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Sample records for acta cryst d65

  1. Crystallization reports are the backbone of Acta Cryst. F, but do they have any spine?

    PubMed Central

    Newman, Janet; Burton, Denis R.; Caria, Sofia; Desbois, Sebastien; Gee, Christine L.; Fazio, Vincent J.; Kvansakul, Marc; Marshall, Bevan; Mills, Grant; Richter, Viviane; Seabrook, Shane A.; Wu, Mingbo; Peat, Thomas S.

    2013-01-01

    Crystallization of macromolecules is famously difficult. By knowing what has worked for others, researchers can ease the process, both in the case where the protein has already been crystallized and in the situation where more general guidelines are needed. The 264 crystallization communications published in Acta Crystallographica Section F in 2012 have been reviewed, and from this analysis some information about trends in crystallization has been gleaned. More importantly, it was found that there are several ways in which the utility of these communications could be increased: to make each individual paper a more complete crystallization record; and to provide a means for taking a snapshot of what the current ‘best practices’ are in the field. PMID:23832194

  2. Crystallization reports are the backbone of Acta Cryst. F, but do they have any spine?

    PubMed

    Newman, Janet; Burton, Denis R; Caria, Sofia; Desbois, Sebastien; Gee, Christine L; Fazio, Vincent J; Kvansakul, Marc; Marshall, Bevan; Mills, Grant; Richter, Viviane; Seabrook, Shane A; Wu, Mingbo; Peat, Thomas S

    2013-07-01

    Crystallization of macromolecules is famously difficult. By knowing what has worked for others, researchers can ease the process, both in the case where the protein has already been crystallized and in the situation where more general guidelines are needed. The 264 crystallization communications published in Acta Crystallographica Section F in 2012 have been reviewed, and from this analysis some information about trends in crystallization has been gleaned. More importantly, it was found that there are several ways in which the utility of these communications could be increased: to make each individual paper a more complete crystallization record; and to provide a means for taking a snapshot of what the current `best practices' are in the field. PMID:23832194

  3. Recent developments in CrystFEL 1

    PubMed Central

    White, Thomas A.; Mariani, Valerio; Brehm, Wolfgang; Yefanov, Oleksandr; Barty, Anton; Beyerlein, Kenneth R.; Chervinskii, Fedor; Galli, Lorenzo; Gati, Cornelius; Nakane, Takanori; Tolstikova, Alexandra; Yamashita, Keitaro; Yoon, Chun Hong; Diederichs, Kay; Chapman, Henry N.

    2016-01-01

    CrystFEL is a suite of programs for processing data from ‘serial crystallography’ experiments, which are usually performed using X-ray free-electron lasers (FELs) but also increasingly with other X-ray sources. The CrystFEL software suite has been under development since 2009, just before the first hard FEL experiments were performed, and has been significantly updated and improved since then. This article describes the most important improvements which have been made to CrystFEL since the first release version. These changes include the addition of new programs to the suite, the ability to resolve ‘indexing ambiguities’ and several ways to improve the quality of the integrated data by more accurately modelling the underlying diffraction physics. PMID:27047311

  4. Acta Astronautica: 60 years of excellence

    NASA Astrophysics Data System (ADS)

    Chern, Rock Jeng-Shing; Chang, Eva Yi-Wei

    2014-12-01

    The Acta Astronautica is 60 years old [1]. Ever since its first publication in 1955 with the title Astronautica Acta (from 1955 to 1973), 2014 is the 60th year of Acta Astronautica (from 1955 to present). Fig. 1 is a poster to manifest the remarkable milestone during the 65th IAC held in Toronto, Canada on 29 September to 3 October 2014. Under the auspices of the IAA's Publications and Communication Committee, and the seamless cooperation and strong support of IAA, Editor-in-Chief, Co-Editors, Managing Editor, authors, reviewers, readers, publisher and all IAA Academicians, its impact factor and ranking have significant improvements recently. Fig. 2 shows the increase in impact factor from 2008 to 2013. The ranking is 7 out of the 63+ journals in the category of Aerospace Engineering.

  5. Intracellular Induction of Listeria monocytogenes actA Expression

    PubMed Central

    Shetron-Rama, Lynne M.; Marquis, Hélène; Bouwer, H. G. Archie; Freitag, Nancy E.

    2002-01-01

    Following entry into the host cytosol, the bacterial pathogen Listeria monocytogenes dramatically increases the expression of several key virulence factors. The expression of actA, whose protein product is required for L. monocytogenes actin-based intracellular motility, is increased by more than 200-fold in cytosolic bacteria in comparison to broth-grown cultures. Two distinct promoter elements have been reported to regulate actA expression. One promoter is located immediately upstream of actA coding sequences, while the second promoter is contributed by the upstream mpl gene via the generation of an mpl-actA-plcB transcript. A series of L. monocytogenes mutants were constructed to define the contributions of individual promoter elements to actA expression. The intracellular induction of actA expression was found to be dependent upon the actA proximal promoter; the mpl promoter appeared to contribute to the extracellular induction of actA but did not affect intracellular levels of expression. The actA promoter is dependent upon a regulatory factor known as PrfA for transcriptional activation; however, no increase in actA expression was detected following the introduction of a high-affinity PrfA binding site within the actA promoter. The presence of a mutationally activated form of PrfA, known as PrfA*, increased overall actA expression in broth-grown cultures of both wild-type and actA promoter mutant strains, but the levels of induction observed were still approximately 50-fold lower than those observed for intracellularly grown L. monocytogenes. Collectively, these results indicate that the dramatic induction of actA expression that occurs in the host cell cytosol is mediated through a single promoter element. Furthermore, intracellular induction of actA appears to require additional steps or factors beyond those necessary for the activation and binding of PrfA to the actA promoter. PMID:11854187

  6. Entering the 60th year of Acta Astronautica

    NASA Astrophysics Data System (ADS)

    Chang, Yi-Wei; Chern, Jeng-Shing; Marec, Jean-Pierre

    2014-04-01

    The Acta Astronautica Journal was firstly published in 1955 as the official Journal of the International Astronautical Federation (IAF) with the title Astronautica Acta. It is entering its 60th year in 2014. In 1962, the Astronautica Acta became the official Journal of the International Academy of Astronautics (IAA) established in 1960. A total of 18 volumes had been published from 1955 to 1973 under the leadership of three Editor-in-Chiefs: F. Hecht, Theodore von Karman, and Martin Summerfield. In 1974, A.K. Oppenheim became the new Editor-in-Chief and several evolved changes were performed including change of the title to Acta Astronautica (for grammatical correctness), cover page change, and format change. From 1974 to 2010, another three Editor-in-Chiefs led the journal with 67 volumes published. They were A.K. Oppenheim, Jean-Pierre Marec, and Rupert Gerzer. The current Editor-in-Chief Jeng-Shing Chern (Rock) took over the job from 2011. Total pages and articles published in 2012 are 3586 and 356, respectively. Currently, the Acta Astronautica Editorial Board consists of one Editor-in-Chief, 15 Co-Editors, one Managing Editor and one Honorary Editor-in-Chief (Jean-Pierre Marec). After 59 years, the Acta Astronautica has become a well-known journal worldwide. Its current rank and impact factor are 7/63 and 0.701, respectively. This paper presents some of the details as well as new strategies and steps. In particular, supports from the IAA Academicians are mandatory and most welcome.

  7. Elsevier/Spectrochimica Acta Atomic Spectroscopy Award 2014

    NASA Astrophysics Data System (ADS)

    Omenetto, Nicolo'; de Loos, Greet

    2016-03-01

    This is to announce the 2014 Elsevier/Spectrochimica Acta Award, the annual award honoring the most significant article(s) published in a volume. Elsevier makes this award on behalf of Spectrochimica Acta, Part B, to encourage the publication of top articles in this journal. All papers published during one year are considered for this award and the Editorial Advisory Board and the Guest Editor(s) of the special issue(s) are responsible for the selection. The award consists of a monetary prize of 1000 together with a presentation certificate.

  8. Elsevier/Spectrochimica Acta Atomic Spectroscopy Award 2013

    NASA Astrophysics Data System (ADS)

    Omenetto, Nicolo'; de Loos, Greet

    2015-01-01

    This is to announce the 2013 Elsevier/Spectrochimica Acta Award, the annual award honoring the most significant article(s) published in a volume. Elsevier makes this award on behalf of Spectrochimica Acta, Part B, to encourage the publication of top articles in this journal. All papers published during one year are considered for this award and the Editorial Advisory Board and the Guest Editor(s) of the special issue(s) are responsible for the selection. The award consists of a monetary prize of 1000 together with a presentation certificate.

  9. Citation Analysis of "Geochimica et Cosmochimica Acta," 1951-1960.

    ERIC Educational Resources Information Center

    Lifshin, Arthur

    1993-01-01

    A citation analysis of the first 10 years of "Geochimica et Cosmochimica Acta" from 1951 to 1960 is described. A shift from German to English language citations and the emerging importance of the journal in the field, which is undergoing a change resulting from technological innovation, are shown. Tables and graphs are included. (EAM)

  10. Localization of the ActA polypeptide of Listeria monocytogenes in infected tissue culture cell lines: ActA is not associated with actin "comets".

    PubMed Central

    Niebuhr, K; Chakraborty, T; Rohde, M; Gazlig, T; Jansen, B; Köllner, P; Wehland, J

    1993-01-01

    The ActA protein of the gram-positive pathogen Listeria monocytogenes is a 90-kDa polypeptide required for interaction of the bacteria with components of the host cell microfilament system to generate intra- and intercellular movement. To study the localization, distribution, and expression of the ActA polypeptide in L. monocytogenes grown either in broth culture or in infected tissue culture cells, we first isolated ActA by monoclonal antibody-based immunoaffinity chromatography. Polyclonal rabbit antisera raised against purified ActA revealed that ActA was associated with the cell wall and exposed on the surface of the bacteria, readily accessible to ActA antibodies. In contrast, a C-terminally truncated ActA1 polypeptide expressed by the isogenic actA1 mutant was detected only in the supernatant fluids. Immunofluorescence microscopy and electron microscopic studies using immunogold labeling showed that ActA was present on the surface of the bacteria infecting PtK2 and J774 cells at all stages of the infection cycle and was not found to be associated with the actin "tail" of individual bacteria. For the isogenic actA1 mutant strain, which grew as microcolonies within infected cells, only diffuse staining of the secreted ActA1 polypeptide in the host cytoplasm was observed. The ActA polypeptide therefore appears to be required in the initiation of actin accumulation by the bacterium and is apparently not directly involved in the generation of the actin tail. Analysis of strains of several L. monocytogenes serotypes indicated microheterogeneity in the molecular weights of the ActA polypeptides of individual strains and led to the detection of a serotype 3a strain that does not produce ActA. Images PMID:8514381

  11. Aortic Disease Presentation and Outcome Associated with ACTA2 mutations

    PubMed Central

    Regalado, Ellen S.; Guo, Dongchuan; Prakash, Siddharth; Bensend, Tracy A.; Flynn, Kelly; Estrera, Anthony; Safi, Hazim; Liang, David; Hyland, James; Child, Anne; Arno, Gavin; Boileau, Catherine; Jondeau, Guillaume; Braverman, Alan; Moran, Rocio; Morisaki, Takayuki; Morisaki, Hiroko; Consortium, Montalcino Aortic; Pyeritz, Reed; Coselli, Joseph; LeMaire, Scott; Milewicz, Dianna M.

    2015-01-01

    Background ACTA2 mutations are the major cause of familial thoracic aortic aneurysms and dissections. We sought to characterize these aortic diseases in a large case series of individuals with ACTA2 mutations. Methods and Results Aortic disease, management, and outcome associated with the first aortic event (aortic dissection or aneurysm repair) were abstracted from the medical records of 277 individuals with 41 various ACTA2 mutations. Aortic events occurred in 48% of these individuals, with the vast majority presenting with thoracic aortic dissections (88%) associated with 25% mortality. Type A dissections were more common than type B dissections (54% versus 21%), but the median age of onset of type B dissections was significantly younger than type A dissections (27 years, IQR 18–41 versus 36 years, IQR 26–45). Only 12% of aortic events were repair of ascending aortic aneurysms, which variably involved the aortic root, ascending aorta and aortic arch. Overall cumulative risk of an aortic event at age 85 years was 0.76 (95% CI 0.64, 0.86). After adjustment for intra-familial correlation, gender and race, mutations disrupting p.R179 and p.R258 were associated with significantly increased risk for aortic events, whereas p.R185Q and p.R118Q mutations showed significantly lower risk of aortic events compared to other mutations. Conclusions ACTA2 mutations are associated with high risk of presentation with an acute aortic dissection. The lifetime risk for an aortic event is only 76%, suggesting that additional environmental or genetic factors play a role in expression of aortic disease in individuals with ACTA2 mutations. PMID:25759435

  12. Cerebral arteriopathy associated with Arg179His ACTA2 mutation

    PubMed Central

    Amans, Matthew R; Stout, Charles; Fox, Christine; Narvid, Jared; Hetts, Steven W; Cooke, Daniel L; Higashida, Randall T; Dowd, Christopher F; McSwain, Hugh; Halbach, Van V

    2013-01-01

    ACTA2 mutations have recently been shown to cause a multisystem smooth muscle dysfunction syndrome that may result in pediatric stroke. We report a case of ACTA2 mutation in a 3-year-old girl presenting with acute ischemic stroke and provide high resolution imaging of the cerebral arteries demonstrating novel findings of multiple tiny aneurysms (particularly in the posterior circulation), as well as the more characteristic imaging phenotype of straightened and narrowed proximal intracranial vessels, dilated cervical vessels and occlusion of the M1 MCA segment without lenticulostriate collateral formation. This newly identified disease should be added to the differential diagnosis of pediatric stroke and cerebral vasculopathy. Neuroradiologists, interventionalists, surgeons and neurologists should become familiar with this rare disease and its clinical sequelae. PMID:24293535

  13. Cerebral arteriopathy associated with Arg179His ACTA2 mutation.

    PubMed

    Amans, Matthew R; Stout, Charles; Fox, Christine; Narvid, Jared; Hetts, Steven W; Cooke, Daniel L; Higashida, Randall T; Dowd, Christopher F; McSwain, Hugh; Halbach, Van V

    2013-01-01

    ACTA2 mutations have recently been shown to cause a multisystem smooth muscle dysfunction syndrome that may result in pediatric stroke. We report a case of ACTA2 mutation in a 3-year-old girl presenting with acute ischemic stroke and provide high resolution imaging of the cerebral arteries demonstrating novel findings of multiple tiny aneurysms (particularly in the posterior circulation), as well as the more characteristic imaging phenotype of straightened and narrowed proximal intracranial vessels, dilated cervical vessels and occlusion of the M1 MCA segment without lenticulostriate collateral formation. This newly identified disease should be added to the differential diagnosis of pediatric stroke and cerebral vasculopathy. Neuroradiologists, interventionalists, surgeons and neurologists should become familiar with this rare disease and its clinical sequelae. PMID:24293535

  14. Cerebral arteriopathy associated with Arg179His ACTA2 mutation.

    PubMed

    Amans, Matthew R; Stout, Charles; Fox, Christine; Narvid, Jared; Hetts, Steven W; Cooke, Daniel L; Higashida, Randall T; Dowd, Christopher F; McSwain, Hugh; Halbach, Van V

    2014-11-01

    ACTA2 mutations have recently been shown to cause a multisystem smooth muscle dysfunction syndrome that may result in pediatric stroke. We report a case of ACTA2 mutation in a 3-year-old girl presenting with acute ischemic stroke and provide high resolution imaging of the cerebral arteries demonstrating novel findings of multiple tiny aneurysms (particularly in the posterior circulation), as well as the more characteristic imaging phenotype of straightened and narrowed proximal intracranial vessels, dilated cervical vessels and occlusion of the M1 MCA segment without lenticulostriate collateral formation. This newly identified disease should be added to the differential diagnosis of pediatric stroke and cerebral vasculopathy. Neuroradiologists, interventionalists, surgeons and neurologists should become familiar with this rare disease and its clinical sequelae. PMID:24353327

  15. Langkocyclines: novel angucycline antibiotics from Streptomyces sp. Acta 3034(*).

    PubMed

    Kalyon, Bahar; Tan, Geok-Yuan A; Pinto, John M; Foo, Cheau-Yee; Wiese, Jutta; Imhoff, Johannes F; Süssmuth, Roderich D; Sabaratnam, Vikineswary; Fiedler, Hans-Peter

    2013-10-01

    Langkocyclines A1-A3 and B1 and B2, five new angucycline antibiotics produced by Streptomyces sp. Acta 3034, were detected in the course of our HPLC-diode array screening. The producing strain was isolated from the rhizospheric soil of a Clitorea sp. collected from Burau Bay, Langkawi, Malaysia, and was characterized by morphological, physiological and chemotaxonomic features in addition to 16S ribosomal RNA gene sequence information. Strain Acta 3034 is closely related to Streptomyces psammoticus NBRC 13971(T) and Streptomyces lanatus NBRC 12787(T). Langkocyclines consist of an angular tetracyclic benz[a]anthracene skeleton and hydrolyzable O-glycosidic sugar moieties. The yellow-colored A-type langkocyclines differ in their aglycon from the blue-lilac-colored B-type langkocyclines. The A-type langkocycline aglycon is identical to that of aquayamycin and urdamycin A. The chemical structures of the langkocyclines were elucidated by HR-MS, 1D and 2D NMR experiments. They are biologically active against Gram-positive bacteria and exhibit a moderate antiproliferative activity against various human tumor cell lines. PMID:23820614

  16. Comment on "Experimental study of the orientation dependence of indium incorporation in GaInN" [J. Cryst. Growth 433 (2016) 7-12

    NASA Astrophysics Data System (ADS)

    Monavarian, Morteza

    2016-07-01

    The authors of the title paper (J. Cryst. Growth 433 (2016) 7-12) reported on experimental comparison of indium incorporation efficiency in wide variety of orientations tilted from the basal plane toward a-plane (a-family planes) or m-plane (m-family planes) and some mixed planes. Despite a good investigation and useful information reported in this manuscript, some points of criticism, concerning the inclination angle calculations, optical characterizations of the layers, and the final conclusions are highlighted in this comment to consider.

  17. Smooth Muscle α Actin (Acta2) and Myofibroblast Function during Hepatic Wound Healing

    PubMed Central

    Rockey, Don C.; Weymouth, Nate; Shi, Zengdun

    2013-01-01

    Smooth muscle α actin (Acta2) expression is largely restricted to smooth muscle cells, pericytes and specialized fibroblasts, known as myofibroblasts. Liver injury, associated with cirrhosis, induces transformation of resident hepatic stellate cells into liver specific myofibroblasts, also known as activated cells. Here, we have used in vitro and in vivo wound healing models to explore the functional role of Acta2 in this transformation. Acta2 was abundant in activated cells isolated from injured livers but was undetectable in quiescent cells isolated from normal livers. Both cellular motility and contraction were dramatically increased in injured liver cells, paralleled by an increase in Acta2 expression, when compared with quiescent cells. Inhibition of Acta2 using several different techniques had no effect on cytoplasmic actin isoform expression, but led to reduced cellular motility and contraction. Additionally, Acta2 knockdown was associated with a significant reduction in Erk1/2 phosphorylation compared to control cells. The data indicate that Acta2 is important specifically in myofibroblast cell motility and contraction and raise the possibility that the Acta2 cytoskeleton, beyond its structural importance in the cell, could be important in regulating signaling processes during wound healing in vivo. PMID:24204762

  18. Acta Informatica Medica Is Indexed In Pubmed And Archived In Pubmed Central

    PubMed Central

    Masic, Izet

    2013-01-01

    Acta Informatica Medica journal has been accepted for archiving in PubMed Central from 2011 onward. The journal started in 1993 as the official journal of the Society for Medical Informatics of Bosnia and Herzegovina. During the last 3 years, Acta Informatica Medica has een included in almost all prestigious online databases, including PubMed, Scopus and EMBASE. The 20th volume of the journal is fully international, with papers from 18 countries. PMID:23572852

  19. Beitraege zur Astronomiegeschichte, Band 5 (Acta Historica Astronomiae Vol. 18)

    NASA Astrophysics Data System (ADS)

    Duerbeck, H. W.; Dick, W. R.; Hamel, J.

    2003-01-01

    The 18th volume of the Acta Historica Astronomiae is at the same time the sixth collection of essays on the history of astronomy ("Beitræge zur Astronomiegeschichte, Band 6"), edited by the historians of astronomy W.R. Dick (Potsdam) and J. Hamel (Berlin). Besides a few short notices and book reviews, the book contains eight major articles, which deal with astronomical topics covering the time from the 16th to the 19th centuries. The first article by Michael Weichenhan (Berlin) deals with "the invention of the disk-shaped earth: a chapter of Copernican apologetics". The author shows that the concept of a "disc-shaped Earth" was by no means widespread in the middle ages, but restricted to the father of the church Lactantius and some adherents. Nevertheless, it was used by adherents of Copernicus to show the absurd consequences of a strictly literal biblical interpretation -- here concerning the Earth's shape, disc versus sphere, there the geocentric versus the heliocentric system. This thorough philosophical study is followed by two very short articles. "The measuring accuracy of Tycho's large sextant" by Johann Wünsch investigates O-C values of planet-star distances, as based on Tycho's observations as published in the Historia Coelestis (a compilation, which is also based on Tycho's manuscripts, and published in Regensburg in 1672). The result is that standard deviations are 80 arcseconds for Saturn and 89 arcseconds for Jupiter and Mars, an unexpectedly poor result in view of the general opinion that Tycho was famous for his precision work. "The astronomer Christoph Grienberger and the Galilei trial" by Franz Daxecker deals with a Jesuit astronomer who was both the disciple and successor of the mathematician-astronomer Christopher Clavius at the Collegium Romanum. While he was inclined to Galilei early on, he was forced to propagate Aristotelian doctrine. The brief article is very concise, but extremely tiresome to read (3 pages of pure text are embellished by

  20. De Novo ACTA2 Mutation Causes a Novel Syndrome of Multisystemic Smooth Muscle Dysfunction

    PubMed Central

    Milewicz, Dianna M.; Østergaard, John R.; Ala-Kokko, Leena M.; Khan, Nadia; Grange, Dorothy K.; Mendoza-Londono, Roberto; Bradley, Timothy J.; Olney, Ann Haskins; Adès, Lesley; Maher, Joseph F.; Guo, Dongchuan; Buja, L. Maximilian; Kim, Dong; Hyland, James C.; Regalado, Ellen S.

    2011-01-01

    Smooth muscle cells (SMCs) contract to perform many physiological functions, including regulation of blood flow and pressure in arteries, contraction of the pupils, peristalsis of the gut and voiding of the bladder. SMC lineage in these organs is characterized by cellular expression of the SMC isoform of α-actin, encoded by the ACTA2 gene. We report here on a unique and de novo mutation in ACTA2, R179H, that causes a syndrome characterized by dysfunction of SMCs throughout the body, leading to aortic and cerebrovascular disease, fixed dilated pupils, hypotonic bladder, malrotation and hypoperistalsis of the gut and pulmonary hypertension. PMID:20734336

  1. Review of the Journal Acta Informatica Medica During Eight Year Period: 2008-2015

    PubMed Central

    Masic, Izet; Begic, Edin; Zunic, Lejla

    2016-01-01

    Introduction: Acta Informatica Medica is official journal of the Academy for Medical Sciences of Bosnia and Herzegovina (from 2014 Acta Inform Med is published bimonthly). Aim: To evaluate journal “Acta Informatica Medica” in 2015 and compare findings to previous years. Material and methods: The study has retrospective and descriptive character, and included the period 2008-2015 (included 36 issues of journal). Results: A total of 83 (average 13,8 articles per journal) articles were published in Acta Informatica Medica during 2015. Analyzing the type of articles, original articles are present in majority during 2015 (68,6%) (by analyzing last eight years, 310 (67,3%) were original). During 2015, 27,7% of articles were related to the applied of Health informatics in field of clinical medicine, 63,8% preclinical medicine and 8,5% to public health. Collaboration rate in 2015 was 0,84. Most often the time required for decision on acceptance of article in 2015 is between 50 and 60 days. Articles came from 16 countries. According to scimagojr.com for 2014, Acta Informatica Medica has SCImago Journal Rank 0,166, while Cites / Doc. (2 years) parameter (widely used as impact index) is 0,70. According to GoogleScholar, h5 index is 11 and h5 median is 19. We analyzed the Acta Informatica Medica by “Publish or Perish” software - H index was 14, g index was 19 and e-index was 10.39. Conclusion: Year after year the highest number of original articles are published. Although the period of revision of articles is acceptable, the period up to two months is certainly not long, the goal is to reduce this period. Although the magazine in mentioned field found its place, although it is indexed in numerous bases, including: PubMed, PubMed Central, SCOPUS, EMBASE, EBSCO, etc. The main goal for next year is that the magazine becomes part of the Web of Science. Imperative is further internationalization of the magazine. PMID:27147796

  2. Citation analysis of Acta Dermatovenerologica Alpina, Pannonica et Adriatica: 1992-2011.

    PubMed

    Ostrbenk, Anja; Skamperle, Mateja; Poljak, Mario

    2012-09-01

    Acta Dermatovenerologica Alpina, Pannonica et Adriatica is small regional professional journal that started publishing in 1992. Despite the journal's relatively narrow readership, it has significantly improved its quality and global profile during the last 20 years, as shown in this citation analysis update. Since 1992, 654 bibliographical items have been published. Among these, 545 (83.4%) were considered WoS citable items and 109 (16.6%) WoS noncitable items. Since 2008, 90% of all published items have been considered WoS citable items and received an average of 1.9 citations per item. The predicted Acta Dermatovenerol APA impact factor calculated using data from a Cited Reference search of Thomson Scientific's Web of Science has shown steep and continuous increase since 2006, when the journal acquired full indexing status in Index Medicus/Medline, and has been above 0.5 since 2008. PMID:23267871

  3. The action of cytochrome b(5) on CYP2E1 and CYP2C19 activities requires anionic residues D58 and D65.

    PubMed

    Peng, Hwei-Ming; Auchus, Richard J

    2013-01-01

    The capacity of cytochrome b(5) (b(5)) to influence cytochrome P450 activities has been extensively studied and physiologically validated. Apo-b(5) enhances the activities of CYP3A4, CYP2A6, CYP2C19, and CYP17A1 but not that of CYP2E1 or CYP2D6, suggesting that the b(5) interaction varies among P450s. We previously showed that b(5) residues E48 and E49 are required to stimulate the 17,20-lyase activity of CYP17A1, but these same residues might not mediate b(5) activation of other P450 reactions, such as CYP2E1-catalyzed oxygenations, which are insensitive to apo-b(5). Using purified P450, b(5), and reductase (POR) in reconstituted assays, the D58G/D65G double mutation, of residues located in a hydrophilic α-helix of b(5), totally abolished the ability to stimulate CYP2E1-catalyzed chlorzoxazone 6-hydroxylation. In sharp contrast, the D58G/D65G double mutation retained the full ability to stimulate the 17,20-lyase activity of CYP17A1. The D58G/D65G double mutation competes poorly with wild-type b(5) for binding to the CYP2E1·POR complex yet accepts electrons from POR at a similar rate. Furthermore, the phospholipid composition markedly influences P450 turnover and b(5) stimulation and specificity, particularly for CYP17A1, in the following order: phosphatidylserine > phosphatidylethanolamine > phosphatidylcholine. The D58G/D65G double mutation also failed to stimulate CYP2C19-catalyzed (S)-mephenytoin 4-hydroxylation, whereas the E48G/E49G double mutation stimulated these activities of CYP2C19 and CYP2E1 equivalent to wild-type b(5). We conclude that b(5) residues D58 and D65 are essential for the stimulation of CYP2E1 and CYP2C19 activities and that the phospholipid composition significantly influences the b(5)-P450 interaction. At least two surfaces of b(5) differentially influence P450 activities, and the critical residues for individual P450 reactions cannot be predicted from sensitivity to apo-b(5) alone. PMID:23193974

  4. The action of cytochrome b5 on both CYP2E1 and CYP2C19 activities requires the anionic residues D58 and D65

    PubMed Central

    Peng, Hwei-Ming; Auchus, Richard J.

    2013-01-01

    The capacity of cytochrome b5 (b5) to influence cytochrome P450 activities has been extensively studied and physiologically validated. Apo-b5 enhances the activities of CYP3A4, CYP2A6, CYP2C19, and CYP17A1 but not of CYP2E1 or CYP2D6, suggesting that the b5 interaction varies amongst P450s. We previously showed that b5 residues E48 and E49 are required to stimulate the 17,20-lyase activity of CYP17A1, but these same residues might not mediate b5 activation of other P450 reactions, such as CYP2E1-catalyzed oxygenations, which are insensitive to apo-b5. Using purified P450, b5, and reductase (POR) in reconstituted assays, mutation D58G+D65G, residues located in a hydrophilic α-helix of b5, totally abolished the ability to stimulate CYP2E1-catalyzed chlorzoxazone 6-hydroxylation. In sharp contrast, the D58G+D65G mutation retained full capability to stimulate the 17,20 lyase activity of CYP17A1. Mutation D58G+D65G competes poorly with wild-type b5 for binding to the CYP2E1•POR complex yet accepts electrons from POR at a similar rate. Furthermore, the phospholipid composition markedly influences P450 turnover and b5 stimulation and specificity, particularly for CYP17A1, in the order phosphatidylserine > phosphatidylethanolamine > phosphatidylcholine. Mutation D58G+D65G also failed to stimulate CYP2C19-catalyzed (S)-mephenytoin 4-hydroxylation, whereas mutation E48G+E49G stimulated these activities of CYP2C19 and CYP2E1 equivalent to wild-type b5. We conclude that b5 residues D58 and D65 are essential for the stimulation of CYP2E1 and CYP2C19 activities and that phospholipid composition significantly influences the b5-P450 interaction. At least two surfaces of b5 differentially influence P450 activities, and the critical residues for individual P450 reactions cannot be predicted from sensitivity to apo-b5 alone. PMID:23193974

  5. Novel MYH11 and ACTA2 mutations reveal a role for enhanced TGFβ signaling in FTAAD

    PubMed Central

    Renard, Marjolijn; Callewaert, Bert; Baetens, Machteld; Campens, Laurence; MacDermot, Kay; Fryns, Jean-Pierre; Bonduelle, Maryse; Dietz, Hal; Gaspar, Isabel Mendes; Cavaco, Diogo; Stattin, Eva-Lena; Schrander-Stumpel, Constance; Coucke, Paul; Loeys, Bart; De Paepe, Anne; De Backer, Julie

    2011-01-01

    Background Thoracic aortic aneurysm / dissection (TAAD) is a common phenotype that may occur as an isolated manifestation or within the constellation of a defined syndrome. In contrast to syndromic TAAD, the elucidation of the genetic basis of isolated TAAD has only recently started. To date, defects have been found in genes encoding extracellular matrix proteins (fibrillin-1, FBN1; collagen type III alpha 1, COL3A1), proteins involved in transforming growth factor beta (TGFβ) signaling (TGFβ receptor 1 and 2, TGFBR1/2; and SMAD3) or proteins that build up the contractile apparatus of aortic smooth muscle cells (myosin heavy chain 11, MYH11; smooth muscle actin alpha 2, ACTA2; and MYLK). Methods and results In 110 non-syndromic TAAD patients that previously tested negative for FBN1 or TGFBR1/2 mutations, we identified 7 ACTA2 mutations in a cohort of 43 familial TAAD patients, including 2 premature truncating mutations. Sequencing of MYH11 revealed an in frame splice-site alteration in one out of two probands with TAA(D) associated with PDA but none in the series of 22 probands from the cohort of 110 patients with non-syndromic TAAD. Interestingly, immunohistochemical staining of aortic biopsies of a patient and a family member with MYH11 and patients with ACTA2 missense mutations showed upregulation of the TGFβ signaling pathway. Conclusions MYH11 mutations are rare and typically identified in patients with TAAD associated with PDA. ACTA2 mutations were identified in 16% of a cohort presenting familial TAAD. Different molecular defects in TAAD may account for a different pathogenic mechanism of enhanced TGFβ signaling. PMID:21937134

  6. Myopathy-inducing mutation H40Y in ACTA1 hampers actin filament structure and function.

    PubMed

    Chan, Chun; Fan, Jun; Messer, Andrew E; Marston, Steve B; Iwamoto, Hiroyuki; Ochala, Julien

    2016-08-01

    In humans, more than 200 missense mutations have been identified in the ACTA1 gene. The exact molecular mechanisms by which, these particular mutations become toxic and lead to muscle weakness and myopathies remain obscure. To address this, here, we performed a molecular dynamics simulation, and we used a broad range of biophysical assays to determine how the lethal and myopathy-related H40Y amino acid substitution in actin affects the structure, stability, and function of this protein. Interestingly, our results showed that H40Y severely disrupts the DNase I-binding-loop structure and actin filaments. In addition, we observed that normal and mutant actin monomers are likely to form distinctive homopolymers, with mutant filaments being very stiff, and not supporting proper myosin binding. These phenomena underlie the toxicity of H40Y and may be considered as important triggering factors for the contractile dysfunction, muscle weakness and disease phenotype seen in patients. PMID:27112274

  7. Langkolide, a 32-membered macrolactone antibiotic produced by Streptomyces sp. Acta 3062.

    PubMed

    Helaly, Soleiman E; Kulik, Andreas; Zinecker, Heidi; Ramachandaran, Kamalanathan; Tan, Geok Yuan Annie; Imhoff, Johannes F; Süssmuth, Roderich D; Fiedler, Hans-Peter; Sabaratnam, Vikineswary

    2012-06-22

    A new 32-membered macrolactone antibiotic, named langkolide, was isolated from the mycelium of Streptomyces sp. Acta 3062. The langkolide structure was determined by HR-MS and 1D and 2D NMR as a 32-membered macrolactone connected from an overhanging polyketide tail to a naphthoquinone unit mediated by two carbohydrate moieties. The producing strain was isolated from a rhizosphere soil of Clitorea sp. collected at Burau Bay, Langkawi, Malaysia, and was characterized by its morphological and chemotaxonomic features in addition to its 16S rRNA gene sequence. It was identified as a member of the Streptomyces galbus clade. Langkolide exhibited various bioactivities including antimicrobial and antiproliferative activities. Furthermore, langkolide inhibited human recombinant phosphodiesterase 4 with an IC(50) value of 0.48 μM. PMID:22642587

  8. Publications on Albert Einstein, cosmology and theory of relativity in Acta Historica Astronomiae. An annotated bibliography. (German Title: Publikationen zu Albert Einstein, Kosmologie und Relativitätstheorie in Acta Historica Astronomiae. Eine annotierte Bibliographie)

    NASA Astrophysics Data System (ADS)

    Dick, Wolfgang R.

    This bibliography lists 15 publications which appeared in volumes 1 to 26 (1998 to 2005) in the series ``Acta Historica Astronomiae''. They concern life and work of Albert Einstein as well as the history of and modern developments in the theory of relativity and relativistic cosmology.

  9. Avoidance of Autophagy Mediated by PlcA or ActA Is Required for Listeria monocytogenes Growth in Macrophages

    PubMed Central

    Mitchell, Gabriel; Ge, Liang; Huang, Qiongying; Chen, Chen; Kianian, Sara; Roberts, Mary F.; Schekman, Randy

    2015-01-01

    Listeria monocytogenes is a facultative intracellular pathogen that escapes from phagosomes and grows in the cytosol of infected host cells. Most of the determinants that govern its intracellular life cycle are controlled by the transcription factor PrfA, including the pore-forming cytolysin listeriolysin O (LLO), two phospholipases C (PlcA and PlcB), and ActA. We constructed a strain that lacked PrfA but expressed LLO from a PrfA-independent promoter, thereby allowing the bacteria to gain access to the host cytosol. This strain did not grow efficiently in wild-type macrophages but grew normally in macrophages that lacked ATG5, a component of the autophagy LC3 conjugation system. This strain colocalized more with the autophagy marker LC3 (42% ± 7%) at 2 h postinfection, which constituted a 5-fold increase over the colocalization exhibited by the wild-type strain (8% ± 6%). While mutants lacking the PrfA-dependent virulence factor PlcA, PlcB, or ActA grew normally, a double mutant lacking both PlcA and ActA failed to grow in wild-type macrophages and colocalized more with LC3 (38% ± 5%). Coexpression of LLO and PlcA in a PrfA-negative strain was sufficient to restore intracellular growth and decrease the colocalization of the bacteria with LC3. In a cell-free assay, purified PlcA protein blocked LC3 lipidation, a key step in early autophagosome biogenesis, presumably by preventing the formation of phosphatidylinositol 3-phosphate (PI3P). The results of this study showed that avoidance of autophagy by L. monocytogenes primarily involves PlcA and ActA and that either one of these factors must be present for L. monocytogenes growth in macrophages. PMID:25776746

  10. Book Review: Beitraege zur Astronomiegeschichte, Band 5 (Acta Historica Astronomiae Vol. 15)

    NASA Astrophysics Data System (ADS)

    Duerbeck, H. W.; Dick, W. R.; Hamel, J.

    2002-12-01

    The 15th volume of the Acta Historica Astronomiae is at the same time the fifth collection of essays on the history of astronomy (Beitraege zur Astronomiegeschichte, Band 5), edited by the historians of astronomy W.R. Dick (Potsdam) and J. Hamel (Berlin). Besides a few short notices and book reviews, the book contains 11 major articles, which deal with astronomical topics covering the time from the 16th to the 20th centuries. The first article, on the analysis and interpretation of historical horoscopes as a source of the history of science, is based on the inaugural lecture of its author, Guenther Oestmann. After a general introduction, which deals with the principles of horoscope making, the author discusses the horoscope of Count Heinrich Ranzau (1526-1598), the Danish governor of Schleswig-Holstein, who was a friend of Tycho Brahe. Oestmann shows that the astronomical-mathematical basis of such a horoscope can be reconstructed and interpreted. However, it is hardly possible to gain an insight in the process how the interpretation of a horoscope was done in detail. The second and third articles, by Franz Daxecker, deal with Athanasius Kircher and Christoph Scheiner, two catholic astronomers of the 17th century. Kircher's Organum Mathematicum is a calculating device that can be used in the fields of arithmetic, geometry, chronology, astronomy, astrology and others. The author provides extracts of the description of the Organum taken from a book by Caspar Schott, which deal with chronology and astronomy. A photograph of the Organum indicates that this tool consists of a set of tables glued on wooden or cardboard, but details of its contents and applications remain pretty obscure for the reader - a few elaborated examples would have been helpful. The second paper deals with the life of Christoph Scheiner SJ, the co-discoverer of sunspots (next to Galileo), after leaving Rome in 1633 - the year of the Galileo trial. Scheiner spent his later years in the Austrian and

  11. Association of a Novel ACTA1 Mutation With a Dominant Progressive Scapuloperoneal Myopathy in an Extended Family

    PubMed Central

    Zukosky, Kristen; Meilleur, Katherine; Traynor, Bryan J.; Dastgir, Jahannaz; Medne, Livija; Devoto, Marcella; Collins, James; Rooney, Jachinta; Zou, Yaqun; Yang, Michele L.; Gibbs, J. Raphael; Meier, Markus; Stetefeld, Joerg; Finkel, Richard S.; Schessl, Joachim; Elman, Lauren; Felice, Kevin; Ferguson, Toby A.; Ceyhan-Birsoy, Ozge; Beggs, Alan H.; Tennekoon, Gihan; Johnson, Janel O.; Bönnemann, Carsten G.

    2015-01-01

    IMPORTANCE New genomic strategies can now be applied to identify a diagnosis in patients and families with previously undiagnosed rare genetic conditions. The large family evaluated in the present study was described in 1966 and now expands the phenotype of a known neuromuscular gene. OBJECTIVE To determine the genetic cause of a slowly progressive, autosomal dominant, scapuloperoneal neuromuscular disorder by using linkage and exome sequencing. DESIGN, SETTING, AND PARTICIPANTS Fourteen affected individuals in a 6-generation family with a progressive scapuloperoneal disorder were evaluated. Participants were examined at pediatric, neuromuscular, and research clinics from March 1, 2005, to May 31, 2014. Exome and linkage were performed in genetics laboratories of research institutions. MAIN OUTCOMES AND MEASURES Examination and evaluation by magnetic resonance imaging, ultrasonography, electrodiagnostic studies, and muscle biopsies (n = 3). Genetic analysis included linkage analysis (n = 17) with exome sequencing (n = 7). RESULTS Clinical findings included progressive muscle weakness in an initially scapuloperoneal and distal distribution, including wrist extensor weakness, finger and foot drop, scapular winging, mild facial weakness, Achilles tendon contractures, and diminished or absent deep tendon reflexes. Both age at onset and progression of the disease showed clinical variability within the family. Muscle biopsy specimens demonstrated type I fiber atrophy and trabeculated fibers without nemaline rods. Analysis of exome sequences within the linkage region (4.8 megabases) revealed missense mutation c.591C>A p.Glu197Asp in a highly conserved residue in exon 4 of ACTA1. The mutation cosegregated with disease in all tested individuals and was not present in unaffected individuals. CONCLUSIONS AND RELEVANCE This family defines a new scapuloperoneal phenotype associated with an ACTA1 mutation. A highly conserved protein, ACTA1 is implicated in multiple muscle

  12. Book Review: Beitraege zur Astronomiegeschichte, Band 5 (Acta Historica Astronomiae Vol. 15)

    NASA Astrophysics Data System (ADS)

    Duerbeck, H. W.; Dick, W. R.; Hamel, J.

