic factors include transport-induced abrasion (littoral zone of surf-washed beaches), bioerosion and dissolution (mainly sublittoral environments). Diagenetically, fragmentation during compaction mainly occurs when shells are in direct

  3. Computer systems for annotation of single molecule fragments

    Science.gov (United States)

    Schwartz, David Charles; Severin, Jessica

    2016-07-19

    There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.

  4. Nuclear Fragmentation in Clinical Heavy Ion Beams, Should We Worry?

    DEFF Research Database (Denmark)

    Bassler, Niels; Hansen, David Christoffer; Toftegaard, Jakob

    particles is formed beyond the Bragg-peak. This tail may deliver unwanted dose to normal tissue, however the magnitude of the tail is directly depending on the inelastic nuclear reaction cross sections. 2. Dosimetry a. Stopping power ratios: Routine dosimetry is performed with air-filled ionization chambers...... the sensitivity on the three fields mentioned above, including: turning off nuclear fragmentation entirely, changing all ineleastic cross sections +/- 20%, changing key parameters in the Fermi-Breakup (FB) model. Results show nuclear effects have their largest impact on the dose distribution. Stopping power......Particle therapy with fast ions is increasingly applied as a treatment option for localized inoperable tumour sites. One of the reasons for the increased complications of understanding heavy ion dosimetry and radiobiology stems from the mixed particle spectrum which occurs due to nuclear...

  5. First Measurement of the Quark-to-Photon Fragmentation Function

    CERN Document Server

    Thompson, J

    1995-01-01

    Earlier measurements at LEP of isolated hard photons in hadronic $Z$ decays attributed to radiation from primary quark pairs, have been extended in the ALEPH experiment to include hard photon production {\\em inside} hadron jets. Events are selected where all particles combine democratically to form hadron jets, one of which contains a photon with a fractional energy $z\\geq 0.7$. After statistical subtraction of non-prompt photons, the quark- to-photon fragmentation function, $D(z)$, is extracted directly from the measured prompt production rate. By taking into account the perturbative contributions to $D(z)$ obtained from an $\\cal{O}(\\alpha \\alpha_S)$ QCD calculation, the unknown non-perturbative component of $D(z)$ is determined at high $z$. This measurement is compared with an earlier theoretical parametrisation widely used to determine the level of quark bremsstrahlung present in prompt photon production at the hadron colliders.

  6. Effective Fragmentation and Flyrock Control Strategies at Quarries

    Directory of Open Access Journals (Sweden)

    Sedat Esen

    2017-01-01

    Full Text Available This paper presents the effective fragmentation and flyrock control strategies that could be applied at quarries to improve the productivity and safety. Fragmentation measurement and modelling as well as a comprehensive drill and blast audit are essential for improving the fragmentation. Face profiling and bore tracking are good tools to manage the ―as-designed‖ and ―as-drilled‖ conditions to get reasonable fragmentation from face burden zone and minimise the flyrock risk. In general, a large scatter in fragmentation data was observed at sites and the causes should be analysed by a detailed root-cause analysis technique. Two case studies were presented in this paper showing some of the effective fragmentation strategies. Finally, a flyrock model was shown to determine the safe blast exclusion zone for the mining equipment and personnel. Some key guidelines were suggested to minimise the occurrence of the flyrock.

  7. Computational tools for in silico fragment-based drug design.

    Science.gov (United States)

    Mortier, Jeremie; Rakers, Christin; Frederick, Raphael; Wolber, Gerhard

    2012-01-01

    Fragment-based strategy in drug design involves the initial discovery of low-molecular mass molecules. Owing to their small-size, fragments are molecular tools to probe specific sub-pockets within a protein active site. Once their interaction within the enzyme cavity is clearly understood and experimentally validated, they represent a unique opportunity to design potent and efficient larger compounds. Computer-aided methods can essentially support the identification of suitable fragments. In this review, available tools for computational drug design are discussed in the frame of fragmentbased approaches. We analyze and review (i) available commercial fragment libraries with respect to their properties and size, (ii) computational methods for the construction of such a library, (iii) the different strategies and software packages for the selection of the fragments with predicted affinity to a given target, and (iv) tools for the in silico linkage of fragments into an actual high-affinity lead structure candidate.

  8. Antibody Fragments and Their Purification by Protein L Affinity Chromatography

    Directory of Open Access Journals (Sweden)

    Gustav Rodrigo

    2015-09-01

    Full Text Available Antibodies and related proteins comprise one of the largest and fastest-growing classes of protein pharmaceuticals. A majority of such molecules are monoclonal antibodies; however, many new entities are antibody fragments. Due to their structural, physiological, and pharmacological properties, antibody fragments offer new biopharmaceutical opportunities. In the case of recombinant full-length antibodies with suitable Fc regions, two or three column purification processes centered around Protein A affinity chromatography have proven to be fast, efficient, robust, cost-effective, and scalable. Most antibody fragments lack Fc and suitable affinity for Protein A. Adapting proven antibody purification processes to antibody fragments demands different affinity chromatography. Such technology must offer the unit operation advantages noted above, and be suitable for most of the many different types of antibody fragments. Protein L affinity chromatography appears to fulfill these criteria—suggesting its consideration as a key unit operation in antibody fragment processing.

  9. Land reform and land fragmentation in Central and Eastern Europe

    DEFF Research Database (Denmark)

    Hartvigsen, Morten B.

    2014-01-01

    It has often been stated that land fragmentation and farm structures characterized by small agricultural holdings and farms divided in a large number of parcels have been the side-effect of land reform in Central and Eastern Europe. This article reports the findings of a study of land reform in 25...... countries in the region from 1989 and onwards and provides an overview of applied land reform approaches. With a basis in theory on land fragmentation, the linkage between land reform approaches and land fragmentation is explored. It is discussed in which situations land fragmentation is a barrier...... for the development of the agricultural and rural sector. The main finding is that land fragmentation is often hampering agricultural and rural development when both land ownership and land use is highly fragmented....

  10. Hydrogen rearrangement to and from radical z fragments in electron capture dissociation of peptides

    DEFF Research Database (Denmark)

    Savitski, Mikhail M; Kjeldsen, Frank; Nielsen, Michael L

    2007-01-01

    capture dissociation (ECD), including previously unreported double H. losses. Consistent with the radical character of H. abstraction, the residue determining the formation rate of z' = z. + H. species is found to be the N-terminal residue in z. species. The size of the complementary c(m)' fragment turned...... out to be another important factor, with z' species dominating over z. ions for m carbon groups of residues composing the c' species, with Gln and His in the c' fragment promoting H. donation and Asp and Ala...

  11. DYNAMICS OF LARGE FRAGMENTS IN THE TAIL OF ACTIVE ASTEROID P/2010 A2

    Energy Technology Data Exchange (ETDEWEB)

    Agarwal, Jessica [Max Planck Institute for Solar System Research, D-37191 Katlenburg-Lindau (Germany); Jewitt, David [Department of Earth and Space Sciences and Department of Physics and Astronomy, University of California at Los Angeles, Los Angeles, CA 90095-1567 (United States); Weaver, Harold, E-mail: agarwal@mps.mpg.de [Johns Hopkins University Applied Physics Laboratory, Johns Hopkins University, Laurel, MD 20723 (United States)

    2013-05-20

    We examine the motions of large fragments at the head of the dust tail of the active asteroid P/2010 A2. In previous work, we showed that these fragments were ejected from the primary nucleus in early 2009, either following a hypervelocity impact or by rotationally induced breakup. Here, we follow their positions through a series of Hubble Space Telescope images taken during the first half of 2010. The orbital evolution of each fragment allows us to constrain its velocity relative to the main nucleus after leaving its sphere of gravitational influence. We find that the fragments constituting a prominent X-shaped tail feature were emitted in a direction opposite to the motion of the asteroid and toward the south of its orbital plane. Derived emission velocities of these primary fragments range between 0.02 and 0.3 m s{sup -1}, comparable to the {approx}0.08 m s{sup -1} gravitational escape speed from the nucleus. Their sizes are on the order of decimeters or larger. We obtain the best fits to our data with ejection velocity vectors lying in a plane that includes the nucleus. This may suggest that the cause of the disruption of P/2010 A2 is rotational breakup.

  12. IN SITU PLASMA MEASUREMENTS OF FRAGMENTED COMET 73P SCHWASSMANN–WACHMANN 3

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, J. A.; Lepri, S. T.; Combi, M.; Zurbuchen, T. H. [University of Michigan, Ann Arbor, MI 48109 (United States); Rubin, M., E-mail: jagi@umich.edu [Universität Bern, Bern (Switzerland)

    2015-12-10

    The interiors of comets contain some of the most pristine material in the solar system. Comet 73P/Schwassmann–Wachmann 3, discovered in 1930, is a Jupiter-family comet with a 5.34-year period. This comet split into 5 fragments in 1995 and disintegrated into nearly 70 major pieces in 2006. In 2006 May and June, recently ionized cometary particles originating from fragments including and surrounding some of these major objects were collected with the ACE/SWICS and Wind/STICS sensors. Due to a combination of the instrument characteristics and the close proximity of the fragments passing between those spacecraft and the Sun, unique measurements regarding the charge state composition and the elemental abundances of both cometary and heliospheric plasma were made during that time. The cometary material released from some of these fragments can be identified by the concentrations of water-group pickup ions having a mass-per-charge ratio of 16–18 amu e{sup −1}, indicating that while these fragments are small, they are still actively sublimating. We present an analysis of cometary composition, spatial distribution, and heliospheric interactions, with a focus on helium, C{sup +}/O{sup +}, and water-group ions.

  13. Thermochemistry and photochemistry of spiroketals derived from indan-2-one: Stepwise processes versus coarctate fragmentations

    Directory of Open Access Journals (Sweden)

    Götz Bucher

    2013-08-01

    Full Text Available Coarctate reactions are defined as reactions that include atoms at which two bonds are made and two bonds are broken simultaneously. In the pursuit of the discovery of new coarctate reactions we investigate the fragmentation reactions of cyclic ketals. Three ketals with different ring sizes derived from indan-2-one were decomposed by photolysis and pyrolysis. Particularly clean is the photolysis of the indan-2-one ketal 1, which gives o-quinodimethane, carbon dioxide and ethylene. The mechanism formally corresponds to a photochemically allowed coarctate fragmentation. Pyrolysis of the five-ring ketal yields a number of products. This is in agreement with the fact that coarctate fragmentation observed upon irradiation would be thermochemically forbidden, although this exclusion principle does not hold for chelotropic reactions. In contrast, fragmentation of the seven-ring ketal 3 is thermochemically allowed and photochemically forbidden. Upon pyrolysis of 3 several products were isolated that could be explained by a coarctate fragmentation. However, the reaction is less clean and stepwise mechanisms may compete.

  14. Introduction of functionalized mesopores to metal-organic frameworks via metal-ligand-fragment coassembly.

    Science.gov (United States)

    Park, Jinhee; Wang, Zhiyong U; Sun, Lin-Bing; Chen, Ying-Pin; Zhou, Hong-Cai

    2012-12-12

    Introduction of functionalized mesopores into microporous metal-organic frameworks (MOFs) can endow them with suitable properties for applications in gas storage, separation, catalysis, and drug delivery. However, common methods for functionalization (including pre- and post-synthetic modifications) of the internal surface of a MOF reduce the pore size of the MOF because the additional functional groups fill up the pores. We present a metal-ligand-fragment coassembly strategy for the introduction of (meso)pores functionalized with various substituent groups on the ligand fragments. Astonishingly, this new functionalization strategy increases the pore volume of a MOF instead of reducing it. Since the ligand fragments are often readily available or easily prepared, the new procedure for synthesis of the modified MOFs becomes much easier and more applicable than existing approaches. Remarkably, mesopores can be generated conveniently and controllably by the coassembly of a ligand and its fragment containing the desired functional groups. The fragment/ligand ratio has been optimized to preserve the parent structure and to promote maximum mesopore introduction, which has led to a systematic evaluation of the effectiveness of a series of functional groups for the adsorption of guest molecules.

  15. Predictable allele frequency changes due to habitat fragmentation in the Glanville fritillary butterfly.

    Science.gov (United States)

    Fountain, Toby; Nieminen, Marko; Sirén, Jukka; Wong, Swee Chong; Lehtonen, Rainer; Hanski, Ilkka

    2016-03-08

    Describing the evolutionary dynamics of now extinct populations is challenging, as their genetic composition before extinction is generally unknown. The Glanville fritillary butterfly has a large extant metapopulation in the Åland Islands in Finland, but declined to extinction in the nearby fragmented southwestern (SW) Finnish archipelago in the 20th century. We genotyped museum samples for 222 SNPs across the genome, including SNPs from candidate genes and neutral regions. SW Finnish populations had significantly reduced genetic diversity before extinction, and their allele frequencies gradually diverged from those in contemporary Åland populations over 80 y. We identified 15 outlier loci among candidate SNPs, mostly related to flight, in which allele frequencies have changed more than the neutral expectation. At outlier loci, allele frequencies in SW Finland shifted in the same direction as newly established populations deviated from old local populations in contemporary Åland. Moreover, outlier allele frequencies in SW Finland resemble those in fragmented landscapes as opposed to continuous landscapes in the Baltic region. These results indicate selection for genotypes associated with good colonization capacity in the highly fragmented landscape before the extinction of the populations. Evolutionary response to habitat fragmentation may have enhanced the viability of the populations, but it did not save the species from regional extinction in the face of severe habitat loss and fragmentation. These results highlight a potentially common situation in changing environments: evolutionary changes are not strong enough to fully compensate for the direct adverse effects of environmental change and thereby rescue populations from extinction.

  16. Detection of titin fragments in urine in response to exercise-induced muscle damage.

    Directory of Open Access Journals (Sweden)

    Kazue Kanda

    Full Text Available Many studies have attempted to determine the associations between blood biomarkers and exercise-induced muscle damage. However, poor correlations between the changes in biomarker levels and the magnitude of muscle symptoms have been reported. Recent advances in proteomic tools offer a strategy for the comprehensive analysis of protein expression, which can be used to identify biomarkers. Here, we used a proteomic analysis to identify urinary proteins that appear in response to a calf-raise exercise, including repetitive eccentric muscle contractions, and found that a titin (also known as connectin N-terminal fragment molecule appears in the urine after eccentric exercise. We measured the titin fragment in urine samples from nine individuals before and after eccentric exercise using a newly-established enzyme-linked immunosorbent assay and found that the titin fragment excretion rate increased 96 h after the exercise (5.1 to 77.6 pg/min, p <0.01. The changes in the titin fragment excretion rate were correlated strongly with blood markers of muscle damage and with muscle symptoms. These findings suggest that the urinary titin fragment is potentially a noninvasive biomarker of muscle damage.

  17. Purification of high affinity benzodiazepine receptor binding site fragments from rat brain

    Energy Technology Data Exchange (ETDEWEB)

    Klotz, K.L.

    1984-01-01

    In central nervous system benzodiazepine recognition sites occur on neuronal cell surfaces as one member of a multireceptor complex, including recognition sites for benzodiazepines, gamma aminobutyric acid (GABA), barbiturates and a chloride ionophore. During photoaffinity labelling, the benzodiazepine agonist, /sup 3/H-flunitrazepam, is irreversibly bound to central benzodiazepine high affinity recognition sites in the presence of ultraviolet light. In these studies a /sup 3/H-flunitrazepam radiolabel was used to track the isolation and purification of high affinity agonist binding site fragments from membrane-bound benzodiazepine receptor in rat brain. The authors present a method for limited proteolysis of /sup 3/H-flunitrazepam photoaffinity labeled rat brain membranes, generating photolabeled benzodiazepine receptor fragments containing the agonist binding site. Using trypsin chymotrypsin A/sub 4/, or a combination of these two proteases, they have demonstrated the extent and time course for partial digestion of benzodiazepine receptor, yielding photolabeled receptor binding site fragments. These photolabeled receptor fragments have been further purified on the basis of size, using ultrafiltration, gel permeation chromatography, and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) as well as on the basis of hydrophobicity, using a high performance liquid chromatography (HPLC) precolumn, several HPLC elution schemes, and two different HPLC column types. Using these procedures, they have purified three photolabeled benzodiazepine receptor fragments containing the agonist binding site which appear to have a molecular weight of less than 2000 daltons each.

  18. The genetic defect of fragmented coronoid process in Labrador retrievers and other skeletal diseases in dogs

    NARCIS (Netherlands)

    Temwichitr, J.

    2009-01-01

    Fragmented medial coronoid process (FCP) is the main component of elbow dysplasia (ED) in dogs, which also includes osteochondrosis of the humeral condyle (OCD), elbow incongruity (INC), and ununited anconeal process (UAP). FCP is recognized as a hereditary disease in many breeds and is a major

  19. Theory including future not excluded

    DEFF Research Database (Denmark)

    Nagao, K.; Nielsen, H.B.

    2013-01-01

    We study a complex action theory (CAT) whose path runs over not only past but also future. We show that, if we regard a matrix element defined in terms of the future state at time T and the past state at time TA as an expectation value in the CAT, then we are allowed to have the Heisenberg equation......, Ehrenfest's theorem, and the conserved probability current density. In addition,we showthat the expectation value at the present time t of a future-included theory for large T - t and large t - T corresponds to that of a future-not-included theory with a proper inner product for large t - T. Hence, the CAT...

  20. Collisional Fragmentation Is Not a Barrier to Close-in Planet Formation

    Energy Technology Data Exchange (ETDEWEB)

    Wallace, Joshua; Tremaine, Scott [Department of Astrophysical Sciences, Princeton University, Princeton, NJ 08544 (United States); Chambers, John, E-mail: joshuajw@princeton.edu [Department of Terrestrial Magnetism, Carnegie Institution for Science, Washington, DC 20015 (United States)

    2017-11-01

    Collisional fragmentation is shown to not be a barrier to rocky planet formation at small distances from the host star. Simple analytic arguments demonstrate that rocky planet formation via collisions of homogeneous gravity-dominated bodies is possible down to distances of order the Roche radius ( r {sub Roche}). Extensive N -body simulations with initial bodies ≳1700 km that include plausible models for fragmentation and merging of gravity-dominated bodies confirm this conclusion and demonstrate that rocky planet formation is possible down to ∼1.1 r {sub Roche}. At smaller distances, tidal effects cause collisions to be too fragmenting to allow mass buildup to a final, dynamically stable planetary system. We argue that even differentiated bodies can accumulate to form planets at distances that are not much larger than r {sub Roche}.

  1. The soluble urokinase plasminogen activator receptor and its fragments in venous ulcers

    DEFF Research Database (Denmark)

    Ahmad, Anwar; Saha, Prakash; Evans, Colin

    2015-01-01

    functions that include chemotaxis, adhesion, and proliferation, which also have a role in wound healing. The aim of this study was to determine whether suPAR and its cleaved fragments are present in venous ulcers and whether their levels are associated with healing. METHODS: Ulcer exudates were collected...... from patients with venous leg ulcers (n = 30). Healing was defined as complete re-epithelialization within 6 months of compression therapy. Time-resolved fluorescence immunoassays were validated for quantification of suPAR and its fragments in ulcer exudates. The effect of exudates on keratinocyte...... with nonhealers (n = 21). Exudate from healing ulcers stimulated keratinocyte migration (P = .02), whereas depletion of suPAR from exudates resulted in cell apoptosis. CONCLUSIONS: We conclude that suPAR and its fragments are present in the environs of venous ulcers and may act as indicators of the propensity...

  2. Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors.

    Science.gov (United States)

    Murray, Christopher W; Berdini, Valerio; Buck, Ildiko M; Carr, Maria E; Cleasby, Anne; Coyle, Joseph E; Curry, Jayne E; Day, James E H; Day, Phillip J; Hearn, Keisha; Iqbal, Aman; Lee, Lydia Y W; Martins, Vanessa; Mortenson, Paul N; Munck, Joanne M; Page, Lee W; Patel, Sahil; Roomans, Susan; Smith, Kirsten; Tamanini, Emiliano; Saxty, Gordon

    2015-07-09

    The DDR1 and DDR2 receptor tyrosine kinases are activated by extracellular collagen and have been implicated in a number of human diseases including cancer. We performed a fragment-based screen against DDR1 and identified fragments that bound either at the hinge or in the back pocket associated with the DFG-out conformation of the kinase. Modeling based on crystal structures of potent kinase inhibitors facilitated the "back-to-front" design of potent DDR1/2 inhibitors that incorporated one of the DFG-out fragments. Further optimization led to low nanomolar, orally bioavailable inhibitors that were selective for DDR1 and DDR2. The inhibitors were shown to potently inhibit DDR2 activity in cells but in contrast to unselective inhibitors such as dasatinib, they did not inhibit proliferation of mutant DDR2 lung SCC cell lines.

  3. Microevolutionary Effects of Habitat Fragmentation on Plant-Animal Interactions

    OpenAIRE

    Francisco E. Fontúrbel; Maureen M. Murúa

    2014-01-01

    Plant-animal interactions are a key component for biodiversity maintenance, but they are currently threatened by human activities. Habitat fragmentation might alter ecological interactions due to demographic changes, spatial discontinuities, and edge effects. Also, there are less evident effects of habitat fragmentation that potentially alter selective forces and compromise the fitness of the interacting species. Changes in the mutualistic and antagonistic interactions in fragmented habitats ...