    2002-12-01

    The 15th volume of the Acta Historica Astronomiae is at the same time the fifth collection of essays on the history of astronomy (Beitraege zur Astronomiegeschichte, Band 5), edited by the historians of astronomy W.R. Dick (Potsdam) and J. Hamel (Berlin). Besides a few short notices and book reviews, the book contains 11 major articles, which deal with astronomical topics covering the time from the 16th to the 20th centuries. The first article, on the analysis and interpretation of historical horoscopes as a source of the history of science, is based on the inaugural lecture of its author, Guenther Oestmann. After a general introduction, which deals with the principles of horoscope making, the author discusses the horoscope of Count Heinrich Ranzau (1526-1598), the Danish governor of Schleswig-Holstein, who was a friend of Tycho Brahe. Oestmann shows that the astronomical-mathematical basis of such a horoscope can be reconstructed and interpreted. However, it is hardly possible to gain an insight in the process how the interpretation of a horoscope was done in detail. The second and third articles, by Franz Daxecker, deal with Athanasius Kircher and Christoph Scheiner, two catholic astronomers of the 17th century. Kircher's Organum Mathematicum is a calculating device that can be used in the fields of arithmetic, geometry, chronology, astronomy, astrology and others. The author provides extracts of the description of the Organum taken from a book by Caspar Schott, which deal with chronology and astronomy. A photograph of the Organum indicates that this tool consists of a set of tables glued on wooden or cardboard, but details of its contents and applications remain pretty obscure for the reader - a few elaborated examples would have been helpful. The second paper deals with the life of Christoph Scheiner SJ, the co-discoverer of sunspots (next to Galileo), after leaving Rome in 1633 - the year of the Galileo trial. Scheiner spent his later years in the Austrian and

  13. Systematic mutational analysis of the amino-terminal domain of the Listeria monocytogenes ActA protein reveals novel functions in actin-based motility.

    PubMed

    Lauer, P; Theriot, J A; Skoble, J; Welch, M D; Portnoy, D A

    2001-12-01

    The Listeria monocytogenes ActA protein acts as a scaffold to assemble and activate host cell actin cytoskeletal factors at the bacterial surface, resulting in directional actin polymerization and propulsion of the bacterium through the cytoplasm. We have constructed 20 clustered charged-to-alanine mutations in the NH2-terminal domain of ActA and replaced the endogenous actA gene with these molecular variants. These 20 clones were evaluated in several biological assays for phenotypes associated with particular amino acid changes. Additionally, each protein variant was purified and tested for stimulation of the Arp2/3 complex, and a subset was tested for actin monomer binding. These specific mutations refined the two regions involved in Arp2/3 activation and suggest that the actin-binding sequence of ActA spans 40 amino acids. We also identified a 'motility rate and cloud-to-tail transition' region in which nine contiguous mutations spanning amino acids 165-260 caused motility rate defects and changed the ratio of intracellular bacteria associated with actin clouds and comet tails without affecting Arp2/3 activation. Several unusual motility phenotypes were associated with amino acid changes in this region, including altered paths through the cytoplasm, discontinuous actin tails in host cells and the tendency to 'skid' or dramatically change direction while moving. These unusual phenotypes illustrate the complexity of ActA functions that control the actin-based motility of L. monocytogenes. PMID:11886549

  14. Electrostatic and Hydrophobic Interactions Mediate Single-Stranded DNA Recognition and Acta2 Repression by Purine-Rich Element-Binding Protein B.

    PubMed

    Rumora, Amy E; Ferris, Lauren A; Wheeler, Tamar R; Kelm, Robert J

    2016-05-17

    Myofibroblast differentiation is characterized by an increased level of expression of cytoskeletal smooth muscle α-actin. In human and murine fibroblasts, the gene encoding smooth muscle α-actin (Acta2) is tightly regulated by a network of transcription factors that either activate or repress the 5' promoter-enhancer in response to environmental cues signaling tissue repair and remodeling. Purine-rich element-binding protein B (Purβ) suppresses the expression of Acta2 by cooperatively interacting with the sense strand of a 5' polypurine sequence containing an inverted MCAT cis element required for gene activation. In this study, we evaluated the chemical basis of nucleoprotein complex formation between the Purβ repressor and the purine-rich strand of the MCAT element in the mouse Acta2 promoter. Quantitative single-stranded DNA (ssDNA) binding assays conducted in the presence of increasing concentrations of monovalent salt or anionic detergent suggested that the assembly of a high-affinity nucleoprotein complex is driven by a combination of electrostatic and hydrophobic interactions. Consistent with the results of pH titration analysis, site-directed mutagenesis revealed several basic amino acid residues in the intermolecular (R267) and intramolecular (K82 and R159) subdomains that are essential for Purβ transcriptional repressor function in Acta2 promoter-reporter assays. In keeping with their diminished Acta2 repressor activity in fibroblasts, purified Purβ variants containing an R267A mutation exhibited reduced binding affinity for purine-rich ssDNA. Moreover, certain double and triple-point mutants were also defective in binding to the Acta2 corepressor protein, Y-box-binding protein 1. Collectively, these findings establish the repertoire of noncovalent interactions that account for the unique structural and functional properties of Purβ. PMID:27064749

  15. Twenty Years of Society of Medical Informatics of B&H and the Journal Acta Informatica Medica

    PubMed Central

    Masic, Izet

    2012-01-01

    In 2012, Health/Medical informatics profession celebrates five jubilees in Bosnia and Herzegovina: a) Thirty five years from the introduction of the first automatic manipulation of data; b) Twenty five years from establishing Society for Medical Informatics BiH; c) Twenty years from establishing scientific and professional journal of the Society for Medical Informatics of Bosnia and Herzegovina „Acta Informatica Medica“; d) Twenty years from establishing first Cathdra for Medical Informatics on biomedical faculties in Bosnia and Herzegovina and e) Ten years from the introduction of “Distance learning” in medical curriculum. All of the five mentioned activities in the area of Medical informatics had special importance and gave appropriate contribution in the development of Health/Medical informatics in Bosnia And Herzegovina. PMID:23322947

  16. Streptomyces rochei ACTA1551, an Indigenous Greek Isolate Studied as a Potential Biocontrol Agent against Fusarium oxysporum f.sp. lycopersici

    PubMed Central

    Kanini, Grammatiki S.; Katsifas, Efstathios A.; Savvides, Alexandros L.; Karagouni, Amalia D.

    2013-01-01

    Many studies have shown that several Greek ecosystems inhabit very interesting bacteria with biotechnological properties. Therefore Streptomyces isolates from diverse Greek habitats were selected for their antifungal activity against the common phytopathogenic fungus Fusarium oxysporum. The isolate encoded ACTA1551, member of Streptomyces genus, could strongly suppress the fungal growth when examined in antagonistic bioassays in vitro. The isolate was found phylogenetically relative to Streptomyces rochei after analyzing its 16S rDNA sequence. The influence of different environmental conditions, such as medium composition, temperature, and pH on the expression of the antifungal activity was thoroughly examined. Streptomyces rochei ACTA1551 was able to protect tomato seeds from F. oxysporum infection in vivo while it was shown to promote the growth of tomato plants when the pathogen was absent. In an initial effort towards the elucidation of the biochemical and physiological nature of ACTA1551 antifungal activity, extracts from solid streptomycete cultures under antagonistic or/and not antagonistic conditions were concentrated and fractionated. The metabolites involved in the antagonistic action of the isolate showed to be more than one and produced independently of the presence of the pathogen. The above observations could support the application of Streptomyces rochei ACTA1551 as biocontrol agent against F. oxysporum. PMID:23762841

  17. The beginnings of Acta Neurochirurgica and the work of Fritz Loew, chief editor from 1958 - 1997. An historical vignette.

    PubMed

    Reulen, Hans-Jürgen; Collmann, Hartmut

    2012-07-01

    Acta Neurochirurgica was founded in 1950, in the difficult time after World War II, by Mario Milletti (Bologna) and Wolfram Sorgo (Innsbruck), and published by Springer press, Vienna. From the beginning the new journal was conceived as an international journal with an impressive list of outstanding neurosurgeons in the editorial board. Only a few years later the issues appeared at irregular intervals due to individual problems of both editors. Wilhelm Tönnis took the initiative to keep the journal alive, when he asked-in consent with Springer press-his staff member Fritz Loew to continue the editorial work and to assemble a new prestigious editorial board. Loew succeeded with both tasks and remained editor-in-chief for nearly 38 years. Initially, all papers were published in the native languages of the authors: English, French, German, Italian and Spanish. With ongoing time the journal accepted manuscripts in English only. The slow progress of this process exemplifies the slow integration of the European countries. In 1971, at the founding meeting of the European Association of Neurosurgical Societies (EANS) in Prague, Acta Neurochirurgica became the official organ of the EANS. Right from the beginning of Acta Neurochirurgica, Supplement volumes were added. Also, the book series Advances and Technical Standards in Neurosurgery is an offspring of Acta Neurochirurgica. Acta Neurochirurgica has become one of the most important neurosurgical journals worldwide. This historical sketch is based on an interview with Fritz Loew, now 91 years old, to which data from the available literature and the Archives of German Neurosurgery, as well as personal information by several colleagues were added. PMID:22581432

  18. Treatment with ActRIIB-mFc Produces Myofiber Growth and Improves Lifespan in the Acta1 H40Y Murine Model of Nemaline Myopathy.

    PubMed

    Tinklenberg, Jennifer; Meng, Hui; Yang, Lin; Liu, Fujun; Hoffmann, Raymond G; Dasgupta, Mahua; Allen, Kenneth P; Beggs, Alan H; Hardeman, Edna C; Pearsall, R Scott; Fitts, Robert H; Lawlor, Michael W

    2016-06-01

    Nemaline myopathies (NMs) are a group of congenital muscle diseases caused by mutations in at least 10 genes and associated with a range of clinical symptoms. NM is defined on muscle biopsy by the presence of cytoplasmic rod-like structures (nemaline rods) composed of cytoskeletal material. Myofiber smallness is also found in many cases of NM and may represent a cause of weakness that can be counteracted by treatment. We have used i.p. injection of activin type IIB receptor (ActRIIB)-mFc (an inhibitor of myostatin signaling) to promote hypertrophy and increase strength in our prior murine work; we therefore tested whether ActRIIB-mFc could improve weakness in NM mice through myofiber hypertrophy. We report a study of ActRIIB-mFc treatment in the Acta1 H40Y mouse model of NM. Treatment of Acta1 H40Y mice produced significant increases in body mass, muscle mass, quadriceps myofiber size, and survival, but other measurements of strength (forelimb grip strength, ex vivo measurements of contractile function) did not improve. Our studies also identified that the complications of urethral obstruction are associated with mortality in male hemizygote Acta1 H40Y mice. The incidence of urethral obstruction and histologic evidence of chronic obstruction (inflammation) were significantly lower in Acta1 H40Y mice that had been treated with ActRIIB-mFc. ActRIIB-mFc treatment produces a mild benefit to the disease phenotype in Acta1 H40Y mice. PMID:27102768

  19. Advances in membrane protein crystallography: in situ and in meso data collection

    SciTech Connect

    Weyand, Simone; Tate, Christopher G.

    2015-05-23

    Membrane protein structural biology has made tremendous advances over the last decade but there are still many challenges associated with crystallization, data collection and structure determination. Two independent groups, Axford et al. [(2015), Acta Cryst. D71, 1228–1237] and Huang et al. [(2015), Acta Cryst. D71, 1238–1256], have published methods that make a major contribution to addressing these challenges.

  20. Vascular disease-causing mutation R258C in ACTA2 disrupts actin dynamics and interaction with myosin

    PubMed Central

    Lu, Hailong; Fagnant, Patricia M.; Bookwalter, Carol S.; Joel, Peteranne; Trybus, Kathleen M.

    2015-01-01

    Point mutations in vascular smooth muscle α-actin (SM α-actin), encoded by the gene ACTA2, are the most prevalent cause of familial thoracic aortic aneurysms and dissections (TAAD). Here, we provide the first molecular characterization, to our knowledge, of the effect of the R258C mutation in SM α-actin, expressed with the baculovirus system. Smooth muscles are unique in that force generation requires both interaction of stable actin filaments with myosin and polymerization of actin in the subcortical region. Both aspects of R258C function therefore need investigation. Total internal reflection fluorescence (TIRF) microscopy was used to quantify the growth of single actin filaments as a function of time. R258C filaments are less stable than WT and more susceptible to severing by cofilin. Smooth muscle tropomyosin offers little protection from cofilin cleavage, unlike its effect on WT actin. Unexpectedly, profilin binds tighter to the R258C monomer, which will increase the pool of globular actin (G-actin). In an in vitro motility assay, smooth muscle myosin moves R258C filaments more slowly than WT, and the slowing is exacerbated by smooth muscle tropomyosin. Under loaded conditions, small ensembles of myosin are unable to produce force on R258C actin-tropomyosin filaments, suggesting that tropomyosin occupies an inhibitory position on actin. Many of the observed defects cannot be explained by a direct interaction with the mutated residue, and thus the mutation allosterically affects multiple regions of the monomer. Our results align with the hypothesis that defective contractile function contributes to the pathogenesis of TAAD. PMID:26153420

  1. Vascular disease-causing mutation R258C in ACTA2 disrupts actin dynamics and interaction with myosin.

    PubMed

    Lu, Hailong; Fagnant, Patricia M; Bookwalter, Carol S; Joel, Peteranne; Trybus, Kathleen M

    2015-08-01

    Point mutations in vascular smooth muscle α-actin (SM α-actin), encoded by the gene ACTA2, are the most prevalent cause of familial thoracic aortic aneurysms and dissections (TAAD). Here, we provide the first molecular characterization, to our knowledge, of the effect of the R258C mutation in SM α-actin, expressed with the baculovirus system. Smooth muscles are unique in that force generation requires both interaction of stable actin filaments with myosin and polymerization of actin in the subcortical region. Both aspects of R258C function therefore need investigation. Total internal reflection fluorescence (TIRF) microscopy was used to quantify the growth of single actin filaments as a function of time. R258C filaments are less stable than WT and more susceptible to severing by cofilin. Smooth muscle tropomyosin offers little protection from cofilin cleavage, unlike its effect on WT actin. Unexpectedly, profilin binds tighter to the R258C monomer, which will increase the pool of globular actin (G-actin). In an in vitro motility assay, smooth muscle myosin moves R258C filaments more slowly than WT, and the slowing is exacerbated by smooth muscle tropomyosin. Under loaded conditions, small ensembles of myosin are unable to produce force on R258C actin-tropomyosin filaments, suggesting that tropomyosin occupies an inhibitory position on actin. Many of the observed defects cannot be explained by a direct interaction with the mutated residue, and thus the mutation allosterically affects multiple regions of the monomer. Our results align with the hypothesis that defective contractile function contributes to the pathogenesis of TAAD. PMID:26153420

  2. Host cell heparan sulfate proteoglycans mediate attachment and entry of Listeria monocytogenes, and the listerial surface protein ActA is involved in heparan sulfate receptor recognition.

    PubMed

    Alvarez-Domínguez, C; Vázquez-Boland, J A; Carrasco-Marín, E; López-Mato, P; Leyva-Cobián, F

    1997-01-01

    The mechanisms by which the intracellular pathogen Listeria monocytogenes interacts with the host cell surface remain largely unknown. In this study, we investigated the role of heparan sulfate proteoglycans (HSPG) in listerial infection. Pretreatment of bacteria with heparin or heparan sulfate (HS), but not with other glycosaminoglycans, inhibited attachment and subsequent uptake by IC-21 murine macrophages and CHO epithelial-like cells. Specific removal of HS from target cells with heparinase III significantly impaired listerial adhesion and invasion. Mutant CHO cells deficient in HS synthesis bound and internalized significantly fewer bacteria than wild-type cells did. Pretreatment of target cells with the HS-binding proteins fibronectin and platelet factor 4, or with heparinase III, impaired listerial infectivity only in those cells expressing HS. Moreover, a synthetic peptide corresponding to the HS-binding ligand in Plasmodium falciparum circumsporozoite protein (pepPf1) inhibited listerial attachment to IC-21 and CHO cells. A motif very similar to the HS-binding site of pepPf1 was found in the N-terminal region of ActA, the L. monocytogenes surface protein responsible for actin-based bacterial motility and cell-to-cell spread. In the same region of ActA, several clusters of positively charged amino acids which could function as HS-binding domains were identified. An ActA-deficient mutant was significantly impaired in attachment and entry due to altered HS recognition functions. This work shows that specific interaction with an HSPG receptor present on the surface of both professional and nonprofessional phagocytes is involved in L. monocytogenes cytoadhesion and invasion and strongly suggests that the bacterial surface protein ActA may be a ligand mediating HSPG receptor recognition. PMID:8975895

  3. Combined MRI and 31P-MRS Investigations of the ACTA1(H40Y) Mouse Model of Nemaline Myopathy Show Impaired Muscle Function and Altered Energy Metabolism

    PubMed Central

    Gineste, Charlotte; Le Fur, Yann; Vilmen, Christophe; Le Troter, Arnaud; Pecchi, Emilie; Cozzone, Patrick J.; Hardeman, Edna C.; Bendahan, David; Gondin, Julien

    2013-01-01

    Nemaline myopathy (NM) is the most common disease entity among non-dystrophic skeletal muscle congenital diseases. Mutations in the skeletal muscle α-actin gene (ACTA1) account for ∼25% of all NM cases and are the most frequent cause of severe forms of NM. So far, the mechanisms underlying muscle weakness in NM patients remain unclear. Additionally, recent Magnetic Resonance Imaging (MRI) studies reported a progressive fatty infiltration of skeletal muscle with a specific muscle involvement in patients with ACTA1 mutations. We investigated strictly noninvasively the gastrocnemius muscle function of a mouse model carrying a mutation in the ACTA1 gene (H40Y). Skeletal muscle anatomy (hindlimb muscles and fat volumes) and energy metabolism were studied using MRI and 31Phosphorus magnetic resonance spectroscopy. Skeletal muscle contractile performance was investigated while applying a force-frequency protocol (from 1–150 Hz) and a fatigue protocol (80 stimuli at 40 Hz). H40Y mice showed a reduction of both absolute (−40%) and specific (−25%) maximal force production as compared to controls. Interestingly, muscle weakness was associated with an improved resistance to fatigue (+40%) and an increased energy cost. On the contrary, the force frequency relationship was not modified in H40Y mice and the extent of fatty infiltration was minor and not different from the WT group. We concluded that the H40Y mouse model does not reproduce human MRI findings but shows a severe muscle weakness which might be related to an alteration of intrinsic muscular properties. The increased energy cost in H40Y mice might be related to either an impaired mitochondrial function or an alteration at the cross-bridges level. Overall, we provided a unique set of anatomic, metabolic and functional biomarkers that might be relevant for monitoring the progression of NM disease but also for assessing the efficacy of potential therapeutic interventions at a preclinical level. PMID:23613869

  4. BOOK REVIEW: Astronomie von Olbers bis Schwarzschild. Nationale Entwicklungen und internationale Beziehungen im 19. Jahrhundert (Acta Historica Astronomiae Vol. 16)

    NASA Astrophysics Data System (ADS)

    Sterken, C.; Dick, W. R.; Hamel, J.

    2002-12-01

    The 14th volume of the Acta Historica Astronomiae is the Proceedings of a Colloquium International Relationships in Astronomy (in German) organised by the History of Astronomy Section of the Astronomische Gesellschaft held on September 18 in Lilienthal, Germany. The book contains 13 articles on astronomical topics covering the 19th and 20th centuries. The first paper is by Guenther Oestmann and deals with contemporary assessments of Johann Hieronymus Schroeter's (1745-1816) astronomical works and with later judgements of the scientific importance and significance of his observations as seen by astronomers and historians. This report is complemented by a second article on Schroeter's 25-ft reflector in Lilienthal near Bremen. To this end, author Felix Luehning has constructed a scale model of the telescope, and shows how the building of a model brings a deeper understanding of function and handling of this instrument. This brings us to a third paper on telescope building in Lilienthal: Hans-Joachim Leue describes the cooperation of Johann Hieronymus Schroeter and Johann Gottlieb Schrader in developing a white reflecting metal alloy for use as telescope mirror. The fourth article, by Klaus Schillinger, describes on the basis of archival documents the aquisition history of the Herschel telescopes, including telescope quality check, repair and building. Memorial sites referring to Wilhelm Olbers, Johann Hieronymus Schroeter, Friedrich Wilhelm Bessel and Carl Friedrich Gauss are described by Arno Langkavel in two walks outlined in the very last paper of this book. Peter Brosche, in the fifth paper, discusses the rediscovery of Ceres in December1801, a discovery that was the result of the combined efforts of a theoretician (Gauss) and an observer (Zach). Juergen Hamel's paper is based on previously unused archival sources and discusses the outstanding role played by H. C. Schumacher (1780-1850, editor of the Astronomische Nachrichten) in the communication between

  5. Multimodal MRI and 31P-MRS Investigations of the ACTA1(Asp286Gly) Mouse Model of Nemaline Myopathy Provide Evidence of Impaired In Vivo Muscle Function, Altered Muscle Structure and Disturbed Energy Metabolism

    PubMed Central

    Gineste, Charlotte; Duhamel, Guillaume; Le Fur, Yann; Vilmen, Christophe; Cozzone, Patrick J.; Nowak, Kristen J.; Bendahan, David; Gondin, Julien

    2013-01-01

    Nemaline myopathy (NM), the most common non-dystrophic congenital disease of skeletal muscle, can be caused by mutations in the skeletal muscle α-actin gene (ACTA1) (~25% of all NM cases and up to 50% of severe forms of NM). Muscle function of the recently generated transgenic mouse model carrying the human Asp286Gly mutation in the ACTA1 gene (Tg(ACTA1)Asp286Gly) has been mainly investigated in vitro. Therefore, we aimed at providing a comprehensive picture of the in vivo hindlimb muscle function of Tg(ACTA1)Asp286Gly mice by combining strictly noninvasive investigations. Skeletal muscle anatomy (hindlimb muscles, intramuscular fat volumes) and microstructure were studied using multimodal magnetic resonance imaging (Dixon, T2, Diffusion Tensor Imaging [DTI]). Energy metabolism was studied using 31-phosphorus Magnetic Resonance Spectroscopy (31P-MRS). Skeletal muscle contractile performance was investigated while applying a force-frequency protocol (1–150 Hz) and a fatigue protocol (6 min–1.7 Hz). Tg(ACTA1)Asp286Gly mice showed a mild muscle weakness as illustrated by the reduction of both absolute (30%) and specific (15%) maximal force production. Dixon MRI did not show discernable fatty infiltration in Tg(ACTA1)Asp286Gly mice indicating that this mouse model does not reproduce human MRI findings. Increased T2 values were observed in Tg(ACTA1)Asp286Gly mice and might reflect the occurrence of muscle degeneration/regeneration process. Interestingly, T2 values were linearly related to muscle weakness. DTI experiments indicated lower λ2 and λ3 values in Tg(ACTA1)Asp286Gly mice, which might be associated to muscle atrophy and/or the presence of histological anomalies. Finally 31P-MRS investigations illustrated an increased anaerobic energy cost of contraction in Tg(ACTA1)Asp286Gly mice, which might be ascribed to contractile and non-contractile processes. Overall, we provide a unique set of information about the anatomic, metabolic and functional consequences

  6. 1,3,5-Tri-p-tolyl­pentane-1,5-diol

    PubMed Central

    Thiruvalluvar, A.; Chithiravel, R.; Muthusubramanian, S.; Butcher, R. J.

    2014-01-01

    In the title compound, C26H30O2, the central benzene ring forms dihedral angles of 14.85 (15) and 28.17 (14)° with the terminal benzene rings. The dihedral angle between the terminal benzene rings is 32.14 (13)°. The crystal packing exhibits two strong inter­molecular O—H⋯O hydrogen bonds, forming directed four-membered co-operative rings. A region of disordered electron density, most probably disordered ethyl acetate solvent mol­ecules, occupying voids of ca 519 Å3 for an electron count of 59, was treated using the SQUEEZE routine in PLATON [Spek (2009 ▶). Acta Cryst. D65, 148–155]. Their formula mass and unit-cell characteristics were not taken into account during refinement. The structure was refined as an inversion twin [absolute structure parameter = −0.3 (4)]. PMID:24764851

  7. Errors in Crystal structure of HINT from Helicobacter pylori

    PubMed Central

    Maize, Kimberly M.

    2016-01-01

    Inaccuracies in the article, Crystal structure of HINT from Helicobacter pylori by Tarique et al. [(2016) Acta Cryst. F72, 42–48] are presented, and a brief history of HINT nomenclature is discussed. PMID:27050269

  8. Erratum: Di-μ-nitrosyl-bis-[(η-penta-methyl-cyclo-penta-dien-yl)ruthenium(0)](Ru-Ru). Corrigendum.

    PubMed

    Pearsal, Matthew; Gembicky, Milan; Dominiak, Paulina; Larsen, Anna; Coppens, Philip

    2010-01-01

    The acknowledgement in the paper by Pearsal, Gembicky, Dominiak, Larsen & Coppens [Acta Cryst. (2007), E63, m2596] is extended and an omitted reference is added.[This corrects the article DOI: 10.1107/S1600536807045321.]. PMID:21578980

  9. Acta Mechanica Sinica (selected articles)

    NASA Astrophysics Data System (ADS)

    Ling, G.; Yin, X.; Jiang, J.; Li, K.

    1982-08-01

    Selected articles on fluid mechanics and heat transfer are presented. Topics discussed are: (1) the secondary vortex and the karman vortex formation; (2) viscous compressible flow in turbomachinery; (3) partial differential equations satisfied by stream functions in three dimensional turbomachinery flow; and (4) iridium electrostatic probe and its application in a high temperature wind tunnel.

  10. Acta mechanica sinica (Selected articles)

    NASA Astrophysics Data System (ADS)

    Lian, J.; Lu, W.

    1984-05-01

    The coherent structure of a turbulent boundary layer at zero pressure gradient and for the gradient of adverse pressure was investigated. The hydrogen bubble method was employed to examine the turbulent flow in a two dimensional diffusion sector in a water channel. In a separate work, tensor calculus was used to derive three dimensional weak conservation form equations, time dependent flow surface iterative equations, and characteristic theory of non-orthogonal spherical coordinates. These equations and theory are useful in solving the three dimensional turbomachine transonic flow field.

  11. Acta Mechanica Sinica (selected articles)

    NASA Astrophysics Data System (ADS)

    Guocan, L.; Xieyuan, Y.

    1982-05-01

    Articles on the following topics are presented: the early stages of unsteady flow around a cylinder at high Reynolds number and under laminar conditions; methods for solving three dimensional flow in turbomachinery; numerical computation of viscous compressible flow in turbomachinery; a high speed interferograph system for investigating fast phenomena; and statistical simulation of the aerodynamic behavior of the transitional region of flow past combined bodies of revolution at arbitrary angles of attack.

  12. Crystal structure of bis-p-anizidinegossypol with an unknown solvate.

    PubMed

    Honkeldieva, Muhabbat T; Talipov, Samat A; Kunafiev, Rishad; Ibragimov, Bakhtiyar T

    2015-12-01

    The title compound, C44H44N2O8, (systematic name: 1,1',6,6'-tetra-hydroxy-5,5'-diisopropyl-8,8'-bis-{[(4-meth-oxy-phen-yl)iminium-yl]meth-yl}-3,3'-dimethyl-2,2'-bi-naphthalene-7,7'-diolate) has been obtained by the addition of p-anizidine to gossypol dissolved in di-chloro-methane. In the solid state, the title compound exists in the enamine or quinoid form. The two naphthyl moieties are inclined to one another by 72.08 (5)°. The pendant phenyl rings are inclined at 22.26 (14) and 23.86 (13)° to the corresponding naphthyl rings. In the crystal, mol-ecules are incorporated into layers through inversion-related pairs of O-H⋯O inter-actions [graph sets R 2 (2)(20) and R 2 (2)(10)] and translation-related O-H⋯O inter-actions [graph set C(15)]. The packing of these layers in the crystal structure gives rise to channels in the [011] direction, with hydro-phobic inter-actions occurring between adjacent layers. The channels are 5-7 Å wide, and the void volume of each cell is 655 Å(3), corresponding to 26.6% of the cell volume. Disordered guest mol-ecules, probably solvent and water mol-ecules, occupy these voids of the crystal; their contribution to the scattering was removed with the SQUEEZE routine [Spek (2015 ▸). Acta Cryst. C71, 9-18] of PLATON [Spek (2009 ▸). Acta Cryst. D65, 148-155]. PMID:26870395

  13. Re-refinement of 4xan: hen egg-white lysozyme with carboplatin in sodium bromide solution

    PubMed Central

    Tanley, Simon W. M.; Schreurs, Antoine M. M.; Kroon-Batenburg, Loes M. J.; Helliwell, John R.

    2016-01-01

    A re-refinement of 4xan, hen egg-white lysozyme (HEWL) with carboplatin crystallized in NaBr solution, has been made and is published here as an addendum to Tanley et al. [(2014), Acta Cryst. F70, 1135–1142]. This follows a previous re-refinement and PDB deposition (4yem) by Shabalin et al. [(2015), Acta Cryst. D71, 1965–1979]. The critical evaluation of the original PDB deposition (4xan), and the subsequent critical examination of the re-refined structure (4yem), has led to an improved model (PDB code 5hmj). PMID:26919531

  14. Poly[aqua­{μ3-5-[(pyridin-2-ylmeth­yl)amino]­isophthalato-κ5 N,N′:O 1,O 1′:O 3}cobalt(II)

    PubMed Central

    Zhu, Xiao-Hong; Cheng, Xiao-Chun

    2011-01-01

    In the title polymer, {[Co(C14H10N2O4)(H2O)]·3.5H2O}n, the Co2+ ion is coordinated by three carboxyl­ate O atoms from two 5-[(pyridin-2-ylmeth­yl)amino]­isophthalate anions, two N atoms from a (pyridin-2-ylmeth­yl)amino group and an O atom from a water mol­ecule, furnishing a distorted CoO4N2 octa­hedral geometry. Each anion acts as a μ3-bridge, linking cobalt ions into a two-dimensional layer parallel to (100). The asymmetric unit also contains three and a half solvent water mol­ecules, which could not be modeled. Therefore, the diffraction contribution of the solvent water mol­ecules was removed by the subroutine SQUEEZE in PLATON [Spek (2009). Acta Cryst. D65, 148–155]. The crystal structure is stabilized by O—H⋯O hydrogen bonds in which the coordinated water mol­ecule acts as donor and the carboxyl­ate O atoms as acceptors. PMID:22199630

  15. (η6-Benzene)(carbonato-κ2 O,O′)[di­cyclohex­yl(naphthalen-1-ylmeth­yl)phosphane-κP]ruthenium(II) chloro­form tris­olvate

    PubMed Central

    Gowrisankar, Saravanan; Neumann, Helfried; Spannenberg, Anke; Beller, Matthias

    2014-01-01

    The title compound, [Ru(CO3)(η6-C6H6){(C6H11)2P(CH2C10H7)}]·3CHCl3, was synthesized by carbonation of [RuCl2(η6-C6H6){(C6H11)2P(CH2C10H7)}] with NaHCO3 in methanol at room temperature. The RuII atom is surrounded by a benzene ligand, a chelating carbonate group and a phosphane ligand in a piano-stool configuration. The crystal packing is consolidated by C—H⋯O and C—H⋯Cl hydrogen-bonding inter­actions between adjacent metal complexes and between the complexes and the solvent mol­ecules. The asymmetric unit contains one metal complex and three chloro­form solvent mol­ecules of which only one was modelled. The estimated diffraction contributions of the other two strongly disordered chloro­form solvent mol­ecules were substracted from the observed diffraction data using the SQUEEZE procedure in PLATON [Spek (2009 ▶). Acta Cryst. D65, 148–155]. PMID:25161531

  16. (Acetonitrile){2-[bis­(pyridin-2-ylmethyl-κ2 N)amino-κN]-N-(2,6-dimethyl­phen­yl)acetamide-κO}(perchlorato-κO)zinc (acetonitrile){2-[bis­(pyridin-2-ylmethyl-κ2 N)amino-κN]-N-(2,6-dimethyl­phen­yl)acetamide-κO}zinc tris­(perchlorate)

    PubMed Central

    Åstrand, Ove Alexander Høgmoen; Görbitz, Carl Henrik; Kristoffersen, Kenneth Aase; Rongved, Pål

    2013-01-01

    In the title salt, [Zn(C22H24N4O)(CH3CN)][Zn(ClO4)(C22H24N4O)(CH3CN)](ClO4)3, two differently coordinated zinc cations occur. In the first complex, the metal ion is coordinated by the N,N′,N′′,O-tetra­dentate acetamide ligand and an acetonitrile N atom, generating an approximate trigonal–bipyramidal coordination geometry, with the O atom in an equatorial site and the acetonitrile N atom in an axial site. In the second complex ion, a perchlorate ion is also bonded to the zinc ion, generating a distorted trans-ZnO2N4 octa­hedron. Of the uncoordinating perchlorate ions, one lies on a crystallographic twofold axis and one lies close to a twofold axis and has a site occupancy of 0.5. N—H⋯O and N—H⋯(O,O) hydrogen bonds are observed in the crystal. Disordered solvent mol­ecules occupy about 11% of the unit-cell volume; their contribution to the scattering was removed with the SQUEEZE routine of the PLATON program [Spek (2009 ▶). Acta Cryst. D65, 148–155.]. PMID:23424407

  17. Di-μ-carbonyl-bis­[bis­(triphenyl­phos­phane)rhodium(0)](Rh—Rh) acetone disolvate1

    PubMed Central

    Gueorguieva, Petia G.; Laneman, Scott A.; Stanley, George G.; Fronczek, Frank R.; Watkins, Steven F.

    2012-01-01

    The dirhodium complex, [Rh2(C18H15P)4(CO)2]·2(CH3)2CO, has crystallographic twofold symmetry and the Rh—Rh distance is 2.6266 (8) Å. The four atoms proximate to each Rh atom [Rh—P = 2.3222 (7) and 2.3283 (8) Å, and Rh—C = 1.961 (3) and 2.045 (3) Å] form a distorted tetra­hedron with large deviations from the putative tetra­hedral angles [r.m.s. deviation = 23 (1)°]. The six angles more closely approximate those of a trigonal bipyramid [r.m.s. deviation = 14 (1)°] with one missing equatorial ligand. The two bridging carbonyl ligands are much more linearly coordinated to one Rh [Rh—C O = 151.0 (2)°] than to the other [127.0 (2)°], and the two Rh2CO planes form a dihedral angle of 45.43 (5)°. The two acetone solvent mol­ecules are disordered, and their estimated scattering contribution was subtracted from the observed diffraction data using the SQUEEZE routine in PLATON [Spek (2009 ▶). Acta Cryst. D65, 148–155]. PMID:23284375

  18. (2.2.2-Cryptand)potassium bis­(cyanato-κN)(5,10,15,20-tetra­phenyl­por­phy­rin­ato-κ4 N)cobaltate(III) chloro­benzene hemisolvate

    PubMed Central

    Belhaj Ali, Bader; Belkhiria, Mohamed Salah; Daran, Jean-Claude; Nasri, Habib

    2012-01-01

    In the title compound, [K(C18H36N2O6)][Co(NCO)2(C44H28N4)]·0.5C6H5Cl or [K(2,2,2-crypt)+][CoIII(NCO)2(TPP)−]·0.5C6H5Cl, the CoIII ion is octa­hedrally coordin­ated by two axial N-bonded NCO− anions and four pyrrole N atoms of the porphyrin. There is a major ruffling distortion of the porphyrin: the dihedral angles between trans pyrrole rings are 34.32 (14) and 34.72 (14)°. The potassium ion is coordinated by the six O atoms and two N atoms of the cryptand-222 mol­ecule and a weak K—O [3.407 (3) Å] bond to one of the cyanate O atoms also occurs. The packing also features weak C—H⋯O and C—H⋯π inter­actions. The contribution to the scattering of the disordered chloro­benzene solvent mol­ecules was removed with the SQUEEZE function in PLATON [Spek (2009 ▶). Acta Cryst. D65, 148–155]. PMID:23125591

  19. Polarization in RMnO3 multiferroics.

    PubMed

    Pirogov, A N

    2016-02-01

    Some comments on the review by Sim et al. [(2016). Acta Cryst. B72, 3-19] are given. The review is devoted to hexagonal multiferroics RMnO3, in which there are ferroelectric and magnetic orders. Strong interaction between these orders causes a series of interesting properties of multiferroics. PMID:26830791

  20. CrystTwiV: a webserver for automated phase extension and refinement in X-ray crystallography

    PubMed Central

    Thireou, Trias; Atlamazoglou, Vassilis; Levakis, Manolis; Eliopoulos, Elias; Hountas, Athanassios; Tsoucaris, George; Bethanis, Kostas

    2007-01-01

    An important stage in macromolecular crystallography is that of phase extension and refinement when initial phase estimates are available from isomorphous replacement or anomalous scattering or other methods. For this purpose, an alternative method called the twin variables (TwiV) method has been proposed. The algorithm is based on alternately transferring the phase information between the twin variable sets. The phase extension and refinement is evaluated with the crystallographic symmetry test by deliberately sacrificing the space-group symmetry in the starting set, then using its re-appearance as a criterion for correctness. Here we present a software program (CrysTwiV) that runs on the web (freely available at: http://btweb.aua.gr/crystwiv/) implementing the above-mentioned method. PMID:17488848

  1. Ethyl­enedi­ammonium sodium tetra­kis­[bis­(ethyl­enedi­amine-κ2 N,N′)(oxalato-κ2 O 1,O 2)cobalt(III)] [penta­hydrogen di(phosphato­octa­deca­tungstate)] tetra­deca­hydrate

    PubMed Central

    Zhang, Shuzhuo; Wang, Jing; Xu, Yun

    2013-01-01

    The title compound, Na(C2H10N2)[Co(C2O4)(C2H8N2)2]4[H5(P2W18O62)2]·14H2O, prepared under hydro­thermal conditions, consists of two Dawson-type [P2W18O62]6− anions, four isolated [Co(en)2(ox)]+ cations (en = ethyl­enedi­amine and ox = oxalate), one Na+ cation, one [H2en]2+ cation, and a number of ordered (14) and disordered solvent water mol­ecules. The [P2W18O62]6− polyoxidometalate anion has site symmetry 1 and contains two structurally distinct types of W atoms: viz. six W atoms on vertical pseudo-mirror planes grouped in two sets of three, and 12 equatorial W atoms that do not lie in the pseudo-mirror planes grouped in two sets of six. In each [Co(en)2(ox)]+ cation, the CoIII ion is coordinated by four N atoms from two en ligands and two O atoms from the ox ligands, completing a distorted octa­hedral structure. The sodium cation lies on an inversion centre and additionally links the complex cations and anions. In the crystal, the various units are linked by N—H⋯O and O—H⋯O hydrogen bonds, which together with C—H⋯O hydrogen bonds form a three-dimensional structure. The contribution of a region of disordered electron density, possibly highly disordered solvent water mol­ecules, to the scattering was removed with the SQUEEZE option of PLATON [Spek (2009 ▶). Acta Cryst. D65, 148–155]. To equilibrate the charges five H+ ions have been added to the polyoxidometalate. These H+ ions and the disordered solvent contribution were not included in the reported mol­ecular weight and density. PMID:24454036

  2. 3-(1H-Indol-3-yl)-2-(2-nitro­benzene­sulfonamido)­propanoic acid including an unknown solvate

    PubMed Central

    Khan, Islam Ullah; Mubashar-ur-Rehman, Hafiz; Aziz, Salman; Harrison, William T. A.

    2012-01-01

    In the title compound, C17H15N3O6S, which crystallized with highly disordered methanol and/or water solvent mol­ecules, the dihedral angle between the the indole and benzene ring systems is 5.3 (2)°, which allows for the formation of intra­molecular π–π stacking inter­actions [centroid–centroid separations = 3.641 (3) and 3.694 (3) Å] and an approximate overall U-shape for the mol­ecule. In the crystal, dimers linked by pairs of Ns—H⋯Oc (s = sulfonamide and c = carboxyl­ate) hydrogen bonds generate R 2 2(10) loops, whereas Ni—H⋯π (i = indole) inter­actions lead to chains propagating in [100] or [010]. Together, these lead to a three-dimensional network in which the solvent voids are present as inter­secting (two-dimensional) systems of [100] and [010] channels. The title compound was found to contain a heavily disordered solvent mol­ecule, which could be methanol or water or a mixture of the two. Due to its uncertain nature and the unresolvable disorder, the data were processed with the SQUEEZE option in PLATON [Spek (2009 ▶). Acta Cryst. D65, 148–155], which revealed 877.8 Å3 of solvent-accessible volume per unit cell and 126 electron-units of scattering density or 109.7 Å3 (16 electron units) per organic mol­ecule.. This was not included in the calculations of overall formula weight, density and absorption coefficient. PMID:22807845

  3. Second monoclinic polymorph of 4-[(1H-benzimidazol-1-yl)meth­yl]benzoic acid

    PubMed Central

    Kuai, Hai-Wei; Cheng, Xiao-Chun

    2011-01-01

    Recently, we reported the first monoclinic [Kuai & Cheng (2011). Acta Cryst., E67, o2787] and the ortho­rhom­bic polymorph [Kuai & Cheng (2011). Acta Cryst., E67, o3014] of the title compound, C15H12N2O2. Another monoclinic polymorph was obtained accidentally by the hydro­thermal reaction of the title compound with manganese chloride in the presence of potassium hydroxide at 413 K. The asymmetric unit consists of four independent mol­ecules. In the crystal, O—H⋯N hydrogen bonds link the independent mol­ecules into four separate chains parallel to the b axis. PMID:22199726

  4. Periodic entanglement III: tangled degree-3 finite and layer net intergrowths from rare forests.

    PubMed

    Evans, Myfanwy E; Hyde, Stephen T

    2015-11-01

    Entanglements of two-dimensional honeycomb nets are constructed from free tilings of the hyperbolic plane (H2) on triply periodic minimal surfaces. The 2-periodic nets that comprise the structures are guaranteed by considering regular, rare free tilings in H2. This paper catalogues an array of entanglements that are both beautiful and challenging for current classification techniques, including examples that are realized in metal-organic materials. The compactification of these structures to the genus-3 torus is considered as a preliminary method for generating entanglements of finite θ-graphs, potentially useful for gaining insight into the entanglement of the periodic structure. This work builds on previous structural enumerations given in Periodic entanglement Parts I and II [Evans et al. (2013). Acta Cryst. A69, 241-261; Evans et al. (2013). Acta Cryst. A69, 262-275]. PMID:26522409

  5. 4-(3-Fluoro­phen­yl)-1-(propan-2-yl­idene)thio­semicarbazone

    PubMed Central

    Miroslaw, Barbara; Szulczyk, Daniel; Koziol, Anna E.; Struga, Marta

    2011-01-01

    The title compound, C10H12FN3S, crystallizes in the same space group (P21/c) as two polymorphic forms of 4-phenyl-1-(propan-2-yl­idene)thio­semicarbazone [Jian et al. (2005). Acta Cryst. E61, o653–o654; Venkatraman et al. (2005). Acta Cryst. E61, o3914–o3916]. The arrangement of mol­ecules relative to the twofold screw axes is similar to that in the crystal structure of the lower density polymorph. In the solid state, the mol­ecular conformation is stabilized by an intra­molecular N—H⋯N hydrogen bond. The mol­ecules form centrosymmetric R 2 2(8) dimers in the crystal through pairs of N—H⋯S hydrogen bonds. PMID:22220027

  6. Triclinic polymorph of 4-[4-(4-formyl-phen-oxy)but-oxy]benzaldehyde.

    PubMed

    Balić, Tomislav; Marković, Berislav; Balić, Ivana

    2013-01-01

    The title compound, C18H18O4, is a triclinic polymorph of the previously reported monoclinic polymorph [Han & Zhen (2005 ▶). Acta Cryst. E61, o4358-o4359]. In the crystal of the triclinic polymorph, molecules are linked by two pairs of C-H⋯O hydrogen bonds, forming a two-dimensional network parallel to (102), and enclosing loops with graph set motifs of R2(2)(8) and R2(2)(6). PMID:23476387

  7. Triclinic polymorph of 4-[4-(4-formyl­phen­oxy)but­oxy]benzaldehyde

    PubMed Central

    Balić, Tomislav; Marković, Berislav; Balić, Ivana

    2013-01-01

    The title compound, C18H18O4, is a triclinic polymorph of the previously reported monoclinic polymorph [Han & Zhen (2005 ▶). Acta Cryst. E61, o4358–o4359]. In the crystal of the triclinic polymorph, molecules are linked by two pairs of C—H⋯O hydrogen bonds, forming a two-dimensional network parallel to (102), and enclosing loops with graph set motifs of R 2 2(8) and R 2 2(6). PMID:23476387

  8. Bis(1,3-dimethyl-1H-imidazolium) hexa-fluoro-silicate methanol 0.33-solvate.

    PubMed

    Tian, Chong; Nie, Wanli; Borzov, Maxim V

    2013-01-01

    The title compound, 6C5H9N2 (+)·3SiF6 (2-)·CH3OH, (I), was prepared by recrystallization of the crude salt from methanol along with solvent-free 2C5H9N2 (+)·SiF6 (2-) (II). Crystals of these solvatomorphs can be separated manually. The solvate (I) crystallizes in a rare hexa-gonal space group P6/mcc. Its asymmetric unit comprises one half of an imidazolium cation bis-ected by the crystallographic m-plane, one-sixth and one-twelfth of two crystallographically independent SiF6 (2-) dianions (Si atoms are located on the 3.2 and 6/m inversion centres), and one-twelfth of a methanol mol-ecule (C atoms are situated on the 622 inversion centres, other atoms are disordered between general positions). In (I), all F atoms of 3.2-located SiF6 (2-) dianions participate in the formation of symmetry-equivalent contacts to the H atoms of imidazolium fragments, thus forming rod-type ensembles positioned on the -6 axes. These 'pillar' rods are, in turn, F⋯H inter-linked through SiF6 (2-) dianions disordered around the 6/m centres. The twelvefold disordered methanol mol-ecules are appended to this array by O-H⋯F hydrogen bonds to the 6/m located SiF6 (2-) dianions. In terms of graph-set notation, the first and second level networks in (I) are N 1 = C 2 (2)(7)[3R 4 (4)(14)]D 2 (2)(4) and N 2 = D 2 (2)(5) (C-H⋯O hydrogen bonds are not considered). After locating all symmetrically independent atoms in the cation and anions, there remained a strong (> 3 e Å(-3)) residual electron density peak located at the 622 inversion centre. Treatment of this pre-refined model with the SQUEEZE procedure in PLATON [Spek (2009). Acta Cryst. D65, 148-155] revealed two voids per unit cell, indicative of the presence of the solvent methanol mol-ecule disordered about the 622 inversion centre. PMID:24109311

  9. Bis(1,3-dimethyl-1H-imidazolium) hexa­fluoro­silicate methanol 0.33-solvate

    PubMed Central

    Tian, Chong; Nie, Wanli; Borzov, Maxim V.

    2013-01-01

    The title compound, 6C5H9N2 +·3SiF6 2−·CH3OH, (I), was prepared by recrystallization of the crude salt from methanol along with solvent-free 2C5H9N2 +·SiF6 2− (II). Crystals of these solvatomorphs can be separated manually. The solvate (I) crystallizes in a rare hexa­gonal space group P6/mcc. Its asymmetric unit comprises one half of an imidazolium cation bis­ected by the crystallographic m-plane, one-sixth and one-twelfth of two crystallographically independent SiF6 2– dianions (Si atoms are located on the 3.2 and 6/m inversion centres), and one-twelfth of a methanol mol­ecule (C atoms are situated on the 622 inversion centres, other atoms are disordered between general positions). In (I), all F atoms of 3.2-located SiF6 2– dianions participate in the formation of symmetry-equivalent contacts to the H atoms of imidazolium fragments, thus forming rod-type ensembles positioned on the -6 axes. These ‘pillar’ rods are, in turn, F⋯H inter­linked through SiF6 2– dianions disordered around the 6/m centres. The twelvefold disordered methanol mol­ecules are appended to this array by O—H⋯F hydrogen bonds to the 6/m located SiF6 2– dianions. In terms of graph-set notation, the first and second level networks in (I) are N 1 = C 2 2(7)[3R 4 4(14)]D 2 2(4) and N 2 = D 2 2(5) (C—H⋯O hydrogen bonds are not considered). After locating all symmetrically independent atoms in the cation and anions, there remained a strong (> 3 e Å−3) residual electron density peak located at the 622 inversion centre. Treatment of this pre-refined model with the SQUEEZE procedure in PLATON [Spek (2009). Acta Cryst. D65, 148–155] revealed two voids per unit cell, indicative of the presence of the solvent methanol mol­ecule disordered about the 622 inversion centre. PMID:24109311

  10. The Crystallography of Quasicrystals

    NASA Astrophysics Data System (ADS)

    Rabson, David Alan

    A century ago, E. S. Fedorov, A. Schonflies, and W. Barlow, working independently, classified the 230 distinct symmetry groups of objects repeated periodically in three-dimensional space. The 230 space groups determine the symmetries of macroscopic properties and provide crystallographers with their most important tool in deducing structure; as such, they find use in biology, organic chemistry, and virology as well as in physics, geology, and materials science. With the discovery in 1984 of quasicrystals, well-ordered but aperiodic metallic alloys with crystallographically forbidden rotational symmetries, the need arose to develop a space-group theory for these new materials. Based on the work by Rokhsar, Wright, and Mermin^1 in two dimensions, Rabson, Mermin, Rokhsar, and Wright have classified all quasicrystal and crystal three -dimensional axial space groups.^2 Our classification, proceeding in reciprocal space, is elementary, does not rely on projecting higher-dimensional crystallographic space groups, and is valid for arbitrary rotational symmetry. As an additional illustration of quasicrystallographic space groups, I derive and demonstrate algorithms that produce two-dimensional tilings of rhombi with each of the possible plane-group symmetries.^3 While the analogous task for crystallographic plane groups is trivial, the lack of translational symmetry in a quasicrystal tiling makes these constructions interesting. Since the symmetry of a quasicrystal appears more naturally in reciprocal than in direct space, it is not surprising that some of the resulting tilings seem intricate, although in fact their symmetries are quite simple. ftn^1 Acta Cryst. A44, 197-211 (1988). ^2 "The Space Groups of Axial Crystals and Quasicrystals," preprint. ^3See also Rabson, Ho, and Mermin, Acta Cryst. A44, 678 (1988) and Acta Cryst. A45, 538 (1989).

  11. Density- and wavefunction-normalized Cartesian spherical harmonics for l ≤ 20.

    PubMed

    Michael, J Robert; Volkov, Anatoliy

    2015-03-01

    The widely used pseudoatom formalism [Stewart (1976). Acta Cryst. A32, 565-574; Hansen & Coppens (1978). Acta Cryst. A34, 909-921] in experimental X-ray charge-density studies makes use of real spherical harmonics when describing the angular component of aspherical deformations of the atomic electron density in molecules and crystals. The analytical form of the density-normalized Cartesian spherical harmonic functions for up to l ≤ 7 and the corresponding normalization coefficients were reported previously by Paturle & Coppens [Acta Cryst. (1988), A44, 6-7]. It was shown that the analytical form for normalization coefficients is available primarily for l ≤ 4 [Hansen & Coppens, 1978; Paturle & Coppens, 1988; Coppens (1992). International Tables for Crystallography, Vol. B, Reciprocal space, 1st ed., edited by U. Shmueli, ch. 1.2. Dordrecht: Kluwer Academic Publishers; Coppens (1997). X-ray Charge Densities and Chemical Bonding. New York: Oxford University Press]. Only in very special cases it is possible to derive an analytical representation of the normalization coefficients for 4 < l ≤ 7 (Paturle & Coppens, 1988). In most cases for l > 4 the density normalization coefficients were calculated numerically to within seven significant figures. In this study we review the literature on the density-normalized spherical harmonics, clarify the existing notations, use the Paturle-Coppens (Paturle & Coppens, 1988) method in the Wolfram Mathematica software to derive the Cartesian spherical harmonics for l ≤ 20 and determine the density normalization coefficients to 35 significant figures, and computer-generate a Fortran90 code. The article primarily targets researchers who work in the field of experimental X-ray electron density, but may be of some use to all who are interested in Cartesian spherical harmonics. PMID:25727874

  12. A monoclinic form of dendocarbin A: a borderline case of one-dimensional isostructural polymorphism.

    PubMed

    Paz, Cristian; Burgos, Viviana; Suarez, Sebastián; Baggio, Ricardo

    2015-04-01

    The title compound, dendocarbin A [systematic name: (1R,5aS,9aS,9bR)-1-hydroxy-6,6,9a-trimethyldodecahydronaphtho[1,2-c]furan-3-one], C15H22O3, is a sesquiterpene lactone isolated from Drimys winteri var chilensis. The monoclinic phase described herein displays an identical molecular structure to the orthorhombic phase that we reported previously [Paz Robles et al. (2014). Acta Cryst. C70, 1007-1010], while varying significantly in chain pitch, and can thus be considered as a borderline case of one-dimensional isostructural polymorphism. PMID:25836288

  13. (E)-Ethyl 3-(3,4-dihydroxyphenyl)prop-2-enoate: a natural polymorph extracted from Aristotelia chilensis (Maqui).

    PubMed

    Paz, Cristian; Moreno, Yanko; Becerra, José; Silva, Mario; Burgos, Viviana; Freire, Eleonora; Baggio, Ricardo

    2013-07-01

    The natural title compound, C11H12O4, extracted from the Chilean native tree Aristotelia chilensis (Maqui), is a polymorph of the synthetic E form reported by Xia, Hu & Rao [Acta Cryst. (2004), E60, o913-o914]. Both rotational conformers are identical from a metrical point of view, and only differ in the orientation of the 3,4-dihydroxyphenyl ring with respect to the rest of the molecule, which leads to completely different crystal structure arrangements and packing efficiencies. The reasons behind both reside in the different hydrogen-bonding interactions. PMID:23832039

  14. On the effective ionic radii for ammonium.

    PubMed

    Sidey, Vasyl

    2016-08-01

    A set of effective ionic radii corresponding to different coordination numbers (CNs) and compatible with the radii system by Shannon [Acta Cryst. (1976), A32, 751-767] has been derived for ammonium: 1.40 Å (CN = IV), 1.48 Å (CN = VI), 1.54 Å (CN = VIII) and 1.67 Å (CN = XII). The bond-valence parameters r0 = 2.3433 Å and B = 0.262 Å have been determined for ammonium-fluorine bonds. PMID:27484382

  15. The application of eigensymmetries of face forms to X-ray diffraction intensities of crystals twinned by `reticular merohedry'

    NASA Astrophysics Data System (ADS)

    Klapper, H.; Hahn, Th

    2012-01-01

    Crystallographic face forms {hkl} are interpreted as sets of symmetry-equivalent X-ray reflections. Extending an earlier paper on twinning by merohedry [ [Sigma] = 1, Klapper & Hahn (2010). Acta Cryst. A66, 327-346], the eigensymmetry of these forms is used to derive general relations between the diffraction intensities of overlapping twin-related reflections. The following twins by reticular merohedry are treated: [Sigma] 3 twins of rhombohedral and cubic, [Sigma] 5 twins of tetragonal and [Sigma] 7 twins of hexagonal crystals.

  16. Crystal structure of benzene-1,3,5-tri-carb-oxy-lic acid-4-pyridone (1/3).

    PubMed

    Staun, Selena L; Oliver, Allen G

    2015-11-01

    Slow co-crystallization of a solution of benzene-1,3,5-tri-carb-oxy-lic acid with a large excess of 4-hy-droxy-pyridine produces an inter-penetrating, three-dimensional, hydrogen-bonded framework consisting of three 4-pyridone and one benzene-1,3,5-tri-carb-oxy-lic acid mol-ecules, C9H6O6·3C5H5NO. This structure represents an ortho-rhom-bic polymorph of the previously reported C-centered, monoclinic structure [Campos-Gaxiola et al. (2014 ▸). Acta Cryst. E70, o453-o454]. PMID:26594492

  17. Redetermination of tetra­kis(N,N-diethyl­dithio­carbamato)tin(IV)

    PubMed Central

    Okio, Coco K. Y. A.; Speziali, Nivaldo L.

    2009-01-01

    The crystal structure of the title compound, [Sn(C5H10NS2)4], was originally determined by Harreld & Schlemper [Acta Cryst. (1971), B27, 1964–1969] using intensity data estimated from Weissenberg films. In comparison with the previous refinement, the current redetermination reveals anisotropic displacement parameters for all non-H atoms, localization of the H atoms, and higher precision of lattice parameters and inter­atomic distances. The complex features a distorted S6 octa­hedral coordination geometry for tin and a cis disposition of the monodentate dithio­carbamate ligands. PMID:21583036

  18. RbZnFe(PO4)2: synthesis and crystal structure

    PubMed Central

    Badri, Abdessalem; Ben Amara, Mongi

    2016-01-01

    A new iron phosphate, rubidium zinc iron(III) phosphate, RbZnFe(PO4)2, has been synthesized as single crystals by the flux method. This compound is isostructural to the previously reported KCoAl(PO4)2 [Chen et al. (1997 ▸). Acta Cryst. C53,1754–1756]. Its structure consists of a three-dimensional framework built up from corner-sharing PO4 and (Zn,Fe)O4 tetra­hedra. This mode of linkage forms channels parallel to the [100], [010] and [001] directions in which the Rb+ ions are located. PMID:27536385

  19. An amino-imino resonance study of 2-amino-4-methylpyridinium nitrate and 2-amino-5-methylpyridinium nitrate.

    PubMed

    Yan, Xing-Chen; Fan, Yu-Hua; Bi, Cai-Feng; Zhang, Xia; Zhang, Zhong-Yu

    2013-01-01

    The contributions of the amino and imino resonance forms to the ground-state structures of 2-amino-4-methylpyridinium nitrate, C(6)H(9)N(2)(+)·NO(3)(-), and the previously reported 2-amino-5-methylpyridinium nitrate [Yan, Fan, Bi, Zuo & Zhang (2012). Acta Cryst. E68, o2084], were studied using a combination of IR spectroscopy, X-ray crystallography and density functional theory (DFT). The results show that the structures of 2-amino-4-methylpyridine and 2-amino-5-methylpyridine obtained upon protonation are best described as existing largely in the imino resonance forms. PMID:23282916

  20. Structural complexity and configurational entropy of crystals.

    PubMed

    Krivovichev, Sergey V

    2016-04-01

    Using a statistical approach, it is demonstrated that the complexity of a crystal structure measured as the Shannon information per atom [Krivovichev (2012). Acta Cryst. A68, 393-398] represents a negative contribution to the configurational entropy of a crystalline solid. This conclusion is in full accordance with the general agreement that information and entropy are reciprocal variables. It also agrees well with the understanding that complex structures possess lower entropies relative to their simpler counterparts. The obtained equation is consistent with the Landauer principle and points out that the information encoded in a crystal structure has a physical nature. PMID:27048729

  1. RbZnFe(PO4)2: synthesis and crystal structure.

    PubMed

    Badri, Abdessalem; Ben Amara, Mongi

    2016-08-01

    A new iron phosphate, rubidium zinc iron(III) phosphate, RbZnFe(PO4)2, has been synthesized as single crystals by the flux method. This compound is isostructural to the previously reported KCoAl(PO4)2 [Chen et al. (1997 ▸). Acta Cryst. C53,1754-1756]. Its structure consists of a three-dimensional framework built up from corner-sharing PO4 and (Zn,Fe)O4 tetra-hedra. This mode of linkage forms channels parallel to the [100], [010] and [001] directions in which the Rb(+) ions are located. PMID:27536385

  2. Trimethyl-3-meth­oxy-4-oxo-5-triphenyl­phospho­ranyl­idene­cyclo­pent-1-ene-1,2,3-tricarboxyl­ate

    PubMed Central

    Krawczyk, Krzysztof K.; Wojtasiewicz, Krystyna; Maurin, Jan K.; Gronowska, Ewa; Czarnocki, Zbigniew

    2010-01-01

    The title compound, C30H27O8P (2), was formed as one of two products {(1) [Krawczyk et al. (2010 ▶). Acta Cryst. E66 (cv2752)] and (2)} in the reaction of dimethyl acetyl­enedicarboxyl­ate with triphenyl­phosphine. The mol­ecule of (2) consists of a five-membered carbocyclic ring. The P atom is a part of a triphenylphosphoranylidene substituent. In contrast to (1), the five-membered ring of (2) is planar, the r.m.s. deviation being only 0.009 (2) Å. PMID:21588989

  3. Hobartine: a tetracyclic indole alkaloid extracted from Aristotelia chilensis (maqui).

    PubMed

    Paz Robles, Cristian; Badilla Vidal, Natalia; Suarez, Sebastián; Baggio, Ricardo

    2014-11-01

    The natural compound hobartine {systematic name: (1R)-3-[(1S,5S)-(4,4,8-trimethylbicyclo[3.3.1]non-7-en-2-yl)methyl]-2,3-dihydro-1H-indole}, C20H26N2, (I), is an indole alkaloid isolated from Aristotelia chilensis as part of a study of secondary metabolites from Chilean flora. The colourless compound has a tetracyclic structure closely related to the strongly coloured polymorphic structures discussed in Paz et al. [Acta Cryst. (2013), C69, 1509-1512] and Watson et al. [Acta Cryst. (1989), C45, 1322-1324]. The main differences reside in the absence of a keto group in (I) compared with the previous structures, as well as an endo double bond in (I) contrasting with the exo double bond found in the previous structures. The supramolecular structure of (I) in strongly related to the twofold screw axis, around which isolated chains build up, internally linked by an N-H···N hydrogen bond which is the only significant intermolecular interaction present in the structure. PMID:25370110

  4. Proceedings of the second international symposium on molecular markers in horticulture Acta Horticulturae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The second International Symposium on Molecular Markers in Horticulture was held at the CH2M Hill Alumni Center at Oregon State University (OSU), Corvallis (Oregon, US), from July 29 to August 1st, 2009. This symposium was convened by a scientist at the National Clonal Germplasm Repository (NCGR) of...

  5. Comment on "Investigations of interstitial generations near growth interface depending on crystal pulling rates during CZ silicon growth by detaching from the melt" by T. Abe et al. [J. Cryst. Growth 434 (2016) 128-137] and on "Observations of secondary defects and vacancies in CZ silicon crystals detached from melt using four different types of characterization technique" by T. Abe et al. [J. Cryst. Growth 436 (2016) 23-33

    NASA Astrophysics Data System (ADS)

    Vanhellemont, Jan; Kamiyama, Eiji; Nakamura, Kozo; Sueoka, Koji

    2016-09-01

    In the papers mentioned above, Abe et al. published beautiful experimental data on intrinsic point defect related defect distributions in detached growing Czochralski Si crystals with and without additional thermal anneals [1,2]. The new fact compared to the results published before [3] is that the crystals are pulled with decreasing speed before detaching, resulting in crystals that vary along the axis from initially vacancy-rich to interstitial-rich for the slowest pulling speed before detaching.

  6. Mechanism of amorphous silica particles precipitation: simulation approach compared to experimental results

    NASA Astrophysics Data System (ADS)

    Noguera, Claudine; Fritz, Bertrand; Clement, Alain

    2015-04-01

    Despite its importance in numerous industrial and natural processes, many unsolved questions remain regarding the mechanism of silica precipitation in aqueous solutions: order of the reaction, role of silica oligomers, existence of an induction time and characteristics of the particle population. Beyond empirical approaches used in the past, we demonstrate that the classical nucleation theory associated to a size dependent growth law, as embedded in the NANOKIN code (1-3), allows a quantitative description of precipitation occurring under largely different experimental conditions : preexisting initial supersaturation in a large domain of temperature (5-150°C) and chemical composition (4), supersaturation reached by neutralization of a high pH silica solution (5) or by fast cooling (6). In that way, the mechanism of silica precipitation can be unraveled. We are able to discard the hypothesis of an induction time as an explanation for the plateaus observed in the saturation curves in these experiments. We challenge the role of oligomer incorporation at the growth stage to account for the observed rate laws and we stress the difference between the order of the growth law and the order of the total reaction rate. We also demonstrate that the characteristics of the particle population are strongly dependent on the way supersaturation is reached (7). Such a microscopic approach thus proves to be well suited to elucidate the mechanism of nanoparticle formation in natural and industrial contexts, involving silica, but also other mineral phases produced as nanoparticles (8). (1) Noguera C., Fritz B., Clément A. and Barronet A., J. Cryst. Growth, 2006, 297, 180. (2) Noguera C., Fritz B., Clément A. and Barronet A., J. Cryst. Growth, 2006, 297, 187. (3) Fritz B., Clément A., Amal Y. and Noguera C., Geochim. Cosmochim. Acta, 2009, 73, 1340. (4) Rothbaum, H.P. and Rohde A.G., J. Colloid Interf. Sci., 1979,71, 533. (5) Tobler D.J., Shaw S. and Benning L.G., Geochim

  7. Crystal structure of bis­(2-amino-5-chloro­pyridinium) tetra­chlorido­cobaltate(II)

    PubMed Central

    Mghandef, Marwa; Boughzala, Habib

    2015-01-01

    The title salt, (C5H6ClN2)2[CoCl4], was synthesized by slow evaporation of an aqueous solution at room temperature. The asymmetric unit consists of two essentially planar (C5H6ClN2)+ cations [maximum deviations = 0.010 (3) and 0.014 (3) Å] that are nearly perpendicular to each other [dihedral angle = 84.12 (7)°]. They are bonded through N—H⋯Cl hydrogen bonds to distorted [CoCl4]2− tetra­hedra, leading to the formation of undulating layers parallel to (100). The structure is isotypic with the Zn analogue [Kefi et. al (2011). Acta Cryst. E67, m355–m356.] PMID:25995878

  8. Redetermination of cytosinium hydrogen maleate–cytosine (1/1) from the original data

    PubMed Central

    Fábry, Jan

    2016-01-01

    The title salt, C4H6N3O+·C4H3O4 −·C4H5N3O, has been redetermined from the data published by Benali-Cherif, Falek & Direm [Acta Cryst. (2009), E65, o3058–o3059]. The improvement of the present redetermination consists in the discovery of the splitting of one of the H atoms into two disordered positions, the occupancies of which are equal to 0.55 (2) and 0.45 (2). These H atoms are involved in an N⋯N hydrogen bond and are shifted towards its centre. The disorder of these H atoms is in agreement with a similar environment of the two independent, but chemically equivalent, cytosinium/cytosine mol­ecules. PMID:27375877

  9. 3α-Hy­droxy­tirucalla-8,24-dien-21-oic acid

    PubMed Central

    Yousuf, S.; Kamdem, R. S. T.; Ngadjui, B. T.; Wafo, P.; Fun, Hoong-Kun

    2011-01-01

    The title compound, C30H48O3, a triterpene isolated from the resin of canarium schweinfurthiiand, is an isomer of the previously reported triterpene 3α-hy­droxy­tirucalla-7,24-dien-21-oic acid [Mora et al. (2001 ▶). Acta Cryst. C57, 638–640], which crystallizes in the same trigonal space group. The title mol­ecule consists of four fused rings having chair, half-chair, half-chair and envelope conformations for rings A, B, C and D, respectively (steroid labelling). An intra­molecular C—H⋯O hydrogen bond generates an S(7) ring. In the crystal, mol­ecules are linked by O—H⋯O and C—H⋯O inter­actions, forming (001) sheets. PMID:21754206

  10. Tetra-amminepalladium(II) dichloride ammonia tetra-solvate.

    PubMed

    Grassl, Tobias; Korber, Nikolaus

    2014-07-01

    The title compound, [Pd(NH3)4]Cl2·4NH3, was crystallized in liquid ammonia from the salt Pd(en)Cl2 (en is ethylenediamine) and is isotypic with [Pt(NH3)4]Cl2·4NH3 [Grassl & Korber (2014 ▶). Acta Cryst. E70, i31]. The Pd(2+) cation is coordinated by four ammonia mol-ecules, exhibiting a square-planar geometry. The chloride anions are surrounded by nine ammonia mol-ecules. These are either bound in the palladium complex or solvent mol-ecules. The packing of the ammonia solvent mol-ecules enables the formation of an extended network of N-H⋯N and N-H⋯Cl inter-actions with nearly ideal hydrogen-bonding geometry. PMID:25161505

  11. Tetra-ammineplatinum(II) dichloride ammonia tetra-solvate.

    PubMed

    Grassl, Tobias; Korber, Nikolaus

    2014-07-01

    The title compound, [Pt(NH3)4]Cl2·4NH3, was crystallized in liquid ammonia from the salt PtCl2. The platinum cation is coordinated by four ammonia mol-ecules, forming a square-planar complex. The chloride anions are surrounded by nine ammonia mol-ecules, either bound within the platinum complex or solvent mol-ecules. The solvent ammonia mol-ecules are packed in such a way that an extended network of N-H⋯N and N-H⋯Cl hydrogen bonds is formed. The structure is isotypic with [Pd(NH3)4]Cl2·4NH3 [Grassl & Korber (2014). Acta Cryst. E70, i32]. PMID:25161504

  12. Acanthamoeba polyphaga mimivirus NDK: preliminary crystallographic analysis of the first viral nucleoside diphosphate kinase

    PubMed Central

    Jeudy, Sandra; Coutard, Bruno; Lebrun, Régine; Abergel, Chantal

    2005-01-01

    The complete sequence of the largest known double-stranded DNA virus, Acanthamoeba polyphaga mimivirus, has recently been determined [Raoult et al. (2004 ▶), Science, 306, 1344–1350] and revealed numerous genes not expected to be found in a virus. A comprehensive structural and functional study of these gene products was initiated [Abergel et al. (2005 ▶), Acta Cryst. F61, 212–215] both to better understand their role in the virus physiology and to obtain some clues to the origin of DNA viruses. Here, the preliminary crystallographic analysis of the viral nucleoside diphosphate kinase protein is reported. The crystal belongs to the cubic space group P213, with unit-cell parameter 99.425 Å. The self-rotation function confirms that there are two monomers per asymmetric unit related by a twofold non-crystallographic axis and that the unit cell thus contains four biological entities. PMID:16511098

  13. Redetermination of cytosinium hydrogen maleate-cytosine (1/1) from the original data.

    PubMed

    Fábry, Jan

    2016-04-01

    The title salt, C4H6N3O(+)·C4H3O4 (-)·C4H5N3O, has been redetermined from the data published by Benali-Cherif, Falek & Direm [Acta Cryst. (2009), E65, o3058-o3059]. The improvement of the present redetermination consists in the discovery of the splitting of one of the H atoms into two disordered positions, the occupancies of which are equal to 0.55 (2) and 0.45 (2). These H atoms are involved in an N⋯N hydrogen bond and are shifted towards its centre. The disorder of these H atoms is in agreement with a similar environment of the two independent, but chemically equivalent, cytosinium/cytosine mol-ecules. PMID:27375877

  14. Crystal structure of 2,4-di­nitro­phenyl 4-methyl­benzene­sulfonate: a new polymorph

    PubMed Central

    Cooley, Tyler A.; Riley, Sean; Biros, Shannon M.; Staples, Richard J.; Ngassa, Felix N.

    2015-01-01

    The title compound, C13H10N2O7S, was synthesized via a nucleophilic substitution reaction between 2,4-di­nitro­phenol and p-toluene­sulfonyl chloride. This crystal structure is a polymorph of CSD entry WUVYUH [Vembu et al. (2003). Acta Cryst, E59, o378–380]. The aromatic substituents on the sulfonate group are oriented gauche to one another with a C—O—S—C torsion angle of −62.0 (3)°. The supra­molecular features that contribute to the crystal stability are offset π–π [centroid–centroid distance = 3.729 (2) Å] and multiple C—H⋯O inter­actions. PMID:26396855

  15. A redetermination from the original data of the crystal structure of 2-amino-4,6-di-meth-oxy-pyrimidin-1-ium 4-amino-benzoate.

    PubMed

    Fábry, Jan

    2016-04-01

    The title structure, C6H9.5N3O2 (0.5+)·C7H6.5NO2 (0.5-), which might be named schematically as 2-amino-4,6-di-meth-oxy-pyrimidine-(μ2-hydrogen)-4-amino-benzoate to indicate a bridging H atom, has been redetermined from the data published by Thanigaimani, Mu-thiah & Lynch [Acta Cryst. (2006), E62, o2976-o2978]. The improvement of the present redetermination consists in a released geometry of the primary amine groups, which were originally assumed to be planar, as well as in a redetermination of the position of the hy-droxy H atom. This H atom, whose parameters were originally constrained, turns out to be situated about the centre of the O⋯N hydrogen bond in two disordered positions with occupancies of 0.5 each. PMID:27375878

  16. Crystal structure of bis­[tetra­kis­(tri­phenyl­phosphane-κP)silver(I)] (nitrilo­tri­acetato-κ4 N,O,O′,O′′)(tri­phenyl­phosphane-κP)argentate(I) with an unknown amount of methanol as solvate

    PubMed Central

    Noll, Julian; Korb, Marcus; Lang, Heinrich

    2016-01-01

    The structure of the title compound, [Ag(C18H15P)4]2[Ag(C6H6NO6)(C18H15P)], exhibits trigonal (P-3) symmetry, with a C 3 axis through all three complex ions, resulting in an asymmetric unit that contains one third of the atoms present in the formula unit. The formula unit thus contains two of the cations, one anion and disordered mol­ecules of methanol as the packing solvent. Attempts to refine the solvent model were unsuccessful, indicating uninter­pretable disorder. Thus, the SQUEEZE procedure in PLATON [Spek (2015 ▸). Acta Cryst. C71, 9–18] was applied, accounting for 670 electrons per unit cell, representing approximately 18 mol­ecules of methanol in the formula unit. The stated crystal data for M r, μ etc do not take these into account. PMID:27006796

  17. Crystal structure of bis-[tetra-kis-(tri-phenyl-phosphane-κP)silver(I)] (nitrilo-tri-acetato-κ(4) N,O,O',O'')(tri-phenyl-phosphane-κP)argentate(I) with an unknown amount of methanol as solvate.

    PubMed

    Noll, Julian; Korb, Marcus; Lang, Heinrich

    2016-03-01

    The structure of the title compound, [Ag(C18H15P)4]2[Ag(C6H6NO6)(C18H15P)], exhibits trigonal (P-3) symmetry, with a C 3 axis through all three complex ions, resulting in an asymmetric unit that contains one third of the atoms present in the formula unit. The formula unit thus contains two of the cations, one anion and disordered mol-ecules of methanol as the packing solvent. Attempts to refine the solvent model were unsuccessful, indicating uninter-pretable disorder. Thus, the SQUEEZE procedure in PLATON [Spek (2015 ▸). Acta Cryst. C71, 9-18] was applied, accounting for 670 electrons per unit cell, representing approximately 18 mol-ecules of methanol in the formula unit. The stated crystal data for M r, μ etc do not take these into account. PMID:27006796

  18. Triclinic polymorph of bis­(triphenyl­sil­yl) oxide toluene disolvate

    PubMed Central

    Purdy, Andrew P.; Smoot, Emily; Butcher, Ray J.; Kerr, Andrew

    2012-01-01

    A new polymorph of the title compound, C36H30OSi2·2C7H8, is reported, which is triclinic (P-1) instead of possessing the previously reported rhombohedral symmetry [Hönle et al. (1990). Acta Cryst. C46, 1982–1984]. Each of the –SiPh3 units are related by the inversion center. The Si—O—Si moiety is linear with the O atom sitting on an inversion center, and the O—Si—(toluene ring centroid) angle is 3.69 (15)°. Each toluene mol­ecule is 5.622 (2) Å from the Si atom and has its closest contacts with the phenyl rings outside of the van der Waals radii. PMID:22412504

  19. Crystal structure of (E)-2-(4-chloro­benzyl­idene)-3,4-di­hydro­naphthalen-1(2H)-one: a second monoclinic polymorph

    PubMed Central

    Haroon, Muhammad; Akhtar, Tashfeen; Tahir, Muhammad Nawaz

    2015-01-01

    The title compound, C17H13ClO, is the second monoclinic polymorph to crystallize in the space group P21/c. The first polymorph crystallized with two independent mol­ecules in the asymmetric unit [Bolognesi et al. (1975 ▸). Acta Cryst. A31, S119; Z′ = 2; no atomic coordinates available], whereas the title compound has Z′ = 1. In the title polymorph, the dihedral angle between the plane of the benzene ring of the tetra­lone moiety and that of the 4-chloro­benzyl ring is 52.21 (11)°. The cyclo­hex-2-en-1-one ring of the tetra­lone moiety has a screw-boat conformation. In the crystal, mol­ecules are liked by pairs of C—H⋯π inter­actions forming inversion dimers. There are no other significant inter­molecular inter­actions present. PMID:26594452

  20. A second polymorph of sodium di­hydrogen citrate, NaH2C6H5O7: structure solution from powder diffraction data and DFT comparison

    PubMed Central

    Rammohan, Alagappa; Kaduk, James A.

    2016-01-01

    The crystal structure of a second polymorph of sodium di­hydrogen citrate, Na+·H2C6H5O7 −, has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The powder pattern of the commercial sample used in this study did not match that corresponding to the known crystal structure [Glusker et al. (1965). Acta Cryst. 19, 561–572; refcode NAHCIT]. In this polymorph, the [NaO7] coordination polyhedra form edge-sharing chains propagating along the a axis, while in NAHCIT the octa­hedral [NaO6] groups form edge-sharing pairs bridged by two hy­droxy groups. The most notable difference is that in this polymorph one of the terminal carboxyl groups is deprotonated, while in NAHCIT the central carboxyl­ate group is deprotonated, as is more typical. PMID:27308058

  1. Redetermined crystal structure of N-(β-carb-oxy-eth-yl)-α-isoleucine.

    PubMed

    Chandrarekha, M; Srinivasan, N; Krishnakumar, R V

    2015-09-01

    Redetermination of the crystal structure of N-(β-carb-oxy-eth-yl)-α-isoleucine, C9H18N2O3, reported earlier by Nehls et al. [Acta Cryst. (2013), E69, o172-o173], was undertaken in which the ionization state assigned to the mol-ecule as unionized has been modified as zwitterionic in the present work. Single-crystal X-ray intensity data obtained from freshly grown crystals and freely refining the amino H atoms provide enhanced refinement and structural parameters, particularly the hydrogen-bonding scheme. N-H⋯O hydrogen bonds dominate the inter-molecular inter-actions along with a C-H⋯O hydrogen bond. The inter-molecular inter-action pattern is a three-dimensional network. The structure was refined as a two-component perfect inversion twin. PMID:26396893

  2. Crystal structure of 4-(tri­methyl­germ­yl)benzoic acid

    PubMed Central

    Knauer, Lena; Barth, Eva R.; Golz, Christopher; Strohmann, Carsten

    2015-01-01

    The title compound, [Ge(CH3)3(C7H5O2)], was obtained as a by-product in the synthesis of the corresponding aldehyde. Two slightly different mol­ecules are present in the asymmetric unit. In both mol­ecules, the geometry of the aromatic ring plane is distorted by varying intensities. Additionally, the Ge atoms deviate from the mean aromatic ring planes. Whereas the distance of the Ge atom to the ring plane is only 0.101 (4) Å in the first mol­ecule, this distance is increased to 0.210 (4) Å in the second. In the crystal structure, centrosymmetric O—H⋯O hydrogen-bonded dimers are formed. The title compound is isostructural with the Si analogue [Haberecht et al. (2004 ▸). Acta Cryst. E60, o329–0330]. PMID:26090151

  3. A combinatorial chemistry approach to new materials for non-linear optics. II. 4-(Dimethylamino)cinnamaldehyde and a molecular complex of 4-methoxycinnamaldehyde with 2,4-dinitroaniline

    PubMed

    Nesterov; Timofeeva; Antipin; Clark

    2000-08-01

    The combinatorial chemistry approach has been used to synthesize an array of Schiff bases. The structures of five of these Schiff bases have been confirmed by X-ray analysis [Nesterov, Timofeeva, Borbulevych, Antipin & Clark (2000). Acta Cryst. C56, 971-975]. In two cases, the reaction conditions were not sufficient to obtain the products in question. In one case, a molecular complex, C(10)H(10)O(2).C(6)H(5)N(3)O(4), of the starting products 4-methoxycinnamaldehyde and 2,4-dinitroaniline was found. X-ray analysis revealed hydrogen-bond formation between the molecules of these reagents in the crystal. In the other case, X-ray analysis demonstrated that no chemical reaction occurred under the reaction conditions, and only one starting reagent, 4-(dimethylamino)cinnamaldehyde, C(11)H(13)NO, was found in the precipitate. PMID:10944294

  4. About the hybrid Fourier syntheses: a probabilistic approach.

    PubMed

    Burla, Maria Cristina; Carrozzini, Benedetta; Cascarano, Giovanni Luca; Giacovazzo, Carmelo; Polidori, Giampiero

    2011-09-01

    The difference electron density has recently been revisited via the method of joint probability distribution functions [Burla et al. (2010). Acta Cryst. A 66, 347-361]. New Fourier coefficients were devised which were the basis of a new ab initio method for the solution of the phase problem (i.e. VLD, vive la difference). In this paper we study the joint probability distribution functions P(F, F(p), F(Q)), where F(Q) is the structure factor corresponding to the ideal hybrid Fourier synthesis ρ(Q) = τρ - ωρ(p) and τ and ω are any pair of real numbers. New Fourier coefficients for the calculations of any hybrid synthesis are obtained, and the properties of the corresponding electron-density maps are discussed. The first applications show the correctness of our theoretical approach and suggest possible applications in phasing procedures. PMID:21844649

  5. 3-[1-(3-Hy­droxy­benz­yl)-1H-benzimid­azol-2-yl]phenol dimethyl sulfoxide monosolvate

    PubMed Central

    Quezada-Miriel, Magdalena; Avila-Sorrosa, Alcives; German-Acacio, Juan Manuel; Reyes-Martínez, Reyna; Morales-Morales, David

    2012-01-01

    Crystals of the title compound were obtained as a 1:1 dimethyl sulfoxide solvate, C20H16N2O2·C2H6O. The mol­ecular conformation of the organic mol­ecule is similar to that in the previously reported unsolvated structure [Eltayeb et al. (2009 ▶). Acta Cryst. E65, o1374–o1375]. Thus, the dihedral angles formed by the benzimidazole moiety with the two benzene rings are 57.54 (4) and 76.22 (5)°, and the dihedral angle between the benzene rings is 89.23 (5)°. In the crystal, a three-dimensional network features O—H⋯O, O—H⋯N and O—H⋯S hydrogen bonds, as well as C—H⋯O and C—H⋯π inter­actions. PMID:23125815

  6. Second monoclinic form of (E)-3-(4-fluoro­phen­yl)-1-phenyl­prop-2-en-1-one

    PubMed Central

    Arias-Ruiz, Saira N.; Romero, Nancy; Lobato-García, Carlos E.; Gómez-Rivera, Abraham; Mendoza, Angel

    2013-01-01

    The unit-cell dimensions and space group of the second monoclinic polymorph of the title compound, C15H11FO, differ from those of the previously reported form [Jing (2009 ▶). Acta Cryst. E65, o2515]. The title compound shows an E conformation of the C=C bond with the 4-fluoro­phenyl group opposite to the benzoyl group. The torsion angle of between the planes of the 4-fluoro­phenyl and benzoyl groups is 10.53 (6)°. In the crystal, weak C—H⋯O and C—H⋯F inter­actions form a cross-linked packing motif, building sheets parallel to (-102). PMID:24454121

  7. Properties of X-ray resonant scattering in the Bragg case revealed on the Riemann surface.

    PubMed

    Saka, Takashi

    2016-07-01

    Continuing the work described in the previous paper [Saka (2016). Acta Cryst. A72, 338-348], the dynamical theory for perfect crystals in the Bragg case is reformulated using the Riemann surface. In particular, diffraction under resonant scattering conditions is investigated. The characteristic features of the dispersion surface and the rocking curve are analytically revealed using four parameters, which are the real and imaginary parts of two quantities specifying the degree of departure from the exact Bragg conditions and the reflection strength. Characteristic properties that have been deduced through numerical analysis are derived analytically using these four parameters. Visualization of the geometric relationships between the four parameters on the Riemann surface is useful for understanding many properties such as symmetry and sharpness of the rocking curve under special conditions. Therefore, employing the Riemann surface is instructive for numerical analysis and useful for understanding dynamical diffraction in the Bragg case. PMID:27357849

  8. A triclinic polymorph of (E)-2-(4-iso­butyl­phen­yl)-N′-[1-(4-nitro­phen­yl)ethyl­idene]propano­hydrazide

    PubMed Central

    Manjunath, B. C.; Madan Kumar, S.; Vinayaka, A. C.; Jayasheelan, S.; Sadashiva, M. P.; Lokanath, N. K.