  4. Critical Features of Fragment Libraries for Protein Structure Prediction

    Science.gov (United States)

    dos Santos, Karina Baptista

    2017-01-01

    The use of fragment libraries is a popular approach among protein structure prediction methods and has proven to substantially improve the quality of predicted structures. However, some vital aspects of a fragment library that influence the accuracy of modeling a native structure remain to be determined. This study investigates some of these features. Particularly, we analyze the effect of using secondary structure prediction guiding fragments selection, different fragments sizes and the effect of structural clustering of fragments within libraries. To have a clearer view of how these factors affect protein structure prediction, we isolated the process of model building by fragment assembly from some common limitations associated with prediction methods, e.g., imprecise energy functions and optimization algorithms, by employing an exact structure-based objective function under a greedy algorithm. Our results indicate that shorter fragments reproduce the native structure more accurately than the longer. Libraries composed of multiple fragment lengths generate even better structures, where longer fragments show to be more useful at the beginning of the simulations. The use of many different fragment sizes shows little improvement when compared to predictions carried out with libraries that comprise only three different fragment sizes. Models obtained from libraries built using only sequence similarity are, on average, better than those built with a secondary structure prediction bias. However, we found that the use of secondary structure prediction allows greater reduction of the search space, which is invaluable for prediction methods. The results of this study can be critical guidelines for the use of fragment libraries in protein structure prediction. PMID:28085928

  5. Measurements of Fragmentation Photons with the PHENIX Detector

    OpenAIRE

    Hanks, Ali; Collaboration, for the PHENIX

    2009-01-01

    Direct photons associated with jets provide a direct measurement of the effects of energy loss on the fragmentation of the parton as it propagates through the medium. Perturbative QCD calculations describe the direct photon cross section well at next-to-leading order, predicting a significant contribution from photons produced through parton fragmentation. Non-perturbative quantities such as the photon fragmentation function, which is poorly constrained, lead to large theoretical uncertaintie...

  6. Critical Features of Fragment Libraries for Protein Structure Prediction.

    Science.gov (United States)

    Trevizani, Raphael; Custódio, Fábio Lima; Dos Santos, Karina Baptista; Dardenne, Laurent Emmanuel

    2017-01-01

    The use of fragment libraries is a popular approach among protein structure prediction methods and has proven to substantially improve the quality of predicted structures. However, some vital aspects of a fragment library that influence the accuracy of modeling a native structure remain to be determined. This study investigates some of these features. Particularly, we analyze the effect of using secondary structure prediction guiding fragments selection, different fragments sizes and the effect of structural clustering of fragments within libraries. To have a clearer view of how these factors affect protein structure prediction, we isolated the process of model building by fragment assembly from some common limitations associated with prediction methods, e.g., imprecise energy functions and optimization algorithms, by employing an exact structure-based objective function under a greedy algorithm. Our results indicate that shorter fragments reproduce the native structure more accurately than the longer. Libraries composed of multiple fragment lengths generate even better structures, where longer fragments show to be more useful at the beginning of the simulations. The use of many different fragment sizes shows little improvement when compared to predictions carried out with libraries that comprise only three different fragment sizes. Models obtained from libraries built using only sequence similarity are, on average, better than those built with a secondary structure prediction bias. However, we found that the use of secondary structure prediction allows greater reduction of the search space, which is invaluable for prediction methods. The results of this study can be critical guidelines for the use of fragment libraries in protein structure prediction.

  7. Nondestructive recovery and examination of bullet fragments from brain tissue.

    Science.gov (United States)

    Johnson, A C; Kinard, W D; Washington, W D

    1980-04-01

    A technique providing both analytical and toolmark results for lead fragments from bullets is discussed. It permits the nondestructive recovery of bullet fragments from soft cadaver tissue and was used with a plasma asher in an actual homicide case. The lead fragments are examined by neutron activation analysis (but other analytical techniques can be used) for their antimony and arsenic content and by microscopy for matching toolmarks.

  8. Minimum Conflict Individual Haplotyping from SNP Fragments and Related Genotype

    OpenAIRE

    Ling-Yun Wu; Rui-Sheng Wang; Xiang-Sun Zhang; Wei Zhang

    2006-01-01

    The Minimum Error Correction (MEC) is an important model for haplotype reconstruction from SNP fragments. However, this model is effective only when the error rate of SNP fragments is low. In this paper, we propose a new computational model called Minimum Conflict Individual Haplotyping (MCIH) as an extension to MEC. In contrast to the conventional approaches, the new model employs SNP fragment information and also related genotype information, thereby a high accurate inference can be expecte...

  9. Deformation, Fracture, and Fragmentation in Brittle Geologic Solids

    Science.gov (United States)

    2010-09-01

    Deformation, Fracture, and Fragmentation in Brittle Geologic Solids by J. D. Clayton ARL-RP-299 September 2010 A...Proving Ground, MD 21005-5066 ARL-RP-299 September 2010 Deformation, Fracture, and Fragmentation in Brittle Geologic Solids J. D. Clayton...2010 4. TITLE AND SUBTITLE Deformation, Fracture, and Fragmentation in Brittle Geologic Solids 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM

  10. A note on the self-similar solutions to the spontaneous fragmentation equation

    Science.gov (United States)

    Breschi, Giancarlo; Fontelos, Marco A.

    2017-05-01

    We provide a method to compute self-similar solutions for various fragmentation equations and use it to compute their asymptotic behaviours. Our procedure is applied to specific cases: (i) the case of mitosis, where fragmentation results into two identical fragments, (ii) fragmentation limited to the formation of sufficiently large fragments, and (iii) processes with fragmentation kernel presenting a power-like behaviour.

  11. Transverse momenta of helium fragments in gold fragmentation at 10.6 GeV/nucleon

    Energy Technology Data Exchange (ETDEWEB)

    Cherry, M.L.; Deines-Jones, P. [Dept. of Physics and Astranomy, Louisiana State Univ., Baton Rouge, LA (United States); Dabrowska, A. [The H. Niewodniczanski Inst. of Nuclear Physics, Cracow (Poland)] [and others; KLMM

    1996-12-31

    The transverse momentum (p{sub t}) distributions of helium fragments from gold fragmentation on different nuclei of nuclear emulsion have been measured and a clear increase of average p{sub t} with target mass is seen. The p{sub t} distributions can be parameterized by a sum of three exponential functions of the form {approx}exp(-p{sup 2}{sub t}/B{sub i}). The differences in p{sub t} distributions in interactions on different targets can be explained by different contributions of the three exponential functions. These contributions depend on the projectile breakup in the collision, and for a given degree of the projectile breakup do not depend on the target mass. (author) 12 refs, 8 figs, 4 tabs

  12. Oral lead bullet fragment exposure in northern bobwhite (Colinus virginianus).

    Science.gov (United States)

    Kerr, Richard; Holladay, Jeremy; Holladay, Steven; Tannenbaum, Lawrence; Selcer, Barbara; Meldrum, Blair; Williams, Susan; Jarrett, Timothy; Gogal, Robert

    2011-11-01

    Lead (Pb) is a worldwide environmental contaminant known to adversely affect multiple organ systems in both mammalian and avian species. In birds, a common route of exposure is via oral ingestion of lead particles. Data are currently lacking for the retention and clearance of Pb bullet fragments in gastrointestinal (GI) tract of birds while linking toxicity with blood Pb levels. In the present study, northern bobwhite quail fed a seed-based diet were orally gavaged with Pb bullet fragments (zero, one or five fragments/bird) and evaluated for rate of fragment clearance, and changes in peripheral blood, renal, immune, and gastrointestinal parameters. Based on radiographs, the majority of the birds cleared or absorbed the fragments by seven days, with the exception of one five-fragment bird which took between 7 and 14 days. Blood Pb levels were higher in males than females, which may be related to egg production in females. In males but not females, feed consumption, body weight gain, packed cell volume (PCV), plasma protein concentration, and δ-aminolevulinic acid dehydratase (δ-ALAD) activity were all adversely affected by five Pb fragments. Birds of both sexes that received a single Pb fragment displayed depressed δ-ALAD, suggesting altered hematologic function, while all birds dosed with five bullet fragments exhibited greater morbidity.

  13. Fluctuations and symmetry energy in nuclear fragmentation dynamics.

    Science.gov (United States)

    Colonna, M

    2013-01-25

    Within a dynamical description of nuclear fragmentation, based on the liquid-gas phase transition scenario, we explore the relation between neutron-proton density fluctuations and nuclear symmetry energy. We show that, along the fragmentation path, isovector fluctuations follow the evolution of the local density and approach an equilibrium value connected to the local symmetry energy. Higher-density regions are characterized by smaller average asymmetry and narrower isotopic distributions. This dynamical analysis points out that fragment final state isospin fluctuations can probe the symmetry energy of the density domains from which fragments originate.

  14. Habitat fragmentation and its lasting impact on Earth's ecosystems.

    Science.gov (United States)

    Haddad, Nick M; Brudvig, Lars A; Clobert, Jean; Davies, Kendi F; Gonzalez, Andrew; Holt, Robert D; Lovejoy, Thomas E; Sexton, Joseph O; Austin, Mike P; Collins, Cathy D; Cook, William M; Damschen, Ellen I; Ewers, Robert M; Foster, Bryan L; Jenkins, Clinton N; King, Andrew J; Laurance, William F; Levey, Douglas J; Margules, Chris R; Melbourne, Brett A; Nicholls, A O; Orrock, John L; Song, Dan-Xia; Townshend, John R

    2015-03-01

    We conducted an analysis of global forest cover to reveal that 70% of remaining forest is within 1 km of the forest's edge, subject to the degrading effects of fragmentation. A synthesis of fragmentation experiments spanning multiple biomes and scales, five continents, and 35 years demonstrates that habitat fragmentation reduces biodiversity by 13 to 75% and impairs key ecosystem functions by decreasing biomass and altering nutrient cycles. Effects are greatest in the smallest and most isolated fragments, and they magnify with the passage of time. These findings indicate an urgent need for conservation and restoration measures to improve landscape connectivity, which will reduce extinction rates and help maintain ecosystem services.

  15. Habitat specialization predicts genetic response to fragmentation in tropical birds.

    Science.gov (United States)

    Khimoun, Aurélie; Eraud, Cyril; Ollivier, Anthony; Arnoux, Emilie; Rocheteau, Vincent; Bely, Marine; Lefol, Emilie; Delpuech, Martin; Carpentier, Marie-Laure; Leblond, Gilles; Levesque, Anthony; Charbonnel, Anaïs; Faivre, Bruno; Garnier, Stéphane

    2016-08-01

    Habitat fragmentation is one of the most severe threats to biodiversity as it may lead to changes in population genetic structure, with ultimate modifications of species evolutionary potential and local extinctions. Nonetheless, fragmentation does not equally affect all species and identifying which ecological traits are related to species sensitivity to habitat fragmentation could help prioritization of conservation efforts. Despite the theoretical link between species ecology and extinction proneness, comparative studies explicitly testing the hypothesis that particular ecological traits underlies species-specific population structure are rare. Here, we used a comparative approach on eight bird species, co-occurring across the same fragmented landscape. For each species, we quantified relative levels of forest specialization and genetic differentiation among populations. To test the link between forest specialization and susceptibility to forest fragmentation, we assessed species responses to fragmentation by comparing levels of genetic differentiation between continuous and fragmented forest landscapes. Our results revealed a significant and substantial population structure at a very small spatial scale for mobile organisms such as birds. More importantly, we found that specialist species are more affected by forest fragmentation than generalist ones. Finally, our results suggest that even a simple habitat specialization index can be a satisfying predictor of genetic and demographic consequences of habitat fragmentation, providing a reliable practical and quantitative tool for conservation biology. © 2016 John Wiley & Sons Ltd.

  16. J/Psi Production from Electromagnetic Fragmentation in Z decay

    OpenAIRE

    Fleming, Sean

    1994-01-01

    The rate for $ Z^{0}\\to J/ \\psi + \\ell^{+}\\ell^{-} $ is suprisingly large with about one event for every million $Z^{0}$ decays. The reason for this is that there is a fragmentation contribution that is not suppressed by a factor of $M^{2}_{\\psi}/M^{2}_{Z}$. In the fragmentation limit $ M_{Z}\\to\\infty$ with $E_{\\psi}/M_{Z}$ fixed, the differential decay rate for $ Z^{0}\\to J/ \\psi + \\ell^{+}\\ell^{-} $ factors into electromagnetic decay rates and universal fragmentation functions. The fragment...

  17. The fragmentation of expanding shells III: Oligarchic accretion and the mass spectrum of fragments

    OpenAIRE

    Dale, James E.; Wunsch, Richard; Smith, Rowan J.; Whitworth, Anthony; Palous, Jan

    2010-01-01

    We use SPH simulations to investigate the gravitational fragmentation of expanding shells through the linear and non--linear regimes. The results are analysed using spherical harmonic decomposition to capture the initiation of structure during the linear regime; the potential-based method of Smith et al. (2009) to follow the development of clumps in the mildly non-linear regime; and sink particles to capture the properties of the final bound objects during the highly non-linear regime. In the...

  18. Effect of sperm DNA fragmentation on embryo development: clinical and biological aspects.

    Science.gov (United States)

    Alvarez Sedó, Cristian; Bilinski, Melina; Lorenzi, Daniela; Uriondo, Heydy; Noblía, Felicitas; Longobucco, Valeria; Lagar, Estefanía Ventimiglia; Nodar, Florencia

    2017-12-01

    The aim of this study was to investigate the effect of sperm DNA fragmentation on fertilization rate, embryo development (blastulation rate), and pregnancy outcomes for ICSI cycles performed in a cohort of couples using donor eggs and to assess the remaining embryos that were not transferred or frozen for apoptotic markers. Eighty-two women (egg recipients) were included in the study (2016) were included in the study. The recipients' mean age was 41.8±5.1 y/o (36-49), while the egg donors' mean age was 30.8±2.1 y/o (27-33). Even though donor egg cycles with frozen sperm samples are performed regularly in our center, 35 cycles were done using fresh sperm samples. The mean age of the males involved in the procedure was 40.1±5.2 y/o. Fertilization, blastulation, and pregnancy rates were assessed. The patients were divided into two groups, TUNEL fragmentation and blastulation rate. High levels of DNA fragmentation were associated with low blastulation and pregnancy rates (per transfer); however, fertilization rate was not affected. Samples with higher levels of DNA fragmentation were associated with higher levels of DNA fragmentation in blastomeres without activating the apoptotic pathway (9.1% vs. 15.9%) (pfragmentation activated the apoptotic pathway in higher levels than samples with TUNEL fragmentation was negatively correlated with blastulation and pregnancy rates even in good quality oocytes. High levels of DNA damage promote embryo arrest and induce the activation of the apoptotic pathway.

  19. DNA fragmentation in chicken spermatozoa during cryopreservation.

    Science.gov (United States)

    Gliozzi, T M; Zaniboni, L; Cerolini, S

    2011-06-01

    Semen cryopreservation is fundamental both for the practice of artificial insemination, and for the conservation of genetic resources in cryobanks; nevertheless, there is still not an efficient standard freezing procedure assuring a steady and suitable level of fertility in fowl, and consequently there is no systematic use of frozen semen in the poultry industry. This study examined changes in motility (CASA), cell membrane integrity (Ethidium Bromide (EtBr) exclusion procedure and stress test) and DNA fragmentation (neutral comet assay) in fowl spermatozoa before, during and after cryopreservation and storage at -196 °C. An optimized comet assay for chicken semen was studied and applied to the analyses. Semen collected from 18 Mericanel della Brianza (local Italian breed) male chicken breeders was frozen in pellets and thawed in a water bath at 60 °C. Measurements were performed on fresh semen soon after dilution, after equilibration with 6% dimethylacetamide at 4 °C (processed semen) and after thawing. Sperm DNA damage occurred during cryopreservation of chicken semen and the proportion of spermatozoa with damaged DNA significantly increased from 6.2% in fresh and 6.4% in processed semen to 19.8% in frozen-thawed semen. The proportion of DNA in the comet tail of damaged spermatozoa was also significantly affected by cryopreservation, with an increase found from fresh (26.3%) to frozen-thawed (30.9%) sperm, whereas processed semen (30.1%) didn't show significant differences. The proportion of total membrane damaged spermatozoa (EtBr exclusion procedure) did not increase by 4 °C equilibration time, and greatly and significantly increased by cryopreservation; the values recorded in fresh, processed and frozen semen were 2.9, 5.6, and 66.7% respectively. As regards the proportion of damaged cells in the stress test, all values differed significantly (7.1% fresh semen, 11.7% processed semen, 63.7% frozen semen). Total motility was not affected by equilibration (52

  20. Epidural catheter fragment entrapment: a case report

    Directory of Open Access Journals (Sweden)

    Mohammadi M

    2010-07-01

    Full Text Available "n Normal 0 false false false EN-US X-NONE AR-SA MicrosoftInternetExplorer4 st1":*{behavior:url(#ieooui } /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:Arial; mso-bidi-theme-font:minor-bidi;} Background: Epidural catheters are seldom difficult to remove from patients. The breakage of the catheters is uncommon, troublesome and occasionally dangerous. "n"nCase presentation: A lumbar epidural catheter inserted in a 17 year-old man for applying anesthesia for internal fixation of femur fracture and subsequent postoperative epidural analgesia. In the third postoperative day, during unsuccessful attempt for removing the catheter, it was broken and was retained in his back. A CT- scan was performed and shows a fragment of catheter in the sub- laminar ligament between L3 and L4 without any connection with epidural space. As the patient had no complaint the fractured fragment was left in site and he was just followed up in the clinic."n"nConclusion: The knowledge of practical method in locating the retained epidural catheter, and the indication for surgical removal are very important. CT- scan is useful in showing the mechanism and locating the epidural catheter entrapment and facilitating surgical follow-up.

  1. Plasminogen fragments K 1-3 and K 5 bind to different sites in fibrin fragment DD

    Directory of Open Access Journals (Sweden)

    T. V. Grinenko

    2016-06-01

    Full Text Available Specific plasminogen-binding sites of fibrin molecule are located in Аα148-160 regions of C-terminal domains. Plasminogen interaction with these sites initiates the activation process of proenzyme and subsequent fibrin lysis. In this study we investigated the binding of plasminogen fragments K 1-3 and K 5 with fibrin fragment DD and their effect on Glu-plasminogen interaction with DD. It was shown that the level of Glu-plasminogen binding to fibrin fragment DD is decreased by 50-60% in the presence of K 1-3 and K 5. Fragments K 1-3 and K 5 have high affinity to fibrin fragment DD (Kd is 0.02 for K 1-3 and 0.054 μМ for K 5. K 5 interaction is independent and K 1-3 is partly dependent on C-terminal lysine residues. K 1-3 interacts with complex of fragment DD-immobilized K 5 as well as K 5 with complex of fragment DD-immobilized K 1-3. The plasminogen fragments do not displace each other from binding sites located in fibrin fragment DD, but can compete for the interaction. The results indicate that fibrin fragment DD contains different binding sites for plasminogen kringle fragments K 1-3 and K 5, which can be located close to each other. The role of amino acid residues of fibrin molecule Аα148-160 region in interaction with fragments K 1-3 and K 5 is discussed.

  2. Plasminogen fragments K 1-3 and K 5 bind to different sites in fibrin fragment DD.

    Science.gov (United States)

    Grinenko, T V; Kapustianenko, L G; Yatsenko, T A; Yusova, O I; Rybachuk, V N

    2016-01-01

    Specific plasminogen-binding sites of fibrin molecule are located in Аα148-160 regions of C-terminal domains. Plasminogen interaction with these sites initiates the activation process of proenzyme and subsequent fibrin lysis. In this study we investigated the binding of plasminogen fragments K 1-3 and K 5 with fibrin fragment DD and their effect on Glu-plasminogen interaction with DD. It was shown that the level of Glu-plasminogen binding to fibrin fragment DD is decreased by 50-60% in the presence of K 1-3 and K 5. Fragments K 1-3 and K 5 have high affinity to fibrin fragment DD (Kd is 0.02 for K 1-3 and 0.054 μМ for K 5). K 5 interaction is independent and K 1-3 is partly dependent on C-terminal lysine residues. K 1-3 interacts with complex of fragment DD-immobilized K 5 as well as K 5 with complex of fragment DD-immobilized K 1-3. The plasminogen fragments do not displace each other from binding sites located in fibrin fragment DD, but can compete for the interaction. The results indicate that fibrin fragment DD contains different binding sites for plasminogen kringle fragments K 1-3 and K 5, which can be located close to each other. The role of amino acid residues of fibrin molecule Аα148-160 region in interaction with fragments K 1-3 and K 5 is discussed.

  3. Evaluating differences in forest fragmentation and restoration between western natural forests and southeastern plantation forests in the United States.

    Science.gov (United States)

    Ren, Xinyu; Lv, Yingying; Li, Mingshi

    2017-03-01

    Changes in forest ecosystem structure and functions are considered some of the research issues in landscape ecology. In this study, advancing Forman's theory, we considered five spatially explicit processes associated with fragmentation, including perforation, dissection, subdivision, shrinkage, and attrition, and two processes associated with restoration, i.e., increment and expansion processes. Following this theory, a forest fragmentation and restoration process model that can detect the spatially explicit processes and ecological consequences of forest landscape change was developed and tested in the current analysis. Using the National Land Cover Databases (2001, 2006 and 2011), the forest fragmentation and restoration process model was applied to US western natural forests and southeastern plantation forests to quantify and classify forest patch losses into one of the four fragmentation processes (the dissection process was merged into the subdivision process) and to classify the newly gained forest patches based on the two restoration processes. At the same time, the spatio-temporal differences in fragmentation and restoration patterns and trends between natural forests and plantations were further compared. Then, through overlaying the forest fragmentation/restoration processes maps with targeting year land cover data and land ownership vectors, the results from forest fragmentation and the contributors to forest restoration in federal and nonfederal lands were identified. Results showed that, in natural forests, the forest change patches concentrated around the urban/forest, cultivated/forest, and shrubland/forest interfaces, while the patterns of plantation change patches were scattered sparsely and irregularly. The shrinkage process was the most common type in forest fragmentation, and the average size was the smallest. Expansion, the most common restoration process, was observed in both natural forests and plantations and often occurred around the

  4. Release and characteristics of fungal fragments in various conditions

    Energy Technology Data Exchange (ETDEWEB)

    Mensah-Attipoe, Jacob [Department of Environmental Science, University of Eastern Finland, Yliopistonranta 1D, P. O. Box 1627, FI-70211 Kuopio (Finland); Saari, Sampo [Department of Physics, Tampere University of Technology, Korkeakoulunkatu 3, 33720 Tampere (Finland); Veijalainen, Anna-Maria; Pasanen, Pertti [Department of Environmental Science, University of Eastern Finland, Yliopistonranta 1D, P. O. Box 1627, FI-70211 Kuopio (Finland); Keskinen, Jorma [Department of Physics, Tampere University of Technology, Korkeakoulunkatu 3, 33720 Tampere (Finland); Leskinen, Jari T.T. [SIB Labs, University of Eastern Finland, Yliopistonranta 1E, P. O. Box 1627, FI-70211, Kuopio (Finland); Reponen, Tiina, E-mail: reponeta@ucmail.uc.edu [Department of Environmental Science, University of Eastern Finland, Yliopistonranta 1D, P. O. Box 1627, FI-70211 Kuopio (Finland); Department of Environmental Health, University of Cincinnati, P.O. Box 670056, Cincinnati, OH 45267-0056 (United States)

    2016-03-15

    Intact spores and submicrometer size fragments are released from moldy building materials during growth and sporulation. It is unclear whether all fragments originate from fungal growth or if small pieces of building materials are also aerosolized as a result of microbial decomposition. In addition, particles may be formed through nucleation from secondary metabolites of fungi, such as microbial volatile organic compounds (MVOCs). In this study, we used the elemental composition of particles to characterize the origin of submicrometer fragments released from materials contaminated by fungi. Particles from three fungal species (Aspergillus versicolor, Cladosporium cladosporioides and Penicillium brevicompactum), grown on agar, wood and gypsum board were aerosolized using the Fungal Spore Source Strength Tester (FSSST) at three air velocities (5, 16 and 27 m/s). Released spores (optical size, d{sub p} ≥ 0.8 μm) and fragments (d{sub p} ≤ 0.8 μm) were counted using direct-reading optical aerosol instruments. Particles were also collected on filters, and their morphology and elemental composition analyzed using scanning electron microscopes (SEMs) coupled with an Energy-Dispersive X-ray spectroscopy (EDX). Among the studied factors, air velocity resulted in the most consistent trends in the release of fungal particles. Total concentrations of both fragments and spores increased with an increase in air velocity for all species whereas fragment–spore (F/S) ratios decreased. EDX analysis showed common elements, such as C, O, Mg and Ca, for blank material samples and fungal growth. However, N and P were exclusive to the fungal growth, and therefore were used to differentiate biological fragments from non-biological ones. Our results indicated that majority of fragments contained N and P. Because we observed increased release of fragments with increased air velocities, nucleation of MVOCs was likely not a relevant process in the formation of fungal fragments. Based

  5. Ecological study of social fragmentation, poverty, and suicide

    Science.gov (United States)

    Whitley, Elise; Gunnell, David; Dorling, Daniel; Smith, George Davey

    1999-01-01

    Objectives To investigate the association between suicide and area based measures of deprivation and social fragmentation. Design Ecological study. Setting 633 parliamentary constituencies of Great Britain as defined in 1991. Main outcome measures Age and sex specific mortality rates for suicide and all other causes for 1981-92. Results Mortality from suicide and all other causes increased with increasing Townsend deprivation score, social fragmentation score, and abstention from voting in all age and sex groups. Suicide mortality was most strongly related to social fragmentation, whereas deaths from other causes were more closely associated with Townsend score. Constituencies with absolute increases in social fragmentation and Townsend scores between 1981 and 1991 tended to have greater increases in suicide rates over the same period. The relation between change in social fragmentation and suicide was largely independent of Townsend score, whereas the association with Townsend score was generally reduced after adjustment for social fragmentation. Conclusions Suicide rates are more strongly associated with measures of social fragmentation than with poverty at a constituency level. Key messagesPlace of residence may affect health, and mortality from most common diseases tends to be higher in areas characterised by low socioeconomic positionResearch dating back over 100 years suggests that social fragmentation may influencesuicideIn the 1980s and 1990s, parliamentary constituencies with high levels of social fragmentation had high rates of suicide, independent of deprivationConstituencies with the greatest increases in social fragmentation between 1981 and 1991 also had the greatest increases in suicide rates over the same periodAny targeting of suicide prevention may be more effective if aimed at socially fragmented rather than deprived areas PMID:10521194

  6. Sustained sleep fragmentation induces sleep homeostasis in mice

    KAUST Repository

    Baud, Maxime O.

    2015-04-01

    Study Objectives: Sleep fragmentation (SF) is an integral feature of sleep apnea and other prevalent sleep disorders. Although the effect of repetitive arousals on cognitive performance is well documented, the effects of long-term SF on electroencephalography (EEG) and molecular markers of sleep homeostasis remain poorly investigated. To address this question, we developed a mouse model of chronic SF and characterized its effect on EEG spectral frequencies and the expression of genes previously linked to sleep homeostasis including clock genes, heat shock proteins, and plasticity-related genes. Design: N/A. Setting: Animal sleep research laboratory. Participants : Sixty-six C57BL6/J adult mice. Interventions: Instrumental sleep disruption at a rate of 60/h during 14 days Measurements and Results: Locomotor activity and EEG were recorded during 14 days of SF followed by recovery for 2 days. Despite a dramatic number of arousals and decreased sleep bout duration, SF minimally reduced total quantity of sleep and did not significantly alter its circadian distribution. Spectral analysis during SF revealed a homeostatic drive for slow wave activity (SWA; 1-4 Hz) and other frequencies as well (4-40 Hz). Recordings during recovery revealed slow wave sleep consolidation and a transient rebound in SWA, and paradoxical sleep duration. The expression of selected genes was not induced following chronic SF. Conclusions: Chronic sleep fragmentation (SF) increased sleep pressure confirming that altered quality with preserved quantity triggers core sleep homeostasis mechanisms. However, it did not induce the expression of genes induced by sleep loss, suggesting that these molecular pathways are not sustainably activated in chronic diseases involving SF.

  7. The speed of range shifts in fragmented landscapes.

    Directory of Open Access Journals (Sweden)

    Jenny A Hodgson

    Full Text Available Species may be driven extinct by climate change, unless their populations are able to shift fast enough to track regions of suitable climate. Shifting will be faster as the proportion of suitable habitat in the landscape increases. However, it is not known how the spatial arrangement of habitat will affect the speed of range advance, especially when habitat is scarce, as is the case for many specialist species. We develop methods for calculating the speed of advance that are appropriate for highly fragmented, stochastic systems. We reveal that spatial aggregation of habitat tends to reduce the speed of advance throughout a wide range of species parameters: different dispersal distances and dispersal kernel shapes, and high and low extinction probabilities. In contrast, aggregation increases the steady-state proportion of habitat that is occupied (without climate change. Nonetheless, we find that it is possible to achieve both rapid advance and relatively high patch occupancy when the habitat has a "channeled" pattern, resembling corridors or chains of stepping stones. We adapt techniques from electrical circuit theory to predict the rate of advance efficiently for complex, realistic landscape patterns, whereas the rate cannot be predicted by any simple statistic of aggregation or fragmentation. Conservationists are already advocating corridors and stepping stones as important conservation tools under climate change, but they are vaguely defined and have so far lacked a convincing basis in fundamental population biology. Our work shows how to discriminate properties of a landscape's spatial pattern that affect the speed of colonization (including, but not limited to, patterns like corridors and chains of stepping stones, and properties that affect a species' probability of persistence once established. We can therefore point the way to better land use planning approaches, which will provide functional habitat linkages and also maintain local

  8. Fragmentation modeling of a resin bonded sand

    Science.gov (United States)

    Hilth, William; Ryckelynck, David

    2017-06-01

    Cemented sands exhibit a complex mechanical behavior that can lead to sophisticated models, with numerous parameters without real physical meaning. However, using a rather simple generalized critical state bonded soil model has proven to be a relevant compromise between an easy calibration and good results. The constitutive model formulation considers a non-associated elasto-plastic formulation within the critical state framework. The calibration procedure, using standard laboratory tests, is complemented by the study of an uniaxial compression test observed by tomography. Using finite elements simulations, this test is simulated considering a non-homogeneous 3D media. The tomography of compression sample gives access to 3D displacement fields by using image correlation techniques. Unfortunately these fields have missing experimental data because of the low resolution of correlations for low displacement magnitudes. We propose a recovery method that reconstructs 3D full displacement fields and 2D boundary displacement fields. These fields are mandatory for the calibration of the constitutive parameters by using 3D finite element simulations. The proposed recovery technique is based on a singular value decomposition of available experimental data. This calibration protocol enables an accurate prediction of the fragmentation of the specimen.

  9. A LTL Fragment for GR(1-Synthesis

    Directory of Open Access Journals (Sweden)

    Klaus Schneider

    2011-02-01

    Full Text Available The idea of automatic synthesis of reactive programs starting from temporal logic (LTL specifications is quite old, but was commonly thought to be infeasible due to the known double exponential complexity of the problem. However, new ideas have recently renewed the interest in LTL synthesis: One major new contribution in this area is the recent work of Piterman et al. who showed how polynomial time synthesis can be achieved for a large class of LTL specifications that is expressive enough to cover many practical examples. These LTL specifications are equivalent to omega-automata having a so-called GR(1 acceptance condition. This approach has been used to automatically synthesize implementations of real-world applications. To this end, manually written deterministic omega-automata having GR(1 conditions were used instead of the original LTL specifications. However, manually generating deterministic monitors is, of course, a hard and error-prone task. In this paper, we therefore present algorithms to automatically translate specifications of a remarkable large fragment of LTL to deterministic monitors having a GR(1 acceptance condition so that the synthesis algorithms can start with more readable LTL specifications.

  10. Gold fragmentation induced by stopped antiprotons

    CERN Document Server

    Lubinski, P.; Von Egidy, T.; Gulda, K.; Hartmann, F.J.; Jastrzebski, J.; Kurcewicz, W.; Pienkowski, L.; Stolarz, A.; Trzcinska, A.

    2002-01-01

    A natural gold target was irradiated with the antiproton beam from the Low Energy Antiproton Ring at CERN. Antiprotons of 200 MeV/c momentum were stopped in a thick target, products of their annihilations on Au nuclei were detected using the off-line gamma-ray spectroscopy method. In total, yields for 114 residual nuclei were determined, providing a data set to deduce the complete mass and charge distribution of all products with A > 20 from a fitting procedure. The contribution of evaporation and fission decay modes to the total reaction cross section as well as the mean mass loss were estimated. The fission probability for Au absorbing antiprotons at rest was determined to be equal to (3.8+-0.5)%, in good agreement with an estimation derived using other techniques. The mass-charge yield distribution was compared with the results obtained for proton and pion induced gold fragmentation. On the average, the energy released in pbar annihilation is similar to that introduced by ~ 1 GeV protons. However, compared...

  11. Physiognomy and Eschatology: Some More Fragments of 4Q561

    DEFF Research Database (Denmark)

    Holst, Søren; Høgenhaven, Jesper

    2006-01-01

    Text, translation and discussion of previously unpublished fragments of "4Q561 Physiognomy". The content of the newly published fragments is of a narrative, and possibly eschatological nature, in contradistinction to the physiognomic divination in the previously known ones, causing the authors to...

  12. Avian guild assemblages in forest fragments around Budongo ...

    African Journals Online (AJOL)

    The findings show that bird assemblages vary in their response to habitat fragmentation but within guilds the response to fragmentation can be consistent, and can make ecological sense. Forest bird conservation can therefore benefit from information on species ecology when deciding which bird species and which parts of ...

  13. Quantifying Urban Fragmentation under Economic Transition in Shanghai City, China

    Directory of Open Access Journals (Sweden)

    Heyuan You

    2015-12-01

    Full Text Available Urban fragmentation affects sustainability through multiple impacts on economic, social, and environmental cost. Characterizing the dynamics of urban fragmentation in relation to economic transition should provide implications for sustainability. However, rather few efforts have been made in this issue. Using the case of Shanghai (China, this paper quantifies urban fragmentation in relation to economic transition. In particular, urban fragmentation is quantified by a time-series of remotely sensed images and a set of landscape metrics; and economic transition is described by a set of indicators from three aspects (globalization, decentralization, and marketization. Results show that urban fragmentation presents an increasing linear trend. Multivariate regression identifies positive linear correlation between urban fragmentation and economic transition. More specifically, the relative influence is different for the three components of economic transition. The relative influence of decentralization is stronger than that of globalization and marketization. The joint influences of decentralization and globalization are the strongest for urban fragmentation. The demonstrated methodology can be applicable to other places after making suitable adjustment of the economic transition indicators and fragmentation metrics.

  14. Projectile fragmentation studies using F, Ne, and Na isotopes

    Science.gov (United States)

    Mazza, Maria; MoNA Collaboration

    2017-09-01

    Projectile fragmentation is one of the techniques used at nuclear science facilities around the world for the production and study of rare isotopes. In the inverse kinematics reaction, a heavy high energy primary beam impinges on a reaction target producing an excited pre-fragment that soon decays - in a time range between 10-9 and 10-21 s - by emission of neutrons and gamma rays. The result is a secondary beam of radioactive nuclei suited for each experiment's needs, but the short lifetime of the pre-fragments prevents direct observation. However, an indirect analysis can be conducted from the reaction products. Neutron multiplicities and the excitation energies of the final fragments are in fact related to the pre-fragments produced in the target and this relationship is expected to be enhanced for final fragments with mass number closest to the reacting beam. The experiment was performed at the National Superconducting Cyclotron Laboratory (NSCL), where a 32Mg beam at 86 MeV/u was impinged on a 9Be reaction target. The MoNA Collaboration measured neutron multiplicities and kinetic energy spectra for neutrons in coincidence with sodium, neon, and fluorine final fragments in order to study the reaction mechanisms in the production of specific pre-fragments.

  15. Characterization of Soil-Water Retention with Coarse Fragments in ...

    African Journals Online (AJOL)

    The presence of coarse fragments can have profound impact on soil moisture retention characteristics. The study was conducted to assess the effects of coarse fragments on the moisture retention characteristics of 16 soil series, developed over five different parent materials in the Densu basin. Soil profiles were excavated ...

  16. Who wants to conserve remaining forest fragments in the ...

    African Journals Online (AJOL)

    Contiguous forests in Madagascar are continuously converted into forest fragments due to deforestation, and dispersed into landscape mosaics dominated by agriculture. These fragments are of increasing importance for biodiversity conservation as well as for the well being of rural inhabitants, providing a high diversity of ...

  17. Cloning and expression of cell wall acid invertase gene fragment ...

    African Journals Online (AJOL)

    A fragment of invertase gene containing catalytic sites of cysteine was cloned from poinsettia (Euphorbia pulcherrima wild.) by using the polymerase chain reaction (PCR) method. The length of the fragment was 521 bp, encoding 173 amino acids and containing a part of open reading frames, but no intron. It had a high ...

  18. Production of a phage-displayed single chain variable fragment ...

    African Journals Online (AJOL)

    Purpose: To develop specific single chain variable fragments (scFv) against infectious bursal disease virus (IBDV) via phage display technology. Methods: Purified viruses were initially applied for iterative panning rounds of scFv phage display libraries. The binding ability of the selected scFv antibody fragments against the ...

  19. Public Values in Water Law : A Case of Substantive Fragmentation?

    NARCIS (Netherlands)

    Ambrus, Monika; Gilissen, Herman Kasper; van Kempen, Jasper JH

    2014-01-01

    Horizontal fragmentation, from a public-values perspective, is a quite well-documented phenomenon in international (water) law. However, the literature does not provide any insight into vertical or substantive fragmentation, i.e. differences in the protection of public values at the various

  20. Identifying protein domains by global analysis of soluble fragment data.

    Science.gov (United States)

    Bulloch, Esther M M; Kingston, Richard L

    2014-11-15

    The production and analysis of individual structural domains is a common strategy for studying large or complex proteins, which may be experimentally intractable in their full-length form. However, identifying domain boundaries is challenging if there is little structural information concerning the protein target. One experimental procedure for mapping domains is to screen a library of random protein fragments for solubility, since truncation of a domain will typically expose hydrophobic groups, leading to poor fragment solubility. We have coupled fragment solubility screening with global data analysis to develop an effective method for identifying structural domains within a protein. A gene fragment library is generated using mechanical shearing, or by uracil doping of the gene and a uracil-specific enzymatic digest. A split green fluorescent protein (GFP) assay is used to screen the corresponding protein fragments for solubility when expressed in Escherichia coli. The soluble fragment data are then analyzed using two complementary approaches. Fragmentation "hotspots" indicate possible interdomain regions. Clustering algorithms are used to group related fragments, and concomitantly predict domain location. The effectiveness of this Domain Seeking procedure is demonstrated by application to the well-characterized human protein p85α. Copyright © 2014 Elsevier Inc. All rights reserved.

  1. Habitat connectivity and fragmented nuthatch populations in agricultural landscapes

    NARCIS (Netherlands)

    Langevelde, van F.

    1999-01-01

    In agricultural landscapes, the habitat of many species is subject to fragmentation. When the habitat of a species is fragmented and the distances between patches of habitat are large relative to the movement distances of the species, it can be expected that the degree of habitat

  2. Adaptation to fragmentation: evolutionary dynamics driven by human influences.

    Science.gov (United States)

    Cheptou, Pierre-Olivier; Hargreaves, Anna L; Bonte, Dries; Jacquemyn, Hans

    2017-01-19

    Fragmentation-the process by which habitats are transformed into smaller patches isolated from each other-has been identified as a major threat for biodiversity. Fragmentation has well-established demographic and population genetic consequences, eroding genetic diversity and hindering gene flow among patches. However, fragmentation should also select on life history, both predictably through increased isolation, demographic stochasticity and edge effects, and more idiosyncratically via altered biotic interactions. While species have adapted to natural fragmentation, adaptation to anthropogenic fragmentation has received little attention. In this review, we address how and whether organisms might adapt to anthropogenic fragmentation. Drawing on selected case studies and evolutionary ecology models, we show that anthropogenic fragmentation can generate selection on traits at both the patch and landscape scale, and affect the adaptive potential of populations. We suggest that dispersal traits are likely to experience especially strong selection, as dispersal both enables migration among patches and increases the risk of landing in the inhospitable matrix surrounding them. We highlight that suites of associated traits are likely to evolve together. Importantly, we show that adaptation will not necessarily rescue populations from the negative effects of fragmentation, and may even exacerbate them, endangering the entire metapopulation.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'. © 2016 The Author(s).

  3. Fission fragment mass distributions via prompt γ-ray spectroscopy

    Indian Academy of Sciences (India)

    2015-07-24

    Jul 24, 2015 ... The distribution of fragment masses formed in nuclear fission is one of the most striking features of the process. Such measurements are very important to understand the shape evolution of the nucleus from ground state to scission through intermediate saddle points. The fission fragment mass distributions, ...