    2013-01-01

    The asymmetric unit of the triclinic polymorph of the title compound, C21H25N3O3, consists of two mol­ecules, whereas for the monoclinic polymorph Z′ = 1 [Fun et al. (2009 ▶). Acta Cryst. E65, o445]. The two mol­ecules exhibit an E configuration with respect to the C=N bond. The mol­ecules are linked into dimers by N—H⋯O and C—H⋯O hydrogen bonds forming R 2 2(8) ring motifs. In addition, π–π inter­actions occur between nitro­phenyl groups [minimum centroid–centroid distance 3.940 (2) Å], stacking the molecules along the ac plane. PMID:24109404

  9. A redetermination of the structure of poly[[μ4-(R)-2-ammonio-3-sulfonato­propano­ato]aqua­sodium], originally reported as poly[[μ7-l-cysteato(2−)]disodium

    PubMed Central

    Brown, I. David

    2012-01-01

    The structure originally reported as poly[[μ7-l-cysteato(2−)]disodium], [Na2(C3H5NO5S)]n [Liu (2002). Acta Cryst. E67, m1346–m1347], has been redetermined with one of the sodium atoms replaced with a water mol­ecule and an additional proton attached to the amine group, resulting in the revised formula [Na{CO2CH(CH2SO3)NH3}(H2O)]n. The agreement index, wR, has been reduced from 0.159 to 0.087 and the global instability index from 0.56 vu (valence units) to the acceptable value of 0.11 vu. PMID:22606082

  10. A family of ternary decagonal tilings

    NASA Astrophysics Data System (ADS)

    Fujita, Nobuhisa

    2010-04-01

    A new family of decagonal quasiperiodic tilings are constructed by the use of generalized point substitution processes, which is a new substitution formalism developed by the author [N. Fujita, Acta Cryst. A 65, 342 (2009)]. These tilings are composed of three prototiles: an acute rhombus, a regular pentagon and a barrel shaped hexagon. In the perpendicular space, these tilings have windows with fractal boundaries, and the windows are analytically derived as the fixed sets of the conjugate maps associated with the relevant substitution rules. It is shown that the family contains an infinite number of local isomorphism classes which can be grouped into several symmetry classes (e.g., C10, D5, etc.). The member tilings are transformed into one another through collective simpleton flips, which are associated with the reorganization in the window boundaries.

  11. 3-[2-(3-Methyl­quinoxalin-2-yl­oxy)eth­yl]-1,3-oxazolidin-2-one

    PubMed Central

    Ahoya, Caleb Anothane; Bouhfid, Rachid; Daouda, Ballo; Essassi, El Mokhtar; El Ammari, Lahcen

    2010-01-01

    Two isomers were isolated during the reaction between 3-methyl­quinoxalin-2-one and bis­(2-chloro­ethyl)amine hydro­chloride. The crystal structure of one isomer has already been reported [Caleb, Bouhfid, Essassi & El Ammari (2009). Acta Cryst. E65, o2024–o2025], while that of the second isomer is the subject of this work. The title compound, C14H15N3O3, has a new structure containing oxazolidine and quinoxaline rings linked by an eth­oxy group. The main difference between the two isomers is the position of the oxazolidine group with respect to the quinoxaline system. The dihedral angle between the fused planar rings and the oxazolidin-2-one ring is 41.63 (8)° in the title mol­ecule. PMID:21579110

  12. Trimesic acid dimethyl sulfoxide solvate: space group revision

    PubMed Central

    Bernès, Sylvain; Hernández, Guadalupe; Portillo, Roberto; Gutiérrez, René

    2008-01-01

    The structure of the title solvate, C9H6O6·C2H6OS, was determined 30 years ago [Herbstein, Kapon & Wasserman (1978 ▶). Acta Cryst. B34, 1613–1617], with data collected at room temperature, and refined in the space group P21. The present redetermination, based on high-resolution diffraction data, shows that the actual space group is more likely to be P21/m. The crystal structure contains layers of trimesic acid molecules lying on mirror planes. A mirror plane also passes through the S and O atoms of the solvent molecule. The molecules in each layer are inter­connected through strong O—H⋯O hydrogen bonds, forming a two-dimensional supra­molecular network within each layer. The donor groups are the hydroxyls of the trimesic acid mol­ecules, while the acceptors are the carbonyl or the sulfoxide O atoms. PMID:21202984

  13. Redetermination of AgPO(3).

    PubMed

    Terebilenko, Katherina V; Zatovsky, Igor V; Ogorodnyk, Ivan V; Baumer, Vyacheslav N; Slobodyanik, Nikolay S

    2011-01-01

    Single crystals of silver(I) polyphosphate(V), AgPO(3), were prepared via a phospho-ric acid melt method using a solution of Ag(3)PO(4) in H(3)PO(4). In comparison with the previous study based on single-crystal Weissenberg photographs [Jost (1961 ▶). Acta Cryst. 14, 779-784], the results were mainly confirmed, but with much higher precision and with all displacement parameters refined anisotropically. The structure is built up from two types of distorted edge- and corner-sharing [AgO(5)] polyhedra, giving rise to multidirectional ribbons, and from two types of PO(4) tetra-hedra linked into meandering chains (PO(3))(n) spreading parallel to the b axis with a repeat unit of four tetra-hedra. The calculated bond-valence sum value of one of the two Ag(I) ions indicates a significant strain of the structure. PMID:21522230

  14. Is it jolly SAD?

    PubMed

    Dodson, Eleanor

    2003-11-01

    Examples of phasing macromolecular crystal structures based on single-wavelength anomalous dispersion (SAD) have demonstrated that this approach may have general applications in structural biology. With better data-collection facilities and cryogenic techniques, combined with powerful data-processing, phasing and density-modification programs, the SAD approach may prove simpler than phasing from multi-wavelength (MAD) measurements. It can be performed at any wavelength where anomalous scattering can be observed, in many cases using laboratory X-ray sources. However, there is still a need for accurate data, successful phase improvement and a certain amount of luck. This paper extends the discussion of Jolly SAD in Dauter et al. [Dauter, Z., Dauter, M. & Dodson, E. (2002), Acta Cryst. D58, 494-506]. PMID:14573950

  15. 2,2′-(1,3-Diazinane-1,3-di­yl)diaceto­nitrile: a second monoclinic polymorph

    PubMed Central

    Rivera, Augusto; Maldonado, Mauricio; Ríos-Motta, Jaime; Fejfarová, Karla; Dušek, Michal

    2011-01-01

    A new monoclinic polymorph of the title compound, C8H12N4, in the space group P21/n (Z = 4) is reported. The previously known form was also monoclinic, P21 /c (Z = 4), but the unit-cell parameters and crystal packing were different [Shoja & Saba (1993 ▶). Acta Cryst. C49, 354–355]. The hexa­hydro­pyrimidine ring of the title compound adopts a chair conformation with a diequatorial substitution and with the CH2-C N groups oriented nearly parallel and in the same direction [NC—CH2⋯CH2—CN pseudo torsion angle = −6.27 (18)°]. In the crystal, inter­molecular C—H⋯ N hydrogen bonds connects the mol­ecules into a chain along the b axis. PMID:22065712

  16. Refining a model electron-density map via the Phantom Derivative method.

    PubMed

    Burla, Maria Cristina; Carrozzini, Benedetta; Cascarano, Giovanni Luca; Giacovazzo, Carmelo; Polidori, Giampiero

    2015-09-01

    The Phantom Derivative (PhD) method [Giacovazzo (2015), Acta Cryst. A71, 483-512] has recently been described for ab initio and non-ab initio phasing. It is based on the random generation of structures with the same unit cell and the same space group as the target structure (called ancil structures), which are used to create derivatives devoid of experimental diffraction amplitudes. In this paper, the non-ab initio variant of the method was checked using phase sets obtained by molecular-replacement techniques as a starting point for phase extension and refinement. It has been shown that application of PhD is able to extend and refine phases in a way that is competitive with other electron-density modification techniques. PMID:26327376

  17. Tetra­methyl 1,1,2-triphenyl-2H-1λ5-phosphole-2,3,4,5-tetra­carboxyl­ate

    PubMed Central

    Krawczyk, Krzysztof K.; Wojtasiewicz, Krystyna; Maurin, Jan K.; Gronowska, Ewa; Czarnocki, Zbigniew

    2010-01-01

    The title compound, C30H27O8P (1), was formed as one of two products {(1) and (2) [Krawczyk et al. (2010 ▶). Acta Cryst. E66 (cv2753)]} in the reaction of dimethyl acetyl­enedicarboxyl­ate with triphenyl­phosphine. The mol­ecule of (1) consists of a five-membered ring, in which the P atom is incorporated. One of the phenyl groups of the triphenyl­phosphine migrated to a vicinal C atom during the reaction. The five-membered ring of (1) is corrugated [r.m.s. deviation = 0.0719 (8) Å], whereas that in compound (2) is planar, the r.m.s. deviation being only 0.009 (2) Å. PMID:21588988

  18. Two new polytypes of 2,4,6-tri­bromo­benzo­nitrile

    PubMed Central

    Britton, Doyle; Noland, Wayland E.; Tritch, Kenneth J.

    2016-01-01

    Three polymorphs of 2,4,6-tri­bromo­benzo­nitrile (RCN), C7H2Br3N, two of which are novel and one of which is a redetermination of the original structure first determined by Carter & Britton [(1972). Acta Cryst. B28, 945–950] are found to be polytypic. Each has a layer structure which differs only in the stacking of the layers. Each layer is composed of mol­ecules associated through C N⋯Br contacts which form R 2 2(10) rings. Two such rings are associated with each N atom; one with each ortho-Br atom. No new polytypes of 1,3,5-tri­bromo-2-iso­cyano­benzene (RNC) were found but a re-determination of the original structure by Carter et al. [(1977). Cryst. Struct. Commun. 6, 543–548] is presented. RNC was found to be isostructural with one of the novel polytypes of RCN. Unit cells were determined for 23 RCN samples and 11 RNC samples. Polytypes could not be distinguished based on crystal habits. In all four structures, each mol­ecule of the asymmetric unit lies across a mirror plane. PMID:26958382

  19. Assessment of radiation damage behaviour in a large collection of empirically optimized datasets highlights the importance of unmeasured complicating effects.

    PubMed

    Krojer, Tobias; von Delft, Frank

    2011-05-01

    The radiation damage behaviour in 43 datasets of 34 different proteins collected over a year was examined, in order to gauge the reliability of decay metrics in practical situations, and to assess how these datasets, optimized only empirically for decay, would have benefited from the precise and automatic prediction of decay now possible with the programs RADDOSE [Murray, Garman & Ravelli (2004). J. Appl. Cryst. 37, 513-522] and BEST [Bourenkov & Popov (2010). Acta Cryst. D66, 409-419]. The results indicate that in routine practice the diffraction experiment is not yet characterized well enough to support such precise predictions, as these depend fundamentally on three interrelated variables which cannot yet be determined robustly and practically: the flux density distribution of the beam; the exact crystal volume; the sensitivity of the crystal to dose. The former two are not satisfactorily approximated from typical beamline information such as nominal beam size and transmission, or two-dimensional images of the beam and crystal; the discrepancies are particularly marked when using microfocus beams (<20 µm). Empirically monitoring decay with the dataset scaling B factor (Bourenkov & Popov, 2010) appears more robust but is complicated by anisotropic and/or low-resolution diffraction. These observations serve to delineate the challenges, scientific and logistic, that remain to be addressed if tools for managing radiation damage in practical data collection are to be conveniently robust enough to be useful in real time. PMID:21525647

  20. Redetermination of Zn2Mo3O8

    PubMed Central

    Cuny, Jerome; Gougeon, Patrick; Gall, Philippe

    2009-01-01

    The crystal structure of dizinc trimolybdenum(IV) octa­oxide, Zn2Mo3O8, has been redetermined from single-crystal X-ray data. The structure has been reported previously based on neutron powder diffraction data [Hibble et al. (1999 ▶). Acta Cryst. B55, 683-697] and single-crystal data [McCarroll et al. (1957 ▶). J. Am. Chem. Soc. 79, 5410–5414; Ansell & Katz (1966 ▶) Acta Cryst. 21, 482–485]. The results of the current redetermination show an improvement in the precision of the structural and geometric parameters with all atoms refined with anisotropic displacement parameters. The crystal structure consists of distorted hexa­gonal-close-packed oxygen layers with stacking sequence abac along [001] and is held together by alternating zinc and molybdenum layers. The Zn atoms occupy both tetra­hedral and octa­hedral inter­stices with a ratio of 1:1. The Mo atoms occupy octa­hedral sites and form strongly bonded triangular clusters involving three MoO6 octa­hedra that are each shared along two edges, forming a Mo3O13 unit. All atoms lie on special positions. The Zn atoms are in 2b Wyckoff positions with 3m. site symmetry, the Mo atoms are in 6c Wyckoff positions with . m. site symmetry and the O atoms are in 2a, 2b and 6c Wyckoff positions with 3m. and . m. site symmetries, respectively. PMID:21582645

  1. Crystallization of Chicken Egg White Lysozyme from Sulfate Salts

    NASA Technical Reports Server (NTRS)

    Forsythe, Elizabeth; Pusey, Marc

    1998-01-01

    It has been "known" that chicken egg white lysozyme does not crystallize from sulfate, particularly ammonium sulfate, salts, but instead gives amorphous precipitates. This has been the basis of several studies using lysozyme comparing macromolecule crystal nucleation and amorphous precipitation. Recently Ries-Kautt et al (Acta Cryst D50, (1994) 366) have shown that purified isoionic CEWL could be crystallized from low concentrations of sulfate at basic pH, and we subsequently showed that in fact CEWL could be purified in both the tetragonal and orthorhombic forms using ammonium sulfate over the pH range 4.0 to 7.8 (Acta Cryst D53, (1997) 795). We have now extended these observations to include a range of common sulfate salts, specifically sodium, potassium, rubidium, magnesium, and manganese sulfates. In all cases but the manganese sulfates both the familiar tetragonal and orthorhombic forms were obtained, with unit cell dimensions close to those known for the "classic" sodium chloride crystallized forms. Manganese sulfate has only yielded orthorhombic crystals to date. All crystallizations were carried out using low (typically less than or equal to 6 M) salt and high (greater than approximately 90 mg/ml) protein concentrations. As with ammonium sulfate, the tetragonal - orthorhombic phase shift appears to be a function of both the temperature and the protein concentration, with higher temperatures and concentrations favoring the orthorhombic and lower the tetragonal form. The phase change range is somewhat reduced for the sulfate salts, depending upon conditions being typically between approximately 15 - 20 C. Both the magnesium and manganese sulfates gave crystals at salt concentrations over 0.6 M as well, with magnesium sulfate giving a very slowly nucleating and growing hexagonal form. A triclinic crystal form, characterized by aggressively small crystals (typically 0.1 mm in size) has been occasionally obtained from ammonium sulfate. Finally, preliminary spot

  2. Comment on "Apatite: A new redox proxy for silicic magmas?" [Geochimica et Cosmochimica Acta 132 (2014) 101-119

    NASA Astrophysics Data System (ADS)

    Marks, Michael A. W.; Scharrer, Manuel; Ladenburger, Sara; Markl, Gregor

    2016-06-01

    Recently Miles et al. (2014) proposed that a negative correlation between oxygen fugacity (expressed as logfO2 and the Mn content of apatite from a range of intermediate to silicic igneous rocks could be used as an oxybarometer (Eq. (1)).

  3. Towards Understanding Leadership in Early Childhood Context: Cross-Cultural Perspectives. Acta Universitatis Ouluensis, E Scientique Rerum Socialium 35.

    ERIC Educational Resources Information Center

    Hujala, Eeva, Ed.; Puroila, Anna-Maija, Ed.

    Recognizing the importance of leadership in determining the quality of early care and education programs, the International Leadership Project (ILP) was initiated in 1996 to develop an understanding of cross-cultural perspectives on leadership, to develop a conceptual framework of leadership, and to develop cross-cultural methodologies for…

  4. Crystal structure of a Pd4 carbonyl tri-phenyl-phosphane cluster [Pd4(CO)5(PPh3)4]·2C4H8O, comparing solvates.

    PubMed

    Robeyns, Koen; Willocq, Christopher; Tinant, Bernard; Devillers, Michel; Hermans, Sophie

    2016-02-01

    Attempts to synthesize Au-Pd heterometallic compounds from homonuclear palladium or gold complexes, [Pd(PtBu2)2] and [Au(PPh3)Cl] in a tetra-hydro-furan (THF) solution under a CO atmosphere resulted in a homonuclear Pd cluster, namely penta-kis-(μ-carbonyl-κ(2) C:C)tetra-kis-(tri-phenyl-phosphane-κP)tetrapalladium(5 Pd-Pd) tetra-hydro-furan disolvate, [Pd4(CO)5(C18H15P)4]·2C4H8O. The complex mol-ecule lies on a twofold rotation axis. The crystal structure is described in relation to the CH2Cl2 solvate previously determined by our group [Willocq et al. (2011 ▸). Inorg. Chim. Acta, 373, 233-242], and in particular to the desolvated structure [Feltham et al. (1985 ▸). Inorg. Chem. 24, 1503-1510]. It is assumed that the title compound transforms into the latter structure, upon gradual loss of solvent mol-ecules. In the title compound, the symmetry-unique THF solvent mol-ecule is linked to the complex mol-ecule by a weak C-H⋯O hydrogen bond. Contributions of disordered solvent molecules to the diffraction intensities, most likely associated with methanol, were removed with the SQUEEZE [Spek (2015). Acta Cryst. C71, 9-18] algorithm. PMID:26958368

  5. Crystal structure of a Pd4 carbonyl tri­phenyl­phosphane cluster [Pd4(CO)5(PPh3)4]·2C4H8O, comparing solvates

    PubMed Central

    Robeyns, Koen; Willocq, Christopher; Tinant, Bernard; Devillers, Michel; Hermans, Sophie

    2016-01-01

    Attempts to synthesize Au–Pd heterometallic compounds from homonuclear palladium or gold complexes, [Pd(PtBu2)2] and [Au(PPh3)Cl] in a tetra­hydro­furan (THF) solution under a CO atmosphere resulted in a homonuclear Pd cluster, namely penta­kis­(μ-carbonyl-κ2 C:C)tetra­kis­(tri­phenyl­phosphane-κP)tetrapalladium(5 Pd—Pd) tetra­hydro­furan disolvate, [Pd4(CO)5(C18H15P)4]·2C4H8O. The complex mol­ecule lies on a twofold rotation axis. The crystal structure is described in relation to the CH2Cl2 solvate previously determined by our group [Willocq et al. (2011 ▸). Inorg. Chim. Acta, 373, 233–242], and in particular to the desolvated structure [Feltham et al. (1985 ▸). Inorg. Chem. 24, 1503–1510]. It is assumed that the title compound transforms into the latter structure, upon gradual loss of solvent mol­ecules. In the title compound, the symmetry-unique THF solvent mol­ecule is linked to the complex mol­ecule by a weak C—H⋯O hydrogen bond. Contributions of disordered solvent molecules to the diffraction intensities, most likely associated with methanol, were removed with the SQUEEZE [Spek (2015). Acta Cryst. C71, 9–18] algorithm. PMID:26958368

  6. A comparison of two algorithms for electron-density map improvement by introduction of atomicity: skeletonization, and map sorting followed by refinement.

    PubMed

    Vellieux, F M

    1998-01-01

    A comparison has been made of two methods for electron-density map improvement by the introduction of atomicity, namely the iterative skeletonization procedure of the CCP4 program DM [Cowtan & Main (1993). Acta Cryst. D49, 148-157] and the pseudo-atom introduction followed by the refinement protocol in the program suite DEMON/ANGEL [Vellieux, Hunt, Roy & Read (1995). J. Appl. Cryst. 28, 347-351]. Tests carried out using the 3.0 A resolution electron density resulting from iterative 12-fold non-crystallographic symmetry averaging and solvent flattening for the Pseudomonas aeruginosa ornithine transcarbamoylase [Villeret, Tricot, Stalon & Dideberg (1995). Proc. Natl Acad. Sci. USA, 92, 10762-10766] indicate that pseudo-atom introduction followed by refinement performs much better than iterative skeletonization: with the former method, a phase improvement of 15.3 degrees is obtained with respect to the initial density modification phases. With iterative skeletonization a phase degradation of 0.4 degrees is obtained. Consequently, the electron-density maps obtained using pseudo-atom phases or pseudo-atom phases combined with density-modification phases are much easier to interpret. These tests also show that for ornithine transcarbamoylase, where 12-fold non-crystallographic symmetry is present in the P1 crystals, G-function coupling leads to the simultaneous decrease of the conventional R factor and of the free R factor, a phenomenon which is not observed when non-crystallographic symmetry is absent from the crystal. The method is far less effective in such a case, and the results obtained suggest that the map sorting followed by refinement stage should be by-passed to obtain interpretable electron-density distributions. PMID:9761819

  7. The active site of hen egg-white lysozyme: flexibility and chemical bonding

    SciTech Connect

    Held, Jeanette Smaalen, Sander van

    2014-04-01

    Chemical bonding at the active site of lysozyme is analyzed on the basis of a multipole model employing transferable multipole parameters from a database. Large B factors at low temperatures reflect frozen-in disorder, but therefore prevent a meaningful free refinement of multipole parameters. Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader’s quantum theory of atoms in molecules [QTAIM; Bader (1994 ▶), Atoms in Molecules: A Quantum Theory. Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) of HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wang et al. (2007), Acta Cryst. D63, 1254–1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagala et al. (2012), Acta Cryst. A68, 337–351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C

  8. Four supramolecular isomers of dichloridobis(1,10-phenanthroline)cobalt(II): synthesis, structure characterization and isomerization.

    PubMed

    Chen, Xiaocui; Han, Shumin; Wang, Ruiyao; Li, Yuan

    2016-01-01

    Crystal engineering can be described as the understanding of intermolecular interactions in the context of crystal packing and the utilization of such understanding to design new solids with desired physical and chemical properties. Free-energy differences between supramolecular isomers are generally small and minor changes in the crystallization conditions may result in the occurrence of new isomers. The study of supramolecular isomerism will help us to understand the mechanism of crystallization, a very central concept of crystal engineering. Two supramolecular isomers of dichloridobis(1,10-phenanthroline-κ(2)N,N')cobalt(II), [CoCl2(C12H8N2)2], i.e. (IA) (orthorhombic) and (IB) (monoclinic), and two supramolecular isomers of dichloridobis(1,10-phenanthroline-κ(2)N,N')cobalt(II) N,N-dimethylformamide monosolvate, [CoCl2(C12H8N2)2]·C3H7NO, i.e. (IIA) (orthorhombic) and (IIB) (monoclinic), were synthesized in dimethylformamide (DMF) and structurally characterized. Of these, (IA) and (IIA) have been prepared and structurally characterized previously [Li et al. (2007). Acta Cryst. E63, m1880-m1880; Cai et al. (2008). Acta Cryst. E64, m1328-m1329]. We found that the heating rate is a key factor for the crystallization of (IA) or (IB), while the temperature difference is responsible for the crystallization of (IIA) or (IIB). Based on the crystallization conditions, isomerization behaviour, the KPI (Kitajgorodskij packing index) values and the density data, (IB) and (IIA) are assigned as the thermodynamic and stable kinetic isomers, respectively, while (IA) and (IIB) are assigned as the metastable kinetic products. The 1,10-phenanthroline (phen) ligands interact with each other through offset face-to-face (OFF) π-π stacking in (IB) and (IIB), but by edge-to-face (EF) C-H...π interactions in (IA) and (IIA). Meanwhile, the DMF molecules in (IIB) connect to neighbouring [CoCl2(phen)2] units through two C-H...Cl hydrogen bonds, whereas there are no obvious interactions

  9. Reply to "Comments on 'Extended electron energy loss fine structure simulation of the local boron environment in sodium aluminoborosilicate glasses containing gadolinium' by M. Qian, H. Li, L. Li and D. M. Strachan [J. Non-Cryst. Solids 328 (2003) 90

    SciTech Connect

    Li, Hong; Qian, Maoxu; Buck, Edgar C.; Strachan, Denis M.

    2005-04-24

    The nature of ^*-band, near 188-194 eV, from B K EELS spectra of borate minerals and boron containing glasses has been well documented. The ban results rom teh transition of B 1s to P ^* in B with sp hybridization. Similarly, the higher energy broad band is attributed to the transition from B 1s to P in B Radiation effects on B04 conversion to Bo3 was also studied in details for crystalline solids by Sauer et al.

  10. Reply to "Comment on papers by K. Shanahan that propose to explain anomalous heat generated by cold fusion", E. Storms, Thermochim. Acta (2005)

    SciTech Connect

    Shanahan, Kirk

    2005-09-21

    Dr. E. Storms has published a Letter [1] in which he argues that in a sequence of recent papers [2-5], the apparent excess heat signal claimed by Dr. Shanahan to arise from a calibration constant shift is actually true excess heat. In particular he proposes that the mechanisms proposed that foster the proposed calibration constant shifts [3,5] cannot occur as postulated for several reasons. As well, he proposes Shanahan has ignored the extant data proving this. Because this Letter may lend unwarranted support to acceptance of cold fusion claims, these erroneous arguments used by Storms need to be answered.

  11. Corrigendum to "Occurrence and abundance of 6-methyl branched glycerol dialkyl glycerol tetraethers in soils: Implications for palaeoclimate reconstruction" [Geochim. Cosmochim. Acta 141 (2014) 97-112

    NASA Astrophysics Data System (ADS)

    De Jonge, Cindy; Hopmans, Ellen C.; Zell, Claudia I.; Kim, Jung-Hyun; Schouten, Stefan; Sinninghe Damsté, Jaap S.

    2016-06-01

    The authors regret that the r2 values (squared pearson correlation coefficient values) reported in Figs. 7 and 8 and in the text, are instead the non-squared r values. This has no direct influence on our interpretation. We have included the corrected Figs. 7 and 8. The text describing these results should read as follows:

  12. Reply to comment by Marks et al. (2016) on "Apatite: A new redox proxy for silicic magmas?" [Geochimica et Cosmochimica Acta 132 (2014) 101-119

    NASA Astrophysics Data System (ADS)

    Miles, Andrew; Graham, Colin; Hawkesworth, Chris; Gillespie, Martin; Hinton, Richard; Bromiley, Geoffrey

    2016-06-01

    Marks et al. (2016) investigate the applicability of the Mn-in-apatite oxybarometer proposed by Miles et al. (2014) across a range of magma compositions using published data on well-characterised samples. The authors show that for magma compositions outside of the calc-alkaline and intermediate to silicic range used in the preliminary calibration, fO2 values calculated from Mn-in-apatite vary significantly from independently constrained estimates. These data are used to reiterate our warnings that other controls that are additional to oxygen fugacity are likely to affect Mn partitioning into apatite in some rock types, and particularly so in magmas that lie outside of the range of compositions and conditions used in the calibration. Marks et al. (2016) highlight that temperature may have an especially important effect on Mn partitioning in apatite in some rock types.

  13. Simposio sobre Educacion de Ninas: Evidencias, Temas, Acciones. Actas de sesiones. (Symposium on Girls Education: Evidence, Issues, Actions. Proceedings). (Washington, DC, May 17-18, 2000).

    ERIC Educational Resources Information Center

    Agency for International Development (IDCA), Washington, DC.

    This symposium highlighted core issues of controversy in girls' education and developed implications for policy and practice. Its evidence-based discussion forum encouraged dialogue, debate, and increased interaction and developed partnerships among academic institutions, nongovernmental organizations, multilateral development agencies, and other…

  14. A monoclinic polymorph of [(Z)-N-(3-chloro­phen­yl)-O-methyl­thio­carbamato-κS](tri­phenyl­phosphane-κP)gold(I): crystal structure and Hirshfeld surface analysis

    PubMed Central

    Yeo, Chien Ing; Tan, Sang Loon; Tiekink, Edward R. T.

    2016-01-01

    The title compound, [Au(C8H7ClNOS)(C18H15P)], is a monoclinic (P21/n, Z′ = 1; form β) polymorph of the previously reported triclinic form (P-1, Z′ = 1; form α) [Tadbuppa & Tiekink (2010 ▸). Acta Cryst. E66, m664]. The mol­ecular structures of both forms feature an almost linear gold(I) coordination geometry [P—Au—S = 175.62 (5)° in the title polymorph], being coordinated by thiol­ate S and phosphane P atoms, a Z conformation about the C=N bond and an intra­molecular Au⋯O contact. The major conformational difference relates to the relative orientations of the residues about the Au—S bond: the P—Au—S—C torsion angles are −8.4 (7) and 106.2 (7)° in forms α and β, respectively. The mol­ecular packing of form β features centrosymmetric aggregates sustained by aryl-C—H⋯O inter­actions, which are connected into a three-dimensional network by aryl-C—H⋯π contacts. The Hirshfeld analysis of forms α and β shows many similarities with the notable exception of the influence of C—H⋯O inter­actions in form β. PMID:27536384

  15. Crystal structure of a new monoclinic polymorph of N-(4-methyl­phen­yl)-3-nitro­pyridin-2-amine

    PubMed Central

    Aznan, Aina Mardia Akhmad; Abdullah, Zanariah; Lee, Vannajan Sanghiran; Tiekink, Edward R. T.

    2014-01-01

    The title compound, C12H11N3O2, is a second monoclinic polymorph (P21, with Z′ = 4) of the previously reported monoclinic (P21/c, with Z′ = 2) form [Akhmad Aznan et al. (2010 ▶). Acta Cryst. E66, o2400]. Four independent mol­ecules comprise the asymmetric unit, which have the common features of a syn disposition of the pyridine N atom and the toluene ring, and an intra­molecular amine–nitro N—H⋯O hydrogen bond. The differences between mol­ecules relate to the dihedral angles between the rings which range from 2.92 (19) to 26.24 (19)°. The geometry-optimized structure [B3LYP level of theory and 6–311 g+(d,p) basis set] has the same features except that the entire mol­ecule is planar. In the crystal, the three-dimensional architecture is consolidated by a combination of C—H⋯O, C—H⋯π, nitro-N—O⋯π and π–π inter­actions [inter-centroid distances = 3.649 (2)–3.916 (2) Å]. PMID:25249854

  16. A log-likelihood-gain intensity target for crystallographic phasing that accounts for experimental error.

    PubMed

    Read, Randy J; McCoy, Airlie J

    2016-03-01

    The crystallographic diffraction experiment measures Bragg intensities; crystallographic electron-density maps and other crystallographic calculations in phasing require structure-factor amplitudes. If data were measured with no errors, the structure-factor amplitudes would be trivially proportional to the square roots of the intensities. When the experimental errors are large, and especially when random errors yield negative net intensities, the conversion of intensities and their error estimates into amplitudes and associated error estimates becomes nontrivial. Although this problem has been addressed intermittently in the history of crystallographic phasing, current approaches to accounting for experimental errors in macromolecular crystallography have numerous significant defects. These have been addressed with the formulation of LLGI, a log-likelihood-gain function in terms of the Bragg intensities and their associated experimental error estimates. LLGI has the correct asymptotic behaviour for data with large experimental error, appropriately downweighting these reflections without introducing bias. LLGI abrogates the need for the conversion of intensity data to amplitudes, which is usually performed with the French and Wilson method [French & Wilson (1978), Acta Cryst. A35, 517-525], wherever likelihood target functions are required. It has general applicability for a wide variety of algorithms in macromolecular crystallography, including scaling, characterizing anisotropy and translational noncrystallographic symmetry, detecting outliers, experimental phasing, molecular replacement and refinement. Because it is impossible to reliably recover the original intensity data from amplitudes, it is suggested that crystallographers should always deposit the intensity data in the Protein Data Bank. PMID:26960124

  17. Dynamical calculations for RHEED from a partially-ordered Cu 3Au(111) surface

    NASA Astrophysics Data System (ADS)

    Ma, Y.; Lordi, S.; Flynn, C. P.; Eades, J. A.

    1994-01-01

    A multislice formalism of Cowley and Moodie [Acta Cryst. 10 (1957) 609] with a recently developed edge patching method has been applied to the RHEED analyses on the order-disorder transition of the Cu 3Au(111) surfaces. The results give the RI- S relation as RI = 0.4 S2.224 ( RI — ratio of reflection intensities, S — long-range orde By combining the RI- T relation experimentally observable by RHEED with the simulated RI- S relation, the needed S- T relation for the transition can be resolved in a straightforward way. The results confirm what was suggested by the experiments [Mater. Res. Soc. Symp. Proc. 237 (1993) 517]: the intensities of the RHEED superstructure reflections from ordering of the Cu and Au is more than 90% sensitive to the outer monolayer alone, thus making RHEED valuable for studies of surface order. The results of the analyses on the attenuation of elastically scattered electrons inside crystal in RHEED are useful to RHEED-related surface analytical techniques: AES, REEL, EDS and RHEED-TRAXS. The investigation on the errors resulting from potential sampling has shown that choosing proper sampling rates in all three dimensions is important to the multislice simulation of RHEED.

  18. Structure of Physarum polycephalum cytochrome b{sub 5} reductase at 1.56 Å resolution

    SciTech Connect

    Kim, Sangwoo; Suga, Michihiro; Ogasahara, Kyoko; Ikegami, Terumi; Minami, Yoshiko; Yubisui, Toshitsugu; Tsukihara, Tomitake

    2007-04-01

    The structure of P. polycephalum cytochrome b{sub 5} reductase, an enzyme which catalyzes the reduction of cytochrome b{sub 5} by NADH, was determined at a resolution of 1.56 Å. Physarum polycephalum cytochrome b{sub 5} reductase catalyzes the reduction of cytochrome b{sub 5} by NADH. The structure of P. polycephalum cytochrome b{sub 5} reductase was determined at a resolution of 1.56 Å. The molecular structure was compared with that of human cytochrome b{sub 5} reductase, which had previously been determined at 1.75 Å resolution [Bando et al. (2004 ▶), Acta Cryst. D60, 1929–1934]. The high-resolution structure revealed conformational differences between the two enzymes in the adenosine moiety of the FAD, the lid region and the linker region. The structural properties of both proteins were inspected in terms of hydrogen bonding, ion pairs, accessible surface area and cavity volume. The differences in these structural properties between the two proteins were consistent with estimates of their thermostabilities obtained from differential scanning calorimetry data.

  19. Improving experimental phases for strong reflections prior to density modification

    SciTech Connect

    Uervirojnangkoorn, Monarin; Hilgenfeld, Rolf; Terwilliger, Thomas C.; Read, Randy J.

    2013-09-20

    Experimental phasing of diffraction data from macromolecular crystals involves deriving phase probability distributions. These distributions are often bimodal, making their weighted average, the centroid phase, improbable, so that electron-density maps computed using centroid phases are often non-interpretable. Density modification brings in information about the characteristics of electron density in protein crystals. In successful cases, this allows a choice between the modes in the phase probability distributions, and the maps can cross the borderline between non-interpretable and interpretable. Based on the suggestions by Vekhter [Vekhter (2005), Acta Cryst. D61, 899–902], the impact of identifying optimized phases for a small number of strong reflections prior to the density-modification process was investigated while using the centroid phase as a starting point for the remaining reflections. A genetic algorithm was developed that optimizes the quality of such phases using the skewness of the density map as a target function. Phases optimized in this way are then used in density modification. In most of the tests, the resulting maps were of higher quality than maps generated from the original centroid phases. In one of the test cases, the new method sufficiently improved a marginal set of experimental SAD phases to enable successful map interpretation. Lastly, a computer program,SISA, has been developed to apply this method for phase improvement in macromolecular crystallography.

  20. Protein energy landscapes determined by five-dimensional crystallography

    SciTech Connect

    Schmidt, Marius; Srajer, Vukica; Henning, Robert; Ihee, Hyotcherl; Purwar, Namrta; Tenboer, Jason; Tripathi, Shailesh

    2013-12-01

    Barriers of activation within the photocycle of a photoactive protein were extracted from comprehensive time courses of time resolved crystallographic data collected at multiple temperature settings. Free-energy landscapes decisively determine the progress of enzymatically catalyzed reactions [Cornish-Bowden (2012 ▶), Fundamentals of Enzyme Kinetics, 4th ed.]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [Moffat (2001 ▶), Chem. Rev.101, 1569–1581; Schmidt et al. (2005 ▶), Methods Mol. Biol.305, 115–154; Schmidt (2008 ▶), Ultrashort Laser Pulses in Medicine and Biology] because both can be determined from the same set of X-ray data. Here, it is demonstrated how barriers of activation can be determined solely from five-dimensional crystallography, where in addition to space and time, temperature is a variable as well [Schmidt et al. (2010 ▶), Acta Cryst. A66, 198–206]. Directly linking molecular structures with barriers of activation between them allows insight into the structural nature of the barrier to be gained. Comprehensive time series of crystallographic data at 14 different temperature settings were analyzed and the entropy and enthalpy contributions to the barriers of activation were determined. One hundred years after the discovery of X-ray scattering, these results advance X-ray structure determination to a new frontier: the determination of energy landscapes.

  1. Crystal structure of ethyl 3-amino-6-methyl-2-[(4-methyl-phen-yl)carbamo-yl]-4-[(E)-2-phenyl-ethen-yl]thieno[2,3-b]pyridine-5-carboxyl-ate monohydrate.