  4. Charge distribution in the ternary fragmentation of {sup 252}Cf

    Energy Technology Data Exchange (ETDEWEB)

    Senthil Kannan, M.T.; Balasubramaniam, M. [Bharathiar University, Department of Physics, Coimbatore (India)

    2017-08-15

    We present here, for the first time, a study on ternary fragmentation charge distribution of {sup 252}Cf using the convolution integral method and the statistical theory. The charge distribution for all possible charge combinations of a ternary breakup are grouped as a bin containing different mass partitions. Different bins corresponding to various third fragments with mass numbers from A{sub 3} = 16 to 84 are identified with the available experimental masses. The corresponding potential energy surfaces are calculated using the three cluster model for the two arrangements A{sub 1} + A{sub 2} + A{sub 3} and A{sub 1} + A{sub 3} + A{sub 2}. The ternary fragmentation yield values are calculated for the ternary combination from each bin possessing minimum potential energy. The yields of the resulting ternary combinations as a function of the charge numbers of the three fragments are analyzed for both the arrangements. The calculations are carried out at different excitation energies of the parent nucleus. For each excitation energy the temperature of the three fragments are iteratively computed conserving the total energy. The distribution of fragment temperatures corresponding to different excitation energies for some fixed third fragments are discussed. The presence of the closed shell nucleus Sn in the favourable ternary fragmentation is highlighted. (orig.)

  5. Fragmentation of protonated oligonucleotides by energetic photons and Cq+ ions

    NARCIS (Netherlands)

    Gonzalez-Magana, O.; Tiemens, M.; Reitsma, G.; Boschman, L.; Door, M.; Bari, S.; Lahaie, P. O.; Wagner, J. R.; Huels, M. A.; Hoekstra, R.; Schlathölter, Thomas

    2013-01-01

    The ionization and fragmentation of trapped protonated dGCAT oligonucleotides upon interaction with energetic photons (h nu = 10-570 eV) and keV Cq+ ions was investigated by means of time-of-flight mass spectrometry. The observed fragmentation patterns are dominated by protonated and nonprotonated

  6. Public Values in Water Law: A Case of Substantive Fragmentation?

    NARCIS (Netherlands)

    Ambrus, M.; Gilissen, Herman Kasper|info:eu-repo/dai/nl/314838732; van Kempen, Jasper|info:eu-repo/dai/nl/314011900

    2014-01-01

    Horizontal fragmentation, from a public-values perspective, is a quite well-documented phenomenon in international (water) law. However, the literature does not provide any insight into vertical or substantive fragmentation, i.e. differences in the protection of public values at the various

  7. Quantifying terrestrial habitat loss and fragmentation: A protocol

    Science.gov (United States)

    Kevin McGarigal; Samuel Cushman; Claudia Regan

    2005-01-01

    Anthropogenic habitat loss and fragmentation have been implicated as among the key drivers of the burgeoning global biodiversity crisis. In response, there is a growing mandate among natural resource managers to evaluate the impacts of proposed management actions on the extent and fragmentation of habitats. Unfortunately, few guidelines exist to help managers...

  8. Habitat fragmentation and the Burrowing Owls (Speotyto cunicularia) in Saskatchewan

    Science.gov (United States)

    Robert G. Warnock; Paul C. James

    1997-01-01

    The relationship between landscape (125,664 ha circular plots) fragmentation patterns and the spatial distribution of Burrowing Owls (Speotyto cunicularia) was investigated in the heavily fragmented grasslands of Saskatchewan. Data were collected from 152 Burrowing Owl sites and 250 random sites located on 1990 LANDSAT-TM satellite images and 1:250,...

  9. Session A6 Rangelands as dynamic systems — Fragmentation of ...

    African Journals Online (AJOL)

    Fragmentation is the breaking apart of habitat without incurring habitat loss — in grazed ecosystems this usually implies a diminished ability of large herbivores to access natural heterogeneity in vegetation and topography. As fragmentation occurs, ecosystems are simplified by breaking up interdependent spatial units into ...

  10. Modelling the negative effects of landscape fragmentation on habitat selection

    NARCIS (Netherlands)

    Langevelde, van F.

    2015-01-01

    Landscape fragmentation constrains movement of animals between habitat patches. Fragmentation may, therefore, limit the possibilities to explore and select the best habitat patches, and some animals may have to cope with low-quality patches due to these movement constraints. If so, these individuals

  11. The Progressive Fragmentation of 332P/Ikeya-Murakami

    Science.gov (United States)

    Kleyna, J. T.; Ye, Q.-Z.; Hui, M.-T.; Meech, K. J.; Wainscoat, R.; Micheli, M.; Keane, J. V.; Weaver, H. A.; Weryk, R.

    2016-08-01

    We describe 2016 January-April observations of the fragments of 332P/Ikeya-Murakami, a comet earlier observed in a 2010 October outburst. We present photometry of the fragments and perform simulations to infer the time of breakup. We argue that the eastern-most rapidly brightening fragment (F4) best corresponds to the original nucleus, rather than the initial bright fragment F1. We compute radial and tangential nongravitational parameters, A 1 = (1.5 ± 0.4) × 10-8 au day-2 and (7.2 ± 1.9) × 10-9 au day-2 both are consistent with zero at the 4σ level. Monte Carlo simulations indicate that the fragments were emitted on the outbound journey well after the 2010 outburst, with bright fragment F1 splitting in early 2014 and the fainter fragments within months of the 2016 January recovery. Western fragment F7 is the oldest, dating from 2011. We suggest that the delayed onset of the splitting is consistent with a self-propagating crystallization of water ice.

  12. Enabling short fragments for uncoordinated spread spectrum communication

    DEFF Research Database (Denmark)

    Ahmed, Naveed; Pöpper, Christina; Capkun, Srdjan

    2014-01-01

    Uncoordinated spread spectrum (USS) protocols have been proposed for anti-jamming communication in wireless settings without shared secrets. The existing USS protocols assume that fragments of hundreds of bits can be transmitted on different channels in order to identify fragments that belong...

  13. Fragmentation and momentum correlations in heavy-ion collisions

    Indian Academy of Sciences (India)

    Sakshi Gautam and Rajni Kant is very dilute. But, the fragments formed by the MST method will be highly unstable. (especially in central collisions) as there the two nucleons may not be well formed and therefore can be unstable and decay after a while. To filter out such unstable fragments, we impose another cut in terms of ...

  14. Fission fragment mass distributions via prompt γ-ray spectroscopy

    Indian Academy of Sciences (India)

    5 units. On the other hand, by employing the γ-ray spectroscopy, it is possible to estimate the yield of individual fission fragments. In this work, determination of the fission fragment mass distribution by employing prompt γ-ray spectroscopy is described along with the recent results on 238U(18O, f) and 238U(32S, f) systems.

  15. Simulation of natural fragmentation of rings cut from warheads

    Directory of Open Access Journals (Sweden)

    John F. Moxnes

    2015-12-01

    Full Text Available Natural fragmentation of warheads that detonates causes the casing of the warhead to split into various sized fragments through shear or radial fractures depending on the toughness, density, and grain size of the material. The best known formula for the prediction of the size distribution is the Mott formulae, which is further examined by Grady and Kipp by investigating more carefully the statistical most random way of portioning a given area into a number of entities. We examine the fragmentation behavior of radially expanding steel rings cut from a 25 mm warhead by using an in house smooth particle hydrodynamic (SPH simulation code called REGULUS. Experimental results were compared with numerical results applying varying particle size and stochastic fracture strain. The numerically obtained number of fragments was consistent with experimental results. Increasing expansion velocity of the rings increases the number of fragments. Statistical variation of the material parameters influences the fragment characteristics, especially for low expansion velocities. A least square regression fit to the cumulative number of fragments by applying a generalized Mott distribution shows that the shape parameter is around 4 for the rings, which is in contrast to the Mott distribution with a shape parameter of ½. For initially polar distributed particles, we see signs of a bimodal cumulative fragment distribution. Adding statistical variation in material parameters of the fracture model causes the velocity numerical solutions to become less sensitive to changes in resolution for Cartesian distributed particles.

  16. Quantum fluctuation effects on nuclear fragment and atomic cluster formation

    Energy Technology Data Exchange (ETDEWEB)

    Ohnishi, Akira [Hokkaido Univ., Sapporo (Japan). Dept. of Physics; Randrup, J.

    1997-05-01

    We investigate the nuclear fragmentation and atomic cluster formation by means of the recently proposed quantal Langevin treatment. It is shown that the effect of the quantal fluctuation is in the opposite direction in nuclear fragment and atomic cluster size distribution. This tendency is understood through the effective classical temperature for the observables. (author)

  17. Fragmentation and momentum correlations in heavy-ion collisions

    Indian Academy of Sciences (India)

    The role of momentum correlations in the production of light and medium mass fragments is studied by imposing momentum cut in the clusterization of the phase space. Our detailed investigation shows that momentum cut has a major role to play in the emission of fragments. A comparison with the experimental data is also ...

  18. Land fragmentation and its driving forces in China

    NARCIS (Netherlands)

    Tan, S.; Heerink, N.; Qu, F.

    2006-01-01

    Fragmentation of landholdings is commonly regarded as a major obstacle to agricultural production growth in China. This study analyses the factors contributing to land fragmentation, and uses household- and village-level data from 11 villages in Jiangxi Province to test these factors empirically.

  19. Analysis of fragmentations of coumarins in mass spectrometry using ...

    African Journals Online (AJOL)

    A good correlation was found between electronic charges of atoms and fragmentation processes. In the present study, another series of coumarins with nitrogenated moieties is used to verify the reliability of this method. KEY WORDS: 4,7-Disubstituted coumarins, Nitrogenated moiety, AM1, Electronic charge, Fragmentation, ...

  20. Complex transitive closure queries on a fragmented graph

    NARCIS (Netherlands)

    Houtsma, M.A.W.; Houtsma, Maurice A.W.; Apers, Peter M.G.; Ceri, Stefano; Abiteboul, Serge; Kanellakis, Paris C.

    1990-01-01

    In this paper we study the reformulation of transitive closure queries on a fragmented graph. We split a query into several subqueries, each requiring only a fragment of the graph. We prove this reformulation to be correct for shortest path and bill of material queries. Here we describe the

  1. Reattachment of dehydrated tooth fragments: Two case reports

    African Journals Online (AJOL)

    2014-07-14

    Jul 14, 2014 ... reviewed, and there was no remarkable report. The palatal gingiva was elevated by a flap surgery, and the mobile root fragment was removed. After checking the fracture lines, etch and dry adhesive (S3 Bond Plus, Kuraray, Japan) was applied to the tooth and the fragment with a brush by scrubbing for 20 s ...

  2. Cloning and expression of cell wall acid invertase gene fragment ...

    African Journals Online (AJOL)

    ONOS

    2010-01-25

    Jan 25, 2010 ... A fragment of invertase gene containing catalytic sites of cysteine was cloned from poinsettia. (Euphorbia pulcherrima wild.) by using the polymerase chain reaction (PCR) method. The length of the fragment was 521 bp, encoding 173 amino acids and containing a part of open reading frames, but no intron.

  3. Structure-guided fragment-based in silico drug design of dengue protease inhibitors

    Science.gov (United States)

    Knehans, Tim; Schüller, Andreas; Doan, Danny N.; Nacro, Kassoum; Hill, Jeffrey; Güntert, Peter; Madhusudhan, M. S.; Weil, Tanja; Vasudevan, Subhash G.

    2011-03-01

    An in silico fragment-based drug design approach was devised and applied towards the identification of small molecule inhibitors of the dengue virus (DENV) NS2B-NS3 protease. Currently, no DENV protease co-crystal structure with bound inhibitor and fully formed substrate binding site is available. Therefore a homology model of DENV NS2B-NS3 protease was generated employing a multiple template spatial restraints method and used for structure-based design. A library of molecular fragments was derived from the ZINC screening database with help of the retrosynthetic combinatorial analysis procedure (RECAP). 150,000 molecular fragments were docked to the DENV protease homology model and the docking poses were rescored using a target-specific scoring function. High scoring fragments were assembled to small molecule candidates by an implicit linking cascade. The cascade included substructure searching and structural filters focusing on interactions with the S1 and S2 pockets of the protease. The chemical space adjacent to the promising candidates was further explored by neighborhood searching. A total of 23 compounds were tested experimentally and two compounds were discovered to inhibit dengue protease (IC50 = 7.7 μM and 37.9 μM, respectively) and the related West Nile virus protease (IC50 = 6.3 μM and 39.0 μM, respectively). This study demonstrates the successful application of a structure-guided fragment-based in silico drug design approach for dengue protease inhibitors providing straightforward hit generation using a combination of homology modeling, fragment docking, chemical similarity and structural filters.

  4. A general approach to the screening and confirmation of tryptamines and phenethylamines by mass spectral fragmentation.

    Science.gov (United States)

    Chen, Bo-Hong; Liu, Ju-Tsung; Chen, Wen-Xiong; Chen, Hung-Ming; Lin, Cheng-Huang

    2008-01-15

    Certain characteristic fragmentations of tryptamines (indoleethylamine) and phenethylamines are described. Based on the GC-EI/MS, LC-ESI/MS and MALDI/TOFMS, the mass fragmentations of 13 standard compounds, including alpha-methyltryptamine (AMT), N,N-dimethyltryptamine (DMT), 5-methoxy-alpha-methyltryptamine (5-MeO-AMT), N,N-diethyltryptamine (DET), N,N-dipropyltryptamine (DPT), N,N-dibutyltryptamine (DBT), N,N-diisopropyltryptamine (DIPT), 5-methoxy-N,N-dimethyltryptamine (5-MeO-DMT), 5-methoxy-N,N-diisopropyltryptamine (5-MeO-DIPT), methamphetamine (MAMP), 3,4-methylenedioxyamphetamine (3,4-MDA), 3,4-methylenedioxymethamphetamine (3,4-MDMA) and 2-methylamino-1-(3,4-methylenedioxyphenyl)butane (MBDB), were compared. As a result, the parent ions of these analytes were hard to be obtained by GC/MS whereas the protonated molecular ions can be observed clearly by means of ESI/MS and MALDI/TOFMS. Furthermore, two major characteristic fragmentations, namely and alpha-cleavage ([M+H](+)-->[3-vinylindole](+)) and beta-cleavage ([M+H](+)-->[CH(2)N(+)R(N1)R(N2)]), are produced when the ESI and MALDI modes are used, respectively. In the case of ESI/MS, the fragment obtained from alpha-cleavage is the major process. In contrast to this, in the case of MALDI/TOFMS, the major fragment is produced via beta-cleavage. The ionization efficiency and fragments formed from either alpha- or beta-cleavages are closely related to the degree of alkylation of the side chain nitrogen in both cases.

  5. Structure-guided fragment-based in silico drug design of dengue protease inhibitors.

    Science.gov (United States)

    Knehans, Tim; Schüller, Andreas; Doan, Danny N; Nacro, Kassoum; Hill, Jeffrey; Güntert, Peter; Madhusudhan, M S; Weil, Tanja; Vasudevan, Subhash G

    2011-03-01

    An in silico fragment-based drug design approach was devised and applied towards the identification of small molecule inhibitors of the dengue virus (DENV) NS2B-NS3 protease. Currently, no DENV protease co-crystal structure with bound inhibitor and fully formed substrate binding site is available. Therefore a homology model of DENV NS2B-NS3 protease was generated employing a multiple template spatial restraints method and used for structure-based design. A library of molecular fragments was derived from the ZINC screening database with help of the retrosynthetic combinatorial analysis procedure (RECAP). 150,000 molecular fragments were docked to the DENV protease homology model and the docking poses were rescored using a target-specific scoring function. High scoring fragments were assembled to small molecule candidates by an implicit linking cascade. The cascade included substructure searching and structural filters focusing on interactions with the S1 and S2 pockets of the protease. The chemical space adjacent to the promising candidates was further explored by neighborhood searching. A total of 23 compounds were tested experimentally and two compounds were discovered to inhibit dengue protease (IC(50) = 7.7 μM and 37.9 μM, respectively) and the related West Nile virus protease (IC(50) = 6.3 μM and 39.0 μM, respectively). This study demonstrates the successful application of a structure-guided fragment-based in silico drug design approach for dengue protease inhibitors providing straightforward hit generation using a combination of homology modeling, fragment docking, chemical similarity and structural filters.

  6. Inter- and intra-laboratory standardization of TUNEL assay for assessment of sperm DNA fragmentation.

    Science.gov (United States)

    Ribeiro, S; Sharma, R; Gupta, S; Cakar, Z; De Geyter, C; Agarwal, A

    2017-05-01

    One of the challenges with the sperm DNA fragmentation results is the inconsistency and the large variability in the results obtained by different techniques. The terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay quantifies the incorporation of fluoresceinated dUTP into single- and double-strand DNA breaks by labeling the 3'-OH terminal with TdT. The goal of this study was optimize the TUNEL protocol for assessment of sperm DNA fragmentation by standardization of the method and comparison of the data across two reference laboratories (i) at Basel, Switzerland and (ii) Cleveland Clinic, Ohio, USA. Semen samples from 31 subjects grouped into three cohorts. Sperm DNA fragmentation was data measured by two experienced operators at two different laboratories using identical semen samples, assay kit, protocol and acquisition settings using identical flow cytometers (BD Accuri C6). No significant differences were observed between the duplicates in any of the experiments performed. By including an additional washing step after fixation in paraformaldehyde, a high correlation was seen between the two laboratories (r = 0.94). A strong positive correlation was observed between the average sperm DNA fragmentation rates (r = 0.719). The mean sperm DNA fragmentation measured in each laboratory was similar. Both flow cytometers were identical in their settings and performance. This inter- and intra-laboratory study establishes that TUNEL is a reproducible assay when utilizing a standardized staining protocol and flow cytometer acquisition settings. Standardization and consensual guidelines for TUNEL validate the assay and establishes TUNEL as a robust test for measuring sperm DNA fragmentation especially in a multicenter setting. © 2017 American Society of Andrology and European Academy of Andrology.

  7. Forest fragmentation and rhinocryptid nest predation in central Chile

    Science.gov (United States)

    Vergara, Pablo M.; Simonetti, Javier A.

    2003-12-01

    Fragmentation of forest landscapes can raise the intensity of nest predation by increasing the abundance and richness of generalist or introduced predators. Understory foraging birds, such as rhinocryptids, can be highly vulnerable to nest predation in fragmented landscapes because they often place their nests on the ground. Temperate deciduous forests in Chile have been intensively fragmented in the last centuries, causing changes in nest predator densities. We tested if predation of artificial nests, mimicking those of rhinocryptids, placed on and above ground was higher in the remnant fragments of central Chile due to an increase in predator abundance. The rate of nest predation in forest remnants was larger than in native continuous forest. Small mammals were the main nest predators. Despite high predation rates, the abundance of rhinocryptids is higher in forest remnants, suggesting that fragments might constitute ecological traps.

  8. Observation of different isoscaling behavior between emitted fragments and residues

    Energy Technology Data Exchange (ETDEWEB)

    Youngs, M., E-mail: mdyoungs@comp.tamu.edu [Cyclotron Institute, Texas A& M University, College Station, TX 77843 (United States); McIntosh, A.B.; Hagel, K. [Cyclotron Institute, Texas A& M University, College Station, TX 77843 (United States); Heilborn, L. [Cyclotron Institute, Texas A& M University, College Station, TX 77843 (United States); Chemistry Department, Texas A& M University, College Station, TX 77843 (United States); Huang, M. [Cyclotron Institute, Texas A& M University, College Station, TX 77843 (United States); Jedele, A.; Kohley, Z.; May, L.W. [Cyclotron Institute, Texas A& M University, College Station, TX 77843 (United States); Chemistry Department, Texas A& M University, College Station, TX 77843 (United States); McCleskey, E. [Cyclotron Institute, Texas A& M University, College Station, TX 77843 (United States); Zarrella, A.; Yennello, S.J. [Cyclotron Institute, Texas A& M University, College Station, TX 77843 (United States); Chemistry Department, Texas A& M University, College Station, TX 77843 (United States)

    2017-06-15

    The traditional isoscaling technique has been used to analyze all isotopically identified particles from {sup 70}Zn+{sup 70}Zn and {sup 64}Zn+{sup 64}Zn collisions at 35 MeV/u. Two additional techniques, using an energy-averaged ratio and using the data present in the tail of energy spectra, are compared to the traditional method and show similar results. Isoscaling fit parameters α and β are found both globally and for each individual series of constant Z and N. The data are then split up between emitted fragments and projectile-like fragments. Isoscaling values for the two different types of fragments are shown to be different, emphasizing the importance of experimentally distinguishing between projectile-like fragments and emitted fragments in order to achieve accurate isoscaling parameters.