    PubMed

    Mague, Joel T; Akkurt, Mehmet; Mohamed, Shaaban K; Bakhite, Etify A; Albayati, Mustafa R

    2016-03-01

    In the title mol-ecule, C27H25N3O3S·H2O, the dihedral angle between the planes of the thienyl ring and the pendant p-tolyl group is 39.25 (6)°, while that between the pyridine ring and the pendant phenyl ring is 44.37 (6)°. In addition, there is a slight twist in the bicyclic core, with a dihedral angle of 2.39 (4)° between the thienyl and pyridine rings. The conformation of the carbamoyl moiety is partially determined by an intra-molecular N-H⋯O hydrogen bond. In the crystal, complementary N-H⋯O hydrogen bonds form dimers which are then associated into chains parallel to the c axis through O-H⋯N hydrogen bonds involving the water mol-ecule of crystallization. Electron density associated with an additional solvent mol-ecule of partial occupancy and disordered about a twofold axis was removed with the SQUEEZE procedure in PLATON [Spek (2015 ▸). Acta Cryst. C71, 9-18]. The given chemical formula and other crystal data do not take into account the unknown solvent molecule(s). PMID:27006791

  2. A redetermination from the original data of the crystal structure of 2-amino-4,6-di­meth­oxy­pyrimidin-1-ium 4-amino­benzoate

    PubMed Central

    Fábry, Jan

    2016-01-01

    The title structure, C6H9.5N3O2 0.5+·C7H6.5NO2 0.5−, which might be named schematically as 2-amino-4,6-di­meth­oxy­pyrimidine-(μ2-hydrogen)-4-amino­benzoate to indicate a bridging H atom, has been redetermined from the data published by Thanigaimani, Mu­thiah & Lynch [Acta Cryst. (2006), E62, o2976–o2978]. The improvement of the present redetermination consists in a released geometry of the primary amine groups, which were originally assumed to be planar, as well as in a redetermination of the position of the hy­droxy H atom. This H atom, whose parameters were originally constrained, turns out to be situated about the centre of the O⋯N hydrogen bond in two disordered positions with occupancies of 0.5 each. PMID:27375878

  3. Etude structurale et vibrationnelle d'un nouveau composé complexe de cobalt: [Co(imidazole)4Cl]Cl.

    PubMed

    Derbel, Amira; Mhiri, Tahar; Graia, Mohsen

    2015-10-01

    In the title complex, chlorido-tetra-kis-(1H-imidazole-κN (3))cobalt(II) chloride, [CoCl(C3H4N2)4]Cl, the Co(II) cation has a distorted square-pyramidal coordination environment. It is coordinated by four N atoms of four imidazole (Im) groups in the basal plane, and by a Cl atom in the apical position. It is isostructural with [Cu(Im)4Cl]Cl [Morzyk-Ociepa et al. (2012 ▸). J. Mol. Struct. 1028, 49-56] and [Cu(Im)4Br]Br [Hossaini Sadr et al. (2004 ▸). Acta Cryst. E60, m1324-m1326]. In the crystal, the [CoCl(C3H4N2)4](+) cations and Cl(-) anions are linked via N-H⋯Cl hydrogen bonds, forming layers parallel to (010). These layers are linked via C-H⋯Cl hydrogen bonds and C-H⋯π and π-π [inter-centroid distance = 3.794 (2) Å] inter-actions, forming a three-dimensional framework. The IR spectrum shows vibrational bands typical for imidazol groups. The monoclinic unit cell of the title compound emulates an ortho-rhom-bic cell as its β angle is close to 90°. The crystal is twinned, with the refined ratio of twin components being 0.569 (1):0.431 (1). PMID:26594402

  4. Crystal structure of an unknown tetra-hydro-furan solvate of tetra-kis-(μ 3-cyanato-κ(3) N:N:N)tetra-kis-[(triphenyl-phosphane-κP)-silver(I)].

    PubMed

    Frenzel, Peter; Schaarschmidt, Dieter; Jakob, Alexander; Lang, Heinrich

    2015-10-01

    In the title compound, [{[(C6H5)3P]Ag}4{NCO}4], a distorted Ag4N4-heterocubane core is set up by four Ag(I) ions being coordinated by the N atoms of the cyanato anions in a μ 3-bridging mode. In addition, a tri-phenyl-phosphine ligand is datively bonded to each of the Ag(I) ions. Intra-molecular Ag⋯Ag distances as short as 3.133 (9) Å suggest the presence of argentophilic (d (10)⋯d (10)) inter-actions. Five moderate-to-weak C-H⋯O hydrogen-bonding inter-actions are observed in the crystal structure, spanning a three-dimensional network. A region of electron density was treated with the SQUEEZE procedure in PLATON [Spek (2015). Acta Cryst. C71, 9-18] following unsuccessful attempts to model it as being part of disordered tetra-hydro-furan solvent mol-ecules. The given chemical formula and other crystal data do not take into account these solvent mol-ecules. PMID:26594421

  5. Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal

    DOE PAGESBeta

    Terwilliger, Thomas C.; Bunkóczi, Gábor; Hung, Li-Wei; Zwart, Peter H.; Smith, Janet L.; Akey, David L.; Adams, Paul D.

    2016-03-01

    A key challenge in the SAD phasing method is solving a structure when the anomalous signal-to-noise ratio is low. Here, we describe algorithms and tools for evaluating and optimizing the useful anomalous correlation and the anomalous signal in a SAD experiment. A simple theoretical framework [Terwilliger et al.(2016),Acta Cryst.D72, 346–358] is used to develop methods for planning a SAD experiment, scaling SAD data sets and estimating the useful anomalous correlation and anomalous signal in a SAD data set. Thephenix.plan_sad_experimenttool uses a database of solved and unsolved SAD data sets and the expected characteristics of a SAD data set to estimatemore » the probability that the anomalous substructure will be found in the SAD experiment and the expected map quality that would be obtained if the substructure were found. Thephenix.scale_and_mergetool scales unmerged SAD data from one or more crystals using local scaling and optimizes the anomalous signal by identifying the systematic differences among data sets, and thephenix.anomalous_signaltool estimates the useful anomalous correlation and anomalous signal after collecting SAD data and estimates the probability that the data set can be solved and the likely figure of merit of phasing.« less

  6. Improving experimental phases for strong reflections prior to density modification

    DOE PAGESBeta

    Uervirojnangkoorn, Monarin; Hilgenfeld, Rolf; Terwilliger, Thomas C.; Read, Randy J.

    2013-09-20

    Experimental phasing of diffraction data from macromolecular crystals involves deriving phase probability distributions. These distributions are often bimodal, making their weighted average, the centroid phase, improbable, so that electron-density maps computed using centroid phases are often non-interpretable. Density modification brings in information about the characteristics of electron density in protein crystals. In successful cases, this allows a choice between the modes in the phase probability distributions, and the maps can cross the borderline between non-interpretable and interpretable. Based on the suggestions by Vekhter [Vekhter (2005), Acta Cryst. D61, 899–902], the impact of identifying optimized phases for a small number ofmore » strong reflections prior to the density-modification process was investigated while using the centroid phase as a starting point for the remaining reflections. A genetic algorithm was developed that optimizes the quality of such phases using the skewness of the density map as a target function. Phases optimized in this way are then used in density modification. In most of the tests, the resulting maps were of higher quality than maps generated from the original centroid phases. In one of the test cases, the new method sufficiently improved a marginal set of experimental SAD phases to enable successful map interpretation. Lastly, a computer program,SISA, has been developed to apply this method for phase improvement in macromolecular crystallography.« less

  7. Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal

    PubMed Central

    Terwilliger, Thomas C.; Bunkóczi, Gábor; Hung, Li-Wei; Zwart, Peter H.; Smith, Janet L.; Akey, David L.; Adams, Paul D.

    2016-01-01

    A key challenge in the SAD phasing method is solving a structure when the anomalous signal-to-noise ratio is low. Here, algorithms and tools for evaluating and optimizing the useful anomalous correlation and the anomalous signal in a SAD experiment are described. A simple theoretical framework [Terwilliger et al. (2016 ▸), Acta Cryst. D72, 346–358] is used to develop methods for planning a SAD experiment, scaling SAD data sets and estimating the useful anomalous correlation and anomalous signal in a SAD data set. The phenix.plan_sad_experiment tool uses a database of solved and unsolved SAD data sets and the expected characteristics of a SAD data set to estimate the probability that the anomalous substructure will be found in the SAD experiment and the expected map quality that would be obtained if the substructure were found. The phenix.scale_and_merge tool scales unmerged SAD data from one or more crystals using local scaling and optimizes the anomalous signal by identifying the systematic differences among data sets, and the phenix.anomalous_signal tool estimates the useful anomalous correlation and anomalous signal after collecting SAD data and estimates the probability that the data set can be solved and the likely figure of merit of phasing. PMID:26960123

  8. Theoretical study of the properties of X-ray diffraction moiré fringes. I

    PubMed Central

    Yoshimura, Jun-ichi

    2015-01-01

    A detailed and comprehensive theoretical description of X-ray diffraction moiré fringes for a bicrystal specimen is given on the basis of a calculation by plane-wave dynamical diffraction theory. Firstly, prior to discussing the main subject of the paper, a previous article [Yoshimura (1997 ▸). Acta Cryst. A53, 810–812] on the two-dimensionality of diffraction moiré patterns is restated on a thorough calculation of the moiré interference phase. Then, the properties of moiré fringes derived from the above theory are explained for the case of a plane-wave diffraction image, where the significant effect of Pendellösung intensity oscillation on the moiré pattern when the crystal is strained is described in detail with theoretically simulated moiré images. Although such plane-wave moiré images are not widely observed in a nearly pure form, knowledge of their properties is essential for the understanding of diffraction moiré fringes in general. PMID:25970298

  9. A P212121 polymorph of (+)-clusianone

    PubMed Central

    Vaneesa Nagalingam, Sree; Wong Pik Ching, Janet; Khaled bin Break, Mohammed; Tahir, M. Ibrahim M.; Khoo, Teng-Jin

    2013-01-01

    The title compound, C33H42O4 [systematic name: (1S,5S,7R)-3-benzoyl-4-hy­droxy-8,8-dimethyl-1,5,7-tris­(3-methyl­but-2-­enyl)bi­cyclo­[3.3.1]nona-3-ene-2,9-dione], has a central bi­cyclo­[3.3.1]nonane-2,4,9-trione surrounded by tetra­prenyl­ated and benzoyl groups. The compound was recrystallized several times in methanol using both a slow evaporation method and with a crystal-seeding technique. This subsequently produced diffraction-quality crystals which crystallize in the ortho­rhom­bic space group P212121, in contrast to a previous report of a structure determination in the Pna21 space group [McCandlish et al. (1976 ▶). Acta Cryst. B32, 1793–1801]. The title compound has a melting point of 365–366 K, and a specific rotation [α]20 value of +51.94°. A strong intra­molecular O—H⋯O hydrogen bond is noted. In the crystal, mol­ecules are assembled in the ab plane by weak C—H⋯O inter­actions. PMID:24860292

  10. Magnetic structure determination from the magnetic pair distribution function (mPDF): ground state of MnO.

    PubMed

    Frandsen, Benjamin A; Billinge, Simon J L

    2015-05-01

    An experimental determination of the magnetic pair distribution function (mPDF) defined in an earlier paper [Frandsen et al. (2014). Acta Cryst. A70, 3-11] is presented for the first time. The mPDF was determined from neutron powder diffraction data from a reactor and a neutron time-of-flight total scattering source on a powder sample of the antiferromagnetic oxide MnO. A description of the data treatment that allowed the measured mPDF to be extracted and then modelled is provided and utilized to investigate the low-temperature structure of MnO. Atomic and magnetic co-refinements support the scenario of a locally monoclinic ground-state atomic structure, despite the average structure being rhombohedral, with the mPDF analysis successfully recovering the known antiferromagnetic spin configuration. The total scattering data suggest a preference for the spin axis to lie along the pseudocubic [10{\\overline 1}] direction. Finally, r-dependent PDF refinements indicate that the local monoclinic structure tends toward the average rhombohedral R{\\overline 3}m symmetry over a length scale of approximately 100 Å. PMID:25921501

  11. Direct phasing in femtosecond nanocrystallography. I. Diffraction characteristics

    PubMed Central

    Chen, Joe P. J.; Spence, John C. H.; Millane, Rick P.

    2014-01-01

    X-ray free-electron lasers solve a number of difficulties in protein crystallography by providing intense but ultra-short pulses of X-rays, allowing collection of useful diffraction data from nanocrystals. Whereas the diffraction from large crystals corresponds only to samples of the Fourier amplitude of the molecular transform at the Bragg peaks, diffraction from very small crystals allows measurement of the diffraction amplitudes between the Bragg samples. Although highly attenuated, these additional samples offer the possibility of iterative phase retrieval without the use of ancillary experimental data [Spence et al. (2011 ▸). Opt. Express, 19, 2866–2873]. This first of a series of two papers examines in detail the characteristics of diffraction patterns from collections of nanocrystals, estimation of the molecular transform and the noise characteristics of the measurements. The second paper [Chen et al. (2014 ▸). Acta Cryst. A70, 154–161] examines iterative phase-retrieval methods for reconstructing molecular structures in the presence of the variable noise levels in such data. PMID:24572315

  12. Crystal structure of a new monoclinic polymorph of N-(4-methyl-phen-yl)-3-nitro-pyridin-2-amine.

    PubMed

    Aznan, Aina Mardia Akhmad; Abdullah, Zanariah; Lee, Vannajan Sanghiran; Tiekink, Edward R T

    2014-08-01

    The title compound, C12H11N3O2, is a second monoclinic polymorph (P21, with Z' = 4) of the previously reported monoclinic (P21/c, with Z' = 2) form [Akhmad Aznan et al. (2010 ▶). Acta Cryst. E66, o2400]. Four independent mol-ecules comprise the asymmetric unit, which have the common features of a syn disposition of the pyridine N atom and the toluene ring, and an intra-molecular amine-nitro N-H⋯O hydrogen bond. The differences between mol-ecules relate to the dihedral angles between the rings which range from 2.92 (19) to 26.24 (19)°. The geometry-optimized structure [B3LYP level of theory and 6-311 g+(d,p) basis set] has the same features except that the entire mol-ecule is planar. In the crystal, the three-dimensional architecture is consolidated by a combination of C-H⋯O, C-H⋯π, nitro-N-O⋯π and π-π inter-actions [inter-centroid distances = 3.649 (2)-3.916 (2) Å]. PMID:25249854

  13. Crystal structure of cis-bis­{4-phenyl-1-[(3R)-1,7,7-tri­methyl-2-oxobi­cyclo­[2.2.1]heptan-3-ylidene]thio­semicarbazidato-κ3 O,N 1,S}cadmium(II) with an unknown solvent mol­ecule

    PubMed Central

    Nogueira, Vanessa Senna; Bresolin, Leandro; Näther, Christian; Jess, Inke; de Oliveira, Adriano Bof

    2015-01-01

    The reaction between the racemic mixture of the camphor-4-phenyl­thio­semicarbazone derivative and cadmium acetate dihydrate yielded the title compound, [Cd(C17H20N3OS)2]. The CdII ion is six-coordinated in a distorted octa­hedral environment by two deprotonated thio­semicarbazone ligands acting as an O,N,S-donor in a tridentate chelating mode, forming five-membered chelate rings. In the crystal, the mol­ecules are connected via pairs of N—H⋯S and C—H⋯S inter­actions, building centrosymmetric dimers. One of the ligands is disordered in the campher unit over two sets of sites with site-occupancy factors of 0.7 and 0.3. The structure contains additional solvent mol­ecules, which are disordered and for which no reasonable split model was found. Therefore, the data were corrected for disordered solvent using the SQUEEZE routine [Spek (2015 ▸). Acta Cryst. C71, 9–18] in PLATON. Since the disordered solvents were removed by data processing, and the number of solvent entities was a suggestion only, they were not considered in the chemical formula and subsequent chemical or crystal information. PMID:26870441

  14. (1-Methyl-1H-imidazole-κN 3)(1-methyl-2-nitroso­benzene-κN)(5,10,15,20-tetra­phenyl­porphyrinato-κ4 N)iron(II) di­chloro­methane monosolvate

    PubMed Central

    Abucayon, Erwin G.; Awasabisah, Dennis; Powell, Douglas R.; Richter-Addo, George B.

    2014-01-01

    The solvated title compound, [Fe(C44H28N4)(C4H6N2)(C7H7NO)]·CH2Cl2, is a porphyrin complex containing an octahedrally coordinated FeII atom with 1-methylimidazole [Fe—N = 2.0651 (17) Å] and o-nitro­sotoluene ligands at the axial positions. The o-nitro­sotoluene ligand is N-bound to iron(II) [Fe—N = 1.8406 (18)Å and Fe—N—O = 122.54 (14)°]. The axial N—Fe—N linkage is almost linear, with a bond angle of 177.15 (7)°. One phenyl group of the porphyrin ligand is disordered over two orientations in a 0.710 (3):0.290 (3) ratio. The di­chloro­methane solvent mol­ecule was severely disordered and its contribution to the scattering was removed with the SQUEEZE routine [van der Sluis & Spek (1990 ▶). Acta Cryst. A46, 194–201]. PMID:24764819

  15. Comparison of racemic epi-inosose and (-)-epi-inosose.

    PubMed

    Krishnaswamy, Shobhana; Patil, Madhuri T; Shashidhar, Mysore S

    2011-11-01

    The conversion of myo-inositol to epi-inositol can be achieved by the hydride reduction of an intermediate epi-inosose derived from myo-inositol. (-)-epi-Inosose, (I), crystallized in the monoclinic space group P2(1), with two independent molecules in the asymmetric unit [Hosomi et al. (2000). Acta Cryst. C56, e584-e585]. On the other hand, (2RS,3SR,5SR,6SR)-epi-inosose, C(6)H(10)O(6), (II), crystallized in the orthorhombic space group Pca2(1). Interestingly, the conformation of the molecules in the two structures is nearly the same, the only difference being the orientation of the C-3 and C-4 hydroxy H atoms. As a result, the molecular organization achieved mainly through strong O-H···O hydrogen bonding in the racemic and homochiral lattices is similar. The compound also follows Wallach's rule, in that the racemic crystals are denser than the optically active form. PMID:22051958

  16. Crystal structure of [(E)-({2-[3-(2-{(1E)-[(carbamo­thioyl­amino)­imino]­meth­yl}phen­oxy)prop­oxy]phen­yl}methyl­idene)amino]­thio­urea with an unknown solvate

    PubMed Central

    Mague, Joel T.; Mohamed, Shaaban K.; Akkurt, Mehmet; Younes, Sabry H. H.; Albayati, Mustafa R.

    2015-01-01

    The title mol­ecule, C19H22N6O2S2, has crystallographically imposed C 2 symmetry, with the central C atom lying on the rotation axis. The O—C—C—C torsion angle for the central chain is −59.22 (16)° and the dihedral angle between the planes of the benzene rings is 75.20 (7)°. In the crystal, N—H⋯O and N—H⋯S inter­actions link the mol­ecules, forming a three-dimensional network encompassing channels running parallel to the c axis, which account for about 20% of the unit-cell volume. The contribution to the scattering from the highly disordered solvent mol­ecules in these channels was removed with the SQUEEZE routine [Spek (2015). Acta Cryst. C71, 9–18] in PLATON. The stated crystal data for M r, μ etc. do not take these into account. PMID:26279946

  17. Theoretical study of the properties of X-ray diffraction moiré fringes. I

    SciTech Connect

    Yoshimura, Jun-ichi

    2015-05-14

    A detailed and comprehensive theoretical description of X-ray diffraction moiré fringes for a bicrystal specimen is given on the basis of a calculation by plane-wave dynamical diffraction theory, where the effect of the Pendellösung intensity oscillation on the moiré pattern is explained in detail. A detailed and comprehensive theoretical description of X-ray diffraction moiré fringes for a bicrystal specimen is given on the basis of a calculation by plane-wave dynamical diffraction theory. Firstly, prior to discussing the main subject of the paper, a previous article [Yoshimura (1997 ▸). Acta Cryst. A53, 810–812] on the two-dimensionality of diffraction moiré patterns is restated on a thorough calculation of the moiré interference phase. Then, the properties of moiré fringes derived from the above theory are explained for the case of a plane-wave diffraction image, where the significant effect of Pendellösung intensity oscillation on the moiré pattern when the crystal is strained is described in detail with theoretically simulated moiré images. Although such plane-wave moiré images are not widely observed in a nearly pure form, knowledge of their properties is essential for the understanding of diffraction moiré fringes in general.

  18. A monoclinic polymorph of [(Z)-N-(3-chloro-phen-yl)-O-methyl-thio-carbamato-κS](tri-phenyl-phosphane-κP)gold(I): crystal structure and Hirshfeld surface analysis.

    PubMed

    Yeo, Chien Ing; Tan, Sang Loon; Tiekink, Edward R T

    2016-08-01

    The title compound, [Au(C8H7ClNOS)(C18H15P)], is a monoclinic (P21/n, Z' = 1; form β) polymorph of the previously reported triclinic form (P-1, Z' = 1; form α) [Tadbuppa & Tiekink (2010 ▸). Acta Cryst. E66, m664]. The mol-ecular structures of both forms feature an almost linear gold(I) coordination geometry [P-Au-S = 175.62 (5)° in the title polymorph], being coordinated by thiol-ate S and phosphane P atoms, a Z conformation about the C=N bond and an intra-molecular Au⋯O contact. The major conformational difference relates to the relative orientations of the residues about the Au-S bond: the P-Au-S-C torsion angles are -8.4 (7) and 106.2 (7)° in forms α and β, respectively. The mol-ecular packing of form β features centrosymmetric aggregates sustained by aryl-C-H⋯O inter-actions, which are connected into a three-dimensional network by aryl-C-H⋯π contacts. The Hirshfeld analysis of forms α and β shows many similarities with the notable exception of the influence of C-H⋯O inter-actions in form β. PMID:27536384

  19. Redetermined structure of 4,4'-bi-pyridine-1,4-phenyl-enedi-acetic acid (1/1) co-crystal.

    PubMed

    Paul, Rima; Bora, Sanchay Jyoti

    2015-10-01

    The asymmetric unit of the title 1:1 co-crystal, C10H8N2·C10H10O4, consists of one half-mol-ecule each of 4,4'-bi-pyridine and 1,4-phenyl-enedi-acetic acid: the complete mol-ecules are generated by crystallographic inversion centres. The dihedral angle between the -CO2H group and the benzene ring in the diacid is 73.02 (7)°. In the crystal, the components are linked by O-H⋯N hydrogen bonds, generating [1-2-1] chains of alternating amine and carb-oxy-lic acid mol-ecules. The chains are cross-linked by C-H⋯O inter-actions. This structure was previously incorrectly described as a (C10H10N2)(2+)·(C10H8O4)(2-) mol-ecular salt [Jia et al. (2009 ▸). Acta Cryst. E65, o2490-o2490]. PMID:26594486

  20. Azole. 44. Uber morpholinonitroimidazolderivate

    PubMed

    Gzella; Wrzeciono; Poppel

    2000-09-01

    The structure analyses of racemic 3-chloro-1-(4-morpholino-5-nitroimidazol-1-yl)propan-2-ol, C(10)H(15)ClN(4)O(4), (II), and 3-chloro-1-(5-morpholino-4-nitroimidazol-1-yl)propan-2-ol, C(10)H(15)ClN(4)O(4), (III), have been undertaken in order to determine the position of the morpholine residue in these two isomers. The morpholine residue in (II) is connected at the 4-position, while in (III), it is connected at the 5-position of the imidazole ring. The morpholine mean planes and nitro groups in the two compounds deviate from the imidazole planes to different extents. The nitro groups in (II) and (III) take part in the conjugation system of the imidazole rings. In consequence, the exocyclic C-N bonds are significantly shorter than the normal single Csp(2)-NO(2) bond and the nitro groups in (II) and (III) show an extraordinary stability on treatment with morpholine and piperidine [Gzella, Wrzeciono & Poppel (1999). Acta Cryst. C55, 1562-1565]. In the crystal lattice, the molecules of both compounds are linked by O-H.N and C-H.O intermolecular hydrogen bonds. PMID:10986519

  1. Enhanced rigid-bond restraints

    SciTech Connect

    Thorn, Andrea; Dittrich, Birger; Sheldrick, George M.

    2012-07-01

    An extension is proposed to the rigid-bond description of atomic thermal motion in crystals. The rigid-bond model [Hirshfeld (1976 ▶). Acta Cryst. A32, 239–244] states that the mean-square displacements of two atoms are equal in the direction of the bond joining them. This criterion is widely used for verification (as intended by Hirshfeld) and also as a restraint in structure refinement as suggested by Rollett [Crystallographic Computing (1970 ▶), edited by F. R. Ahmed et al., pp. 167–181. Copenhagen: Munksgaard]. By reformulating this condition, so that the relative motion of the two atoms is required to be perpendicular to the bond, the number of restraints that can be applied per anisotropic atom is increased from about one to about three. Application of this condition to 1,3-distances in addition to the 1,2-distances means that on average just over six restraints can be applied to the six anisotropic displacement parameters of each atom. This concept is tested against very high resolution data of a small peptide and employed as a restraint for protein refinement at more modest resolution (e.g. 1.7 Å)

  2. Maximum-likelihood density modification using pattern recognition of structural motifs

    SciTech Connect

    Terwilliger, Thomas C.

    2001-12-01

    A likelihood-based density-modification method is extended to include pattern recognition of structural motifs. The likelihood-based approach to density modification [Terwilliger (2000 ▶), Acta Cryst. D56, 965–972] is extended to include the recognition of patterns of electron density. Once a region of electron density in a map is recognized as corresponding to a known structural element, the likelihood of the map is reformulated to include a term that reflects how closely the map agrees with the expected density for that structural element. This likelihood is combined with other aspects of the likelihood of the map, including the presence of a flat solvent region and the electron-density distribution in the protein region. This likelihood-based pattern-recognition approach was tested using the recognition of helical segments in a largely helical protein. The pattern-recognition method yields a substantial phase improvement over both conventional and likelihood-based solvent-flattening and histogram-matching methods. The method can potentially be used to recognize any common structural motif and incorporate prior knowledge about that motif into density modification.

  3. A new polymorph of 2,6-dimeth­oxy­benzoic acid

    PubMed Central

    Portalone, Gustavo

    2011-01-01

    A new crystalline form of 2,6-dimeth­oxy­benzoic acid, C9H10O4, crystallizing in a tetra­gonal unit cell has been identified during screening for co-crystals. The asymmetric unit comprises a non-planar independent mol­ecule with a synplanar conformation of the carb­oxy group. The sterically bulky o-meth­oxy substituents force the carb­oxy group to be twisted away from the plane of the benzene ring by 65.72 (15)°. The carb­oxy group is disordered over two sites about the C—C bond [as indicated by the almost equal C—O distances of 1.254 (3) and 1.250 (3) Å], the occupancies of the disordered carboxym H atoms being 0.53 (5) and 0.47 (5). In the known ortho­rhom­bic form reported by Swaminathan et al. [Acta Cryst. (1976), B32, 1897–1900], due to the anti­planar conformation adopted by the OH group, the mol­ecular components are associated in the crystal in chains stabilized by linear O—H⋯O hydrogen bonds. However, in the new tetra­gonal polymorph, mol­ecules form dimeric units via pairs of O—H⋯O hydrogen bonds between the carb­oxy groups. PMID:22199883

  4. Bis[2-(hy-droxy-imino-meth-yl)phenolato]nickel(II): a second monoclinic polymorph.

    PubMed

    Rusanova, Julia A; Buvaylo, Elena A; Rusanov, Eduard B

    2011-01-01

    The title compound, [Ni(C(7)H(6)NO(2))(2)], (I), is a second monoclinic polymorph of the compound, (II), reported by Srivastava et al. [Acta Cryst. (1967), 22, 922] and Mereiter [Private communication (2002) CCDC refcode NISALO01]. The bond lengths and angles are similar in both structures. The mol-ecule in both structures lies on a crystallographic inversion center and both have an inter-nal hydrogen bond. The title compound crystallizes in the space group P2(1)/c (Z = 2), whereas compound (II) is in the space group P2(1)/n (Z = 2) with a similar cell volume but different cell parameters. In both polymorphs, mol-ecules are arranged in the layers but in contrast to the previously published compound (II) where the dihedral angle between the layers is 86.3°, in the title polymorph the same dihedral angle is 29.4°. The structure of (I) is stabilized by strong intra-molecular O-H⋯O hydrogen bonding between the O-H group and the phenolate O atom. PMID:21522882

  5. A computational study into the (tetrahedral) distortion of TX {sub 2} {alpha}-quartz materials: The effect of changing the chemical composition away from SiO{sub 2}

    SciTech Connect

    Zwijnenburg, Martijn A. . E-mail: martijn@ri.ac.uk; Huenerbein, Robert; Bell, Robert G.; Cora, Furio

    2006-11-15

    We report a periodic density functional study into the tetrahedral distortion of a range of quartz-like TX {sub 2} materials. The total tetrahedral distortion and its most sizable contribution, the angular part (angular tetrahedral distortion), are found to be strongly dependent on the chemical composition and to increase in the order of BeF{sub 2}Acta. Cryst. 16 (1963) 542-545], demonstrating that regular tetrahedra are in principle possible in quartz but that distortions from ideality are energetically advantageous. The energetic reason for this distortion is still an open question; we propose a simple electrostatic model that explains the ease with which tetrahedra can be distorted in terms of charge transfer and the relative charge on the X (O,S,F) atom. - Graphical Abstract: View on a quartz unit-cell with TX {sub 4} tetrahedra. Display Omitted.

  6. Crystal structure of the Anderson-type hetero­polyoxometalate; K2[H7CrIIIMo6O24]·8H2O: a redetermination revealing the position of the extra H atom in the polyanion

    PubMed Central

    Joo, Hea-Chung; Park, Ki-Min; Lee, Uk

    2015-01-01

    The title compound contains a symmetric hydrogen bond in which the H atom does not lie on a crystallographic centre of symmetry. The structure of K2[H7CrIIIMo6O24]·8H2O, namely dipotassium hepta­hydrogen hexa­molybdochromate(III) octa­hydrate, previously reported by Lee [Acta Cryst. (2007), E63, i5–i7], has been redetermined in order to locate the position of the seventh H atom in the anion. Six of the H atoms are bonded to the six μ3-O atoms and form hydrogen bonds of medium strength either to water mol­ecules or to the terminal O atoms of other polyanions. The seventh H atom forms a very short hydrogen bond between two μ2-O atoms on adjacent polyanions. This short bond, together with two normal hydrogen bonds, link the two crystallographically distinct centrosymmetric polyanions into chains along [011], while the length of this bond [2.461 (3) Å] suggests that the H atom lies at its centre, but unusually for such a bond, this point is not a crystallographic centre of symmetry. PMID:25878807

  7. Protein energy landscapes determined by five-dimensional crystallography

    PubMed Central

    Schmidt, Marius; Srajer, Vukica; Henning, Robert; Ihee, Hyotcherl; Purwar, Namrta; Tenboer, Jason; Tripathi, Shailesh

    2013-01-01

    Free-energy landscapes decisively determine the progress of enzymatically catalyzed reactions [Cornish-Bowden (2012 ▶), Fundamentals of Enzyme Kinetics, 4th ed.]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [Moffat (2001 ▶), Chem. Rev. 101, 1569–1581; Schmidt et al. (2005 ▶), Methods Mol. Biol. 305, 115–154; Schmidt (2008 ▶), Ultrashort Laser Pulses in Medicine and Biology] because both can be determined from the same set of X-ray data. Here, it is demonstrated how barriers of activation can be determined solely from five-dimensional crystallo­graphy, where in addition to space and time, temperature is a variable as well [Schmidt et al. (2010 ▶), Acta Cryst. A66, 198–206]. Directly linking molecular structures with barriers of activation between them allows insight into the structural nature of the barrier to be gained. Comprehensive time series of crystallo­graphic data at 14 different temperature settings were analyzed and the entropy and enthalpy contributions to the barriers of activation were determined. One hundred years after the discovery of X-ray scattering, these results advance X-ray structure determination to a new frontier: the determination of energy landscapes. PMID:24311594

  8. A second ortho­rhom­bic polymorph of (Z)-3-(9-anthr­yl)-1-(2-thien­yl)prop-2-en-1-one1

    PubMed Central

    Chantrapromma, Suchada; Suwunwong, Thitipone; Boonnak, Nawong; Fun, Hoong-Kun

    2010-01-01

    The title heteroaryl chalcone, C21H14OS, is a second ortho­rhom­bic polymorph which crystallizes in the space group P212121. The structure was previously reported [Fun et al. (2009 ▶). Acta Cryst. E65, o2168-o2169] in the space group Pna21. The bond distances and angles are similar in both structures. In contrast, the overall crystal packing is different from that in the first ortho­rhom­bic Pna21 polymorph in which mol­ecules were stacked into columns along the b axis and the thio­phene units of two adjacent columns were stacked in a head to tail fashion. In the present polymorph, mol­ecules are found to dimerize through a weak S⋯S inter­action [3.6513 (7) Å] and these dimers are arranged into sheets parallel to the bc plane. There are no classical hydrogen bonds in the packing which features short C⋯O [3.2832 (2)–3.6251 (9) Å], C⋯S [3.4879 (17)–3.6251 (19) Å] and S⋯O [2.9948 (16) Å] contacts, together with C—H⋯π inter­actions. Similar contacts were found in the other polymorph. PMID:21579743

  9. Probability density functions of the average and difference intensities of Friedel opposites.

    PubMed

    Shmueli, U; Flack, H D

    2010-11-01

    Trigonometric series for the average (A) and difference (D) intensities of Friedel opposites were carefully rederived and were normalized to minimize their dependence on sin(theta)/lambda. Probability density functions (hereafter p.d.f.s) of these series were then derived by the Fourier method [Shmueli, Weiss, Kiefer & Wilson (1984). Acta Cryst. A40, 651-660] and their expressions, which admit any chemical composition of the unit-cell contents, were obtained for the space group P1. Histograms of A and D were then calculated for an assumed random-structure model and for 3135 Friedel pairs of a published solved crystal structure, and were compared with the p.d.f.s after the latter were scaled up to the histograms. Good agreement was obtained for the random-structure model and a qualitative one for the published solved structure. The results indicate that the residual discrepancy is mainly due to the presumed statistical independence of the p.d.f.'s characteristic function on the contributions of the interatomic vectors. PMID:20962376

  10. On the group-theoretical approach to the study of interpenetrating nets.

    PubMed

    Baburin, Igor A

    2016-05-01

    Using group-subgroup and group-supergroup relations, a general theoretical framework is developed to describe and derive interpenetrating 3-periodic nets. The generation of interpenetration patterns is readily accomplished by replicating a single net with a supergroup G of its space group H under the condition that site symmetries of vertices and edges are the same in both H and G. It is shown that interpenetrating nets cannot be mapped onto each other by mirror reflections because otherwise edge crossings would necessarily occur in the embedding. For the same reason any other rotation or roto-inversion axes from G \\ H are not allowed to intersect vertices or edges of the nets. This property significantly narrows the set of supergroups to be included in the derivation of interpenetrating nets. A procedure is described based on the automorphism group of a Hopf ring net [Alexandrov et al. (2012). Acta Cryst. A68, 484-493] to determine maximal symmetries compatible with interpenetration patterns. The proposed approach is illustrated by examples of twofold interpenetrated utp, dia and pcu nets, as well as multiple copies of enantiomorphic quartz (qtz) networks. Some applications to polycatenated 2-periodic layers are also discussed. PMID:27126113

  11. Redetermined structure of 4,4′-bi­pyridine–1,4-phenyl­enedi­acetic acid (1/1) co-crystal

    PubMed Central

    Paul, Rima; Bora, Sanchay Jyoti

    2015-01-01

    The asymmetric unit of the title 1:1 co-crystal, C10H8N2·C10H10O4, consists of one half-mol­ecule each of 4,4′-bi­pyridine and 1,4-phenyl­enedi­acetic acid: the complete mol­ecules are generated by crystallographic inversion centres. The dihedral angle between the –CO2H group and the benzene ring in the diacid is 73.02 (7)°. In the crystal, the components are linked by O—H⋯N hydrogen bonds, generating [1-2-1] chains of alternating amine and carb­oxy­lic acid mol­ecules. The chains are cross-linked by C—H⋯O inter­actions. This structure was previously incorrectly described as a (C10H10N2)2+·(C10H8O4)2− mol­ecular salt [Jia et al. (2009 ▸). Acta Cryst. E65, o2490–o2490]. PMID:26594486

  12. Crystal structure of 2-methyl­amino-4-(6-methyl-4-oxo-4H-chromen-3-yl)-3-nitro­pyrano[3,2-c]chromen-5(4H)-one with an unknown solvate

    PubMed Central

    Raja, Rajamani; Kandhasamy, Subramani; Perumal, Paramasivam T.; SubbiahPandi, A.

    2015-01-01

    In the title compound, C23H16N2O7, the mean planes of the two chromene units (r.m.s. deviations = 0.031 and 0.064 Å) are almost normal to one another with a dihedral angle of 85.59 (6)°. The central six-membered pyran ring has a distorted envelope conformation, with the methine C atom at the flap. There is an intra­molecular N—H⋯O hydrogen bond, which generates an S(6) ring motif. In the crystal, mol­ecules are linked by pairs of N—H⋯O hydrogen bonds, forming inversion dimers with an R 2 2(12) ring motif. The dimers are linked by pairs of C—H⋯O hydrogen bonds, enclosing R 2 2(6) ring motifs, forming zigzag chains along [001]. The chains are linked by a second pair of C—H⋯O hydrogen bonds, forming slabs parallel to (110). Within the slabs there are C—H⋯π inter­actions present. A region of disordered electron density was treated with the SQUEEZE procedure in PLATON [Spek (2015 ▸). Acta Cryst. C71, 9–18] following unsuccessful attempts to model it as plausible solvent mol­ecule(s). The given chemical formula and other crystal data do not take into account the unknown solvent mol­ecule(s). PMID:26396882

  13. Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal.

    PubMed

    Terwilliger, Thomas C; Bunkóczi, Gábor; Hung, Li Wei; Zwart, Peter H; Smith, Janet L; Akey, David L; Adams, Paul D

    2016-03-01

    A key challenge in the SAD phasing method is solving a structure when the anomalous signal-to-noise ratio is low. Here, algorithms and tools for evaluating and optimizing the useful anomalous correlation and the anomalous signal in a SAD experiment are described. A simple theoretical framework [Terwilliger et al. (2016), Acta Cryst. D72, 346-358] is used to develop methods for planning a SAD experiment, scaling SAD data sets and estimating the useful anomalous correlation and anomalous signal in a SAD data set. The phenix.plan_sad_experiment tool uses a database of solved and unsolved SAD data sets and the expected characteristics of a SAD data set to estimate the probability that the anomalous substructure will be found in the SAD experiment and the expected map quality that would be obtained if the substructure were found. The phenix.scale_and_merge tool scales unmerged SAD data from one or more crystals using local scaling and optimizes the anomalous signal by identifying the systematic differences among data sets, and the phenix.anomalous_signal tool estimates the useful anomalous correlation and anomalous signal after collecting SAD data and estimates the probability that the data set can be solved and the likely figure of merit of phasing. PMID:26960123

  14. Crystal structure of ethyl 3-amino-6-methyl-2-[(4-methyl­phen­yl)carbamo­yl]-4-[(E)-2-phenyl­ethen­yl]thieno[2,3-b]pyridine-5-carboxyl­ate monohydrate

    PubMed Central

    Mague, Joel T.; Akkurt, Mehmet; Mohamed, Shaaban K.; Bakhite, Etify A.; Albayati, Mustafa R.

    2016-01-01

    In the title mol­ecule, C27H25N3O3S·H2O, the dihedral angle between the planes of the thienyl ring and the pendant p-tolyl group is 39.25 (6)°, while that between the pyridine ring and the pendant phenyl ring is 44.37 (6)°. In addition, there is a slight twist in the bicyclic core, with a dihedral angle of 2.39 (4)° between the thienyl and pyridine rings. The conformation of the carbamoyl moiety is partially determined by an intra­molecular N—H⋯O hydrogen bond. In the crystal, complementary N—H⋯O hydrogen bonds form dimers which are then associated into chains parallel to the c axis through O—H⋯N hydrogen bonds involving the water mol­ecule of crystallization. Electron density associated with an additional solvent mol­ecule of partial occupancy and disordered about a twofold axis was removed with the SQUEEZE procedure in PLATON [Spek (2015 ▸). Acta Cryst. C71, 9–18]. The given chemical formula and other crystal data do not take into account the unknown solvent molecule(s). PMID:27006791

  15. Crystal structure of an unknown tetra­hydro­furan solvate of tetra­kis­(μ 3-cyanato-κ3 N:N:N)tetra­kis­[(triphenyl­phosphane-κP)­silver(I)

    PubMed Central

    Frenzel, Peter; Schaarschmidt, Dieter; Jakob, Alexander; Lang, Heinrich

    2015-01-01

    In the title compound, [{[(C6H5)3P]Ag}4{NCO}4], a distorted Ag4N4-heterocubane core is set up by four AgI ions being coordinated by the N atoms of the cyanato anions in a μ 3-bridging mode. In addition, a tri­phenyl­phosphine ligand is datively bonded to each of the AgI ions. Intra­molecular Ag⋯Ag distances as short as 3.133 (9) Å suggest the presence of argentophilic (d 10⋯d 10) inter­actions. Five moderate-to-weak C—H⋯O hydrogen-bonding inter­actions are observed in the crystal structure, spanning a three-dimensional network. A region of electron density was treated with the SQUEEZE procedure in PLATON [Spek (2015). Acta Cryst. C71, 9–18] following unsuccessful attempts to model it as being part of disordered tetra­hydro­furan solvent mol­ecules. The given chemical formula and other crystal data do not take into account these solvent mol­ecules. PMID:26594421

  16. 2-[(1,3-Benzo­thia­zol-2-yl)imino­meth­yl]-6-meth­oxy­phenol: a new monoclinic polymorph

    PubMed Central

    Affan, Md. Abu; Jessop, Philip G.; Salam, Md. Abdus; Halim, Siti Nadiah Binti Abdul; Tiekink, Edward R. T.