  9. Fragment-based discovery of a potent NAMPT inhibitor.

    Science.gov (United States)

    Korepanova, Alla; Longenecker, Kenton L; Pratt, Steve D; Panchal, Sanjay C; Clark, Richard F; Lake, Marc; Gopalakrishnan, Sujatha M; Raich, Diana; Sun, Chaohong; Petros, Andrew M

    2017-12-12

    NAMPT expression is elevated in many cancers, making this protein a potential target for anticancer therapy. We have carried out both NMR based and TR-FRET based fragment screens against human NAMPT and identified six novel binders with a range of potencies. Co-crystal structures were obtained for two of the fragments bound to NAMPT while for the other four fragments force-field driven docking was employed to generate a bound pose. Based on structural insights arising from comparison of the bound fragment poses to that of bound FK866 we were able to synthetically elaborate one of the fragments into a potent NAMPT inhibitor. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Nuclear fragmentation measurements for hadrontherapy and space radiation protection

    Energy Technology Data Exchange (ETDEWEB)

    De Napoli, M. [INFN - Sezione di Catania (Italy); Agodi, C.; Blancato, A. A.; Cavallaro, M.; Cirrone, G. A. P.; Cuttone, G.; Sardina, D.; Scuderi, V. [INFN - Laboratori Nazionali del Sud (Italy); Battistoni, G. [INFN - Sezione di Milano (Italy); Bondi, M.; Cappuzzello, F.; Carbone, D.; Nicolosi, D.; Raciti, G.; Tropea, S. [INFN - Laboratori Nazionali del Sud, Italy and Dipartimento di Fisica e Astronomia, Universita degli Studi di Catania (Italy); Giacoppo, F. [Department of Physics, University of Oslo (Norway); Morone, M. C. [Dipartimento di Biopatologia e Diagnostica per Immagini, Universita di Roma Tor Vergata (Italy); Pandola, L. [INFN-Laboratori Nazionali del Gran Sasso (Italy); Rapisarda, E. [Nuclear and Radiation Physics Section, Katholieke Universiteit Leuven Celestijnenlaan Heverlee (Belgium); Romano, F. [INFN - Laboratori Nazionali del Sud (Italy) and Museo Storico della Fisica e Centro Studi e Ricerche E. Fermi Roma (Italy); and others

    2013-04-19

    Nuclear fragmentation measurements are necessary in hadrontherapy and space radiation protection, to predict the effects of the ion nuclear interactions within the human body. Nowadays, a very limited set of carbon fragmentation cross sections has been measured and in particular, to our knowledge, no double differential fragmentation cross sections at intermediate energies are available in literature. We have measured the double differential cross sections and the angular distributions of the secondary fragments produced in the {sup 12}C fragmentation at 62 AMeV on a thin carbon target. The experimental data have been also used to benchmark the prediction capability of the Geant4 Monte Carlo code at intermediate energies, where it was never tested before.

  11. Habitat fragmentation, climate change, and inbreeding in plants.

    Science.gov (United States)

    Leimu, Roosa; Vergeer, Philippine; Angeloni, Francesco; Ouborg, N Joop

    2010-05-01

    Habitat fragmentation and climate change are recognized as major threats to biodiversity. The major challenge for present day plant populations is how to adapt and cope with altered abiotic and biotic environments caused by climate change, when at the same time adaptive and evolutionary potential is decreased as habitat fragmentation reduces genetic variation and increases inbreeding. Although the ecological and evolutionary effects of fragmentation and climate change have been investigated separately, their combined effects remained largely unexplored. In this review, we will discuss the individual and joint effects of habitat fragmentation and climate change on plants and how the abilities and ways in which plants can respond and cope with climate change may be compromised due to habitat fragmentation.

  12. Quantification of projection angle in fragment generator warhead

    Directory of Open Access Journals (Sweden)

    K.D. Dhote

    2014-06-01

    Full Text Available Tactical Ballistic Missile (TBM class target neutralization by the fragment spray of a Fragment Generator Warhead (FGW calls for quantification of fragment projection angle scatter to finalize the end game engagement logic. For conventional axi-symmetric warhead, dispersion is assumed to be normal with a standard deviation of 30. However, such information is not available in case of FGW. Hence, a set of experiments are conducted to determine the dispersion of fragments. The experiments are conducted with a specific configuration of FGW in an identical arena to quantify the scatter and then verified its applicability to other configurations having a range of L/D and C/M ratios, and contoured fragmenting discs. From the experimental study, it is concluded that the scatter in projection angle follows normal distribution with a standard deviation of 0.75° at Chi-square significance level of 0.01(χ20.99.

  13. Policy Options to Reduce Fragmentation in the Pooling of Health Insurance Funds in Iran

    Science.gov (United States)

    Bazyar, Mohammad; Rashidian, Arash; Kane, Sumit; Vaez Mahdavi, Mohammad Reza; Akbari Sari, Ali; Doshmangir, Leila

    2016-01-01

    There are fragmentations in Iran’s health insurance system. Multiple health insurance funds exist, without adequate provisions for transfer or redistribution of cross subsidy among them. Multiple risk pools, including several private secondary insurance schemes, have resulted in a tiered health insurance system with inequitable benefit packages for different segments of the population. Also fragmentation might have contributed to inefficiency in the health insurance systems, a low financial protection against healthcare expenditures for the insured persons, high coinsurance rates, a notable rate of insurance coverage duplication, low contribution of well-funded institutes with generous benefit package to the public health insurance schemes, underfunding and severe financial shortages for the public funds, and a lack of transparency and reliable data and statistics for policy-making. We have conducted a policy analysis study, including qualitative interviews of key informants and document analysis. As a result we introduce three policy options: keeping the existing structural fragmentations of social health insurance (SHI)schemes but implementing a comprehensive "policy integration" strategy; consolidation of existing health insurance funds and creating a single national health insurance scheme; and reducing fragmentation by merging minor well-resourced funds together and creating two or three large insurance funds under the umbrella of the existing organizations. These policy options with their advantages and disadvantages are explained in the paper. PMID:27239868

  14. Policy Options to Reduce Fragmentation in the Pooling of Health Insurance Funds in Iran

    Directory of Open Access Journals (Sweden)

    Mohammad Bazyar

    2016-04-01

    Full Text Available There are fragmentations in Iran’s health insurance system. Multiple health insurance funds exist, without adequate provisions for transfer or redistribution of cross subsidy among them. Multiple risk pools, including several private secondary insurance schemes, have resulted in a tiered health insurance system with inequitable benefit packages for different segments of the population. Also fragmentation might have contributed to inefficiency in the health insurance systems, a low financial protection against healthcare expenditures for the insured persons, high coinsurance rates, a notable rate of insurance coverage duplication, low contribution of well-funded institutes with generous benefit package to the public health insurance schemes, underfunding and severe financial shortages for the public funds, and a lack of transparency and reliable data and statistics for policy-making. We have conducted a policy analysis study, including qualitative interviews of key informants and document analysis. As a result we introduce three policy options: keeping the existing structural fragmentations of social health insurance (SHI schemes but implementing a comprehensive “policy integration” strategy; consolidation of existing health insurance funds and creating a single national health insurance scheme; and reducing fragmentation by merging minor well-resourced funds together and creating two or three large insurance funds under the umbrella of the existing organizations. These policy options with their advantages and disadvantages are explained in the paper.

  15. Charmed-meson fragmentation functions with finite-mass corrections and their application in various processes

    Energy Technology Data Exchange (ETDEWEB)

    Kneesch, Torben

    2010-12-15

    We have calculated the single-inclusive production cross section of massive quarks in electron-positron-annihilation with next-to-leading order QCD corrections. With these results we have extracted fragmentation functions for the fragmentation from partons into D{sup 0}, D{sup +} and D{sup *} mesons, where we have used experimental data from the B factories Belle and CLEO and from the ALEPH and OPAL experiments at the LEP collider. In our analysis we have included the masses of c and b quarks and of the D mesons and tested the evolution of fragmentation functions with a global fit spanning the B factories' center-of-mass energy of {radical}(s)=10.5 GeV to LEP's run at the Z boson resonance at M{sub Z}. We have applied this fragmentation functions in deep inelastic scattering for comparisons with HERA data using parton cross sections from the literature available in program form. We have then modified this cross section to calculate predictions for deep inelastic two-photon-scattering. By applying the Weizsaecker-Williams spectrum on the real photon we have calculated predictions for LEP1, LEP2 and the future ILC experiments. For ILC we have also included a beamstrahlung spectrum. Finally we have calculated production cross sections for the planned e{gamma} mode of the ILC with the help of a Compton spectrum. (orig.)

  16. Gene flow and pathogen transmission among bobcats (Lynx rufus) in a fragmented urban landscape

    Science.gov (United States)

    Lee, Justin S.; Ruell, Emily W.; Boydston, Erin E.; Lyren, Lisa M.; Alonso, Robert S.; Troyer, Jennifer L.; Crooks, Kevin R.; VandeWoude, Sue

    2012-01-01

    Urbanization can result in the fragmentation of once contiguous natural landscapes into a patchy habitat interspersed within a growing urban matrix. Animals living in fragmented landscapes often have reduced movement among habitat patches because of avoidance of intervening human development, which potentially leads to both reduced gene flow and pathogen transmission between patches. Mammalian carnivores with large home ranges, such as bobcats (Lynx rufus), may be particularly sensitive to habitat fragmentation. We performed genetic analyses on bobcats and their directly transmitted viral pathogen, feline immunodeficiency virus (FIV), to investigate the effects of urbanization on bobcat movement. We predicted that urban development, including major freeways, would limit bobcat movement and result in genetically structured host and pathogen populations. We analysed molecular markers from 106 bobcats and 19 FIV isolates from seropositive animals in urban southern California. Our findings indicate that reduced gene flow between two primary habitat patches has resulted in genetically distinct bobcat subpopulations separated by urban development including a major highway. However, the distribution of genetic diversity among FIV isolates determined through phylogenetic analyses indicates that pathogen genotypes are less spatially structured--exhibiting a more even distribution between habitat fragments. We conclude that the types of movement and contact sufficient for disease transmission occur with enough frequency to preclude structuring among the viral population, but that the bobcat population is structured owing to low levels of effective bobcat migration resulting in gene flow. We illustrate the utility in using multiple molecular markers that differentially detect movement and gene flow between subpopulations when assessing connectivity.

  17. Policy Options to Reduce Fragmentation in the Pooling of Health Insurance Funds in Iran.

    Science.gov (United States)

    Bazyar, Mohammad; Rashidian, Arash; Kane, Sumit; Vaez Mahdavi, Mohammad Reza; Akbari Sari, Ali; Doshmangir, Leila

    2016-02-11

    There are fragmentations in Iran's health insurance system. Multiple health insurance funds exist, without adequate provisions for transfer or redistribution of cross subsidy among them. Multiple risk pools, including several private secondary insurance schemes, have resulted in a tiered health insurance system with inequitable benefit packages for different segments of the population. Also fragmentation might have contributed to inefficiency in the health insurance systems, a low financial protection against healthcare expenditures for the insured persons, high coinsurance rates, a notable rate of insurance coverage duplication, low contribution of well-funded institutes with generous benefit package to the public health insurance schemes, underfunding and severe financial shortages for the public funds, and a lack of transparency and reliable data and statistics for policy-making. We have conducted a policy analysis study, including qualitative interviews of key informants and document analysis. As a result we introduce three policy options: keeping the existing structural fragmentations of social health insurance (SHI)schemes but implementing a comprehensive "policy integration" strategy; consolidation of existing health insurance funds and creating a single national health insurance scheme; and reducing fragmentation by merging minor well-resourced funds together and creating two or three large insurance funds under the umbrella of the existing organizations. These policy options with their advantages and disadvantages are explained in the paper. © 2016 by Kerman University of Medical Sciences.

  18. Primary and secondary fragmentation of crystal-bearing intermediate magma

    Science.gov (United States)

    Jones, Thomas J.; McNamara, Keri; Eychenne, Julia; Rust, Alison C.; Cashman, Katharine V.; Scheu, Bettina; Edwards, Robyn

    2016-11-01

    Crystal-rich intermediate magmas are subjected to both primary and secondary fragmentation processes, each of which may produce texturally distinct tephra. Of particular interest for volcanic hazards is the extent to which each process contributes ash to volcanic plumes. One way to address this question is by fragmenting pyroclasts under controlled conditions. We fragmented pumice samples from Soufriere Hills Volcano (SHV), Montserrat, by three methods: rapid decompression in a shock tube-like apparatus, impact by a falling piston, and milling in a ball mill. Grain size distributions of the products reveal that all three mechanisms produce fractal breakage patterns, and that the fractal dimension increases from a minimum of 2.1 for decompression fragmentation (primary fragmentation) to a maximum of 2.7 by repeated impact (secondary fragmentation). To assess the details of the fragmentation process, we quantified the shape, texture and components of constituent ash particles. Ash shape analysis shows that the axial ratio increases during milling and that particle convexity increases with repeated impacts. We also quantify the extent to which the matrix is separated from the crystals, which shows that secondary processes efficiently remove adhering matrix from crystals, particularly during milling (abrasion). Furthermore, measurements of crystal size distributions before (using x-ray computed tomography) and after (by componentry of individual grain size classes) decompression-driven fragmentation show not only that crystals influence particular size fractions across the total grain size distribution, but also that free crystals are smaller in the fragmented material than in the original pumice clast. Taken together, our results confirm previous work showing both the control of initial texture on the primary fragmentation process and the contributions of secondary processes to ash formation. Critically, however, our extension of previous analyses to characterisation

  19. Observations of Titan 3C-4 Transtage Fragmentation Debris

    Science.gov (United States)

    Cowardin, Heather; Seitzer, P.; Abercromby, K.; Barker, E.; Cardona, T.; Krisko, P.; Lederer, S.

    2013-01-01

    The fragmentation of a Titan 3C-4 Transtage (1968-081) on 21 February 1992 is one of only two known break-ups in or near geosynchronous orbit. The original rocket body and 24 pieces of debris are currently being tracked by the US Space Surveillance Network (SSN). The rocket body (SSN# 3432) and several of the original fragments (SSN# 25000, 25001, 30000, and 33511) were observed in survey mode during 2004-2010 using the 0.6-m Michigan Orbital DEbris Survey Telescope (MODEST) in Chile using a broad R filter. This paper will present a size distribution for all calibrated magnitude data acquired on MODEST. Size distribution plots will also be shown using historical models for small fragmentation debris (down to 10 cm) believed to be associated with the Titan break-up. In November 2010, visible broadband photometry (Johnson/Kron-Cousins BVRI) was acquired with the 0.9-m Small and Moderate Aperture Research Telescope System (SMARTS) at the Cerro Tololo Inter-American Observatory (CTIO) in Chile on several Titan fragments (SSN# 25001, 33509, 33510) and the parent rocket body. Color index data will be used to determine the fragment brightness distribution and how the data compares to spacecraft materials measured in the laboratory using similar photometric measurement techniques. In 2012, the SSN added 16 additional fragments to the catalogue. MODEST acquired magnitude data on ten Titan fragments in late 2012 and early 2013. The magnitude distribution of all the observed fragments are analyzed as a function of time. In order to better characterize the breakup fragments spectral measurements were acquired on the original rocket body and five Titan fragments using the 6.5-m Magellan telescopes at Las Campanas Observatory in Chile. The telescopic spectra are compared with laboratory acquired spectra of materials (e.g., Aluminum and various paints) and categorized based on known absorption features for spacecraft materials.

  20. The Complex Stratigraphy of the Highland Crust in the Serenitatis Region of the Moon Inferred from Mineral Fragment Chemistry

    Science.gov (United States)

    Ryder, Graham; Norman, Marc D.; Taylor, G. Jeffrey

    1997-01-01

    Large impact basins are natural drill holes into the Moon, and their ejecta carries unique information about the rock types and stratigraphy of the lunar crust. We have conducted an electron microprobe study of mineral fragments in the poikilitic melt breccias collected from the Taurus Mountains at the Apollo 17 landing site. These breccias are virtually unanimously agreed to be impact melt produced in the Serenitatis impact event. They contain lithic fragments and much more abundant mineral fragments of crustal origin. We have made precise microprobe analyses of minor element abundances in fragments of olivine, pyroxene, and plagioclase to provide new information on the possible source rocks and the crustal stratigraphy in the Serenitatis region. These data were also intended to elucidate the nature of the cryptic geochemical component in breccias such as these with low-K Fra Mauro basalt compositions. We chose the finest-grained (i.e., most rapidly quenched) breccias for study, to avoid reacted and partly assimilated fragments as much as possible. Most of the mineral fragments appear to have been derived from rocks that would fall into the pristine igneous Mg-suite as represented by lithic fragments in the Apollo collection, or reasonable extensions of it. Gabbroic rocks were more abundant in the target stratigraphy than is apparent from the Apollo sample collection. Some pyroxene and plagiociase, but probably not much olivine, could be derived from feldspathic granulites, which are metamorphosed polymict breccias. Some mineral fragments are from previously unknown rocks. These include highly magnesian olivines (up to Fo(sub 94)), possibly volcanic in origin, that exacerbate the difficulty in explaining highly magnesian rocks in the lunar crust. It appears that some part of the lunar interior has an mg*(= 100 x Mg/(Mg/Fe) atomic) greater than the conventional bulk Moon value of 80-84. Other volcanic rocks, including mare basalts, and rapidly- cooled impact melt

  1. Social network fragmentation and community health.

    Science.gov (United States)

    Chami, Goylette F; Ahnert, Sebastian E; Kabatereine, Narcis B; Tukahebwa, Edridah M

    2017-09-05

    Community health interventions often seek to intentionally destroy paths between individuals to prevent the spread of infectious diseases. Immunizing individuals through direct vaccination or the provision of health education prevents pathogen transmission and the propagation of misinformation concerning medical treatments. However, it remains an open question whether network-based strategies should be used in place of conventional field approaches to target individuals for medical treatment in low-income countries. We collected complete friendship and health advice networks in 17 rural villages of Mayuge District, Uganda. Here we show that acquaintance algorithms, i.e., selecting neighbors of randomly selected nodes, were systematically more efficient in fragmenting all networks than targeting well-established community roles, i.e., health workers, village government members, and schoolteachers. Additionally, community roles were not good proxy indicators of physical proximity to other households or connections to many sick people. We also show that acquaintance algorithms were effective in offsetting potential noncompliance with deworming treatments for 16,357 individuals during mass drug administration (MDA). Health advice networks were destroyed more easily than friendship networks. Only an average of 32% of nodes were removed from health advice networks to reduce the percentage of nodes at risk for refusing treatment in MDA to below 25%. Treatment compliance of at least 75% is needed in MDA to control human morbidity attributable to parasitic worms and progress toward elimination. Our findings point toward the potential use of network-based approaches as an alternative to role-based strategies for targeting individuals in rural health interventions.

  2. Beyond the fragmentation threshold hypothesis: regime shifts in biodiversity across fragmented landscapes.

    Directory of Open Access Journals (Sweden)

    Renata Pardini

    Full Text Available Ecological systems are vulnerable to irreversible change when key system properties are pushed over thresholds, resulting in the loss of resilience and the precipitation of a regime shift. Perhaps the most important of such properties in human-modified landscapes is the total amount of remnant native vegetation. In a seminal study Andrén proposed the existence of a fragmentation threshold in the total amount of remnant vegetation, below which landscape-scale connectivity is eroded and local species richness and abundance become dependent on patch size. Despite the fact that species patch-area effects have been a mainstay of conservation science there has yet to be a robust empirical evaluation of this hypothesis. Here we present and test a new conceptual model describing the mechanisms and consequences of biodiversity change in fragmented landscapes, identifying the fragmentation threshold as a first step in a positive feedback mechanism that has the capacity to impair ecological resilience, and drive a regime shift in biodiversity. The model considers that local extinction risk is defined by patch size, and immigration rates by landscape vegetation cover, and that the recovery from local species losses depends upon the landscape species pool. Using a unique dataset on the distribution of non-volant small mammals across replicate landscapes in the Atlantic forest of Brazil, we found strong evidence for our model predictions--that patch-area effects are evident only at intermediate levels of total forest cover, where landscape diversity is still high and opportunities for enhancing biodiversity through local management are greatest. Furthermore, high levels of forest loss can push native biota through an extinction filter, and result in the abrupt, landscape-wide loss of forest-specialist taxa, ecological resilience and management effectiveness. The proposed model links hitherto distinct theoretical approaches within a single framework

  3. A rapid, strong, and convergent genetic response to urban habitat fragmentation in four divergent and widespread vertebrates.

    Science.gov (United States)

    Delaney, Kathleen Semple; Riley, Seth P D; Fisher, Robert N

    2010-09-16

    Urbanization is a major cause of habitat fragmentation worldwide. Ecological and conservation theory predicts many potential impacts of habitat fragmentation on natural populations, including genetic impacts. Habitat fragmentation by urbanization causes populations of animals and plants to be isolated in patches of suitable habitat that are surrounded by non-native vegetation or severely altered vegetation, asphalt, concrete, and human structures. This can lead to genetic divergence between patches and in turn to decreased genetic diversity within patches through genetic drift and inbreeding. We examined population genetic patterns using microsatellites in four common vertebrate species, three lizards and one bird, in highly fragmented urban southern California. Despite significant phylogenetic, ecological, and mobility differences between these species, all four showed similar and significant reductions in gene flow over relatively short geographic and temporal scales. For all four species, the greatest genetic divergence was found where development was oldest and most intensive. All four animals also showed significant reduction in gene flow associated with intervening roads and freeways, the degree of patch isolation, and the time since isolation. Despite wide acceptance of the idea in principle, evidence of significant population genetic changes associated with fragmentation at small spatial and temporal scales has been rare, even in smaller terrestrial vertebrates, and especially for birds. Given the striking pattern of similar and rapid effects across four common and widespread species, including a volant bird, intense urbanization may represent the most severe form of fragmentation, with minimal effective movement through the urban matrix.

  4. Comparing binding modes of analogous fragments using NMR in fragment-based drug design: application to PRDX5.

    Directory of Open Access Journals (Sweden)

    Clémentine Aguirre

    Full Text Available Fragment-based drug design is one of the most promising approaches for discovering novel and potent inhibitors against therapeutic targets. The first step of the process consists of identifying fragments that bind the protein target. The determination of the fragment binding mode plays a major role in the selection of the fragment hits that will be processed into drug-like compounds. Comparing the binding modes of analogous fragments is a critical task, not only to identify specific interactions between the protein target and the fragment, but also to verify whether the binding mode is conserved or differs according to the fragment modification. While X-ray crystallography is the technique of choice, NMR methods are helpful when this fails. We show here how the ligand-observed saturation transfer difference (STD experiment and the protein-observed 15N-HSQC experiment, two popular NMR screening experiments, can be used to compare the binding modes of analogous fragments. We discuss the application and limitations of these approaches based on STD-epitope mapping, chemical shift perturbation (CSP calculation and comparative CSP sign analysis, using the human peroxiredoxin 5 as a protein model.

  5. Validating fragment-based drug discovery for biological RNAs: lead fragments bind and remodel the TPP riboswitch specifically.

    Science.gov (United States)

    Warner, Katherine Deigan; Homan, Philip; Weeks, Kevin M; Smith, Alison G; Abell, Chris; Ferré-D'Amaré, Adrian R

    2014-05-22

    Thiamine pyrophosphate (TPP) riboswitches regulate essential genes in bacteria by changing conformation upon binding intracellular TPP. Previous studies using fragment-based approaches identified small molecule "fragments" that bind this gene-regulatory mRNA domain. Crystallographic studies now show that, despite having micromolar Kds, four different fragments bind the TPP riboswitch site-specifically, occupying the pocket that recognizes the aminopyrimidine of TPP. Unexpectedly, the unoccupied site that would recognize the pyrophosphate of TPP rearranges into a structure distinct from that of the cognate complex. This idiosyncratic fragment-induced conformation, also characterized by small-angle X-ray scattering and chemical probing, represents a possible mechanism for adventitious ligand discrimination by the riboswitch, and suggests that off-pathway conformations of RNAs can be targeted for drug development. Our structures, together with previous screening studies, demonstrate the feasibility of fragment-based drug discovery against RNA targets. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. Statistical universalities in fragmentation under scaling symmetry with a constant frequency of fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    Gorokhovski, M A [Laboratoire de Mecanique des Fluides et d' Acoustique, CNRS - Ecole Centrale de Lyon - INSA Lyon - Universite Claude Bernard Lyon 1, 36 Avenue Guy de Collongue, 69134 Ecully Cedex (France); Saveliev, V L [Institut of Ionosphere, Kamenskoe Plato, 050020 Almaty (Kazakhstan)], E-mail: mikhael.gorokhovski@ec-lyon.fr, E-mail: saveliev@topmail.kz

    2008-04-21

    This paper analyses statistical universalities that arise over time during constant frequency fragmentation under scaling symmetry. The explicit expression of particle-size distribution obtained from the evolution kinetic equation shows that, with increasing time, the initial distribution tends to the ultimate steady-state delta function through at least two intermediate universal asymptotics. The earlier asymptotic is the well-known log-normal distribution of Kolmogorov (1941 Dokl. Akad. Nauk. SSSR 31 99-101). This distribution is the first universality and has two parameters: the first and the second logarithmic moments of the fragmentation intensity spectrum. The later asymptotic is a power function (stronger universality) with a single parameter that is given by the ratio of the first two logarithmic moments. At large times, the first universality implies that the evolution equation can be reduced exactly to the Fokker-Planck equation instead of making the widely used but inconsistent assumption about the smallness of higher than second order moments. At even larger times, the second universality shows evolution towards a fractal state with dimension identified as a measure of the fracture resistance of the medium.

  7. Imaging three-body breakup involving two identical fragments

    Science.gov (United States)

    Feizollah, Peyman; Severt, T.; Jochim, Bethany; Berry, Ben; Kanaka Raju, P.; Zohrabi, M.; Rajput, Jyoti; Ablikim, U.; Kaderiya, B.; Ziaee, Farzaneh; Rudenko, A.; Rolles, D.; Carnes, K. D.; Esry, B. D.; Ben-Itzhak, I.

    2017-04-01

    We study the strong-field fragmentation of CO2 and CO2+ into C++O++O+ as examples of three-body breakup involving two identical fragments. This process can happen through concerted- or sequential-breakup mechanisms. In concerted breakup, the two O+ fragments play indistinguishable roles. In sequential breakup, however, one of the O+ fragments comes from the first fragmentation step of CO23+, and the other one comes from unimolecular dissociation of CO2+ in the second step. Therefore, in sequential breakup the two O+ fragments may be distinguished. A method is proposed that allows us to separate the concerted and sequential processes when the lifetime of the intermediate molecule is much longer than its rotational period. As a result, it is possible to experimentally distinguish the two O+ fragments in the sequential process. This work was supported by the Chemical Sciences, Geosciences, and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U. S. Department of Energy.

  8. Roles of tRNA-derived fragments in human cancers.

    Science.gov (United States)

    Sun, Chunxiao; Fu, Ziyi; Wang, Siwei; Li, Jun; Li, Yongfei; Zhang, Yanhong; Yang, Fan; Chu, Jiahui; Wu, Hao; Huang, Xiang; Li, Wei; Yin, Yongmei

    2018-02-01

    Transfer RNAs (tRNAs) were traditionally considered to participate in protein translation. Recent studies have identified a novel class of small non-coding RNAs (sncRNAs), produced by the specific cleavage of pre- and mature tRNAs, which have been named tRNA-derived fragments. tRNA-derived fragments are classified into diverse subtypes based on the different cleavage positions of the pre- and mature tRNAs. Recently, accumulated evidence has shown that these tRNA-derived fragments are frequently dysregulated in several cancers. Several tRNA-derived fragments were found to participate in cell proliferation, apoptosis, and invasive metastasis in several malignant human tumors. These dysregulated fragments are able to bind both Argonaute proteins and Piwi proteins to regulate gene expression. Some of the newly identified tRNA-derived fragments have been considered as the new biomarkers and therapeutic targets for the treatment of cancer. This review summarizes the biogenesis and biological functions of different subtypes of tRNA-derived fragments and discusses their molecular mechanisms in cancer progression. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Forest Fragmentation and Driving Forces in Yingkou, Northeastern China

    Directory of Open Access Journals (Sweden)

    Lei Zhang

    2017-03-01

    Full Text Available Forest fragmentation, the process of changing original large and intact forest patches into smaller and isolated areas, significantly influences the balance of surface physical environment, biodiversity, and species richness. Sufficient knowledge of forest fragmentation is necessary to maintain ecological balance and promote sustainable resource utilization. This study combines remote sensing, geographical information systems, and landscape metrics to assess forest fragmentation at landscape and pixel levels during different time periods (2000–2005, 2005–2010, and 2010–2015 in the Yingkou region. Spatial statistical analysis is also used to analyze the relationship between forest landscape fragmentation and its determinants (e.g., natural factors, socioeconomic factors, and proximity factors. Results show that forest patches became smaller, subdivided, and isolated during 2010–2015 at the total landscape level. Local changes occurred in the southwest of the study region or around the development area. Our data also indicate that shrinkage and subdivision were the main forest fragmentation processes during three times, and attrition became the main forest fragmentation process from 2010 to 2015. These changes were significantly influenced by natural factors (e.g., elevation and slope, proximity factors (e.g., distance to city and distance to province roads, and socioeconomic factors (e.g., gross domestic product. Results presented in this study provide valuable insights into the pattern and processes of forest fragmentation and present direct implications for the protection and reasonable utilization of forest resources.

  10. Geometry analysis for landscape fragmentation in coastal areas of China

    Science.gov (United States)

    Zhang, Tianhai; Yu, Ning; Mu, Hongdu; Tuo, Tao

    2017-08-01

    In recent years, the continuous expansion of urban-transport networks in China has aggravated the fragmentation of regional landscapes and led to the degradation of multiple ecological functions. In this study, Geographic Information System (GIS) techniques, patch size of fragmentation geometry were used to identify and monitor spatial distribution patterns of landscape fragmentation due to urban-transport networks in Fujian Province. This network has caused serious damage to regional ecological functions, and risks to the persistence of animal populations and biodiversity. This analysis revealed that the smallest patch class (0-15 km2) occurred with a much greater frequency than all other larger patch sizes. In the coastal cities of Xiamen, Zhangzhou and Quanzhou, the percentage of the number of patches less than 300 km2 was higher than in the western cities of Nanping, Sanming and Longyan, and the percentage of the area of patches less than 300 km2 was also higher. Based on a holistic identification of the structure of the network and its landscape division, we found that: Fujian Province has a spatial pattern of landscape fragmentation, with less fragmentation in western and northern regions, and most fragmentation in southern and eastern regions. Coastal regions and areas close to the main transport routes were more seriously fragmented and contained most of the small patches.

  11. Bootstrap embedding: An internally consistent fragment-based method

    Science.gov (United States)

    Welborn, Matthew; Tsuchimochi, Takashi; Van Voorhis, Troy

    2016-08-01

    Strong correlation poses a difficult problem for electronic structure theory, with computational cost scaling quickly with system size. Fragment embedding is an attractive approach to this problem. By dividing a large complicated system into smaller manageable fragments "embedded" in an approximate description of the rest of the system, we can hope to ameliorate the steep cost of correlated calculations. While appealing, these methods often converge slowly with fragment size because of small errors at the boundary between fragment and bath. We describe a new electronic embedding method, dubbed "Bootstrap Embedding," a self-consistent wavefunction-in-wavefunction embedding theory that uses overlapping fragments to improve the description of fragment edges. We apply this method to the one dimensional Hubbard model and a translationally asymmetric variant, and find that it performs very well for energies and populations. We find Bootstrap Embedding converges rapidly with embedded fragment size, overcoming the surface-area-to-volume-ratio error typical of many embedding methods. We anticipate that this method may lead to a low-scaling, high accuracy treatment of electron correlation in large molecular systems.

  12. DNA fragmentation in spermatozoa and its relationship with impaired spermatogenesis

    Directory of Open Access Journals (Sweden)

    S. A. Rudneva

    2014-01-01

    Full Text Available Sperm cells DNA fragmentation is one of the factors of male sub-/infertility discovered recently. At present, pathophysiological mechanisms that cause DNA fragmentation have not been studied completely. It is suggested that they may be caused with defects of chromatin remodeling, apoptosis, and oxidative stress. Spermiological examination was performed in 461 infertile men. With 23 % of the patients examined, the frequency of sperm cells DNA fragmentation comprises over 15 %, with that, 18 % of the patients demonstrated its range from 15.1 to 30 %, and with 5 % of patients, it exceeded 30 %. We found that the amount of sperm cells with fragmented DNA with severe forms of pathozoospermia is higher that with less manifested disturbances of spermatogenesis. Negative dynamics was revealed regarding the change in sperm concentration in men that have increased frequency of DNA fragmentation. Obtained results confirm the suggestion of the correlation between some semen parameters (concentration, motility, and morphology and sperm DNA fragmentation. Thus, one can state that the DNA fragmentation parameter of sperm cells has a certain diagnostic and forecasting value for married couples with reproduction disorders.

  13. DNA fragmentation in spermatozoa and its relationship with impaired spermatogenesis

    Directory of Open Access Journals (Sweden)

    S. A. Rudneva

    2015-02-01

    Full Text Available Sperm cells DNA fragmentation is one of the factors of male sub-/infertility discovered recently. At present, pathophysiological mechanisms that cause DNA fragmentation have not been studied completely. It is suggested that they may be caused with defects of chromatin remodeling, apoptosis, and oxidative stress. Spermiological examination was performed in 461 infertile men. With 23 % of the patients examined, the frequency of sperm cells DNA fragmentation comprises over 15 %, with that, 18 % of the patients demonstrated its range from 15.1 to 30 %, and with 5 % of patients, it exceeded 30 %. We found that the amount of sperm cells with fragmented DNA with severe forms of pathozoospermia is higher that with less manifested disturbances of spermatogenesis. Negative dynamics was revealed regarding the change in sperm concentration in men that have increased frequency of DNA fragmentation. Obtained results confirm the suggestion of the correlation between some semen parameters (concentration, motility, and morphology and sperm DNA fragmentation. Thus, one can state that the DNA fragmentation parameter of sperm cells has a certain diagnostic and forecasting value for married couples with reproduction disorders.

  14. Microevolutionary Effects of Habitat Fragmentation on Plant-Animal Interactions

    Directory of Open Access Journals (Sweden)

    Francisco E. Fontúrbel

    2014-01-01

    Full Text Available Plant-animal interactions are a key component for biodiversity maintenance, but they are currently threatened by human activities. Habitat fragmentation might alter ecological interactions due to demographic changes, spatial discontinuities, and edge effects. Also, there are less evident effects of habitat fragmentation that potentially alter selective forces and compromise the fitness of the interacting species. Changes in the mutualistic and antagonistic interactions in fragmented habitats could significantly influence the plant reproductive output and the fauna assemblage associated with. Fragmented habitats may trigger contemporary evolution processes and open new evolutionary opportunities. Interacting parties with a diffuse and asymmetric relationship are less susceptible to local extinction but more prone to evolve towards new interactions or autonomy. However, highly specialized mutualisms are likely to disappear. On the other hand, ecological interactions may mutually modulate their response in fragmented habitats, especially when antagonistic interactions disrupt mutualistic ones. Ecoevolutionary issues of habitat fragmentation have been little explored, but the empiric evidence available suggests that the complex modification of ecological interactions in fragmented habitats might lead to nonanalogous communities on the long term.

  15. Causes and consequences of habitat fragmentation in river networks.

    Science.gov (United States)

    Fuller, Matthew R; Doyle, Martin W; Strayer, David L

    2015-10-01

    Increases in river fragmentation globally threaten freshwater biodiversity. Rivers are fragmented by many agents, both natural and anthropogenic. We review the distribution and frequency of these major agents, along with their effects on connectivity and habitat quality. Most fragmentation research has focused on terrestrial habitats, but theories and generalizations developed in terrestrial habitats do not always apply well to river networks. For example, terrestrial habitats are usually conceptualized as two-dimensional, whereas rivers often are conceptualized as one-dimensional or dendritic. In addition, river flow often leads to highly asymmetric effects of barriers on habitat and permeability. New approaches tailored to river networks can be applied to describe the network-wide effects of multiple barriers on both connectivity and habitat quality. The net effects of anthropogenic fragmentation on freshwater biodiversity are likely underestimated, because of time lags in effects and the difficulty of generating a single, simple signal of fragmentation that applies to all aquatic species. We conclude by presenting a decision tree for managing freshwater fragmentation, as well as some research horizons for evaluating fragmented riverscapes. © 2015 New York Academy of Sciences.

  16. Fragmentation mechanisms of cytosine, adenine and guanine ionized bases.

    Science.gov (United States)

    Sadr-Arani, Leila; Mignon, Pierre; Chermette, Henry; Abdoul-Carime, Hassan; Farizon, Bernadette; Farizon, Michel

    2015-05-07

    The different fragmentation channels of cytosine, adenine and guanine have been studied through DFT calculations. The electronic structure of bases, their cations, and the fragments obtained by breaking bonds provides a good understanding of the fragmentation process that can complete the experimental approach. The calculations allow assigning various fragments to the given peaks. The comparison between the energy required for the formation of fragments and the peak intensity in the mass spectrum is used. For cytosine and guanine the elimination of the HNCO molecule is a major route of dissociation, while for adenine multiple loss of HCN or HNC can be followed up to small fragments. For cytosine, this corresponds to the initial bond cleavage of N3-C4/N1-C2, which represents the main dissociation route. For guanine the release of HNCO is obtained through the N1-C2/C5-C6 bond cleavage (reverse order also possible) leading to the largest peak of the spectrum. The corresponding energies of 3.5 and 3.9 eV are typically in the range available in the experiments. The loss of NH3 or HCN is also possible but requires more energy. For adenine, fragmentation consists of multiple loss of the HCN molecule and the main route corresponding to HC8N9 loss is followed by the release of HC2N1.

  17. Global patterns of fragmentation and connectivity of mammalian carnivore habitat.

    Science.gov (United States)

    Crooks, Kevin R; Burdett, Christopher L; Theobald, David M; Rondinini, Carlo; Boitani, Luigi

    2011-09-27

    Although mammalian carnivores are vulnerable to habitat fragmentation and require landscape connectivity, their global patterns of fragmentation and connectivity have not been examined. We use recently developed high-resolution habitat suitability models to conduct comparative analyses and to identify global hotspots of fragmentation and connectivity for the world's terrestrial carnivores. Species with less fragmentation (i.e. more interior high-quality habitat) had larger geographical ranges, a greater proportion of habitat within their range, greater habitat connectivity and a lower risk of extinction. Species with higher connectivity (i.e. less habitat isolation) also had a greater proportion of high-quality habitat, but had smaller, not larger, ranges, probably reflecting shorter distances between habitat patches for species with restricted distributions; such species were also more threatened, as would be expected given the negative relationship between range size and extinction risk. Fragmentation and connectivity did not differ among Carnivora families, and body mass was associated with connectivity but not fragmentation. On average, only 54.3 per cent of a species' geographical range comprised high-quality habitat, and more troubling, only 5.2 per cent of the range comprised such habitat within protected areas. Identification of global hotspots of fragmentation and connectivity will help guide strategic priorities for carnivore conservation.

  18. Genetic consequences of habitat fragmentation during a range expansion.

    Science.gov (United States)

    Mona, S; Ray, N; Arenas, M; Excoffier, L

    2014-03-01

    We investigate the effect of habitat fragmentation on the genetic diversity of a species experiencing a range expansion. These two evolutionary processes have not been studied yet, at the same time, owing to the difficulties of deriving analytic results for non-equilibrium models. Here we provide a description of their interaction by using extensive spatial and temporal coalescent simulations and we suggest guidelines for a proper genetic sampling to detect fragmentation. To model habitat fragmentation, we simulated a two-dimensional lattice of demes partitioned into groups (patches) by adding barriers to dispersal. After letting a population expand on this grid, we sampled lineages from the lattice at several scales and studied their coalescent history. We find that in order to detect fragmentation, one needs to extensively sample at a local level rather than at a landscape level. This is because the gene genealogy of a scattered sample is less sensitive to the presence of genetic barriers. Considering the effect of temporal changes of fragmentation intensities, we find that at least 10, but often >100, generations are needed to affect local genetic diversity and population structure. This result explains why recent habitat fragmentation does not always lead to detectable signatures in the genetic structure of populations. Finally, as expected, long-distance dispersal increases local genetic diversity and decreases levels of population differentiation, efficiently counteracting the effects of fragmentation.

  19. Prolonged incubation of processed human spermatozoa will increase DNA fragmentation.

    Science.gov (United States)

    Nabi, A; Khalili, M A; Halvaei, I; Roodbari, F

    2014-05-01

    One of the causes of failure in ART is sperm DNA fragmentation which may be associated with long period of spermatozoa incubation at 37 °C. The objective was to evaluate the rate of sperm DNA fragmentation using the sperm chromatin dispersion (SCD) test after swim-up at different time intervals prior to use. In this prospective study, 21 normozoospermic specimens were analysed. The samples were incubated at 37 °C after preparation by direct swim-up. DNA fragmentation was assessed at different time intervals (0, 1, 2 and 3 h) using SCD test. Spermatozoa with no DNA fragmentation showed large- or medium-sized halos, and sperm cells with DNA fragmentation showed either a small halo or no halo. The rates of normal morphology and progressive motility after sperm processing were 72.33 ± 2.53% and 90 ± 1.02%, respectively. The rate of sperm DNA fragmentation was significantly higher after 2 h (8.81 ± 0.93%, P = 0.004) and 3 h (10.76 ± 0.89%, P fragmentation. Therefore, sperm samples intended for ART procedures should be used within 2 h of incubation at 37 °C. © 2013 Blackwell Verlag GmbH.

  20. Advancement of magma fragmentation by inhomogeneous bubble distribution.

    Science.gov (United States)

    Kameda, M; Ichihara, M; Maruyama, S; Kurokawa, N; Aoki, Y; Okumura, S; Uesugi, K

    2017-12-01

    Decompression times reported in previous studies suggest that thoroughly brittle fragmentation is unlikely in actual explosive volcanic eruptions. What occurs in practice is brittle-like fragmentation, which is defined as the solid-like fracture of a material whose bulk rheological properties are close to those of a fluid. Through laboratory experiments and numerical simulation, the link between the inhomogeneous structure of bubbles and the development of cracks that may lead to brittle-like fragmentation was clearly demonstrated here. A rapid decompression test was conducted to simulate the fragmentation of a specimen whose pore morphology was revealed by X-ray microtomography. The dynamic response during decompression was observed by high-speed photography. Large variation was observed in the responses of the specimens even among specimens with equal bulk rheological properties. The stress fields of the specimens under decompression computed by finite element analysis shows that the presence of satellite bubbles beneath a large bubble induced the stress concentration. On the basis of the obtained results, a new mechanism for brittle-like fragmentation is proposed. In the proposed scenario, the second nucleation of bubbles near the fragmentation surface is an essential process for the advancement of fragmentation in an upward magma flow in a volcanic conduit.