    2013-01-01

    The title compound, C15H12N2O2S, is a P21/c polymorph of a previously reported P21/n polymorph [Büyükgüngör et al. (2004 ▶). Acta Cryst. E60, o1414–o1416]. The dihedral angle between the benzo­thia­zole (r.m.s. deviation = 0.010 Å) and the benzene ring of 7.86 (6)° compares with 10.76 (10)° in the literature structure. The meth­oxy substituent is almost coplanar with the benzene ring to which it is attached [C—O—C—C torsion angle = 178.31 (14)°] and the conformation about the imine bond [1.287 (2) Å] is E. There is an intra­molecular O—H⋯N hydrogen bond and the hy­droxy O and thio­ether S atoms are syn. In the crystal, columns are formed along the b axis as centrosymmetric dimeric aggregates, mediated by C—H⋯O inter­actions and linked by π–π inter­actions between the thia­zole and benzene rings [centroid-to-centroid distance = 3.8256 (10) Å]. PMID:24109355

  17. Crystal structure of an unknown solvate of bis­(tetra-n-butyl­ammonium) [N,N′-(4-tri­fluoro­methyl-1,2-phenyl­ene)bis­(oxamato)-κ4 O,N,N′,O′]nickelate(II)

    PubMed Central

    Eya’ane Meva, François; Schaarschmidt, Dieter; Rüffer, Tobias

    2015-01-01

    In the title compound, [N(C4H9)4]2[Ni(C11H3F3N2O6)] or [N(n-Bu)4]2[Ni(topbo)] [n-Bu = n-butyl and topbo = 4-tri­fluoro­methyl-1,2-phenyl­enebis(oxamate)], the Ni2+ cation is coordinated by two deprotonated amido N atoms and two carboxyl­ate O atoms, setting up a slightly distorted square-planar coordination environment. The [Ni(topbo]2− anion lies on a twofold rotation axis. Due to an incompatibility with the point-group symmetry of the complete mol­ecule, orientational disorder of the CF3 group is observed. The tetra­hedral ammonium cations and the anion are linked by weak inter­molecular C—H⋯O and C—H⋯F hydrogen-bonding inter­actions into a three-dimensional network. A region of electron density was treated with the SQUEEZE procedure in PLATON [Spek (2015). Acta Cryst. C71, 9–18] following unsuccessful attempts to model it as plausible solvent mol­ecule(s). The given chemical formula and other crystal data do not take into account the unknown solvent mol­ecule. PMID:26090126

  18. Revision of pyrrhotite structures within a common superspace model.

    PubMed

    Izaola, Zunbeltz; González, Santiago; Elcoro, Luis; Perez-Mato, J M; Madariaga, Gotzon; García, Alberto

    2007-10-01

    The structure of pyrrhotite (Fe(1 - x)S with 0.05 < or = x < or = 0.125) has been reinvestigated in the framework of the superspace formalism. A common model with a centrosymmetric superspace group is proposed for the whole family. The atomic domains in the internal space representing the Fe atoms are parametrized as crenel functions that fulfil the closeness condition. The proposed model explains the x-dependent space groups observed and the basic features of the structures reported up to now. Our model yields for any x value a well defined ordered distribution of Fe vacancies in contrast to some of the structural models proposed in the literature. A new (3 + 1)-dimensional refinement of Fe(0.91)S using the deposited dataset [Yamamoto & Nakazawa (1982). Acta Cryst. A38, 79-86] has been performed as a benchmark of the model. The consistency of the proposed superspace symmetry and its validity for other compositions has been further checked by means of ab initio calculations of both atomic forces and equilibrium atomic positions in non-relaxed and relaxed structures, respectively. PMID:17873438

  19. Crystal structure of cis-bis-{4-phenyl-1-[(3R)-1,7,7-tri-methyl-2-oxobi-cyclo-[2.2.1]heptan-3-ylidene]thio-semicarbazidato-κ(3) O,N (1),S}cadmium(II) with an unknown solvent mol-ecule.

    PubMed

    Nogueira, Vanessa Senna; Bresolin, Leandro; Näther, Christian; Jess, Inke; de Oliveira, Adriano Bof

    2015-12-01

    The reaction between the racemic mixture of the camphor-4-phenyl-thio-semicarbazone derivative and cadmium acetate dihydrate yielded the title compound, [Cd(C17H20N3OS)2]. The Cd(II) ion is six-coordinated in a distorted octa-hedral environment by two deprotonated thio-semicarbazone ligands acting as an O,N,S-donor in a tridentate chelating mode, forming five-membered chelate rings. In the crystal, the mol-ecules are connected via pairs of N-H⋯S and C-H⋯S inter-actions, building centrosymmetric dimers. One of the ligands is disordered in the campher unit over two sets of sites with site-occupancy factors of 0.7 and 0.3. The structure contains additional solvent mol-ecules, which are disordered and for which no reasonable split model was found. Therefore, the data were corrected for disordered solvent using the SQUEEZE routine [Spek (2015 ▸). Acta Cryst. C71, 9-18] in PLATON. Since the disordered solvents were removed by data processing, and the number of solvent entities was a suggestion only, they were not considered in the chemical formula and subsequent chemical or crystal information. PMID:26870441

  20. Maximum-likelihood density modification

    PubMed Central

    Terwilliger, Thomas C.

    2000-01-01

    A likelihood-based approach to density modification is developed that can be applied to a wide variety of cases where some information about the electron density at various points in the unit cell is available. The key to the approach consists of developing likelihood functions that represent the probability that a particular value of electron density is consistent with prior expectations for the electron density at that point in the unit cell. These likelihood functions are then combined with likelihood functions based on experimental observations and with others containing any prior knowledge about structure factors to form a combined likelihood function for each structure factor. A simple and general approach to maximizing the combined likelihood function is developed. It is found that this likelihood-based approach yields greater phase improvement in model and real test cases than either conventional solvent flattening and histogram matching or a recent reciprocal-space solvent-flattening procedure [Terwilliger (1999 ▶), Acta Cryst. D55, 1863–1871]. PMID:10944333

  1. Maximum-likelihood density modification using pattern recognition of structural motifs

    PubMed Central

    Terwilliger, Thomas C.

    2001-01-01

    The likelihood-based approach to density modification [Terwilliger (2000 ▶), Acta Cryst. D56, 965–972] is extended to include the recognition of patterns of electron density. Once a region of electron density in a map is recognized as corresponding to a known structural element, the likelihood of the map is reformulated to include a term that reflects how closely the map agrees with the expected density for that structural element. This likelihood is combined with other aspects of the likelihood of the map, including the presence of a flat solvent region and the electron-density distribution in the protein region. This likelihood-based pattern-recognition approach was tested using the recognition of helical segments in a largely helical protein. The pattern-recognition method yields a substantial phase improvement over both conventional and likelihood-based solvent-flattening and histogram-matching methods. The method can potentially be used to recognize any common structural motif and incorporate prior knowledge about that motif into density modification. PMID:11717487

  2. V1.42In1.83Mo15Se19

    PubMed Central

    Gougeon, Patrick; Gall, Philippe; Salloum, Diala; Potel, Michel

    2010-01-01

    The structure of the title compound, vanadium indium penta­deca­molybdenum nona­deca­selenide, V1.42In1.83Mo15Se19, is isotypic with In2.9Mo15Se19 [Grüttner et al. (1979 ▶). Acta Cryst. B35, 285–292]. It is characterized by two cluster units Mo6Sei 8Sea 6 and Mo9Sei 11Sea 6 (where i represents inner and a apical atoms) that are present in a 1:1 ratio. The cluster units are centered at Wyckoff positions 2b and 2c and have point-group symmetry and , respectively. The clusters are inter­connected through additional Mo—Se bonds. In the title compound, the V3+ cations replace the trivalent indium atoms present in In2.9Mo15Se19, and a deficiency is observed on the monovalent indium site. One Mo, one Se and the V atom are situated on mirror planes, and two other Se atoms and the In atom are situated on threefold rotation axes. PMID:21587348

  3. Na4.25Mo15S19: a novel ternary reduced molybdenum sulfide containing Mo6 and Mo9 clusters

    PubMed Central

    Salloum, D.; Gougeon, P.; Gall, P.

    2014-01-01

    The structure of tetra­sodium penta­deca­molybdenum nona­deca­sulfide, Na4.25Mo15S19, is isotypic with Na3.9Mo15Se19 [Salloum et al. (2013 ▶). Acta Cryst. E69, i67–i68]. It is characterized by Mo6Si 8Sa 6 and Mo9Si 11Sa 6 (where i represents inner and a apical atoms) cluster units that are present in a 1:1 ratio. The cluster units are centered at Wyckoff positions 2b and 2c, and have point-group symmetry -3 and -6, respectively. The clusters are inter­connected through additional Mo—S bonds. The Na+ cations occupy inter­unit voids formed by six or seven S atoms. One Mo, one S and one Na site [occupancy 0.751 (12)] are situated on mirror planes, and two other S atoms and one Na site (full occupancy) are situated on threefold rotation axes. PMID:24940190

  4. Na3.88Mo15Se19: a novel ternary reduced molybdenum selenide containing Mo6 and Mo9 clusters

    PubMed Central

    Salloum, Diala; Gougeon, Patrick; Gall, Philippe

    2013-01-01

    The structure of tetrasodium penta­deca­molybdenum nona­deca­selenide, Na3.88Mo15Se19, is isotypic with the In3+xMo15Se19 compounds [Grüttner et al. (1979 ▶). Acta Cryst. B35, 285–292]. It is characterized by two cluster units, Mo6Sei 8Sea 6 and Mo9Sei 11Sea 6 (where i represents inner and a apical atoms), that are present in a 1:1 ratio. The cluster units are centered at Wyckoff positions 2b and 2c and have point-group symmetry -3 and -6, respectively. The clusters are inter­connected through additional Mo—Se bonds. In the title compound, the Na+ cations replace the trivalent as well as the monovalent indium atoms present in In3.9Mo15Se19. One Mo, one Se and one Na atom are situated on mirror planes, and two other Se atoms and one Na atom [occupancy 0.628 (14)] are situated on threefold rotation axes. The crystal studied was twinned by merohedry with refined components of 0.4216 (12) and 0.5784 (12). PMID:24098158

  5. Ring-strain release in neutral and dicationic 7,8,17,18-tetra-bromo-5,10,15,20-tetra-phenyl-porphyrin: crystal structures of C44H26Br4N4 and C44H28Br4N4 (2+)·2ClO4 (-)·3CH2Cl2.

    PubMed

    Scheidt, W Robert; Duval, Hugues F; Oliver, Allen G

    2016-06-01

    Two porphyrin complexes were studied to determine the effects of protonation on ring deformation within the porphyrin. The porphyrin 7,8,17,18-tetra-bromo-5,10,15,20-tetra-phenyl-porphyrin, C44H26Br4N4, was selected because the neutral species is readily doubly protonated to yield a dication, which was crystallized here with perchlorate counter-ions as a di-chloro-methane tris-olvate, C44H28Br4N4 (2+)·2ClO4 (-)·3CH2Cl2. The centrosymmetric neutral species is observed to have a mild 'ruffling' of the pyrrole rings and is essentially planar throughout; intra-molecular N-H⋯N hydrogen bonds occur. In contrast, the dication exhibits considerable deformation, with the pyrrole rings oriented well out of the plane of the porphyrin, resulting in a 'saddle' conformation of the ring. The charged species forms N-H⋯O hydrogen bonds to the perchlorate anions, which lie above and below the plane of the porphyrin ring. Distortions to the planarity of the pyrrole rings in both cases are very minor. The characterization of the neutral species represents a low-temperature redetermination of the previous room-temperature analyses [Zou et al. (1995 ▸). Acta Cryst. C51, 760-761; Rayati et al. (2008 ▸). Polyhedron, pp. 2285-2290], which showed disorder and physically unrealistic displacement parameters. PMID:27308051

  6. Diosgenin hemihydrate

    PubMed Central

    Hernández Linares, María-Guadalupe; Bernès, Sylvain; Flores-Alamo, Marcos; Guerrero-Luna, Gabriel; Martínez-Gallegos, Anselmo A.

    2012-01-01

    Diosgenin [or (22R,25R)-spirost-5-en-3β-ol] is the starting material of the Marker degradation, a cheap semi-synthesis of progesterone, which has been designated as an Inter­national Historic Chemical Landmark. Thus far, a single X-ray structure for diosgenin is known, namely its dimethyl sulfoxide solvate [Zhang et al. (2005 ▶). Acta Cryst. E61, o2324–o2325]. We have now determined the structure of the hemihydrate, C27H42O3·0.5H2O. The asymmetric unit contains two diosgenin mol­ecules, with quite similar conformations, and one water mol­ecule. Hy­droxy groups in steroids and water mol­ecules form O—H⋯O hydrogen-bonded R 5 4(10) ring motifs. Fused edge-sharing R(10) rings form a backbone oriented along [100], which aggregates the diosgenin mol­ecules in the crystal structure. PMID:22904823

  7. Succinate esters: odd-even effects in melting points.

    PubMed

    Joseph, Sumy; Sathishkumar, Ranganathan

    2014-10-01

    Dialkyl succinates show a pattern of alternating behavior in their melting points, as the number of C atoms in the alkane side chain increases, unlike in the dialkyl oxalates [Joseph et al. (2011). Acta Cryst. B67, 525-534]. Dialkyl succinates with odd numbers of C atoms in the alkyl side chain show higher melting points than the immediately adjacent analogues with even numbers. The crystal structures and their molecular packing have been analyzed for a series of dialkyl succinates with 1-4 C atoms in the alkyl side chain. The energy difference (ΔE) between the optimized and observed molecular conformations, density, Kitaigorodskii packing index (KPI) and C-H...O interactions are considered to rationalize this behavior. In contrast to the dialkyl oxalates where a larger number of moderately strong C-H...O interactions were characteristic of oxalates with elevated melting points, here the molecular packing and the density play a major role in raising the melting point. On moving from oxalate to succinate esters the introduction of the C2 spacer adds two activated H atoms to the asymmetric unit, resulting in the formation of stronger C-H...O hydrogen bonds in all succinates. As a result the crystallinity of long-chain alkyl substituted esters improves enormously in the presence of hydrogen bonds from activated donors. PMID:25274517

  8. Phasing in the presence of severe site-specific radiation damage through dose-dependent modelling of heavy atoms.

    PubMed

    Schiltz, M; Dumas, P; Ennifar, E; Flensburg, C; Paciorek, W; Vonrhein, C; Bricogne, G

    2004-06-01

    The case of a brominated RNA crystal structure determination in which standard three-wavelength MAD phasing was unsuccessful because of fast X-ray-induced debromination was reinvestigated [Ennifar et al. (2002), Acta Cryst. D58, 1262-1268]. It was found that if the data are kept unmerged and if a dose-stamp is associated with each reflection measurement, dose-dependent occupancies can be refined for the Br atoms. Such a parametrization has been implemented in the macromolecular phasing program SHARP. Refining such dose-dependent occupancies on an unmerged data set gave a dramatic improvement, even for SAD phases from only the first wavelength (peak), and resulted in a good electron-density map after solvent flattening. The adverse effect of radiation damage has been turned into a beneficial one. The crucial difference is made by the use of unmerged data: phasing power is generated through the intensity differences of symmetry-related reflections recorded at different doses, i.e. corresponding to different states of the X-ray-induced debromination. This approach should prove useful in all situations of experimental phasing where site-specific radiation damage occurs unavoidably and undesirably and not only in cases in which radiation damage is purposely being created in order to demonstrate its potential usefulness. PMID:15159561

  9. Crystal structure of 2-[(3S,4S)-4-(anthracen-9-yl)-1-(4-meth­oxy­phen­yl)-2-oxoazetidin-3-yl]-2-aza-2H-phenalene-1,3-dione unknown solvate

    PubMed Central

    Çelik, Ísmail; Akkurt, Mehmet; Jarrahpour, Aliasghar; Rad, Javad Ameri; Çelik, Ömer

    2015-01-01

    The central β-lactam ring of the title compound, C36H24N2O4, is almost planar (r.m.s. deviation = 0.003 Å) and makes dihedral angles of 17.17 (19), 89.76 (17) and 78.44 (17)° with the benzene ring, the anthracene ring (r.m.s. deviation = 0.003 Å) and the 1H-benzo[de]iso­quinoline-1,3(2H)-dione moiety, which is nearly planar [maximum deviation = 0.098 (2) Å], respectively. The mol­ecular structure is stabilized by an intra­molecular C—H⋯N hydrogen bond. In the crystal, mol­ecules are linked via C—H⋯π and π–π stacking inter­actions [centroid–centroid distances = 3.5270 (19) and 3.779 (2) Å], forming a three-dimensional structure. A region of disordered electron density, probably disordered solvent mol­ecules, was treated with the SQUEEZE procedure in PLATON [Spek (2015 ▸). Acta Cryst. C71, 9–18], which indicated a solvent cavity of 322 Å3 containing approximately 91 electrons. Their formula mass and unit-cell characteristics were not taken into account during the refinement. PMID:25844239

  10. A log-likelihood-gain intensity target for crystallographic phasing that accounts for experimental error

    PubMed Central

    Read, Randy J.; McCoy, Airlie J.

    2016-01-01

    The crystallographic diffraction experiment measures Bragg intensities; crystallo­graphic electron-density maps and other crystallographic calculations in phasing require structure-factor amplitudes. If data were measured with no errors, the structure-factor amplitudes would be trivially proportional to the square roots of the intensities. When the experimental errors are large, and especially when random errors yield negative net intensities, the conversion of intensities and their error estimates into amplitudes and associated error estimates becomes nontrivial. Although this problem has been addressed intermittently in the history of crystallographic phasing, current approaches to accounting for experimental errors in macromolecular crystallography have numerous significant defects. These have been addressed with the formulation of LLGI, a log-likelihood-gain function in terms of the Bragg intensities and their associated experimental error estimates. LLGI has the correct asymptotic behaviour for data with large experimental error, appropriately downweighting these reflections without introducing bias. LLGI abrogates the need for the conversion of intensity data to amplitudes, which is usually performed with the French and Wilson method [French & Wilson (1978 ▸), Acta Cryst. A35, 517–525], wherever likelihood target functions are required. It has general applicability for a wide variety of algorithms in macromolecular crystallography, including scaling, characterizing anisotropy and translational noncrystallographic symmetry, detecting outliers, experimental phasing, molecular replacement and refinement. Because it is impossible to reliably recover the original intensity data from amplitudes, it is suggested that crystallographers should always deposit the intensity data in the Protein Data Bank. PMID:26960124

  11. Structure and molecular model refinement of Aspergillus oryzae (TAKA) alpha-amylase: an application of the simulated-annealing method.

    PubMed

    Swift, H J; Brady, L; Derewenda, Z S; Dodson, E J; Dodson, G G; Turkenburg, J P; Wilkinson, A J

    1991-08-01

    Monoclinic crystals of a neutral alpha-amylase from Aspergillus oryzae, containing three molecules in the asymmetric unit, have been reported previously and studied at 3 A resolution [Matsuura, Kunusoki, Harada & Kakudo (1984). J. Biochem. 95, 697-702]. Here we report the solution of the structure of this enzyme in a different crystal form (space group P2(1)2(1)2(1), a = 50.9, b = 67.2, c = 132.7 A), with only one molecule in the asymmetric unit. The structure was solved by the molecular replacement method, using a model of acid alpha-amylase from a related fungus A. niger [Brady, Brzozowski, Derewenda, Dodson & Dodson (1991). Acta Cryst. B47, 527-535]. Conventional least-squares crystallographic refinement failed to converge in a satisfactory manner, and the technique of molecular dynamics in the form of the XPLOR package [Brunger (1988). XPLOR Manual. Yale Univ., USA] was used to overcome the problem. A large rigid-body type movement of the C-terminal domain was identified and accounted for. The final round of restrained least-squares refinement (at 2.1 A resolution) including 3675 protein atoms and 247 water molecules resulted in a conventional crystallographic R factor of 0.183 and an atomic model which conforms well to standard stereochemical parameters (standard deviation of bond lengths from their expected values is 0.028 A, while that for planar groups is 0.029 A). PMID:1930835

  12. Orientation relationship of eutectoid FeAl and FeAl2

    PubMed Central

    Scherf, A.; Kauffmann, A.; Kauffmann-Weiss, S.; Scherer, T.; Li, X.; Stein, F.; Heilmaier, M.

    2016-01-01

    Fe–Al alloys in the aluminium range of 55–65 at.% exhibit a lamellar microstructure of B2-ordered FeAl and triclinic FeAl2, which is caused by a eutectoid decomposition of the high-temperature Fe5Al8 phase, the so-called ∊ phase. The orientation relationship of FeAl and FeAl2 has previously been studied by Bastin et al. [J. Cryst. Growth (1978 ▸), 43, 745] and Hirata et al. [Philos. Mag. Lett. (2008 ▸), 88, 491]. Since both results are based on different crystallographic data regarding FeAl2, the data are re-evaluated with respect to a recent re-determination of the FeAl2 phase provided by Chumak et al. [Acta Cryst. (2010 ▸), C66, i87]. It is found that both orientation relationships match subsequent to a rotation operation of 180° about a 〈112〉 crystallographic axis of FeAl or by applying the inversion symmetry of the FeAl2 crystal structure as suggested by the Chumak data set. Experimental evidence for the validity of the previously determined orientation relationships was found in as-cast fully lamellar material (random texture) as well as directionally solidified material (∼〈110〉FeAl || solidification direction) by means of orientation imaging microscopy and global texture measurements. In addition, a preferential interface between FeAl and FeAl2 was identified by means of trace analyses using cross sectioning with a focused ion beam. On the basis of these habit planes the orientation relationship between the two phases can be described by (01)FeAl || (114) and [111]FeAl || [10]. There is no evidence for twinning within FeAl lamellae or alternating orientations of FeAl lamellae. Based on the determined orientation and interface data, an atomistic model of the structure relationship of Fe5Al8, FeAl and FeAl2 in the vicinity of the eutectoid decomposition is derived. This model is analysed with respect to the strain which has to be accommodated at the interface of FeAl and FeAl2. PMID:27047304

  13. The properties of (2Fo - Fc) and (Fo - Fc) electron-density maps at medium-to-high resolutions.

    PubMed

    Minichino, A; Habash, J; Raftery, J; Helliwell, J R

    2003-05-01

    This paper reports on the efficacy of (F(o) - F(c)) versus (2F(o) - F(c)) electron-density maps at 3.2 A resolution. Firstly, a study is reported of a simple truncation at 2.3 and 3.2 A of the 1.6 A resolution crystal structure of concanavalin A at room temperature [Emmerich et al. (1994), Acta Cryst. D50, 749-756] with 149 known bound water molecules. Secondly, the concanavalin A 1.6 A resolution model was re-refined but with the data truncated to 3.2 A. In a similar evaluation, these procedures were repeated for the apocrustacyanin A1 cryotemperature 1.4 A resolution model [Cianci et al. (2001), Acta Cryst. D57, 1219-1229]. Maps at 1.4, 2.3 and 3.2 A resolutions were first generated and the structure was then re-refined at 3.2 A and additionally at 2.3 A resolution. The results on concanavalin A show that the number of bound water molecules that are resolved decreases by two thirds from 1.6 to 3.2 A, but that key structural waters, for example at the transition metal and the calcium ion, are still resolved in the (F(o) - F(c)) map but not in the (2F(o) - F(c)) map. For apocrustacyanin A1, the results with these two difference maps were less clear-cut. Two key structural bound waters (w93 and w105) were selected that had been previously identified in beta-crustacyanin [Cianci et al. (2002), Proc. Natl Acad. Sci. USA, 99, 9795-9800] in protein-carotenoid interactions. The behaviour of w93 is similar to that of concanavalin A key waters, but that of w105 is not. These behaviours were therefore explored in finer resolution increments, namely 2.9, 2.7 and 2.5 A. Finally, further tests on "real" data sets for peanut lectin and concanavalin A at medium resolution confirm these map properties, namely that an (F(o) - F(c)) difference electron-density map is more effective than a (2F(o) - F(c)) map in showing bound water structure at lower resolutions ( approximately 3.2 A). This result is important since a growing number of protein crystal structure studies are concerned

  14. Comments on "Synthesis aspects, structural, spectroscopic, antimicrobial and room temperature ferromagnetism of zinc iodide complex with Schiff based ligand" by K. Shakila and S. Kalainathan, Spectrochim. Acta 135 A (2015) 1059-1065.

    PubMed

    Srinivasan, Bikshandarkoil R; Nadkarni, V S

    2016-06-15

    Shakila and Kalainathan report on the synthetic and structural aspects of a zinc iodide complex with Schiff based ligand, which exhibits room temperature ferromagnetism. In this comment, many points of criticism, concerning the characterization of this so called zinc iodide complex of Schiff based ligand are highlighted to prove that the title paper is completely erroneous. PMID:27037763

  15. Comments on "Synthesis aspects, structural, spectroscopic, antimicrobial and room temperature ferromagnetism of zinc iodide complex with Schiff based ligand" by K. Shakila and S. Kalainathan, Spectrochim. Acta 135 A (2015) 1059-1065

    NASA Astrophysics Data System (ADS)

    Srinivasan, Bikshandarkoil R.; Nadkarni, V. S.

    2016-06-01

    Shakila and Kalainathan report on the synthetic and structural aspects of a zinc iodide complex with Schiff based ligand, which exhibits room temperature ferromagnetism. In this comment, many points of criticism, concerning the characterization of this so called zinc iodide complex of Schiff based ligand are highlighted to prove that the title paper is completely erroneous.

  16. Comment on "Behavior of Re and Os during contact between an aqueous solution and oil: Consequences for the application of the Re-Os geochronometer to petroleum" [Geochim. Cosmochim. Acta 158 (2015) 1-21

    NASA Astrophysics Data System (ADS)

    Wu, Jia; Li, Zhen; Wang, Xuan-ce

    2016-08-01

    In a recent study, Mahdaoui et al. (2015) simulated the contact of oil with Re/Os-bearing aqueous fluids in petroleum reservoirs and concluded that both metals could be rapidly and substantially enriched in the oil fraction. These findings could have significant geological ramifications for the use of rhenium-osmium (Re-Os) geochronology in the age-dating of oil deposits. However, the lack of data reproducibility between parallel experiments and misused parameter of "recovery rate" has cast doubt on the main conclusions of the paper. Re-analyses of the raw data provided sufficient evidence to suggest that in petroleum basins with very low abundances of Re and Os, the extraction of these metals to oil is unlikely to be a geologically instantaneous process as the authors implied in their study. In addition, the possibility of reactor leakage in the contacting experiments cannot be completely ruled out.

  17. Coping with Social Change: Programs That Work. Proceedings of a Conference (Acapulco, Mexico, June 1989) = Como enfrentarse al cambio social: programas eficaces. Actas de uno Conferencia (Acapulco, Mexico, Junio de 1989).

    ERIC Educational Resources Information Center

    Hoskins, Irene, Ed.

    Written in English and Spanish, this document contains the proceedings of the 14th International Congress of Gerontology on concerns about the impact of rapid social change on the well-being of older women and families in Latin American and the Caribbean and about effective programs that address the needs of the older populations. The first…

  18. Corrigendum to "Recycling of crustal material by the Iceland mantle plume: New evidence from nitrogen elemental and isotope systematics of subglacial basalts" [Geochim. Cosmochim. Acta 176 (2016) 206-226

    NASA Astrophysics Data System (ADS)

    Halldórsson, Sæmundur A.; Hilton, David R.; Barry, Peter H.; Füri, Evelyn; Grönvold, Karl

    2016-08-01

    In Table 1 of the above published paper, N2/40Ar* ratios (column 13) are incorrect. A corrected table and updated figures (Figs. 6-8) are shown below. The correct N2/40Ar* values vary between 178 and 2.6 × 104, with a mean of 4.1 ± 2.1 (×103). Although this range in N2/40Ar* ratios is somewhat smaller compared to what was reported, it still displays considerably more heterogeneity compared to the DMM database. The new mean value is also significantly higher than the DMM mean (138 ± 65), as discussed. Therefore, the findings in the paper concerning heterogeneous and elevated N2/40Ar* ratios in Icelandic subglacial basalts still stand.

  19. Corrigendum to "Historical review: Anders Jonas Ångström and the foundation of spectroscopy - Commemorative article on the second centenary of his birth" [Spectrochim. Acta Part B, 102 (2014) 12-23

    NASA Astrophysics Data System (ADS)

    Reif-Acherman, Simón

    2015-07-01

    The following addendum should be added to the Acknowledgments of the above article. Due to the multiplicity of simultaneous activities in which I am continuously involved, I forgot mentioning that Prof. Dr. Klaus Hentschel, of the History Department of the University of Stuttgart (Germany) was helpful in obtaining some of the source material used in my review. In particular, Prof. Hentschel provided the scans of Anne Beckmann's work to which I was guided by passages in his book on "Mapping the spectrum", Oxford University Press (2002). I also followed his recommendation of contacting the Swedish historians of science, and Prof. Sven Widmalm among them; however, the correspondence was not successful.

  20. Corrigendum to "Isotopic and geochemical characterization of fossil brines of the Cambrian Mt. Simon sandstone and Ironton-Galesville formation from the Illinois Basin, USA" [Geochim. Cosmochim. Acta 165 (2015) 342-360

    NASA Astrophysics Data System (ADS)

    Labotka, Dana M.; Panno, Samuel V.; Locke, Randall A.; Freiburg, Jared T.

    2016-08-01

    The original Fig. 4 incorrectly represented data from Clayton et al. (1966). The deuterium values were reported in percent deuterium and mistaken by the authors as per mille. The corrected Fig. 4 Corrigendum is given and shows the data from Clayton et al. (1966) plotting in a similar manner as other published data for groundwater in the Illinois Basin. The data from Clayton et al. (1966) was not used in the discussion of the deep-seated Cambrian brines, and, therefore, this misrepresentation does not affect the conclusions of the original manuscript. The authors apologize for the oversight.

  1. Actas de la 4th mesa redonda sobre investigacion en "Lenguas Extranjeras" en la Universidad Autonoma Metropolitana 1996. (Proceedings from the 4th Roundtable on Investigation in Foreign Languages in the Autonomous Metropolitan University 1996).

    ERIC Educational Resources Information Center

    Zoreda, Margaret Lee, Comp.; Diop, Mamoudou Si, Comp.; Vivaldo Lima, Javier, Comp.

    The articles included in this volume were selected as exemplary papers from the conference in Mexico. The goal of the forum was to provide an opportunity for researchers from the three branches of the Universidad Autonoma Metropolitana (UAM) to meet and discuss research projects currently in progress at the university. The works presented here…

  2. Corrigendum to ‘Evidence for shock heating and constraints on Martian surface temperatures revealed by 40Ar/39Ar thermochronometry of Martian meteorites’ [Geochim. Cosmochim. Acta (2010) 6900–6920

    DOE PAGESBeta

    Cassata, William S.; Shuster, David L.; Renne, Paul R.; Weiss, Benjamin P.

    2014-10-23

    Here, the authors regret they have discovered errors in Eq. (3) and in a spreadsheet used to calculate cosmogenic exposure ages shown in Table 1. Eq. (3) is missing a term. The spreadsheet errors concerned an incorrect cell reference and application of Eq. (3). Correction of these errors results in ~15–20% changes to the exposure ages of all samples, minor (generally <0.2%) changes to the radioisotopic ages of some samples (those that entailed a correction for chlorine-derived 38Ar calculated based on the exposure age; see Section 3.3), and statistically insignificant changes to the inferred trapped components identified through isochron analyses.more » These modifications have no impact on the modeling, discussions, or conclusions in the paper, nor do the changes to radioisotopic ages exceed the 1 sigma uncertainties.« less

  3. Corrigendum to ‘Evidence for shock heating and constraints on Martian surface temperatures revealed by 40Ar/39Ar thermochronometry of Martian meteorites’ [Geochim. Cosmochim. Acta (2010) 6900–6920

    SciTech Connect

    Cassata, William S.; Shuster, David L.; Renne, Paul R.; Weiss, Benjamin P.

    2014-10-23

    Here, the authors regret they have discovered errors in Eq. (3) and in a spreadsheet used to calculate cosmogenic exposure ages shown in Table 1. Eq. (3) is missing a term. The spreadsheet errors concerned an incorrect cell reference and application of Eq. (3). Correction of these errors results in ~15–20% changes to the exposure ages of all samples, minor (generally <0.2%) changes to the radioisotopic ages of some samples (those that entailed a correction for chlorine-derived 38Ar calculated based on the exposure age; see Section 3.3), and statistically insignificant changes to the inferred trapped components identified through isochron analyses. These modifications have no impact on the modeling, discussions, or conclusions in the paper, nor do the changes to radioisotopic ages exceed the 1 sigma uncertainties.

  4. Corrigendum to "Synthesis and spectral characterization of new homologous 1,3,5-triaryl-2-pyrazolines: Influence of alkyloxy chain length on fluorescence" [Spectrochim. Acta Part A: Mol. Biomol. Spectrosc. 133 (2014) 182-189

    NASA Astrophysics Data System (ADS)

    Abbas, Asghar; Hussain, Safdar; Hafeez, Noureen; Naseer, Muhammad Moazzam

    2015-03-01

    The authors regret to inform that the affiliation of one of the authors, namely, Noureen Hafeez has been written as Department of Forensic Medicine & Toxicology, Rawalpindi Institute of Health Sciences (RIHS), Bahria University, Islamabad, Pakistan in the published article. The correct address is shown above.

  5. Western Hemisphere Conference on Persons with Disabilities. Conference Proceedings (Washington, D.C., March 14-18, 1993) = Conferencia Hemisferica Occidental sobre Personas con Discapacidades. Actas de la Conferencia. (Washington, D.C., 14 al 18 de Marzo de 1993).

    ERIC Educational Resources Information Center

    Kelley, Jerry D., Ed.; And Others

    This document presents the proceedings of a conference which brought together delegates and First Ladies representing western hemisphere nations to address needs and issues affecting people with disabilities in the Americas. It presents the texts of two keynote addresses: "Small Triumphs, Big Victories: A Global View of Persons with Disabilities,"…

  6. Corrigendum to "Basin-scale controls on the molybdenum-isotope composition of seawater during Oceanic Anoxic Event 2 (Late Cretaceous)" [Geochim. Cosmochim. Acta 178 (2016) 291-306

    NASA Astrophysics Data System (ADS)

    Dickson, Alexander J.; Jenkyns, Hugh C.; Porcelli, Donald; van den Boorn, Sander; Idiz, Erdem; Owens, Jeremy D.

    2016-09-01

    A recent molybdenum-isotope estimate of the extent of anoxic and euxinic conditions in the world ocean during Oceanic Anoxic Event 2 (∼94 Ma) concluded by discussing a contrast between the new results with existing estimates of marine euxinia based on sulphur isotopes. This suggested contrast was erroneous; when areal extents of marine anoxia and euxinia are calculated for both isotopic proxies, the agreement is actually striking, and highlights the fact that large areas of the global ocean probably remained well ventilated during this event.

  7. Corrigendum to "Natural dye extract of lawsonia inermis seed as photo sensitizer for titanium dioxide based dye sensitized solar cells" [Spectrochim. Acta A Mol. Biomol. Spectrosc. 128 (2014) 420-426

    NASA Astrophysics Data System (ADS)

    Ananth, S.; Vivek, P.; Arumanayagam, T.; Murugakoothan, P.

    2015-05-01

    The authors regret to inform that the following text in page No. 425, "The conventionally prepared TiO2 based DSSC exhibits the observed values of Isc = 1.6 mA cm-2, Voc = 0.48 V and the calculated value of FF is 64.32%. Similarly, for pre dye treated TiO2 based DSSC, the observed values of Isc = 2.99 mA cm-2, Voc = 0.50 V and the calculated value of FF is 66.9%" should be read as, "The conventionally prepared TiO2 based DSSC exhibits the observed values of Isc = 2.99 mA cm-2, Voc = 0.50 V and the calculated value of FF is 66.9%. Similarly, for pre dye treated TiO2 based DSSC, the observed values of Isc = 4.2 mA cm-2, Voc = 0.56 V and the calculated value of FF is 62.5%". Though the text is typed wrongly, the I-V graph, the discussions and our conclusions are as same as that of our published article.

  8. Improving experimental phases for strong reflections prior to density modification

    SciTech Connect

    Uervirojnangkoorn, Monarin; Hilgenfeld, Rolf; Terwilliger, Thomas C.; Read, Randy J.

    2013-10-01

    A genetic algorithm has been developed to optimize the phases of the strongest reflections in SIR/SAD data. This is shown to facilitate density modification and model building in several test cases. Experimental phasing of diffraction data from macromolecular crystals involves deriving phase probability distributions. These distributions are often bimodal, making their weighted average, the centroid phase, improbable, so that electron-density maps computed using centroid phases are often non-interpretable. Density modification brings in information about the characteristics of electron density in protein crystals. In successful cases, this allows a choice between the modes in the phase probability distributions, and the maps can cross the borderline between non-interpretable and interpretable. Based on the suggestions by Vekhter [Vekhter (2005 ▶), Acta Cryst. D61, 899–902], the impact of identifying optimized phases for a small number of strong reflections prior to the density-modification process was investigated while using the centroid phase as a starting point for the remaining reflections. A genetic algorithm was developed that optimizes the quality of such phases using the skewness of the density map as a target function. Phases optimized in this way are then used in density modification. In most of the tests, the resulting maps were of higher quality than maps generated from the original centroid phases. In one of the test cases, the new method sufficiently improved a marginal set of experimental SAD phases to enable successful map interpretation. A computer program, SISA, has been developed to apply this method for phase improvement in macromolecular crystallography.

  9. A polymorphic form of 4,4-dimethyl-8-methylene-3-azabicyclo[3.3.1]non-2-en-2-yl 3-indolyl ketone, an indole alkaloid extracted from Aristotelia chilensis (maqui).

    PubMed

    Paz, Cristian; Becerra, José; Silva, Mario; Freire, Eleonora; Baggio, Ricardo

    2013-12-15

    The title compound [systematic name: (4,4-dimethyl-8-methylene-3-azabicyclo[3.3.1]non-2-en-2-yl)(1H-indol-3-yl)methanone], C20H22N2O, (II), was obtained from mother liquors extracted from Aristotelia chilensis (commonly known as maqui), a native Chilean tree. The compound is a polymorphic form of that obtained from the same source and reported by Watson, Nagl, Silva, Cespedes & Jakupovic [Acta Cryst. (1989), C45, 1322-1324], (Ia). The molecule consists of an indolyl ketone fragment and a nested three-ring system, with both groups linked by a C-C bridge. Comparison of both forms shows that they do not differ in their gross features but in the relative orientation of the two ring systems, due to different rotations around the bridge, as measured by the O=C-C=N torsion angle [130.0 (7)° in (Ia) and 161.6 (2)° in (II)]. The resulting slight conformational differences are reflected in a number of intramolecular contacts being observed in (II) but not in (Ia). Regarding intermolecular interactions, both forms share a similar N-H···O synthon but with differing hydrogen-bonding strength, leading in both cases to C(6) catemers with different chain motifs. There are marked differences between the two forms regarding colour and the (de)localization of a double bond, which allows speculation about the possible existence of different variants of this type of molecule. PMID:24311501

  10. Crystallography without Crystals: An Overview

    NASA Astrophysics Data System (ADS)

    Ourmazd, Abbas

    2007-03-01

    Protein X-ray crystallography, an ``outgrowth of physics,'' is now the mainstay of biology, biochemistry, and the pharmaceutical industry. However, roughly 40% of biological molecules do not crystallize. And although more than half a million proteins have been sequenced, the structure of less than 40,000 has been determined. By obviating the need for purification and crystallization, the ability to determine the structure of individual biological molecules would constitute a fundamental breakthrough. The confluence of four developments has generated intense interest in achieving this by short-pulse X-ray scattering: *The advent of algorithms capable of ``solving the phase problem'' with practical demonstrations in astronomy, high-energy electron diffraction, and protein crystallography [1,2,3]. *Development of sophisticated techniques for determining the relative orientation of electron microscope images of biological entities such as cells and large macromolecules [4]. *Development of techniques for producing beams of hydrated proteins [3,5]. *The promise of ultra-bright, short pulses of X-rays from X-ray Free Electron Lasers (XFELs) under construction in the US, Europe, and Japan. I will describe how these and other key developments have brought the prospect of single-molecule structure determination ``tantalizingly close,'' perhaps even closer than generally realized in the literature. [1] J. R. Fienup, Appl. Opt. 21, 2758 (1982). [2] J. Miao et al. PNAS 98, 6641 (2001). [3] J.C.H. Spence et al. Acta Cryst. A61, 237 (2005) [4] J. Frank, Three-Dimensional Electron Microscopy of Macromolecular Assemblies (OUP Press, 2006) [5] J.B. Fenn, J. Biomolecular Techniques 13, 101 (2002).

  11. Crystal structures of spinel-type Na2MoO4 and Na2WO4 revisited using neutron powder diffraction.

    PubMed

    Fortes, A Dominic

    2015-06-01

    Time-of-flight neutron powder diffraction data have been collected from Na2MoO4 and Na2WO4 to a resolution of sin (θ)/λ = 1.25 Å(-1), which is substanti-ally better than the previous analyses using Mo Kα X-rays, providing roughly triple the number of measured reflections with respect to the previous studies [Okada et al. (1974 ▶). Acta Cryst. B30, 1872-1873; Bramnik & Ehrenberg (2004 ▶). Z. Anorg. Allg. Chem. 630, 1336-1341]. The unit-cell parameters are in excellent agreement with literature data [Swanson et al. (1962 ▶). NBS Monograph No. 25, sect. 1, pp. 46-47] and the structural parameters for the molybdate agree very well with those of Bramnik & Ehrenberg (2004 ▶). However, the tungstate structure refinement of Okada et al. (1974 ▶) stands apart as being conspicuously inaccurate, giving significantly longer W-O distances, 1.819 (8) Å, and shorter Na-O distances, 2.378 (8) Å, than are reported here or in other simple tungstates. As such, this work represents an order-of-magnitude improvement in precision for sodium molybdate and an equally substantial improvement in both accuracy and precision for sodium tungstate. Both compounds adopt the spinel structure type. The Na(+) ions have site symmetry .-3m and are in octa-hedral coordination while the transition metal atoms have site symmetry -43m and are in tetra-hedral coordination. PMID:26090129

  12. Crystal structure of tetra-kis-[μ2-2-(di-methyl-amino)-ethano-lato-κ(3) N,O:O]di-μ3-hydroxido-di-thio-cyanato-κ(2) N-dichromium(III)dilead(II) di-thio-cyanate aceto-nitrile monosolvate.