  1. Habitat Fragmentation and Native Bees: a Premature Verdict?

    Directory of Open Access Journals (Sweden)

    James H. Cane

    2001-06-01

    Full Text Available Few studies directly address the consequences of habitat fragmentation for communities of pollinating insects, particularly for the key pollinator group, bees (Hymenoptera: Apiformes. Bees typically live in habitats where nesting substrates and bloom are patchily distributed and spatially dissociated. Bee studies have all defined habitat fragments as remnant patches of floral hosts or forests, overlooking the nesting needs of bees. Several authors conclude that habitat fragmentation is broadly deleterious, but their own data show that some native species proliferate in sampled fragments. Other studies report greater densities and comparable diversities of native bees at flowers in some fragment size classes relative to undisrupted habitats, but find dramatic shifts in species composition. Insightful studies of habitat fragmentation and bees will consider fragmentation, alteration, and loss of nesting habitats, not just patches of forage plants, as well as the permeability of the surrounding matrix to interpatch movement. Inasmuch as the floral associations and nesting habits of bees are often attributes of species or subgenera, ecological interpretations hinge on authoritative identifications. Study designs must accommodate statistical problems associated with bee community samples, especially non-normal data and frequent zero values. The spatial scale of fragmentation must be appreciated: bees of medium body size can regularly fly 1-2 km from nest site to forage patch. Overall, evidence for prolonged persistence of substantial diversity and abundances of native bee communities in habitat fragments of modest size promises practical solutions for maintaining bee populations. Provided that reserve selection, design, and management can address the foraging and nesting needs of bees, networks of even small reserves may hold hope for sustaining considerable pollinator diversity and the ecological services pollinators provide.

  2. Life history strategy influences parasite responses to habitat fragmentation.

    Science.gov (United States)

    Froeschke, Götz; van der Mescht, Luther; McGeoch, Melodie; Matthee, Sonja

    2013-12-01

    Anthropogenic habitat use is a major threat to biodiversity and is known to increase the abundance of generalist host species such as rodents, which are regarded as potential disease carriers. Parasites have an intimate relationship with their host and the surrounding environment and it is expected that habitat fragmentation will affect parasite infestation levels. We investigated the effect of habitat fragmentation on the ecto- and endoparasitic burdens of a broad niche small mammal, Rhabdomys pumilio, in the Western Cape Province, South Africa. Our aim was to look at the effects of fragmentation on different parasite species with diverse life history characteristics and to determine whether general patterns can be found. Sampling took place within pristine lowland (Fynbos/Renosterveld) areas and at fragmented sites surrounded and isolated by agricultural activities. All arthropod ectoparasites and available gastrointestinal endoparasites were identified. We used conditional autoregressive models to investigate the effects of habitat fragmentation on parasite species richness and abundance of all recovered parasites. Host density and body size were larger in the fragments. Combined ecto- as well as combined endoparasite taxa showed higher parasite species richness in fragmented sites. Parasite abundance was generally higher in the case of R. pumilio individuals in fragmented habitats but it appears that parasites that are more permanently associated with the host's body and those that are host-specific show the opposite trend. Parasite life history is an important factor that needs to be considered when predicting the effects of habitat fragmentation on parasite and pathogen transmission. Copyright © 2013 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

  3. Gene Prediction in Metagenomic Fragments with Deep Learning

    Directory of Open Access Journals (Sweden)

    Shao-Wu Zhang

    2017-01-01

    Full Text Available Next generation sequencing technologies used in metagenomics yield numerous sequencing fragments which come from thousands of different species. Accurately identifying genes from metagenomics fragments is one of the most fundamental issues in metagenomics. In this article, by fusing multifeatures (i.e., monocodon usage, monoamino acid usage, ORF length coverage, and Z-curve features and using deep stacking networks learning model, we present a novel method (called Meta-MFDL to predict the metagenomic genes. The results with 10 CV and independent tests show that Meta-MFDL is a powerful tool for identifying genes from metagenomic fragments.

  4. Gross Properties and Isotopic Phenomena in Spectator Fragmentation

    Science.gov (United States)

    Sfienti, C.; De Napoli, M.; Adrich, P.; Aumann, T.; Bacri, C. O.; Barczyk, T.; Bassini, R.; Bianchin, S.; Boiano, C.; Botvina, A. S.; Boudard, A.; Brzychczyk, J.; Chbihi, A.; Cibor, J.; Czech, B.; Ducret, J.-E.; Emling, H.; Frankland, J.; Hellström, M.; Henzlova, D.; Kezzar, K.; Immé, G.; Iori, I.; Johansson, H.; Lafriakh, A.; Le Fèvre, A.; Le Gentil, E.; Leifels, Y.; Lynch, W. G.; Lühning, J.; Łukasik, J.; Lynen, U.; Majka, Z.; Mocko, M.; Müller, W. F. J.; Mykulyak, A.; Orth, H.; Otte, A. N.; Palit, R.; Pawlowski, P.; Pullia, A.; Raciti, G.; Rapisarda, E.; Sann, H.; Schwarz, C.; Simon, H.; Sümmerer, K.; Trautmann, W.; Volant, C.; Wallace, M.; Weick, H.; Wiechula, J.; Wieloch, A.; Zwieglinski, B.

    2007-05-01

    A systematic study of isotopic effects in the break-up of projectile spectators at relativistic energies has been performed with the ALADiN spectrometer at the GSI laboratory. Searching for signals of criticality in the fragment production we have applied the model-independent universal fluctuations theory already proposed to track criticality signals in multifragmentation to our data. The fluctuation of the largest fragment charge and of the asymmetry of the two and three largest fragments and their bimodal distribution have also been analysed.

  5. Position-sensitive spectroscopy of {sup 252}Cf fission fragments

    Energy Technology Data Exchange (ETDEWEB)

    Granja, C. [Institute of Experimental and Applied Physics, Czech Technical University, 128 00 Prague 2 (Czech Republic)]. E-mail: carlos.granja@utef.cvut.cz; Vykydal, Z. [Institute of Experimental and Applied Physics, Czech Technical University, 128 00 Prague 2 (Czech Republic); Kopatch, Y. [Joint Institute for Nuclear Research, 141 980 Dubna (Russian Federation); Jakubek, J. [Institute of Experimental and Applied Physics, Czech Technical University, 128 00 Prague 2 (Czech Republic); Pospisil, S. [Institute of Experimental and Applied Physics, Czech Technical University, 128 00 Prague 2 (Czech Republic); Telezhnikov, S.A. [Joint Institute for Nuclear Research, 141 980 Dubna (Russian Federation)

    2007-05-11

    The fission fragments from spontaneous fission of {sup 252}Cf have been measured with the spectrometric and position-sensitive semiconductor pixel detector Medipix2. Fragments are identified by pattern recognition of clusters generated in the Medipix2 pixel matrix sensor upon heavy particle hit. From analysis of cluster area, the distribution of kinetic energy of fission fragments is obtained. Together with a novel USB readout interface, the Medipix2/USB system operates as active nuclear emulsion in single-quantum and on-line tracking mode.

  6. Gene Prediction in Metagenomic Fragments with Deep Learning.

    Science.gov (United States)

    Zhang, Shao-Wu; Jin, Xiang-Yang; Zhang, Teng

    2017-01-01

    Next generation sequencing technologies used in metagenomics yield numerous sequencing fragments which come from thousands of different species. Accurately identifying genes from metagenomics fragments is one of the most fundamental issues in metagenomics. In this article, by fusing multifeatures (i.e., monocodon usage, monoamino acid usage, ORF length coverage, and Z-curve features) and using deep stacking networks learning model, we present a novel method (called Meta-MFDL) to predict the metagenomic genes. The results with 10 CV and independent tests show that Meta-MFDL is a powerful tool for identifying genes from metagenomic fragments.

  7. Gluon fragmentation into {sup 3} P{sub J} quarkonium

    Energy Technology Data Exchange (ETDEWEB)

    Ma, J.P.

    1995-10-01

    The functions of the gluon fragmentation into {sup 3}P{sub j} quarkonium are calculated to order {alpha}{sup 2}{sub s}. With the recent progress in analysing quarkonium systems in QCD it is possible show how the so called divergence in the limit of the zero-binding energy, which is related to P-wave quarkonia, is treated correctly in the case of fragmentation functions. The obtained fragmentation functions satisfy explicitly at the order of {alpha} {sup 2}{sub s} the Altarelli-Parisi equation and when z {yields} 0 they behave as z{sup -1} as expected. 19 refs., 7 figs.

  8. To what extent does urbanisation affect fragmented grassland functioning?

    Science.gov (United States)

    van der Walt, L; Cilliers, S S; Kellner, K; Du Toit, M J; Tongway, D

    2015-03-15

    Urbanisation creates altered environments characterised by increased human habitation, impermeable surfaces, artificial structures, landscape fragmentation, habitat loss, resulting in different resource loss pathways. The vulnerable Rand Highveld Grassland vegetation unit in the Tlokwe Municipal area, South Africa, has been extensively affected and transformed by urbanisation, agriculture, and mining. Grassland fragments in urban areas are often considered to be less species rich and less functional than in the more untransformed or "natural" exurban environments, and are therefore seldom a priority for conservation. Furthermore, urban grassland fragments are often being more intensely managed than exurban areas, such as consistent mowing in open urban areas. Four urbanisation measures acting as indicators for patterns and processes associated with urban areas were calculated for matrix areas surrounding each selected grassland fragment to quantify the position of each grassland remnant along an urbanisation gradient. The grassland fragments were objectively classified into two classes of urbanisation, namely "exurban" and "urban" based on the urbanisation measure values. Grazing was recorded in some exurban grasslands and mowing in some urban grassland fragments. Unmanaged grassland fragments were present in both urban and exurban areas. Fine-scale biophysical landscape function was determined by executing the Landscape Function Analysis (LFA) method. LFA assesses fine-scale landscape patchiness (entailing resource conserving potential and erosion resistance) and 11 soil surface indicators to produce three main LFA parameters (stability, infiltration, and nutrient cycling), which indicates how well a system is functioning in terms of fine-scale biophysical soil processes and characteristics. The aim of this study was to determine the effects of urbanisation and associated management practices on fine-scale biophysical landscape function of urban and exurban

  9. New fission-fragment detector for experiments at DANCE

    Science.gov (United States)

    Rusev, G.; Roman, A. R.; Daum, J. K.; Springs, R. K.; Bond, E. M.; Jandel, M.; Baramsai, B.; Bredeweg, T. A.; Couture, A.; Favalli, A.; Ianakiev, K. D.; Iliev, M. L.; Mosby, S.; Ullmann, J. L.; Walker, C. L.

    2015-10-01

    A fission-fragment detector based on thin scintillating films has been built to serve as a veto/trigger detector in neutron-induced fission measurements at DANCE. The fissile material is surrounded by scintillating films providing a 4 π detection of the fission fragments. The scintillation events caused by the fission fragment interactions in the films are registered with silicon photomultipliers. Design of the detector and test measurements are described. Work supported by the U.S. Department of Energy through the LANL/LDRD Program and the U.S. Department of Energy, Office of Science, Nuclear Physics under the Early Career Award No. LANL20135009.

  10. Evaluation of genetic diversity in jackfruit (Artocarpus heterophyllus Lam.) based on amplified fragment length polymorphism markers.

    Science.gov (United States)

    Shyamalamma, S; Chandra, S B C; Hegde, M; Naryanswamy, P

    2008-07-22

    Artocarpus heterophyllus Lam., commonly called jackfruit, is a medium-sized evergreen tree that bears high yields of the largest known edible fruit. Yet, it has been little explored commercially due to wide variation in fruit quality. The genetic diversity and genetic relatedness of 50 jackfruit accessions were studied using amplified fragment length polymorphism markers. Of 16 primer pairs evaluated, eight were selected for screening of genotypes based on the number and quality of polymorphic fragments produced. These primer combinations produced 5976 bands, 1267 (22%) of which were polymorphic. Among the jackfruit accessions, the similarity coefficient ranged from 0.137 to 0.978; the accessions also shared a large number of monomorphic fragments (78%). Cluster analysis and principal component analysis grouped all jackfruit genotypes into three major clusters. Cluster I included the genotypes grown in a jackfruit region of Karnataka, called Tamaka, with very dry conditions; cluster II contained the genotypes collected from locations having medium to heavy rainfall in Karnataka; cluster III grouped the genotypes in distant locations with different environmental conditions. Strong coincidence of these amplified fragment length polymorphism-based groupings with geographical localities as well as morphological characters was observed. We found moderate genetic diversity in these jackfruit accessions. This information should be useful for tree breeding programs, as part of our effort to popularize jackfruit as a commercial crop.

  11. Fragmented Land Cover Types and Estimation of Area with Course Spatial Resolution Imagery

    Science.gov (United States)

    Hlavka, Chris; Dungan, Jennifer; Gore, William (Technical Monitor)

    1998-01-01

    Imagery of coarse resolution, such weather satellite imagery with 1 sq km pixels, is increasingly used to monitor dynamic and fragmented types of land surface types, such as scars from recent fires and ponds in wetlands. Accurate estimates of these land cover types at regional to global scales are required to assess the roles of fires and wetlands in global warming, yet difficult to compute when much of the area is accounted for by fragments about the same size as the pixels. In previous research, we found that size distribution of the fragments in several example scenes fit simple two-parameter models and related effects of coarse resolution to errors in area estimates based on pixel counts. We report on progress to develop accurate area estimates based on modelling the size distribution of the fragments, including analysis of size distributions on an expanded set of maps developed from digital imagery and a test of a procedure to correct for effects of coarse spatial resolution.

  12. Population of high-spin isomeric states following fragmentation of 238U

    Science.gov (United States)

    Bowry, M.; Podolyák, Zs.; Pietri, S.; Kurcewicz, J.; Bunce, M.; Regan, P. H.; Farinon, F.; Geissel, H.; Nociforo, C.; Prochazka, A.; Weick, H.; Al-Dahan, N.; Alkhomashi, N.; Allegro, P. R. P.; Benlliure, J.; Benzoni, G.; Boutachkov, P.; Bruce, A. M.; Denis Bacelar, A. M.; Farrelly, G. F.; Gerl, J.; Górska, M.; Gottardo, A.; Grębosz, J.; Gregor, N.; Janik, R.; Knöbel, R.; Kojouharov, I.; Kubo, T.; Kurz, N.; Litvinov, Yu. A.; Merchan, E.; Mukha, I.; Naqvi, F.; Pfeiffer, B.; Pfützner, M.; Plaß, W.; Pomorski, M.; Riese, B.; Ricciardi, M. V.; Schmidt, K.-H.; Schaffner, H.; Scheidenberger, C.; Simpson, E. C.; Sitar, B.; Spiller, P.; Stadlmann, J.; Strmen, P.; Sun, B.; Tanihata, I.; Terashima, S.; Valiente Dobón, J. J.; Winfield, J. S.; Wollersheim, H.-J.; Woods, P. J.

    2013-08-01

    Isomeric ratios have been determined for 23 metastable states identified in A≈200 nuclei from Pt to Rn near the valley of stability following fragmentation of 238U. This includes high-spin states with angular momenta ranging from (39/2)ℏ to 25ℏ. The experimental results are discussed together with those of similar experiments performed in this mass region. Isomeric ratios are compared with theoretical predictions where the angular momentum of the fragment arises purely due to the angular momentum of nucleons removed from the projectile. The theoretical yield of low-spin states is generally overestimated. In these cases the assumption of 100% feeding of the isomer may require modification. However, the yield of high-spin isomeric states [Im ≥ (39/2)ℏ] is significantly underestimated and highlights the requirement for a more complete theoretical framework in relation to the generation of fragment angular momentum. The enhanced population of high-spin states reported here is advantageous to future studies involving isomeric beams at fragmentation facilities such as the Rikagaku Kenkyusho RI Beam Factory (Japan) and next-generation facilities at the Facility for Antiproton and Ion Research (Germany) and Facility for Rare Isotope Beams (USA).

  13. Vertical distribution of epiphytic bryophytes in Atlantic Forest fragments in northeastern Brazil

    Directory of Open Access Journals (Sweden)

    Hermeson Cassiano de Oliveira

    Full Text Available ABSTRACT The microclimatic gradient established from the forest understory to the canopy provides a range of different conditions for the establishment of bryophytes along the height of a tree. We investigated epiphytic bryophyte communities of four fragments of Atlantic Forest with the aim of describing their vertical zonation and assessing differentiation among the communities of the different fragments. In each fragment, five host trees were selected from which bryophyte samples were collected in four height zones from the base to the canopy. Furthermore, 10 plots were demarcated in each fragment where bryophytes were collected from the understory. In total, 114 bryophyte species were found on the 20 sampled phorophytes, plus an additional 51 species in the understory, for a total of 165 species. Species composition of height zones differed significantly between communities of the trunk base and the canopy. The samples from the understory included 77% of all species. Among all species found, 10 showed a significant preference for a specific height. Around 70% of the bryophyte species grew as mats; this life form occurred in all trees and height zones. The results showed a weak, yet significant, vertical gradient, which differs from what is usually found in the Atlantic Forest.

  14. Typing of Mycobacterium avium Subspecies paratuberculosis Isolates from Newfoundland Using Fragment Analysis

    Science.gov (United States)

    Podder, Milka P.; Banfield, Susan E.; Keefe, Greg P.; Whitney, Hugh G.; Tahlan, Kapil

    2015-01-01

    Short Sequence Repeat (SSR) typing of Mycobacterium avium subspecies paratuberculosis (Map) isolates is one of the most commonly used method for genotyping this pathogen. Currently used techniques have challenges in analyzing mononucleotide repeats >15 bp, which include some of the Map SSRs. Fragment analysis is a relatively simple technique, which can accurately measure the size of DNA fragments and can be used to calculate the repeat length of the target SSR loci. In the present study, fragment analysis was used to analyze 4 Map SSR loci known to provide sufficient discriminatory power to determine the relationship between Map isolates. Eighty-five Map isolates from 18 animals from the island of Newfoundland were successfully genotyped using fragment analysis. To the best of our knowledge, this is the first report on Map SSR diversity from Newfoundland dairy farms. Previously unreported Map SSR-types or combinations were also identified during the course of the described work. In addition, multiple Map SSR-types were isolated from a single animal in many cases, which is not a common finding. PMID:25927612

  15. Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei

    Energy Technology Data Exchange (ETDEWEB)

    Begley, Darren W.; Hartley, Robert C.; Davies, Douglas R.; Edwards, Thomas E.; Leonard, Jess T.; Abendroth, Jan; Burris, Courtney A.; Bhandari, Janhavi; Myler, Peter J.; Staker, Bart L.; Stewart, Lance J. (UWASH); (Emerald)

    2011-09-28

    As part of the Seattle Structural Genomics Center for Infectious Disease, we seek to enhance structural genomics with ligand-bound structure data which can serve as a blueprint for structure-based drug design. We have adapted fragment-based screening methods to our structural genomics pipeline to generate multiple ligand-bound structures of high priority drug targets from pathogenic organisms. In this study, we report fragment screening methods and structure determination results for 2C-methyl-D-erythritol-2,4-cyclo-diphosphate (MECP) synthase from Burkholderia pseudomallei, the gram-negative bacterium which causes melioidosis. Screening by nuclear magnetic resonance spectroscopy as well as crystal soaking followed by X-ray diffraction led to the identification of several small molecules which bind this enzyme in a critical metabolic pathway. A series of complex structures obtained with screening hits reveal distinct binding pockets and a range of small molecules which form complexes with the target. Additional soaks with these compounds further demonstrate a subset of fragments to only bind the protein when present in specific combinations. This ensemble of fragment-bound complexes illuminates several characteristics of MECP synthase, including a previously unknown binding surface external to the catalytic active site. These ligand-bound structures now serve to guide medicinal chemists and structural biologists in rational design of novel inhibitors for this enzyme.

  16. Human impacts affect tree community features of 20 forest fragments of a vanishing neotropical hotspot.

    Science.gov (United States)

    Pereira, José Aldo Alves; de Oliveira-Filho, Ary Teixeira; Eisenlohr, Pedro V; Miranda, Pedro L S; de Lemos Filho, José Pires

    2015-02-01

    The loss in forest area due to human occupancy is not the only threat to the remaining biodiversity: forest fragments are susceptible to additional human impact. Our aim was to investigate the effect of human impact on tree community features (species composition and abundance, and structural descriptors) and check if there was a decrease in the number of slender trees, an increase in the amount of large trees, and also a reduction in the number of tree species that occur in 20 fragments of Atlantic montane semideciduous forest in southeastern Brazil. We produced digital maps of each forest fragment using Landsat 7 satellite images and processed the maps to obtain morphometric variables. We used investigative questionnaires and field observations to survey the history of human impact. We then converted the information into scores given to the extent, severity, and duration of each impact, including proportional border area, fire, trails, coppicing, logging, and cattle, and converted these scores into categorical levels. We used linear models to assess the effect of impacts on tree species abundance distribution and stand structural descriptors. Part of the variation in floristic patterns was significantly correlated to the impacts of fire, logging, and proportional border area. Structural descriptors were influenced by cattle and outer roads. Our results provided, for the first time, strong evidence that tree species occurrence and abundance, and forest structure of Atlantic seasonal forest fragments respond differently to various modes of disturbance by humans.