    PubMed

    Rusanova, Julia A; Semenaka, Valentyna V; Omelchenko, Irina V

    2016-04-01

    The tetra-nuclear complex cation of the title compound, [Cr2Pb2(NCS)2(OH)2(C4H10NO)4](SCN)2·CH3CN, lies on an inversion centre. The main structural feature of the cation is a distorted seco-norcubane Pb2Cr2O6 cage with a central four-membered Cr2O2 ring. The Cr(III) ion is coordinated in a distorted octa-hedron, which involves two N atoms of one bidentate ligand and one thio-cyanate anion, two μ2-O atoms of 2-(di-methyl-amino)-ethano-late ligands and two μ3-O atoms of hydroxide ions. The coordination geometry of the Pb(II) ion is a distorted disphenoid, which involves one N atom, two μ2-O atoms and one μ3-O atom. In addition, weak Pb⋯S inter-actions involving the coordinating and non-coordinating thio-cyanate anions are observed. In the crystal, the complex cations are linked through the thio-cyanate anions via the Pb⋯S inter-actions and O-H⋯N hydrogen bonds into chains along the c axis. The chains are further linked together via S⋯S contacts. The contribution of the disordered solvent aceto-nitrile mol-ecule was removed with the SQUEEZE [Spek (2015 ▸). Acta Cryst. C71, 9-18] procedure in PLATON. The solvent is included in the reported mol-ecular formula, weight and density. PMID:27375871

  13. Crystal structure of tetra­kis­[μ2-2-(di­methyl­amino)­ethano­lato-κ3 N,O:O]di-μ3-hydroxido-di­thio­cyanato-κ2 N-dichromium(III)dilead(II) di­thio­cyanate aceto­nitrile monosolvate

    PubMed Central

    Rusanova, Julia A.; Semenaka, Valentyna V.; Omelchenko, Irina V.

    2016-01-01

    The tetra­nuclear complex cation of the title compound, [Cr2Pb2(NCS)2(OH)2(C4H10NO)4](SCN)2·CH3CN, lies on an inversion centre. The main structural feature of the cation is a distorted seco-norcubane Pb2Cr2O6 cage with a central four-membered Cr2O2 ring. The CrIII ion is coordinated in a distorted octa­hedron, which involves two N atoms of one bidentate ligand and one thio­cyanate anion, two μ2-O atoms of 2-(di­methyl­amino)­ethano­late ligands and two μ3-O atoms of hydroxide ions. The coordination geometry of the PbII ion is a distorted disphenoid, which involves one N atom, two μ2-O atoms and one μ3-O atom. In addition, weak Pb⋯S inter­actions involving the coordinating and non-coordinating thio­cyanate anions are observed. In the crystal, the complex cations are linked through the thio­cyanate anions via the Pb⋯S inter­actions and O—H⋯N hydrogen bonds into chains along the c axis. The chains are further linked together via S⋯S contacts. The contribution of the disordered solvent aceto­nitrile mol­ecule was removed with the SQUEEZE [Spek (2015 ▸). Acta Cryst. C71, 9–18] procedure in PLATON. The solvent is included in the reported mol­ecular formula, weight and density. PMID:27375871

  14. Crystal structure of azido­(η5-cyclo­penta­dien­yl)bis­(tri­phenyl­phosphane-κP)ruthenium(II) di­chloro­methane hemisolvate

    PubMed Central

    Hernández-Calva, Adriana; Meléndez-Balbuena, Lidia; Arroyo, Maribel; Ramírez-Monroy, Armando

    2014-01-01

    The title solvated complex, [Ru(η5-C5H5)(N3){P(C6H5)3}2]·0.5CH2Cl2, displays a typical piano-stool geometry about the RuII atom. The bond lengths and angles of the cyclo­penta­dienyl and phosphane ligands are very similar to that of the unsolvated complex [Taqui Khan et al. (1994 ▶). Acta Cryst. C50, 502–504]. The azide anion displays similar N—N distances of 1.173 (3) and 1.156 (3) Å and has an N—N—Ru angle of 119.20 (15)°, indicating a greater contribution of the canonical form Ru—N=N(+)=N(-) for the bonding situation. An intra­molecular C—H⋯N hydrogen-bonding inter­action between one ortho H atom of a phosphane ligand and the N atom coordinating to the metal is observed. A similar inter­molecular inter­action is observed between a meta H atom of a phosphane ligand and the terminal azide N atom of a neighbouring complex. Finally, two C—H⋯N inter­actions exists between the H atoms of the di­chloro­methane solvent mol­ecule and the terminal N atom of two azide anions. The solvent mol­ecule is located about a twofold rotation axis and shows disorder of the Cl atoms with an occupancy ratio of 0.62 (3):0.38 (3). PMID:25484673

  15. Icosahedral symmetry breaking: C(60) to C(84), C(108) and to related nanotubes.

    PubMed

    Bodner, Mark; Bourret, Emmanuel; Patera, Jiri; Szajewska, Marzena

    2015-05-01

    This paper completes the series of three independent articles [Bodner et al. (2013). Acta Cryst. A69, 583-591, (2014), PLOS ONE, 10.1371/journal.pone.0084079] describing the breaking of icosahedral symmetry to subgroups generated by reflections in three-dimensional Euclidean space {\\bb R}^3 as a mechanism of generating higher fullerenes from C60. The icosahedral symmetry of C60 can be seen as the junction of 17 orbits of a symmetric subgroup of order 4 of the icosahedral group of order 120. This subgroup is noted by A1 × A1, because it is isomorphic to the Weyl group of the semi-simple Lie algebra A1 × A1. Thirteen of the A1 × A1 orbits are rectangles and four are line segments. The orbits form a stack of parallel layers centered on the axis of C60 passing through the centers of two opposite edges between two hexagons on the surface of C60. These two edges are the only two line segment layers to appear on the surface shell. Among the 24 convex polytopes with shell formed by hexagons and 12 pentagons, having 84 vertices [Fowler & Manolopoulos (1992). Nature (London), 355, 428-430; Fowler & Manolopoulos (2007). An Atlas of Fullerenes. Dover Publications Inc.; Zhang et al. (1993). J. Chem. Phys. 98, 3095-3102], there are only two that can be identified with breaking of the H3 symmetry to A1 × A1. The remaining ones are just convex shells formed by regular hexagons and 12 pentagons without the involvement of the icosahedral symmetry. PMID:25921498

  16. Molecular scene analysis: application of a topological approach to the automated interpretation of protein electron-density maps.

    PubMed

    Leherte, L; Fortier, S; Glasgow, J; Allen, F H

    1994-03-01

    Methods to assist in the spatial and visual analysis of electron-density maps have been investigated as part of a project in molecular scene analysis [Fortier, Castleden, Glasgow, Conklin, Walmsley, Leherte & Allen (1993). Acta Cryst. D49, 168-178]. In particular, the usefulness of the topological approach for the segmentation of medium-resolution (3 A) maps of proteins and their interpretation in terms of structural motifs has been assessed. The approach followed is that proposed by Johnson [Johnson (1977). ORCRIT. The Oak Ridge Critical Point Network Program. Chemistry Division, Oak Ridge National Laboratory, USA] which provides a global representation of the electron-density distribution through the location, identification and linkage of its critical points. In the first part of the study, the topological approach was applied to calculated maps of three proteins of small to medium size so as to develop a methodology that could then be used for analyzing maps of medium resolution. The methodology was then applied to both calculated and experimental maps of penicillopepsin at 3 A resolution. The study shows that the networks of critical points can provide a useful segmentation of the maps, tracing the protein main chains and capturing their conformation. In addition, these networks can be parsed in terms of secondary-structure motifs, through a geometrical analysis of the critical points. The procedure adopted for secondary-structure recognition, which was phrased in terms of geometry-based rules, provides a basis for a further automated implementation of a more complete set of recognition operations through the use of artificial-intelligence techniques. PMID:15299453

  17. Predicting the Elastic Moduli of Perovskites in the Earth's Mantle

    NASA Astrophysics Data System (ADS)

    Angel, R. J.; Ross, N. L.; Zhao, J.; Vanpeteghem, C.

    2006-05-01

    Understanding the relationship between the elasticity of a mineral and its composition and structure is essential for building predictive models of mantle flow. Recent advances in laboratory-based single-crystal X- ray diffraction techniques for measuring the intensities of diffraction from crystals held in situ at high pressures in the diamond-anvil cell have been used to determine the role of polyhedral compression in the response of oxide perovskites to high pressure [1]. These new data clearly demonstrate that, contrary to previous belief that perovskites octahedra are essentially incompressible, the compression of the octahedral sites is significant and that the evolution of the perovskite structure with pressure is controlled by a new principle; that of equipartition of bond-valence strain between the A and B cation sites within the structure [2]. The structural response to pressure is thus determined by the compressibility ratio of the A and B cation sites within the structure which can be predicted as inverse of the ratio of the site parameters MA/MB [2] which are completely determined by the room-pressure structure. Further, we find that the bulk elastic properties of perovskites are strongly linearly correlated with this site parameter ratio, thus providing a way to predict the elastic moduli of lower-mantle perovskites from the composition alone. References [1] e.g. Zhao, Ross & Angel (2004) Phys Chem Miner. 31: 299; Ross, Zhao,. & Angel (2004). J. Solid State Chemistry 177:1276, Vanpeteghem CB, Zhao J, Angel RJ, Ross NL, Bolfan-Casanova N (2006) Geophysical Research Letters 33: L03306. [2] Zhao, Ross, & Angel (2004). Acta Cryst. B60:263

  18. Distinguishing tautomerism in the crystal structure of (Z)-N-(5-ethyl-2,3-di-hydro-1,3,4-thiadiazol-2-ylidene) -4-methylbenzenesulfonamide using DFT-D calculations and {sup 13}C solid-state NMR

    SciTech Connect

    Li, Xiaozhou; Bond, Andrew D.; Johansson, Kristoffer E.; Van de Streek, Jacco

    2014-08-01

    The crystal structure of (Z)-N-(5-ethyl-2,3-di-hydro-1,3,4-thiadiazol-2-ylidene) -4-methylbenzenesulfonamide contains an imine tautomer, rather than the previously reported amine tautomer. The tautomers can be distinguished using dispersion-corrected density functional theory calculations and by comparison of calculated and measured {sup 13}C solid-state NMR spectra. The crystal structure of the title compound, C{sub 11}H{sub 13}N{sub 3}O{sub 2}S{sub 2}, has been determined previously on the basis of refinement against laboratory powder X-ray diffraction (PXRD) data, supported by comparison of measured and calculated {sup 13}C solid-state NMR spectra [Hangan et al. (2010 ▶). Acta Cryst. B66, 615–621]. The mol@@ecule is tautomeric, and was reported as an amine tautomer [systematic name: N-(5-ethyl-1,3,4-thia@@diazol-2-yl)-p-toluene@@sulfonamide], rather than the correct imine tautomer. The protonation site on the mol@@ecule’s 1,3,4-thia@@diazole ring is indicated by the inter@@molecular contacts in the crystal structure: N—H⋯O hydrogen bonds are established at the correct site, while the alternative protonation site does not establish any notable inter molecular inter@@actions. The two tautomers provide essentially identical Rietveld fits to laboratory PXRD data, and therefore they cannot be directly distinguished in this way. However, the correct tautomer can be distinguished from the incorrect one by previously reported qu@@anti@@tative criteria based on the extent of structural distortion on optimization of the crystal structure using dispersion-corrected density functional theory (DFT-D) calculations. Calculation of the {sup 13}C SS-NMR spectrum based on the correct imine tautomer also provides considerably better agreement with the measured {sup 13}C SS-NMR spectrum.

  19. Heterocyclic tautomerism: reassignment of two crystal structures of 2-amino-1,3-thiazolidin-4-one derivatives.

    PubMed

    Gzella, Andrzej K; Kowiel, Marcin; Suseł, Aneta; Wojtyra, Magdalena N; Lesyk, Roman

    2014-08-01

    The structures of 5-(2-hydroxyethyl)-2-[(pyridin-2-yl)amino]-1,3-thiazolidin-4-one, C10H11N3O2S, (I), and ethyl 4-[(4-oxo-1,3-thiazolidin-2-yl)amino]benzoate, C12H12N2O3S, (II), which are identical to the entries with refcodes GACXOZ [Váňa et al. (2009). J. Heterocycl. Chem. 46, 635-639] and HEGLUC [Behbehani & Ibrahim (2012). Molecules, 17, 6362-6385], respectively, in the Cambridge Structural Database [Allen (2002). Acta Cryst. B58, 380-388], have been redetermined at 130 K. This structural study shows that both investigated compounds exist in their crystal structures as the tautomer with the carbonyl-imine group in the five-membered heterocyclic ring and an exocyclic amine N atom, rather than the previously reported tautomer with a secondary amide group and an exocyclic imine N atom. The physicochemical and spectroscopic data of the two investigated compounds are the same as those of GACXOZ and HEGLUC, respectively. In the thiazolidin-4-one system of (I), the S and chiral C atoms, along with the hydroxyethyl group, are disordered. The thiazolidin-4-one fragment takes up two alternative locations in the crystal structure, which allows the molecule to adopt R and S configurations. The occupancy factors of the disordered atoms are 0.883 (2) (for the R configuration) and 0.117 (2) (for the S configuration). In (I), the main factor that determines the crystal packing is a system of hydrogen bonds, involving both strong N-H...N and O-H...O and weak C-H...O hydrogen bonds, linking the molecules into a three-dimensional hydrogen-bond network. On the other hand, in (II), the molecules are linked via N-H...O hydrogen bonds into chains. PMID:25093365

  20. A monoclinic polymorph of 4-(2H-1,3-benzodioxol-5-yl)-1-(4-methyl­phen­yl)-1H-pyrazol-5-amine

    PubMed Central

    Jotani, Mukesh M.; Gajera, Nilesh N.; Patel, Mukesh C.; Sung, Herman H. Y.; Tiekink, Edward R. T.

    2015-01-01

    The title compound, C17H15N3O2, is a monoclinic polymorph (P21/c with Z′ = 1) of the previously reported triclinic (P-1 with Z′ = 2) form [Gajera et al. (2013 ▸). Acta Cryst. E69, o736–o737]. The mol­ecule in the monoclinic polymorph features a central pyrazolyl ring with an N-bound p-tolyl group and a C-bound 1,3-benzodioxolyl fused-ring system on either side of the C atom bearing the amino group. The dihedral angles between the central ring and the N- and C-bound rings are 50.06 (5) and 27.27 (5)°, respectively. The angle between the pendent rings is 77.31 (4)°, indicating the mol­ecule has a twisted conformation. The five-membered dioxolyl ring has an envelope conformation with the methyl­ene C atom being the flap. The relative disposition of the amino and dioxolyl substituents is syn. One of the independent mol­ecules in the triclinic form has a similar syn disposition but the other has an anti arrangement of these substituents. In the crystal structure of the monoclinic form, mol­ecules assemble into supra­molecular helical chains via amino–pyrazolyl N—H⋯N hydrogen bonds. These are linked into layers via C—H⋯π inter­actions, and layers stack along the a axis with no specific inter­actions between them. PMID:26594387

  1. X-ray structure of the metcyano form of dehaloperoxidase from Amphitrite ornata: evidence for photoreductive dissociation of the iron-cyanide bond

    SciTech Connect

    de Serrano, V.S.; Davis, M.F.; Gaff, J.F.; Zhang, Q.; Chen, Z.; D'Antonio, E.L.; Bowden, E.F.; Rose, R.; Franzen, S.

    2010-11-09

    X-ray crystal structures of the metcyano form of dehaloperoxidase-hemoglobin (DHP A) from Amphitrite ornata (DHPCN) and the C73S mutant of DHP A (C73SCN) were determined using synchrotron radiation in order to further investigate the geometry of diatomic ligands coordinated to the heme iron. The DHPCN structure was also determined using a rotating-anode source. The structures show evidence of photoreduction of the iron accompanied by dissociation of bound cyanide ion (CN{sup -}) that depend on the intensity of the X-ray radiation and the exposure time. The electron density is consistent with diatomic molecules located in two sites in the distal pocket of DHPCN. However, the identities of the diatomic ligands at these two sites are not uniquely determined by the electron-density map. Consequently, density functional theory calculations were conducted in order to determine whether the bond lengths, angles and dissociation energies are consistent with bound CN{sup -} or O{sub 2} in the iron-bound site. In addition, molecular-dynamics simulations were carried out in order to determine whether the dynamics are consistent with trapped CN{sup -} or O{sub 2} in the second site of the distal pocket. Based on these calculations and comparison with a previously determined X-ray crystal structure of the C73S-O{sub 2} form of DHP [de Serrano et al. (2007), Acta Cryst. D63, 1094-1101], it is concluded that CN{sup -} is gradually replaced by O{sub 2} as crystalline DHP is photoreduced at 100 K. The ease of photoreduction of DHP A is consistent with the reduction potential, but suggests an alternative activation mechanism for DHP A compared with other peroxidases, which typically have reduction potentials that are 0.5 V more negative. The lability of CN{sup -} at 100 K suggests that the distal pocket of DHP A has greater flexibility than most other hemoglobins.

  2. Compounds with a ‘stuffed’ anti-bixbyite-type structure, analysed in terms of the Zintl–Klemm and coordination-defect concepts

    PubMed Central

    Vegas, Angel; Martin, Raymond L.; Bevan, D. J. M.

    2009-01-01

    The bixbyite structure (Mn2O3) () is often described as a distorted face-centered cubic (f.c.c.) array of Mn atoms, with O atoms occupying 3/4 of the tetrahedral holes. The empty M 4 tetrahedra are centred at 16c. In anti-bixbyite structures (Mg3N2), cation vacancies are centred in empty N4 tetrahedra. If 16 hypothetical atoms were located at this site they would form the structure of γ-Si. This means that anti-bixbyite structures are ideally prepared to accommodate Si(Ge) atoms at these holes. Several compounds (Li3AlN2 and Li3ScN2) fully satisfy this expectation. They are really anti-bixbyites ‘stuffed’ with Al(Sc). The presence of these atoms in 16c is illuminated in the light of the extended Zintl–Klemm concept (EZKC) [Vegas & García-Baonza (2007 ▶). Acta Cryst. B63, 339–345], from which a compound would be the result of ‘multiple resonance’ pseudo-structures, emerging from electron transfers between any species pair (like or unlike atoms, cations or anions). The coordination-defect (CD) concept [Bevan & Martin (2008) ▶. J. Solid State Chem. 181, 2250–2259] is also consistent with the EZKC description of the pseudo-structures. A more profound insight into crystal structures is gained if one is not restricted to the contemplation of classical anions and cations in their conventional oxidation states. PMID:19155554

  3. Ir-Spectroscopy of Glycine and its Complexes with Water in Helium Nanodroplets

    NASA Astrophysics Data System (ADS)

    Letzner, M.; Grün, S. A.; Schwaab, G.; Havenith, M.

    2011-06-01

    Glycine is the smallest amino acid, and therefore it is of special interest as a model and starting point for theoretical and experimental studies. Whereas the crystalline form of glycine consists of zwitterions NH_3+-CH_2-COO-, gas phase glycine is known to exist in the nonionized form NH_2-CH_2-COOH. The interaction between glycine and water has been widely studied using a large variety of theoretical methods. Depending on the theoretical level used, a stabilisation of the zwitterionic form is predicted for complexes containing from 2 to 7 water molecules. In low-temperature Ar matrices a set of characteristic IR absorption bands for the zwitterionic form has been observed. The higher stoichiometry complexes (glycine)\\cdots(H_2O)_n with n larger than 3 are demonstrated to be zwitterionic H-bonded complexes. The multitude of conformations expected for these glycine-water complexes makes a combination of low temperature and high resolution spectroscopy essential. We want to use the advantages of our experiment to investigate glycine and its complexes with water in helium-nanodroplets at ultracold temperatures in the range from 3000-3800 Cm-1. Our measurements were carried out using a high power IR-OPO (cw: 2.7 W) as radiation source and a helium nanodroplet spectrometer. Helium-nanodroplets are formed by expansion of helium at 55 bar through a 5 μm nozzle which is kept at a temperature of 16 K. The status of the project is presented. P.-G. Jönsson et al., Acta Crystallogr., Sect. B: Struct. Crystallogr. Cryst. Chem. 28, 1827 (1972) G. Junk et al., J. Am. Chem. Soc. 85, 839 (1963) R. Ramaekers et al., J. Chem. Phys., 120 (2004)

  4. Identification of the critical linker residues conferring differences in the compactness of NS5 from Dengue virus serotype 4 and NS5 from Dengue virus serotypes 1-3.

    PubMed

    Subramanian Manimekalai, Malathy Sony; Saw, Wuan Geok; Pan, Ankita; Grüber, Ardina; Grüber, Gerhard

    2016-06-01

    Dengue virus (DENV) nonstructural protein 5 (NS5) consists of a methyltransferase (MTase) domain and an RNA-dependent RNA polymerase (RdRp) domain. The cross-talk between these domains occurs via a ten-residue linker. Recent solution studies of DENV NS5 from all four serotypes (DENV-1 to DENV-4) showed that NS5 adopts multiple conformations owing to its flexible linker and that DENV-4 NS5 is more compact and less flexible compared with NS5 from DENV-1 to DENV-3 [Saw et al. (2015), Acta Cryst. D71, 2309-2327]. Here, using a variety of single, double, triple and quadruple mutants of DENV-4 NS5 combined with solution X-ray scattering studies, insight into the critical residues responsible for the differential flexibility of DENV-4 NS5 is presented. The DENV-4 NS5 mutants K271T and S266N/T267A as well as the deletion mutant ΔS266T267 showed enlarged dimensions and flexibility similar to those of DENV-3 NS5. The data indicate that the residues Lys271, Ser266 and Thr267 are important for the compactness of DENV-4 NS5 and therefore may be critical for the regulation of virus replication. Furthermore, quantitative characterization of the flexibility of these DENV-4 NS5 linker mutants using the ensemble-optimization method revealed that these mutants possess a similar conformational distribution to DENV-3 NS5, confirming that these residues in the linker region cause the higher compactness of DENV-4 NS5. PMID:27303800

  5. Crystal structure of an unknown solvate of {2,2′-[ethane-1,2-diylbis(nitrilo­methanylyl­idene)]diphenolato-κ4 O,N,N′,O′}(N-ferrocenylisonicotinamide-κN 1)cobalt(II): a CoII–salen complex that forms hydrogen-bonded dimers

    PubMed Central

    Brautigam, Bryan; Herholdt, Chelsea; Farnsworth, William; Brudi, Ellen; McDonald, Eric; Wu, Guang; Contakes, Stephen

    2015-01-01

    The title compound, [CoFe(C5H5)(C16H14N2O2)(C11H9N2O)], was prepared as an air-stable red–brown solid by mixing equimolar amounts of {2,2′-[ethane-1,2-diylbis(nitrilo­methanylyl­idene)]diphenolato}cobalt(II) and N-ferrocenylisonicotinamide in dry di­chloro­methane under nitro­gen and was characterized by ESI–MS, IR, and single-crystal X-ray diffraction. The structure at 100 K has triclinic (P-1) symmetry and indicates that the complex crystallizes as a mixture of λ and δ conformers. It exhibits the expected square pyramidal geometry about Co, and forms hydrogen-bonded dimers through amide N—H groups and phenolate O atoms on an adjacent mol­ecule. The involvement of only half of the salen ring structure in hydrogen-bonding inter­actions results in slight folding of the salen ring away from the pyridine coordination site in the δ conformer with an inter-salicyl­idene fold angle of 9.9 (7)°. In contrast, the λ conformer is nearly planar. The dimers pack into an open structure containing channels filled with highly disordered solvent mol­ecules. These solvent molecules’ contributions to the intensity data were removed with the SQUEEZE procedure [Spek (2015). Acta Cryst. C71, 9–18] available in PLATON. PMID:26396858

  6. Crystal structures of deuterated sodium molybdate dihydrate and sodium tungstate dihydrate from time-of-flight neutron powder diffraction.

    PubMed

    Fortes, A Dominic

    2015-07-01

    Time-of-flight neutron powder diffraction data have been measured from ∼90 mol% deuterated isotopologues of Na2MoO4·2H2O and Na2WO4·2H2O at 295 K to a resolution of sin (θ)/λ = 0.77 Å(-1). The use of neutrons has allowed refinement of structural parameters with a precision that varies by a factor of two from the heaviest to the lightest atoms; this contrasts with the X-ray based refinements where precision may be > 20× poorer for O atoms in the presence of atoms such as Mo and W. The accuracy and precision of inter-atomic distances and angles are in excellent agreement with recent X-ray single-crystal structure refinements whilst also completing our view of the hydrogen-bond geometry to the same degree of statistical certainty. The two structures are isotypic, space-group Pbca, with all atoms occupying general positions, being comprised of edge- and corner-sharing NaO5 and NaO6 polyhedra that form layers parallel with (010) inter-leaved with planes of XO4 (X = Mo, W) tetra-hedra that are linked by chains of water mol-ecules along [100] and [001]. The complete structure is identical with the previously described molybdate [Capitelli et al. (2006 ▸). Asian J. Chem. 18, 2856-2860] but shows that the purported three-centred inter-action involving one of the water mol-ecules in the tungstate [Farrugia (2007 ▸). Acta Cryst. E63, i142] is in fact an ordinary two-centred 'linear' hydrogen bond. PMID:26279871

  7. Ring-strain release in neutral and dicationic 7,8,17,18-tetra­bromo-5,10,15,20-tetra­phenyl­porphyrin: crystal structures of C44H26Br4N4 and C44H28Br4N4 2+·2ClO4 −·3CH2Cl2

    PubMed Central

    Scheidt, W. Robert; Duval, Hugues F.; Oliver, Allen G.

    2016-01-01

    Two porphyrin complexes were studied to determine the effects of protonation on ring deformation within the porphyrin. The porphyrin 7,8,17,18-tetra­bromo-5,10,15,20-tetra­phenyl­porphyrin, C44H26Br4N4, was selected because the neutral species is readily doubly protonated to yield a dication, which was crystallized here with perchlorate counter-ions as a di­chloro­methane tris­olvate, C44H28Br4N4 2+·2ClO4 −·3CH2Cl2. The centrosymmetric neutral species is observed to have a mild ‘ruffling’ of the pyrrole rings and is essentially planar throughout; intra­molecular N—H⋯N hydrogen bonds occur. In contrast, the dication exhibits considerable deformation, with the pyrrole rings oriented well out of the plane of the porphyrin, resulting in a ‘saddle’ conformation of the ring. The charged species forms N—H⋯O hydrogen bonds to the perchlorate anions, which lie above and below the plane of the porphyrin ring. Distortions to the planarity of the pyrrole rings in both cases are very minor. The characterization of the neutral species represents a low-temperature redetermination of the previous room-temperature analyses [Zou et al. (1995 ▸). Acta Cryst. C51, 760–761; Rayati et al. (2008 ▸). Polyhedron, pp. 2285–2290], which showed disorder and physically unrealistic displacement parameters. PMID:27308051

  8. Crystal structure of an unknown solvate of (piperazine-κN){5,10,15,20-tetra­kis­[4-(benzo­yloxy)phen­yl]porphyrinato-κ4 N}zinc

    PubMed Central

    Nasri, Soumaya; Ezzayani, Khaireddine; Turowska-Tyrk, Ilona; Roisnel, Thierry; Nasri, Habib

    2016-01-01

    The title compound, [Zn(C72H44N4O8)(C4H10N2)] or [Zn(TPBP)(pipz] (where TPBP and pipz are 5,10,15,20-tetra­kis­[4-(benzo­yloxy)phen­yl]porphyrinato and piperazine ligands respectively), features a distorted square-pyramidal coordin­ation geometry about the central ZnII atom. This central atom is chelated by the four N atoms of the porphyrinate anion and further coordinated by a nitro­gen atom of the piperazine axial ligand, which adopts a chair confirmation. The average Zn—N(pyrrole) bond length is 2.078 (7) Å and the Zn— N(pipz) bond length is 2.1274 (19) Å. The zinc cation is displaced by 0.4365 (4) Å from the N4C20 mean plane of the porphyrinate anion toward the piperazine axial ligand. This porphyrinate macrocycle exhibits major saddle and moderate ruffling deformations. In the crystal, the supra­molecular structure is made by parallel pairs of layers along (100), with an inter­layer distance of 4.100 Å while the distance between two pairs of layers is 4.047 Å. A region of electron density was treated with the SQUEEZE [Spek (2015 ▸). Acta Cryst. C71, 9–18] procedure in PLATON following unsuccessful attempts to model it as being part of disordered n-hexane solvent and water mol­ecules. The given chemical formula and other crystal data do not take into account these solvent mol­ecules. PMID:27555935

  9. Crystal structure of an unknown solvate of (piperazine-κN){5,10,15,20-tetra-kis-[4-(benzo-yloxy)phen-yl]porphyrinato-κ(4) N}zinc.

    PubMed

    Nasri, Soumaya; Ezzayani, Khaireddine; Turowska-Tyrk, Ilona; Roisnel, Thierry; Nasri, Habib

    2016-07-01

    The title compound, [Zn(C72H44N4O8)(C4H10N2)] or [Zn(TPBP)(pipz] (where TPBP and pipz are 5,10,15,20-tetra-kis-[4-(benzo-yloxy)phen-yl]porphyrinato and piperazine ligands respectively), features a distorted square-pyramidal coordin-ation geometry about the central Zn(II) atom. This central atom is chelated by the four N atoms of the porphyrinate anion and further coordinated by a nitro-gen atom of the piperazine axial ligand, which adopts a chair confirmation. The average Zn-N(pyrrole) bond length is 2.078 (7) Å and the Zn- N(pipz) bond length is 2.1274 (19) Å. The zinc cation is displaced by 0.4365 (4) Å from the N4C20 mean plane of the porphyrinate anion toward the piperazine axial ligand. This porphyrinate macrocycle exhibits major saddle and moderate ruffling deformations. In the crystal, the supra-molecular structure is made by parallel pairs of layers along (100), with an inter-layer distance of 4.100 Å while the distance between two pairs of layers is 4.047 Å. A region of electron density was treated with the SQUEEZE [Spek (2015 ▸). Acta Cryst. C71, 9-18] procedure in PLATON following unsuccessful attempts to model it as being part of disordered n-hexane solvent and water mol-ecules. The given chemical formula and other crystal data do not take into account these solvent mol-ecules. PMID:27555935

  10. Form, symmetry and packing of biomacromolecules. V. Shells with boundaries at anti-nodes of resonant vibrations in icosahedral RNA viruses.

    PubMed

    Janner, A

    2011-11-01

    The RNA viruses cowpea chlorotic mottle, satellite tobacco mosaic, pariacoto and MS2, already considered in part IV of this series of papers [Janner, A. (2011a), Acta Cryst. A67, 517-520], are investigated further, with the aim to arrive at a possible physical basis for their structural properties. The shell structure of the filled capsid is analyzed in terms of successive spherical boundaries of the sets of icosahedral equivalent chains. By inversion in the sphere enclosing the capsid, the internal boundaries are transformed into external ones, which are more easily visualized. This graphical procedure reveals the presence of regularly spaced shells with boundaries fitting with anti-nodal surfaces of the virus considered as an elastic resonator. The centers of gravity of the various chains occur in the nodal regions of eigenvibrations with wavelength λ = R(0)/K(0), where R(0) is the radius of the virus and K(0) takes one of the values 12, 6, 4, 3, depending on the mode. The resonator model is consistent with practically all spherical shell boundaries, whereas deviations are observed for the icosahedral axial modes, which apparently play a secondary role with respect to the spherical ones. Both the spherical and the axial anti-nodal surfaces fit very well with the packed structure of the viruses in the crystal which, accordingly, is expected to have eigenfrequencies related to those of the virus. These results open the way to a better understanding of the possibility of breaking the capsid using resonant forced oscillations excited, for example, by an applied elastic shock or by irradiation with femtosecond laser pulses, as already realised by K.-T. Tsen and co-workers. An alternative `plywood' model connected to the extreme elastic properties of the capsid is also considered. PMID:22011468

  11. Etude structurale et vibrationnelle d’un nouveau composé complexe de cobalt: [Co(imidazole)4Cl]Cl

    PubMed Central

    Derbel, Amira; Mhiri, Tahar; Graia, Mohsen

    2015-01-01

    In the title complex, chlorido­tetra­kis­(1H-imidazole-κN 3)cobalt(II) chloride, [CoCl(C3H4N2)4]Cl, the CoII cation has a distorted square-pyramidal coordination environment. It is coordinated by four N atoms of four imidazole (Im) groups in the basal plane, and by a Cl atom in the apical position. It is isostructural with [Cu(Im)4Cl]Cl [Morzyk-Ociepa et al. (2012 ▸). J. Mol. Struct. 1028, 49–56] and [Cu(Im)4Br]Br [Hossaini Sadr et al. (2004 ▸). Acta Cryst. E60, m1324–m1326]. In the crystal, the [CoCl(C3H4N2)4]+ cations and Cl− anions are linked via N—H⋯Cl hydrogen bonds, forming layers parallel to (010). These layers are linked via C—H⋯Cl hydrogen bonds and C—H⋯π and π–π [inter-centroid distance = 3.794 (2) Å] inter­actions, forming a three-dimensional framework. The IR spectrum shows vibrational bands typical for imidazol groups. The monoclinic unit cell of the title compound emulates an ortho­rhom­bic cell as its β angle is close to 90°. The crystal is twinned, with the refined ratio of twin components being 0.569 (1):0.431 (1). PMID:26594402

  12. Crystal structure of tri­aqua­(2,6-di­methyl­pyrazine-κN 4)bis­(thio­cyanato-κN)manganese(II) 2,5-di­methyl­pyrazine disolvate

    PubMed Central

    Suckert, Stefan; Wöhlert, Susanne; Jess, Inke; Näther, Christian

    2015-01-01

    In the crystal structure of the title complex, [Mn(NCS)2(C6H8N2)(H2O)3]·2C6H8N2, the MnII cation is coordinated by two terminally N-bonded thio­cyanate anions, three water mol­ecules and one 2,6-di­methyl­pyrazine ligand within a slightly distorted N3O3 octa­hedral geometry; the entire complex mol­ecule is generated by the application of a twofold rotation axis. The asymmetric unit also contains an uncoordinating 2,5-di­methyl­pyrazine ligand in a general position. Obviously, the coordination to the 2,6-di­methyl­pyrazine ligand is preferred because coordination to the 2,5-di­methyl­pyrazine is hindered due to the bulky methyl group proximate to the N atom. The discrete complexes are linked by water-O—H⋯N(2,6-di­methyl­pyzazine/2,5-di­methyl­pyza­zine) hydrogen bonding, forming a three-dimensional network. In the crystal, mol­ecules are arranged in a way that cavities are formed in which unspecified, disordered solvent molecules reside. These were modelled employing the SQUEEZE routine in PLATON [Spek (2015 ▸). Acta Cryst. C71, 9–18]. The composition of the unit cell does not take into account the presence of the unspecified solvent. PMID:26870435

  13. Crystal structure of a new monoclinic polymorph of 2,4-di­hydroxy­benzaldehyde 4-methyl­thio­semi­carbazone

    PubMed Central

    Salam, M. A.; Hussein, Mouayed A.; Tiekink, Edward R. T.

    2015-01-01

    The title compound, C9H11N3O2S, is a second monoclinic (P21/c) polymorph of the previously reported Cc form [Tan et al. (2008b ▸). Acta Cryst. E64, o2224]. The mol­ecule is non-planar, with the dihedral angle between the N3CS residue (r.m.s. deviation = 0.0816 Å) and the benzene ring being 21.36 (4)°. The conformation about the C=N bond [1.292 (2) Å] is E, the two N-bound H atoms are anti, and the inner hy­droxy O-bound and outer amide N-bound H atoms form intra­molecular hydrogen bonds to the imine N atom. Crucially, the H atom of the outer hy­droxy group is approximately syn to the H atom of the benzene C atom connecting the two C atoms bearing the hy­droxy substituents. This arrangement enables the formation of supra­molecular tubes aligned along [010] and sustained by N—H⋯O, O—H⋯S and N—H⋯S hydrogen bonds; the tubes pack with no specific inter­actions between them. While the mol­ecular structure in the Cc form is comparable, the H atom of the outer hy­droxy group is approximately anti, rather than syn. This different orientation leads to the formation a three-dimensional architecture based on N—H⋯O and O—H⋯S hydrogen bonds. PMID:25705451

  14. Crystal structures of spinel-type Na2MoO4 and Na2WO4 revisited using neutron powder diffraction

    PubMed Central

    Fortes, A. Dominic

    2015-01-01

    Time-of-flight neutron powder diffraction data have been collected from Na2MoO4 and Na2WO4 to a resolution of sin (θ)/λ = 1.25 Å−1, which is substanti­ally better than the previous analyses using Mo Kα X-rays, providing roughly triple the number of measured reflections with respect to the previous studies [Okada et al. (1974 ▸). Acta Cryst. B30, 1872–1873; Bramnik & Ehrenberg (2004 ▸). Z. Anorg. Allg. Chem. 630, 1336–1341]. The unit-cell parameters are in excellent agreement with literature data [Swanson et al. (1962 ▸). NBS Monograph No. 25, sect. 1, pp. 46–47] and the structural parameters for the molybdate agree very well with those of Bramnik & Ehrenberg (2004 ▸). However, the tungstate structure refinement of Okada et al. (1974 ▸) stands apart as being conspicuously inaccurate, giving significantly longer W—O distances, 1.819 (8) Å, and shorter Na—O distances, 2.378 (8) Å, than are reported here or in other simple tungstates. As such, this work represents an order-of-magnitude improvement in precision for sodium molybdate and an equally substantial improvement in both accuracy and precision for sodium tungstate. Both compounds adopt the spinel structure type. The Na+ ions have site symmetry .-3m and are in octa­hedral coordination while the transition metal atoms have site symmetry -43m and are in tetra­hedral coordination. PMID:26090129

  15. Crystal structures of deuterated sodium molybdate dihydrate and sodium tungstate dihydrate from time-of-flight neutron powder diffraction

    PubMed Central

    Fortes, A. Dominic

    2015-01-01

    Time-of-flight neutron powder diffraction data have been measured from ∼90 mol% deuterated isotopologues of Na2MoO4·2H2O and Na2WO4·2H2O at 295 K to a resolution of sin (θ)/λ = 0.77 Å−1. The use of neutrons has allowed refinement of structural parameters with a precision that varies by a factor of two from the heaviest to the lightest atoms; this contrasts with the X-ray based refinements where precision may be > 20× poorer for O atoms in the presence of atoms such as Mo and W. The accuracy and precision of inter­atomic distances and angles are in excellent agreement with recent X-ray single-crystal structure refinements whilst also completing our view of the hydrogen-bond geometry to the same degree of statistical certainty. The two structures are isotypic, space-group Pbca, with all atoms occupying general positions, being comprised of edge- and corner-sharing NaO5 and NaO6 polyhedra that form layers parallel with (010) inter­leaved with planes of XO4 (X = Mo, W) tetra­hedra that are linked by chains of water mol­ecules along [100] and [001]. The complete structure is identical with the previously described molybdate [Capitelli et al. (2006 ▸). Asian J. Chem. 18, 2856–2860] but shows that the purported three-centred inter­action involving one of the water mol­ecules in the tungstate [Farrugia (2007 ▸). Acta Cryst. E63, i142] is in fact an ordinary two-centred ‘linear’ hydrogen bond. PMID:26279871

  16. A structural study of (1RS,2SR,3RS,4SR,5RS)-2,4-dibenzoyl-1,3,5-triphenylcyclohexan-1-ol chloroform hemisolvate and (1RS,2SR,3RS,4SR,5RS)-2,4-dibenzoyl-1-phenyl-3,5-bis(2-methoxyphenyl)cyclohexan-1-ol.