  17. Number-squeezed and fragmented states of strongly interacting bosons in a double well

    Science.gov (United States)

    Corbo, Joel C.; DuBois, Jonathan L.; Whaley, K. Birgitta

    2017-11-01

    We present a systematic study of the phenomena of number squeezing and fragmentation for a repulsive Bose-Einstein condensate (BEC) in a three-dimensional double-well potential over a range of interaction strengths and barrier heights, including geometries that exhibit appreciable overlap in the one-body wave functions localized in the left and right wells. We compute the properties of the condensate with numerically exact, full-dimensional path-integral ground-state (PIGS) quantum Monte Carlo simulations and compare with results obtained from using two- and eight-mode truncated basis models. The truncated basis models are found to agree with the numerically exact PIGS simulations for weak interactions, but fail to correctly predict the amount of number squeezing and fragmentation exhibited by the PIGS simulations for strong interactions. We find that both number squeezing and fragmentation of the BEC show nonmonotonic behavior at large values of interaction strength a . The number squeezing shows a universal scaling with the product of number of particles and interaction strength (N a ), but no such universal behavior is found for fragmentation. Detailed analysis shows that the introduction of repulsive interactions not only suppresses number fluctuations to enhance number squeezing, but can also enhance delocalization across wells and tunneling between wells, each of which may suppress number squeezing. This results in a dynamical competition whose resolution shows a complex dependence on all three physical parameters defining the system: interaction strength, number of particles, and barrier height.

  18. Ten-Year Follow-Up of a Fragment Reattachment to an Anterior Tooth: A Conservative Approach

    Science.gov (United States)

    Mendes, Luiz; Laxe, Laisa

    2017-01-01

    This report describes the 10-year follow-up data of a patient who underwent fragment reattachment to the maxillary central incisor after coronal fracture with pulp exposure as well as the procedures followed for functional and esthetic adjustments. A 9-year-old female patient presented at the clinic of dentistry at the State University of Rio de Janeiro with a coronal fracture and pulp exposure of the right maxillary central incisor that had occurred immediately after an accident. The intact tooth fragment was recovered at the accident site and stored in milk. The treatment plan followed was to perform direct pulp capping and tooth fragment reattachment. When the patient was 14 years old, adhesion between fragment and remaining tooth was lost, and fragment reattachment was performed. Five years later, the same tooth presented clinical discoloration and absence of sensitivity during pulp vitality tests. Subsequently, a new treatment plan was formulated, which included endodontic treatment, followed by nonvital tooth bleaching and light-cured composite resin restoration. An esthetic and natural-looking restoration was achieved. Tooth fragment reattachment is not a temporary restorative technique and requires functional and esthetic adjustments over time to maintain the biomimetic characteristics of traumatized anterior teeth and predictable outcomes. PMID:28740741

  19. Ten-Year Follow-Up of a Fragment Reattachment to an Anterior Tooth: A Conservative Approach

    Directory of Open Access Journals (Sweden)

    Luiz Mendes

    2017-01-01

    Full Text Available This report describes the 10-year follow-up data of a patient who underwent fragment reattachment to the maxillary central incisor after coronal fracture with pulp exposure as well as the procedures followed for functional and esthetic adjustments. A 9-year-old female patient presented at the clinic of dentistry at the State University of Rio de Janeiro with a coronal fracture and pulp exposure of the right maxillary central incisor that had occurred immediately after an accident. The intact tooth fragment was recovered at the accident site and stored in milk. The treatment plan followed was to perform direct pulp capping and tooth fragment reattachment. When the patient was 14 years old, adhesion between fragment and remaining tooth was lost, and fragment reattachment was performed. Five years later, the same tooth presented clinical discoloration and absence of sensitivity during pulp vitality tests. Subsequently, a new treatment plan was formulated, which included endodontic treatment, followed by nonvital tooth bleaching and light-cured composite resin restoration. An esthetic and natural-looking restoration was achieved. Tooth fragment reattachment is not a temporary restorative technique and requires functional and esthetic adjustments over time to maintain the biomimetic characteristics of traumatized anterior teeth and predictable outcomes.

  20. How does a CC double bond cleave in the gas phase? Fragmentation of protonated ketotifen in mass spectrometry.

    Science.gov (United States)

    Chai, Yunfeng; Wang, Lu; Wang, Lin

    2016-12-01

    In the literature, it is reported that the protonated ketotifen mainly undergoes CC double bond cleavage in electrospray ionization tandem mass spectrometry (ESI-MS/MS); however, there is no explanation on the mechanism of this fragmentation reaction. Therefore, we carried out a combined experimental and theoretical study on this interesting fragmentation reaction. The fragmentation of protonated ketotifen (m/z 310) always generated a dominant fragment ion at m/z 96 in different electrospray ionization mass spectrometers (ion trap, triple quadrupole and linear trap quadrupole (LTQ)-orbitrap). The mechanism of the generation of this product ion (m/z 96) through the CC double bond cleavage was proposed to be a sequential hydrogen migration process (including proton transfer, continuous two-step 1,2-hydride transfer and ion-neutral complex-mediated hydride transfer). This mechanism was supported by density functional theory (DFT) calculations and a deuterium labeling experiment. DFT calculations also showed that the formation of the product ion m/z 96 was most favorable in terms of energy. This study provides a reasonable explanation for the fragmentation of protonated ketotifen in ESI-MS/MS, and the fragmentation mechanism is suitable to explain other CC double bond cleavage reactions in mass spectrometry. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  1. Responses of small mammals to habitat fragmentation: epidemiological considerations for rodent-borne hantaviruses in the Americas.

    Science.gov (United States)

    Rubio, André V; Ávila-Flores, Rafael; Suzán, Gerardo

    2014-12-01

    Rodent-borne hantaviruses are a group of zoonotic agents that cause hemorrhagic fever in humans. The transmission of hantaviruses among rodent hosts may be higher with the increase of reservoir host abundance in a given area (density-dependent transmission) and with the decrease of small mammal diversity (dilution effect phenomenon). These population and community parameters may be modified by habitat fragmentation; however, studies that focus on fragmentation and its effect on hantavirus infection risk are scarce. To further understanding of this issue, we assessed some population and community responses of rodents that may increase the risk for hantavirus transmission among wildlife hosts in the Americas. We conducted a meta-analysis of published studies to assess the responses of small mammals to fragmentation of native habitats, relative to patch size. Our analyses included five countries and 14 case studies for abundance of reservoir hosts (8 species) and 15 case studies for species richness. We found that a reduction of patch area due to habitat fragmentation is associated with increased reservoir host abundances and decreased small mammal richness, which is mainly due to the loss of non-host small mammals. According to these results, habitat fragmentation in the Americas should be considered as an epidemiological risk factor for hantavirus transmission to humans. These findings are important to assess potential risk of infection when fragmentation of native habitats occurs.

  2. High Radiation Environment Nuclear Fragment Separator Magnet

    Energy Technology Data Exchange (ETDEWEB)

    Kahn, Stephen [Muons, Inc., Batavia, IL (United States); Gupta, Ramesh [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2016-01-31

    Superconducting coils wound with HTS conductor can be used in magnets located in a high radiation environment. NbTi and Nb3Sn superconductors must operate at 4.5 K or below where removal of heat is less efficient. The HTS conductor can carry significant current at higher temperatures where the Carnot efficiency is significantly more favorable and where the coolant heat capacity is much larger. Using the HTS conductor the magnet can be operated at 40 K. This project examines the use of HTS conductor for the Michigan State University Facility For Rare Isotope Beams (FRIB) fragment separator dipole magnet which bends the beam by 30° and is located in a high radiation region that will not be easily accessible. Two of these magnets are needed to select the chosen isotope. There are a number of technical challenges to be addressed in the design of this magnet. The separator dipole is 2 m long and subtends a large angle. The magnet should keep a constant transverse field profile along its beam reference path. Winding coils with a curved inner segment is difficult as the conductor will tend to unwind during the process. In the Phase I project two approaches to winding the conductor were examined. The first was to wind the coils with curved sections on the inner and outer segments with the inner segment wound with negative curvature. The alternate approach was to use a straight segment on the inner segment to avoid negative curvature. In Phase I coils with a limited number of turns were successfully wound and tested at 77 K for both coil configurations. The Phase II program concentrated on the design, coil winding procedures, structural analysis, prototyping and testing of an HTS curved dipole coil at 40 K with a heat load representative of the radiation environment. One of the key criteria of the design of this magnet is to avoid the use of organic materials that would degrade rapidly in radiation. The Lorentz forces expected from the coils interacting with the

  3. Detection and location of metal fragments in the human body

    Science.gov (United States)

    Brown, R. L.; Neuschaefer, R. W.

    1970-01-01

    Portable electronic device, based on the design of an eddy current gage, detects ferrous and nonferrous metal fragments. Device is more easily transported than X-ray equipment and does not present a radiation hazard.

  4. Improved Barriers to Turbine Engine Fragments: Final Annual Report

    National Research Council Canada - National Science Library

    Shockey, Donald

    2002-01-01

    This final annual technical report describes the progress rnade during year 4 of the SPI International Phase II effort to develop a computational capability for designing lightweight fragment barriers...

  5. Activation of human monocytes by proteolytic fragments of gliadin

    Czech Academy of Sciences Publication Activity Database

    Jelínková, Lenka; Tučková, Ludmila; Cinová, Jana; Cimburek, Zdeněk; Tlaskalová, Helena

    2003-01-01

    Roč. 87, č. 1 (2003), s. 08 ISSN 0165-2478 Institutional research plan: CEZ:AV0Z5020903 Keywords : proteolytic * fragments * gliadin Subject RIV: EE - Microbiology, Virology Impact factor: 1.710, year: 2003

  6. N-Protonated Isomers as Gateways to Peptide Ion Fragmentation

    National Research Council Canada - National Science Library

    Haeffner, Fredrik; Merle, John K; Irikura, Karl K

    2011-01-01

    .... If the intrinsic barrier to dissociation is the same for all backbone sites, the fragmentation propensity at each amide bond should reflect the stability of the corresponding N-protonated isomer...

  7. Forest fragmentation and avian nest predation in forested landscapes.

    Science.gov (United States)

    Small, M F; Hunter, M L

    1988-06-01

    The size of forest fragments, the use of land bordering fragments, and the distance of nests from an edge all affect the frequency of predation upon bird nests in Maine (USA), an area where the forest has been fragmented by roads, but not significantly reduced in area. We placed artificial nests containing quail eggs in forests of different sizes and at various distances from the edge to test which of these factors was most important in describing predation. Predation was greatest in small tracts surrounded completely by land. Large areas and those bordered on at least one side by a large water body had lower predation rates. This suggests that influx of predators from nearby habitats may be responsible for much of the nest predation in forest fragments.

  8. Dynamic rock fragmentation: thresholds for long runout rock avalanches

    Directory of Open Access Journals (Sweden)

    E.T. Bowman

    2014-10-01

    Full Text Available The dynamic fragmentation of rock within rock avalanches is examined using the fragmentation concepts introduced by Grady and co-workers. The analyses use typical material values for weak chalk and limestone in order to determine theoretical strain rate thresholds for dynamic fragmentation and resulting fragment sizes. These are found to compare favourably with data obtained from field observations of long runout rock avalanches and chalk cliff collapses in spite of the simplicity of the approach used. The results provide insight as to the energy requirements to develop long runout behaviour and hence may help to explain the observed similarities between large rock avalanches and much smaller scale chalk cliff collapses as seen in Europe.

  9. Policing, Community Fragmentation, and Public Health: Observations from Baltimore.

    Science.gov (United States)

    Gomez, Marisela B

    2016-04-01

    Studies show that policing, when violent, and community fragmentation have a negative impact on health outcomes. This current study investigates the connection of policing and community fragmentation and public health. Using an embedded case study analysis, semi-structured interviews were conducted with 21 African-American female and male residents, ages 21-64 years of various neighborhoods of high arrest rates and health and socioeconomic depravation in Baltimore City, MD. Baltimore residents' perceptions of policing, stress, community fragmentation, and solutions are presented. Analysis of the perceptions of these factors suggests that violent policing increases community fragmentation and is a public health threat. Approaches to address this public health threat are discussed.

  10. Amplification of deoxyribonucleic acid (DNA) fragment using two ...

    African Journals Online (AJOL)

    user

    2011-04-11

    extension steps and the fidelity of the ... cant time-savings and a reduction in reagent use, relative .... A, The sequence of the amplified 900 bp DNA fragment by two-step method (Enterobacteria phage lambda, complete genome.

  11. Fragmentation mechanism reflecting the cluster structure of {sup 19}B

    Energy Technology Data Exchange (ETDEWEB)

    Takemoto, H.; Horiuchi, H. [Kyoto Univ., Dept. of Physics, Kyoto (Japan); Ono, A.

    1999-08-01

    Clustering structure of neutron dripline nucleus {sup 19}B which was predicted theoritically is investigated by studying the fragmentation reaction of {sup 19}B. We compare {sup 19}B fragmentation with {sup 13}B fragmentation in {sup 19}B + {sup 14}N and {sup 13}B + {sup 14}N reactions by using antisymmetrized molecular dynamics, where {sup 13}B has no clustering feature in its structure. We find that the cluster structure of the {sup 19}B nucleus is reflected in its fragmentation as the simultaneous production of He and Li isotopes. Furthermore we investigate the dependence of the cluster decay of {sup 19}B on the incident energy, and find that the cluster structure of {sup 19}B in its ground state is more reflected in lower incident-energy reactions. (author)

  12. Charge promotion of low-energy fragmentations of peptide ions.

    Science.gov (United States)

    Burlet, O; Orkiszewski, R S; Ballard, K D; Gaskell, S J

    1992-11-01

    We have examined the hypothesis that structural features which predispose to localization of charge at a strongly favored site are not conducive to the low-energy fragmentation of peptide ions via a multiplicity of pathways. Consistent with this proposal, it is demonstrated that the formation of N- or C-terminal pre-charged derivatives is detrimental to the formation of sequence-specific product ions following low-energy collisional activation. Protonation of pre-charged derivatives (yielding doubly charged ions) restores favorable fragmentation properties; the effect is attributed to the fragmentation-directing properties of the proton which may occupy one of several sites. Similarly, a doubly protonated peptide which incorporates a C-terminal arginine residue as a single strongly favored site of protonation exhibits favored low-energy fragmentations attributable to location of the second proton at one of several sites remote from the C-terminus.

  13. Calibrations for studies of neutron-rich precursor fragments

    Science.gov (United States)

    Mazza, Maria; Parkhurst, Rachel; Wilensky, Samuel; Mosby, Michelle; Stephenson, Sharon; Rogers, Warren; MoNA Collaboration Collaboration

    2015-10-01

    Heavy ion collisions at relativistic energies produce the radioactive beams used at nuclear structure facilities worldwide. However, there are still unanswered questions about the reaction mechanism of projectile fragmentation and the specific roles that ablation, evaporation, and abrasion play. Using the projectile fragmentation of a 32Mg beam at 86 MeV/u on a natural Beryllium target at the National Superconducting Cyclotron Laboratory (NSCL), our experimental goal is to better understand the excitation energy and the momentum distribution of the precursors of the observed final fragments (neon, sodium, and fluorine). A suite of charged particle detectors in conjunction with the Modular Neutron Array (MoNA) allows us to analyze both the charged final fragments as well as the coincident neutrons. Detector calibration results and preliminary results will be presented. This material is based upon work supported by the National Science Foundation under Grants PHY-1205537.

  14. Zinc Mediated Tandem Fragmentation-Allylation of Methyl 5-Iodopentofuranosides

    DEFF Research Database (Denmark)

    Hyldtoft, Lene; Madsen, Robert

    1999-01-01

    In the presence of zinc and allyl bromide methyl 5-iodopentofuranosides undergo a tandem fragmentation alkylation to give functionalized dienes. These can undergo ring-closing olefin metathesis to produce cyclohexenes which on dihydroxylation give quercitols....

  15. Fragmentation patterns of evergreen oak woodlands in Southwestern Iberia

    DEFF Research Database (Denmark)

    Costa, A.; Madeira, M.; Lima Santos, J.

    2014-01-01

    Mediterranean evergreen oak woodlands (composed of Quercus suber L. and Quercus rotundifolia Lam.) are becoming increasingly fragmented in the human-modified landscapes of Southwestern Portugal and Spain. Previous studies have largely neglected to assess the spatial changes of oak woodlands...... in relation to their surrounding landscape matrix, and to characterize and quantify woodland boundaries and edges. The present study aims to fill this gap by analyzing fragmentation patterns of oak woodlands over a 50-year period (1958-2007) in three landscapes. Using archived aerial imagery from 1958, 1995...... and 2007, for two consecutive periods (1958-1995 and 1995-2007), we calculated a set of landscape metrics to compare woodland fragmentation over time. Our results indicated a continuous woodland fragmentation characterized by their edge dynamics. From 1958 to 2007, the replacement of open farmland...

  16. Fragmentation trees for the structural characterisation of metabolites

    Science.gov (United States)

    Kasper, Piotr T; Rojas-Chertó, Miguel; Mistrik, Robert; Reijmers, Theo; Hankemeier, Thomas; Vreeken, Rob J

    2012-01-01

    Metabolite identification plays a crucial role in the interpretation of metabolomics research results. Due to its sensitivity and widespread implementation, a favourite analytical method used in metabolomics is electrospray mass spectrometry. In this paper, we demonstrate our results in attempting to incorporate the potentials of multistage mass spectrometry into the metabolite identification routine. New software tools were developed and implemented which facilitate the analysis of multistage mass spectra and allow for efficient removal of spectral artefacts. The pre-processed fragmentation patterns are saved as fragmentation trees. Fragmentation trees are characteristic of molecular structure. We demonstrate the reproducibility and robustness of the acquisition of such trees on a model compound. The specificity of fragmentation trees allows for distinguishing structural isomers, as shown on a pair of isomeric prostaglandins. This approach to the analysis of the multistage mass spectral characterisation of compounds is an important step towards formulating a generic metabolite identification method. Copyright © 2012 John Wiley & Sons, Ltd. PMID:22956319

  17. Multiplicity distributions of shower particles and target fragments in 7 ...

    Indian Academy of Sciences (India)

    emulsion) collisions at 3 A GeV/c are experimentally studied. In the framework of the multisource thermal model, the multicomponent Erlang distribution is used to describe the experimental multiplicity distributions of shower particles, grey fragments ...

  18. Binding thermodynamics discriminates fragments from druglike compounds: a thermodynamic description of fragment-based drug discovery.

    Science.gov (United States)

    Williams, Glyn; Ferenczy, György G; Ulander, Johan; Keserű, György M

    2017-04-01

    Small is beautiful - reducing the size and complexity of chemical starting points for drug design allows better sampling of chemical space, reveals the most energetically important interactions within protein-binding sites and can lead to improvements in the physicochemical properties of the final drug. The impact of fragment-based drug discovery (FBDD) on recent drug discovery projects and our improved knowledge of the structural and thermodynamic details of ligand binding has prompted us to explore the relationships between ligand-binding thermodynamics and FBDD. Information on binding thermodynamics can give insights into the contributions to protein-ligand interactions and could therefore be used to prioritise compounds with a high degree of specificity in forming key interactions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Fragmentation processes of OCS in collision with highly charged ions

    Science.gov (United States)

    Matsumoto, J.; Tezuka, T.; Fukutome, A.; Karimi, R.; Wales, B.; Sanderson, J. H.; Shiromaru, H.

    2014-04-01

    Fragmentation of (OCS)3+ and (OCS)4+ produced by 120 keV Ar8+ collision was studied by using a position-sensitive time-of-flight (PS-TOF) method. We identified stepwise processes involving CO2+ and CS2+ metastable species as well as the concerted process (simultaneous breakup of the two bonds). For the (OCS)4+ events, the stepwise processes were found for fragmentation channels containing a doubly-charged terminal atom.

  20. Isotopic Scaling and the Symmetry Energy in Spectator Fragmentation

    OpenAIRE

    INDRA, The; collaborations, ALADIN; :; Fèvre, A. Le; Auger, G.; Begemann-Blaich, M.L.; Bellaize, N.; Bittiger, R.; Bocage, F.; Borderie, B.; R. Bougault(LPCC); Bouriquet, B.; Charvet, J. L.; Chbihi, A.; Dayras, R.

    2004-01-01

    Isotopic effects in the fragmentation of excited target residues following collisions of $^{12}$C on $^{112,124}$Sn at incident energies of 300 and 600 MeV per nucleon were studied with the INDRA 4$\\pi$ detector. The measured yield ratios for light particles and fragments with atomic number $Z \\leq$ 5 obey the exponential law of isotopic scaling. The deduced scaling parameters decrease strongly with increasing centrality to values smaller than 50% of those obtained for the peripheral event gr...