    PubMed

    Minyaev, Mikhail E; Roitershtein, Dmitrii M; Nifant'ev, Ilya E; Ananyev, Ivan V; Minyaeva, Tatyana V; Mikhaylyev, Timofey A

    2015-06-01

    (1RS,2SR,3RS,4SR,5RS)-2,4-Dibenzoyl-1,3,5-triphenylcyclohexan-1-ol or (4-hydroxy-2,4,6-triphenylcyclohexane-1,3-diyl)bis(phenylmethanone), C38H32O3, (1), is formed as a by-product in the NaOH-catalyzed synthesis of 1,3,5-triphenylpentane-1,5-dione from acetophenone and benzaldehyde. Single crystals of the chloroform hemisolvate, C38H32O3·0.5CHCl3, were grown from chloroform. The structure has triclinic (P1) symmetry. One diastereomer [as a pair of (1RS,2SR,3RS,4SR,5RS)-enantiomers] of (1) has been found in the crystal structure and confirmed by NMR studies. The dichoromethane hemisolvate has been reported previously [Zhang et al. (2007). Acta Cryst. E63, o4652]. (1RS,2SR,3RS,4SR,5RS)-2,4-Dibenzoyl-3,5-bis(2-methoxyphenyl)-1-phenylcyclohexan-1-ol or [4-hydroxy-2,6-bis(2-methoxyphenyl)-4-phenylcyclohexane-1,3-diyl]bis(phenylmethanone), C40H36O5, (2), is also formed as a by-product, under the same conditions, from acetophenone and 2-methoxybenzaldehyde. Crystals of (2) have been grown from chloroform. The structure has orthorhombic (Pca2₁) symmetry. A diastereomer of (2) possesses the same configuration as (1). In both structures, the cyclohexane ring adopts a chair conformation with all bulky groups (benzoyl, phenyl and 2-methoxyphenyl) in equatorial positions. The molecules of (1) and (2) both display one intramolecular O-H···O hydrogen bond. PMID:26044332

  17. Map-likelihood phasing

    PubMed Central

    Terwilliger, Thomas C.

    2001-01-01

    The recently developed technique of maximum-likelihood density modification [Terwilliger (2000 ▶), Acta Cryst. D56, 965–972] allows a calculation of phase probabilities based on the likelihood of the electron-density map to be carried out separately from the calculation of any prior phase probabilities. Here, it is shown that phase-probability distributions calculated from the map-likelihood function alone can be highly accurate and that they show minimal bias towards the phases used to initiate the calculation. Map-likelihood phase probabilities depend upon expected characteristics of the electron-density map, such as a defined solvent region and expected electron-density distributions within the solvent region and the region occupied by a macromolecule. In the simplest case, map-likelihood phase-probability distributions are largely based on the flatness of the solvent region. Though map-likelihood phases can be calculated without prior phase information, they are greatly enhanced by high-quality starting phases. This leads to the technique of prime-and-switch phasing for removing model bias. In prime-and-switch phasing, biased phases such as those from a model are used to prime or initiate map-likelihood phasing, then final phases are obtained from map-likelihood phasing alone. Map-likelihood phasing can be applied in cases with solvent content as low as 30%. Potential applications of map-likelihood phasing include unbiased phase calculation from molecular-replacement models, iterative model building, unbiased electron-density maps for cases where 2Fo − Fc or σA-weighted maps would currently be used, structure validation and ab initio phase determination from solvent masks, non-crystallographic symmetry or other knowledge about expected electron density. PMID:11717488

  18. Shotgun crystallization strategy for structural genomics: an optimized two-tiered crystallization screen against the Thermotoga maritima proteome.

    PubMed

    Page, Rebecca; Grzechnik, Slawomir K; Canaves, Jaume M; Spraggon, Glen; Kreusch, Andreas; Kuhn, Peter; Stevens, Raymond C; Lesley, Scott A

    2003-06-01

    As the field of structural genomics continues to grow and new technologies are developed, novel strategies are needed to efficiently crystallize large numbers of protein targets, thus increasing output, not just throughput [Chayen & Saridakis (2002). Acta Cryst. D58, 921-927]. One strategy, developed for the high-throughput structure determination of the Thermotoga maritima proteome, is to quickly determine which proteins have a propensity for crystal formation followed by focused SeMet-incorporated protein crystallization attempts. This experimental effort has resulted in over 320 000 individual crystallization experiments. As such, it has provided one of the most extensive systematic data sets of commonly used crystallization conditions against a wide range of proteins to date. Analysis of this data shows that many of the original screening conditions are redundant, as all of the T. maritima proteins that crystallize readily could be identified using just 23% of the original conditions. It also shows that proteins that contain selenomethionine and are more extensively purified often crystallize in distinctly different conditions from those of their native less pure counterparts. Most importantly, it shows that the two-tiered strategy employed here is extremely successful for predicting which proteins will readily crystallize, as greater than 99% of the proteins identified as having a propensity to crystallize under non-optimal native conditions did so again as selenomethionine derivatives during the focused crystallization trials. This crystallization strategy can be adopted for both large-scale genomics programs and individual protein studies with multiple constructs and has the potential to significantly accelerate future crystallographic efforts. PMID:12777766

  19. Derechos Educacionales de los Padres: Una Explicacion de los Procedimientos de Seguridad para los Padres de Ninos con Discapacidades. Bajo la Clausula del Acta de Educacion para Individuos con Discapacidades (IDEA) y las Reglas para la Administracion del Acta de Educacion para Ninos Excepcionales (Educational Rights of Parents: An Explanation of Procedural Safeguards Available to Parents of Children with Disabilities. Under Provisions of the Individuals with Disabilities Education Act (IDEA) and the Rules for the Administration of the Exceptional Children's Educational Act [ECEA]).

    ERIC Educational Resources Information Center

    Mountain Plains Regional Resource Center, Des Moines, IA.

    This pamphlet, in Spanish, describes Colorado parents' educational rights under federal and state special education rules and regulations. It addresses: (1) free appropriate public education and termination of services; (2) required prior notice to parents if there is a proposed change or refusal to change a child's special education program; (3)…

  20. Geometry of trigonal boron coordination sphere in boronic acids derivatives - a bond-valence vector model approach.

    PubMed

    Czerwińska, Karolina; Madura, Izabela D; Zachara, Janusz

    2016-04-01

    The systematic analysis of the geometry of three-coordinate boron in boronic acid derivatives with a common [CBO2] skeleton is presented. The study is based on the bond-valence vector (BVV) model [Zachara (2007). Inorg. Chem. 46, 9760-9767], a simple tool for the identification and quantitative estimation of both steric and electronic factors causing deformations of the coordination sphere. The empirical bond-valence (BV) parameters in the exponential equation [Brown & Altermatt (1985). Acta Cryst. B41, 244-247] rij and b, for B-O and B-C bonds were determined using data deposited in the Cambridge Structural Database. The values obtained amount to rBO = 1.364 Å, bBO = 0.37 Å, rBC = 1.569 Å, bBC = 0.28 Å, and they were further used in the calculation of BVV lengths. The values of the resultant BVV were less than 0.10 v.u. for 95% of the set comprising 897 [CBO2] fragments. Analysis of the distribution of BVV components allowed for the description of subtle in- and out-of plane deviations from the `ideal' (sp(2)) geometry of boron coordination sphere. The distortions specific for distinct groups of compounds such as boronic acids, cyclic and acyclic esters, benzoxaboroles and hemiesters were revealed. In cyclic esters the direction of strains was found to be controlled by the ring size effect. It was shown that the syn or anti location of substituents on O atoms is decisive for the deformations direction for both acids and acyclic esters. The greatest strains were observed in the case of benzoxaboroles which showed the highest deviation from the zero value of the resultant BVV. The out-of-plane distortions, described by the vz component of the resultant BVV, were ascertained to be useful in the identification of weak secondary interactions on the fourth coordination site of the boron centre. PMID:27048726

  1. Orientation and optical properties of methylene blue crystal for better understanding of interactions with clay mineral surface

    NASA Astrophysics Data System (ADS)

    Milošević, Maja; Logar, Mihovil

    2013-04-01

    twinning of feldspar minerals. Final result of molecular polymerization is represented as crystal framework of methylene blue. Model of the MB molecular aggregation in the crystal structure could be used as a way for the interpretation of the thin layer structure and the molecular aggregation on the clay surface. References - Hang P.T. & Brindley G.W., (1970), Clays and Clay Minerals, 18, 203-212. - Bujdak J., Iyi N., Kaneko Y. and Sasai R., (2003), Clay Minerals (2003), 38, 561-572. - Li F. and Zare R.N., (2005), J. Phys. Chem. B 2005, 109, 3330-3333. - Marr III, H.E., Stewart, J.M. and Chiu, M.F., (1973), Acta Cryst. (1973), B29, 847. - Bujdak J., (2006), Applied Clay Science 34 (2006) 58 - 73

  2. Radiation damage effects in zircon

    NASA Astrophysics Data System (ADS)

    Trachenko, Kostya; Dove, Martin; Salje, Ekhard

    2002-03-01

    Zircon, ZrSiO_4, is important for geology and geochronology, and has been proposed as a host material to immobilize highly radioactive materials from dismantled weapons and nuclear waste from power stations [1]. In these applications zircon is exposed to alpha-irradiation. Computer simulations have started to be employed to simulate radiation damage in zircon [2], but the origin and microscopic mechanisms of the most important structural changes in zircon - unit cell expansion and large macroscopic swelling at higher doses, strong shear deformation of the crystalline lattice, and polymerization of SiOn units [3], remain unknown. Here, we perform the molecular dynamics simulation of highly energetic recoils in zircon. Basing on the simulation results, we propose the simple picture of the density change in the damaged region that consists of the depleted and densified matter. We find that the experimentally observed structural changes originate from the interaction of the damaged region with the surrounding crystalline lattice: the shear of the lattice around the damaged region causes shear deformation and expansion of the unit cells. The polymers of connected SiOn polyhedra are most commonly present in the densified shell at the periphery of the damaged region. [1] R C Ewing et al, J. Mater. Res. 10, 243 (1995); W J Weber et al, B E Burakov et al, in Scientific Basis for Nuclear Waste Management XIX, 25-32 and 33-40 (Plenum, New York, 1996); R C Ewing, et al in Crystalline Ceramics: Waste Forms for the Disposal of Weapons Plutonium, NATO Workshop Proceedings 65 (Academic Publishers, Dordrecht, The Netherlands, 1996). [2] B Park et al, Phys. Rev. B, 64, 174108 (1-16) (2001); J P Crocombette and D Ghaleb, J. Nucl. Mater., 295, 167 (2001); K Trachenko et al, J. Appl. Phys., 87, 7702 (2000); K Trachenko et al, J. Phys.: Cond. Matt., 13, 1947 (2001). [3] T Murakami et al, Am. Min., 76, 1510 (1991); H D Holland and D Gottfried, Acta Cryst. 8, 291 (1955).; W J Weber, J. Am

  3. Crystal structures of a copper(II) and the isotypic nickel(II) and palladium(II) complexes of the ligand (E)-1-[(2,4,6-tri-bromo-phen-yl)diazen-yl]naphthalen-2-ol.

    PubMed

    Chetioui, Souheyla; Rouag, Djamil-Azzeddine; Djukic, Jean-Pierre; Bochet, Christian G; Touzani, Rachid; Bailly, Corinne; Crochet, Aurélien; Fromm, Katharina M

    2016-08-01

    In the copper(II) complex, bis-{(E)-1-[(2,4,6-tri-bromo-phen-yl)diazen-yl]naph-thalen-2-olato}copper(II), [Cu(C16H8Br3N2O)2], (I), the metal cation is coord-inated by two N atoms and two O atoms from two bidentate (E)-1-[(2,4,6-tri-bromo-phen-yl)diazen-yl]naphthalen-2-olate ligands, forming a slightly distorted square-planar environment. In one of the ligands, the tri-bromo-benzene ring is inclined to the naphthalene ring system by 37.4 (5)°, creating a weak intra-molecular Cu⋯Br inter-action [3.134 (2) Å], while in the other ligand, the tri-bromo-benzene ring is inclined to the naphthalene ring system by 72.1 (6)°. In the isotypic nickel(II) and palladium(II) complexes, namely bis-{(E)-1-[(2,4,6-tri-bromo-phen-yl)diazen-yl]naphthalen-2-olato}nickel(II), [Ni(C16H8Br3N2O)2], (II), and bis-{(E)-1-[(2,4,6-tri-bromo-phen-yl)diazen-yl]naphthalen-2-olato}palladium(II), [Pd(C16H8Br3N2O)2], (III), respectively, the metal atoms are located on centres of inversion, hence the metal coordination spheres have perfect square-planar geometries. The tri-bromo-benzene rings are inclined to the naphthalene ring systems by 80.79 (18)° in (II) and by 80.8 (3)° in (III). In the crystal of (I), mol-ecules are linked by C-H⋯Br hydrogen bonds, forming chains along [010]. The chains are linked by C-H⋯π inter-actions, forming sheets parallel to (011). In the crystals of (II) and (III), mol-ecules are linked by C-H⋯π inter-actions, forming slabs parallel to (10-1). For the copper(II) complex (I), a region of disordered electron density was corrected for using the SQUEEZE routine in PLATON [Spek (2015 ▸). Acta Cryst. C71, 9-18]. The formula mass and unit-cell characteristics of the disordered solvent mol-ecules were not taken into account during refinement. PMID:27536389

  4. Crystal structures of 2-(4-nitro­phen­yl)-3-phenyl-2,3-di­hydro-4H-1,3-benzo­thia­zin-4-one and 2-(2-nitro­phen­yl)-3-phenyl-2,3-di­hydro-4H-1,3-benzo­thia­zin-4-one

    PubMed Central

    Yennawar, Hemant; Cali, Aaron S.; Xie, Yiwen; Silverberg, Lee J.

    2015-01-01

    The crystal structures are reported of the isomeric compounds 2-(4-nitro­phen­yl)-3-phenyl-2,3-di­hydro-4H-1,3-benzo­thia­zin-4-one, (I), and 2-(2-nitro­phen­yl)-3-phenyl-2,3-di­hydro-4H-1,3-benzo­thia­zin-4-one, (II), both C20H14N2O3S, being the para-nitro and ortho-nitro forms, respectively, the meta-form of which is known [Yennawar et al. (2013). Acta Cryst. E69, o1679]. The six-membered thia­zone ring fused with a benzene ring displays a screw-boat conformation with a total puckering amplitude of 0.627 (1) Å in (I), and a near screw-boat conformation with a total puckering amplitude of 0.600 (1) Å in (II). The dihedral angles between the planes of the substituent nitrophenyl and phenyl and rings with the benzene ring of the parent benzo­thia­zone moiety are 75.93 (5) and 82.61 (5)° [in (I)], and 76.79 (6) and 71.66 (6)° [in (II)]. Weak inter­molecular C—H⋯O hydrogen-bonding inter­actions between aromatic H-atom donors and both a nitro-O atom and a thia­zone O-atom acceptor in (I) and a thia­zone O atom in (II) are present, forming in (I) a centrosymmetric 22-membered cyclic dimer which is extended through a similar inversion-related 14-membered cyclic hydrogen-bonding association into a zigzag chain structure extending along c. In (II), a single inter­molecular C—H⋯O hydrogen bond gives a chain structure extending along b. In addition, weak C—H⋯π inter­actions are present in both structures [minimum C⋯ring-centroid separations = 3.630 (2) and 3.581 (2) Å, respectively]. PMID:26029403

  5. Expanding the structural landscape of niclosamide: a high Z' polymorph, two new solvates and monohydrate H(A).

    PubMed

    Sovago, Ioana; Bond, Andrew D

    2015-05-01

    Three new crystalline phases are reported for the drug niclosamide [5-chloro-N-(2-chloro-4-nitrophenyl)-2-hydroxybenzamide], C13H8Cl2N2O4. A new high-Z' polymorph (denoted Form II) is described, with four molecules in the asymmetric unit in the space group P2/n. The structure exhibits pseudosymmetry, including local translations and screw-type operations. The niclosamide molecules are linked by O-H...O hydrogen bonds into chains, and the chains are packed so that the molecules form face-to-face (stacking) and end-to-end interactions within layers perpendicular to the chains. There are two different layer arrangements, giving a structure that is relatively complex. In the acetone and acetonitrile solvates, the incorporated solvent molecules accept hydrogen bonds from the OH groups of niclosamide, and the niclosamide molecules are stacked in a face-to-face manner. In the acetone solvate, C13H8Cl2N2O4·C3H6O, V-shaped arrangements are formed in which the nitrobenzene ends of the niclosamide molecules are brought into face-to-face contact. In the acetonitrile solvate, C13H8Cl2N2O4·CH3CN, stacking occurs by translation along a short axis (ca 3.8 Å) and the crystals are frequently observed to be twinned by twofold rotation around that axis. The acetonitrile molecules occupy channels in the structure. A complete structure is provided for niclosamide monohydrate, C13H8Cl2N2O4·H2O, polymorph HA, obtained by Rietveld refinement against laboratory powder X-ray diffraction data. It has been suggested that this compound is related to the methanol solvate of niclosamide [Harriss, Wilson & Radosevljevic Evans (2014). Acta Cryst. C70, 758-763], but it is found that the two are not fully isostructural: they contain isostructural two-dimensional layers, but the layers are arranged differently in the two structures. This suggests that HA may have the potential for polytypism, and features in the Rietveld difference curve indicate that a polytype fully isostructural with the

  6. Crystal structures of tris­[1-oxo­pyridine-2-olato(1−)]silicon(IV) chloride chloro­form-d 1 disolvate, tris­[1-oxo­pyridine-2-olato(1−)]silicon(IV) chloride aceto­nitrile unqu­anti­fied solvate, and fac-tris­[1-oxo­pyridine-2-thiol­ato(1−)]silicon(IV) chloride chloro­form-d 1 disolvate

    PubMed Central

    Kraft, Bradley M.; Brennessel, William W.; Ryan, Amy E.; Benjamin, Candace K.

    2015-01-01

    The cations in the title salts, [Si(OPO)3]Cl·2CDCl3, (I), [Si(OPO)3]Cl·xCH3CN, (II), and fac-[Si(OPTO)3]Cl·2CDCl3, (III) (OPO = 1-oxo-2-pyridin­one, C5H4NO2, and OPTO = 1-oxo-2-pyridine­thione, C5H4NOS), have distorted octa­hedral coordination spheres. The first two structures contain the same cation and anion, but different solvents of crystallization led to different solvates and packing arrangements. In structures (I) and (III), the silicon complex cations and chloride anions are well separated, while in (II), there are two C—H⋯Cl distances that fall just within the sum of the van der Waals radii of the C and Cl atoms. The pyridine portions of the OPO ligands in (I) and (II) are modeled as disordered with the planar flips of themselves [(I): 0.574 (15):0.426 (15), 0.696 (15):0.304 (15), and 0.621 (15):0.379 (15); (II): 0.555 (13):0.445 (13), 0.604 (14):0.396 (14) and 0.611 (13):0.389 (13)], demonstrating that both fac and mer isomers are co-crystallized. In (II), highly disordered solvent, located in two independent channels along [100], was unable to be modeled. Reflection contributions from this solvent were fixed and added to the calculated structure factors using the SQUEEZE [Spek (2015 ▸). Acta Cryst. C71, 9–18] function of program PLATON, which determined there to be 54 electrons in 225 Å3 accounted for per unit cell (25 electrons in 109 Å3 in one channel, and 29 electrons in 115 Å3 in the other). In (I) and (II), all species lie on general positions. In (III), all species are located along crystallographic threefold axes. PMID:26870422

  7. Crystal packing in three related disaccharides: precursors to heparan sulfate oligosaccharides

    PubMed Central

    Gainsford, Graeme J.; Schwörer, Ralf; Tyler, Peter C.; Zubkova, Olga V.

    2015-01-01

    The three title compounds form part of a set of important precursor dissacharides which lead to novel therapeutics, in particular for Alzheimer’s disease. All three crystallize as poorly diffracting crystals with one independent mol­ecule in the asymmetric unit. Two of them are isostructural: 4-meth­oxy­phenyl 4-O-[6-O-acetyl-2-azido-3-O-benzyl-2-de­oxy-4-O-(9-fluor­en­yl­methyl­oxycarbon­yl)-α-d-gluco­pyranos­yl]-2-O-benzoyl-3-O-benzyl-6-O-chloro­acetyl-α-l-ido­pyran­oside, C59H56ClN3O16, (I), the ido-relative of a reported gluco-disaccharide [Gainsford et al., 2013 ▸). Acta Cryst. C69, 679–682] and 4-meth­oxy­phenyl 4-O-[6-O-acetyl-2-azido-3-O-benzyl-2-de­oxy-4-O-(9-fluorenyl­methyl­oxycarbon­yl)-α-d-gluco­pyranos­yl]-2-O-benzoyl-3-O-benzyl-6-O-meth­oxy­acetyl-α-l-ido­pyran­oside, C60H59N3O17, (II). Both exhibit similar conformational disorder of pendant groups. The third compound 4-meth­oxy­phenyl 4-O-[6-O-acetyl-2-azido-3,4-di-O-benzyl-2-de­oxy-α-d-gluco­pyranos­yl]-2-O-benzoyl-3-O-benzyl-6-O-meth­oxy­oacetyl-β-d-gluco­pyran­oside, C52H55N3O15, (III), illustrates that a slightly larger set of weak inter­molecular inter­actions can result in a less disordered mol­ecular arrangement. The mol­ecules are bound by weak C—H⋯O(ether) hydrogen bonds in (I) and (II), augmented by C—H⋯π inter­actions in (III). The absolute configurations were determined, although at varying levels of significance from the limited observed data. PMID:26090127

  8. Crystal structure of 4'-{[4-(2,2':6',2''-terpyrid-yl-4'-yl)phen-yl]ethyn-yl}biphenyl-4-yl (2,2,5,5-tetra-methyl-1-oxyl-3-pyrrolin-3-yl)formate benzene 2.5-solvate.

    PubMed

    Meyer, Andreas; Schnakenburg, Gregor; Schiemann, Olav

    2015-10-01

    ethynylphenyl spacer [Meyer et al. (2015). Acta Cryst. E71, 870-874]. PMID:26594417

  9. Crystal structures of a copper(II) and the isotypic nickel(II) and palladium(II) complexes of the ligand (E)-1-[(2,4,6-tri­bromo­phen­yl)diazen­yl]naphthalen-2-ol

    PubMed Central

    Chetioui, Souheyla; Rouag, Djamil-Azzeddine; Djukic, Jean-Pierre; Bochet, Christian G.; Touzani, Rachid; Bailly, Corinne; Crochet, Aurélien; Fromm, Katharina M.

    2016-01-01

    In the copper(II) complex, bis­{(E)-1-[(2,4,6-tri­bromo­phen­yl)diazen­yl]naph­thalen-2-olato}copper(II), [Cu(C16H8Br3N2O)2], (I), the metal cation is coord­inated by two N atoms and two O atoms from two bidentate (E)-1-[(2,4,6-tri­bromo­phen­yl)diazen­yl]naphthalen-2-olate ligands, forming a slightly distorted square-planar environment. In one of the ligands, the tri­bromo­benzene ring is inclined to the naphthalene ring system by 37.4 (5)°, creating a weak intra­molecular Cu⋯Br inter­action [3.134 (2) Å], while in the other ligand, the tri­bromo­benzene ring is inclined to the naphthalene ring system by 72.1 (6)°. In the isotypic nickel(II) and palladium(II) complexes, namely bis­{(E)-1-[(2,4,6-tri­bromo­phen­yl)diazen­yl]naphthalen-2-olato}nickel(II), [Ni(C16H8Br3N2O)2], (II), and bis­{(E)-1-[(2,4,6-tri­bromo­phen­yl)diazen­yl]naphthalen-2-olato}palladium(II), [Pd(C16H8Br3N2O)2], (III), respectively, the metal atoms are located on centres of inversion, hence the metal coordination spheres have perfect square-planar geometries. The tri­bromo­benzene rings are inclined to the naphthalene ring systems by 80.79 (18)° in (II) and by 80.8 (3)° in (III). In the crystal of (I), mol­ecules are linked by C—H⋯Br hydrogen bonds, forming chains along [010]. The chains are linked by C—H⋯π inter­actions, forming sheets parallel to (011). In the crystals of (II) and (III), mol­ecules are linked by C—H⋯π inter­actions, forming slabs parallel to (10-1). For the copper(II) complex (I), a region of disordered electron density was corrected for using the SQUEEZE routine in PLATON [Spek (2015 ▸). Acta Cryst. C71, 9–18]. The formula mass and unit-cell characteristics of the disordered solvent mol­ecules were not taken into account during refinement. PMID:27536389

  10. Crystal structure of an unknown solvate of dodecakis-(μ2-alaninato-1:2κ(2) O:N,O)cerium(III)hexa-nickel(II) aqua-tris-(hydroxido-κO)tris-(nitrato-κ(2) O,O')cerate(III).

    PubMed

    Bezzubov, Stanislav I; Doljenko, Vladimir D; Churakov, Andrei V; Zharinova, Irina S; Kiselev, Yuri M

    2015-10-01

    The chiral title compound, [CeNi6(C3H6NO2)12][Ce(NO3)3(OH)3(H2O)], comprises a complex heterometallic Ni/Ce cation and a homonuclear Ce anion. Both the cation and anion exhibit point group symmetry 3. with the Ce(III) atom situated on the threefold rotation axis. The cation metal core consists of six Ni(II) atoms coordinated in a slightly distorted octa-hedral N2O4 configuration by N and O atoms of 12 deprotonated l-alaninate ligands exhibiting both bridging and chelating modes. This metal-organic coordination motif encapsulates one Ce(III) atom that shows an icosa-hedral coordination by the O-donor atoms of the l-alaninate ligands, with Ce-O distances varying in the range 2.455 (5)-2.675 (3) Å. In the anion, the central Ce(III) ion is bound to three bidentate nitrate ligands, to three hydroxide ligands and to one water mol-ecule, with Ce-O distances in the range 2.6808 (19)-2.741 (2) Å. The H atoms of the coordinating water mol-ecule are disordered over three positions due to its location on a threefold rotation axis. Disorder is also observed in fragments of two l-alaninate ligands, with occupancy ratios of 0.608 (14):0.392 (14) and 0.669 (8):0.331 (8), respectively, for the two sets of sites. In the crystal, the complex cations and anions assemble through O-H⋯O and N-H⋯O hydrogen bonds into a three-dimensional network with large voids of approximately 1020 Å(3). The contributions of highly disordered ethanol and water solvent mol-ecules to the diffraction data were removed with the SQUEEZE procedure [Spek (2015 ▸). Acta Cryst. C71, 9-18]. The given chemical formula and other crystal data do not take into account the unknown amount of these solvent mol-ecules. PMID:26594427

  11. Polymorphism of NaVO2F2: a P2₁/c superstructure with pseudosymmetry of P2₁/m in the subcell.

    PubMed

    Yu, Zi-Qun; Wang, Jing-Quan; Huang, Ya-Xi; Botis, Sanda M; Pan, Yuanming; Mi, Jin-Xiao

    2015-06-01

    The ADDSYM routine in the program PLATON [Spek (2015). Acta Cryst. C71, 9-18] has helped researchers to avoid structures of (metal-)organic compounds being reported in an unnecessarily low symmetry space group. However, determination of the correct space group may get more complicated in cases of pseudosymmetric inorganic compounds. One example is NaVO2F2, which was reported [Crosnier-Lopez et al. (1994). Eur. J. Solid State Inorg. Chem. 31, 957-965] in the acentric space group P2₁ based on properties but flagged by ADDSYM as (pseudo)centrosymmetric P2₁/m within default distance tolerances. Herein a systematic investigation reveals that NaVO2F2 exists in at least four polymorphs: P2₁, (I), P2₁/m, (II), P2₁/c, (III), and one or more low-temperature ones. The new centrosymmetric modification, (III), with the space group P2₁/c has a similar atomic packing geometry to phase (I), except for having a doubled c axis. The double-cell of phase (III) arises from atomic shifts from the glide plane c at (x, ¼, z). With increasing temperature, the number of observed reflections decreases. The odd l reflections gradually become weaker and, correspondingly, all atoms shift towards the glide plane, resulting in a gradual second-order transformation of (III) into high-temperature phase (II) (P2₁/m) at below 493 K. At least one first-order enantiotropic phase transition was observed below 139 K from both the single-crystal X-ray diffraction and the differential scanning calorimetry analyses. Periodic first-principles calculations within density functional theory show that both P2₁/c superstructure (III) and P2₁ substructure (I) are more stable than P2₁/m structure (II), and that P2₁/c superstructure (III) is more stable that P2₁ substructure (I). PMID:26044323

  12. Data processing pipeline for serial femtosecond crystallography at SACLA1

    PubMed Central

    Nakane, Takanori; Joti, Yasumasa; Tono, Kensuke; Yabashi, Makina; Nango, Eriko; Iwata, So; Ishitani, Ryuichiro; Nureki, Osamu

    2016-01-01

    A data processing pipeline for serial femtosecond crystallography at SACLA was developed, based on Cheetah [Barty et al. (2014). J. Appl. Cryst.47, 1118–1131] and CrystFEL [White et al. (2016). J. Appl. Cryst.49, 680–689]. The original programs were adapted for data acquisition through the SACLA API, thread and inter-node parallelization, and efficient image handling. The pipeline consists of two stages: The first, online stage can analyse all images in real time, with a latency of less than a few seconds, to provide feedback on hit rate and detector saturation. The second, offline stage converts hit images into HDF5 files and runs CrystFEL for indexing and integration. The size of the filtered compressed output is comparable to that of a synchrotron data set. The pipeline enables real-time feedback and rapid structure solution during beamtime. PMID:27275146

  13. Response to comments on the papers recently published by Kalaivani et al.

    NASA Astrophysics Data System (ADS)

    Kalaivani, D.; Jayaraman, D.; Joseph, V.

    2016-04-01

    We argue that the crystal 1. L-lysinium succinate (LLMS) (D. Kalaivani et al J. Cryst. Growth 426 (2015) 135-140), 2. Zinc chloride doped lysinium succinate (ZnCl2-Lls) (D. Kalaivani et al. J. Cryst. Growth 428 (2015) 24-28) are not a dubious crystal. EDAX is the primary tool for analyzing the presence of all the elements except lighter elements.

  14. The Behaviors that College Students Classify as Political Bias: Preliminary Findings and Implications

    ERIC Educational Resources Information Center

    Tollini, Craig

    2009-01-01

    There have been a number of recently published books and reports about the existence of a liberal bias in academia (e.g., ACTA 2005, ACTA 2006, Berube 2006, Black 2004, Horowitz 2006, Horowitz 2008, and Shapiro 2004). Sociology is one of the disciplines that is most frequently cited as "producers" of bias in two of these studies (ACTA 2006,…

  15. Reply to the comment by Wu et al. (2016) on "Behavior of Re and Os during contact between an aqueous solution and oil: Consequences for the application of the Re-Os geochronometer to petroleum" [Geochim. Cosmochim. Acta 158 (2015) 1-21

    NASA Astrophysics Data System (ADS)

    Reisberg, Laurie; Michels, Raymond; Mahdaoui, Fatima

    2016-08-01

    We reply here to the questions raised by Wu et al. concerning the results published by Mahdaoui et al. (2015). This paper describes experiments in which aqueous solutions containing ReO4- and OsCl62- were brought in contact with natural oils at various ranges of concentration, time and temperature. The main observation is that the transfer of Re and Os to oils is very efficient under all experimental conditions. Wu et al. argue that thermodynamic equilibrium was not achieved in these experiments as apparent partition coefficients are inconsistent. They conclude that the experiments were flawed by possible leaking of reactors and that the conclusions by Mahdaoui et al. (2015) were not justified. In the following reply we explain that Mahdaoui et al. (2015) never claimed that thermodynamic equilibrium was achieved. Any calculations or considerations in this context are therefore meaningless. We recall the objectives of our publication, which were to experimentally test the behavior of ReO4- and OsCl6- (two plausible chemical forms of Re and Os in deep aquifers of petroleum systems) in aqueous solution-oil systems. To our knowledge these are the first experiments of their kind. The parameters that could influence the precision and reproducibility of our results were discussed in detail in Mahdaoui et al. (2015). The essential point is that all 60 of the experiments provide evidence of substantial transfer of Re and Os from water to oil. In contrast to what was mistakenly understood by Wu et al., the paper does not challenge the use of Re-Os to date geological events affecting petroleum. Instead, by providing a mechanism that might allow Os isotopic homogenization on a basin-wide scale, a critical step missing from most current models, it offers a possible explanation of how Re-Os geochronology in oils could potentially work. More generally, our study suggests that transfer of Re and Os from waters to oil may be an important phenomenon that should not be overlooked.

  16. Comment on "Structural and vibrational studies on 1-(5-Methyl- [1,3,4] thiadiazol-2-yl)-pyrolidin-2-ol" [Spectrochimica Acta Part A, 152 (2016) 252-261]. The importance of intramolecular OH ⋯ N hydrogen bonding in the conformational properties of thiadiazol-pyrrolidin-2-ol bearing species

    NASA Astrophysics Data System (ADS)

    Laurella, Sergio L.; Erben, Mauricio F.

    2016-07-01

    The title paper [1] reports a study on the spectroscopic and physicochemical properties of 1-(5-methyl- [1,3,4]thiadiazol-2-yl)-pyrrolidin-2-ol (MTPN) based on experimental and theoretical data. The latter ones are based on the computed molecular structure for a rather unusual conformer. Here, after a careful analysis of the conformational space of MTPN, the most stable conformation was determined for the molecule isolated in a vacuum, which results to be 21.9 kJ/mol more stable than the conformer reported previously. Our study also includes the closely related species 1-(5-trifluoromethyl- [1,3,4]thiadiazol-2-yl)-pyrrolidin-2-ol (FMTPN). An intramolecular OH ⋯ N hydrogen bond determines the conformational behavior of the [1,3,4]thiadiazol-2-yl)-pyrrolidin-2-ol group as demonstrated by Natural Bond Orbital population analysis.

  17. Guia del Proceso del IFSP de Colorado: Conexiones para la Ninez Temprana, Iniciativa Infantil de Colorado Parte C del Acta de Educacion para Individuos con Desabilidades (Colorado Guidelines for the IFSP Process: Early Childhood Connections, Colorado's Infant/Toddler Initiative for Part C of the Individuals with Disabilities Education Act).

    ERIC Educational Resources Information Center

    Miller, Jerri; Petersen, Sandy

    This booklet for Spanish-speaking parents of young children with disabilities describes Colorado's Individualized Family Service Plan (IFSP) process. It explains guidelines, shares family stories and reflections for families and care providers, and the describes the values that drive the IFSP process in Colorado. Information is provided on…

  18. Comment on "Structural and vibrational studies on 1-(5-Methyl- [1,3,4] thiadiazol-2-yl)-pyrolidin-2-ol" [Spectrochimica Acta Part A, 152 (2016) 252-261]. The importance of intramolecular OH⋯N hydrogen bonding in the conformational properties of thiadiazol-pyrrolidin-2-ol bearing species.

    PubMed

    Laurella, Sergio L; Erben, Mauricio F

    2016-07-01

    The title paper [1] reports a study on the spectroscopic and physicochemical properties of 1-(5-methyl- [1,3,4]thiadiazol-2-yl)-pyrrolidin-2-ol (MTPN) based on experimental and theoretical data. The latter ones are based on the computed molecular structure for a rather unusual conformer. Here, after a careful analysis of the conformational space of MTPN, the most stable conformation was determined for the molecule isolated in a vacuum, which results to be 21.9kJ/mol more stable than the conformer reported previously. Our study also includes the closely related species 1-(5-trifluoromethyl- [1,3,4]thiadiazol-2-yl)-pyrrolidin-2-ol (FMTPN). An intramolecular OH⋯N hydrogen bond determines the conformational behavior of the [1,3,4]thiadiazol-2-yl)-pyrrolidin-2-ol group as demonstrated by Natural Bond Orbital population analysis. PMID:27070529

  19. [Role of Activin A and Myostatin in cancer cachexia].

    PubMed

    Thissen, Jean-Paul; Loumaye, Audrey

    2013-05-01

    Recent works suggest that Activin A (ActA) and Myostatin (Mstn), two members of the TGFβ superfamily, could contribute to skeletal muscle atrophy observed in some cancers. It is known that several human tumoral cell lines synthesize and secrete ActA and Mstn. In addition, systemic treatment with ActA and Mstn in mice induce muscle atrophy. Likewise, Inhibin-α knock-out mice, which are characterized by elevated circulating levels of ActA, exhibit muscle atrophy and die of cachexia. Finally, administration of ActA and Mstn antagonists prevents muscular atrophy and mortality induced by some animal tumors. Collectively, these findings suggest that ActA or Mstn production by several cancers could contribute to cachexia and thus to mortality associated with some cancers in human. This hypothesis is very interesting since new molecules that are able to inhibit ActA and Mstn, in particularly the sActRIIB, are under development. PMID:23566617

  20. Corrosive behavior of chromium carbide-based films formed on steel using a filtered cathodic vacuum arc system

    NASA Astrophysics Data System (ADS)

    Lin, Chun-Chun; Chang, Ku-Ling; Shih, Han C.

    2007-03-01

    The formation of chromium carbide-based hard-coatings on steels using a 90°-bend filtered cathodic vacuum arc (FCVA) has extensive industrial applications; such coatings are free of macroparticles and exhibit excellent characteristics. In this investigation, a working pressure of C 2H 2/Ar was adopted to synthesize amorphous chromium carbide film (a-C:Cr) and crystalline chromium carbide film (cryst-Cr 3C 2) from a Cr target (99.95%) at 500 °C under a substrate voltage of -50 V. The corrosion behavior of a-C:Cr coated on steel (a-C:Cr/steel) and cryst-Cr 3C 2 coated on steel (cryst-Cr 3C 2/steel) were compared in terms of open-circuit potentials (OCP) and polarization resistance ( Rp) in an aerated 3.5 wt% NaCl aqueous solution, as determined by electrochemical impedance spectroscopy (EIS). The XRD results indicated that the transformation of a-C:Cr to cryst-Cr 3C 2 is distinct as the working pressure declines from 1.2 × 10 -2 to 2.9 × 10 -3 Torr. The OCP of a-C:Cr/steel and cryst-Cr 3C 2/steel resemble each other and both assembly are nobler than uncoated steel. The Rp of the coatings exceeds that of the uncoated steel. The SEM observation and the EIS results demonstrate that the cryst-Cr 3C 2/steel more effectively isolates the defects than dose a-C:Cr/steel.

  1. Trinuclear nickel coordination complexes of phenanthrene-9,10-dione dioxime

    PubMed Central

    Williams, Owen M.; Cowley, Alan H.

    2016-01-01

    oriented along the c axis. In the fluorido­boronate structure, the solvent (DCM) was too badly disordered to be modelled, so its contribution was removed using SQUEEZE [Spek (2015 ▸). Acta Cryst. C71, 9–18]. PMID:27375884

  2. Stress-Induced Proton Disorder in Hydrous Ringwoodite

    NASA Astrophysics Data System (ADS)

    Koch-Müller, M.; Rhede, D.; Mrosko, M.; Speziale, S.; Schade, U.

    2008-12-01

    observed up to 30 GPa without any discontinuity and their pressure behaviour (dν/dP) can well be described by linear fits. Molecular vibrations are very sensitive to non-hydrostatic conditions and we interpret the disappearance of the OH-bands as a stress-induced proton disordering in hydrous ringwoodite due to the use of hard pressure transmiting media like CsI or argon without thermal annealing. Thus, our study cannot confirm the phase transition observed by Camorro Perez et al. (2006) in ringwoodite. But as they used Neon as pressure transmitting medium, which is known to become non-hydrostatic at pressure above 16 GPa (Bell and Mao, 1981) we argue that their observation of a sudden disappearance of the OH band may also be related to non-hydrostatic conditions. References Bell P.M. and Mao H.-K. (1981) Carnegie Inst. Wash Yrbk 80: 404-406. Camorro Perez E.M., Daniel I., Chervin J.-C., Dumas P., Bass J.D. and Inoue T. (2006) Phys. Chem. Minerals, 33, 502 - 510. Kudoh Y., Kuribayashi T., Mizohata H., Ohtani E., (2000) Phys. Chem. Mineral. 27, 474-479. Wittlinger J., Fischer R., Wener S., ScheiderJ., Schulz J. (1997) Acta Cryst B53, 745 - 749.

  3. Crystal structure of 4′-{[4-(2,2′:6′,2′′-terpyrid­yl-4′-yl)phen­yl]ethyn­yl}biphenyl-4-yl (2,2,5,5-tetra­methyl-1-oxyl-3-pyrrolin-3-yl)formate benzene 2.5-solvate

    PubMed Central

    Meyer, Andreas; Schnakenburg, Gregor; Schiemann, Olav

    2015-01-01

    ′-terpyridine (3), which has an ethynylphenyl spacer [Meyer et al. (2015). Acta Cryst. E71, 870–874]. PMID:26594417

  4. Trinuclear nickel coordination complexes of phenanthrene-9,10-dione dioxime.

    PubMed

    Williams, Owen M; Cowley, Alan H

    2016-04-01

    the fluorido-boronate structure, the solvent (DCM) was too badly disordered to be modelled, so its contribution was removed using SQUEEZE [Spek (2015 ▸). Acta Cryst. C71, 9-18]. PMID:27375884

  5. XANES and Raman spectrometry on glasses and crystals in the CAS system.

    NASA Astrophysics Data System (ADS)

    Neuville, N.; Cormier, C.; Flank, F.; Massiot, M.

    2003-04-01

    decreasing SiO2, and we interpret this decrease as a substitution of Si by Al in T4 units with other substitution of Si by Al in T3 units. From the Xanes spectra, we observed that : - Al is in tetrahedral site in different Q species in all the CAS system. - Ca is in octahedral site in all the CAS system, with a decrease of the site distorsion with increasing SiO2 content. Finally, the anomalous behavior for the viscosity and glass transition properties in the low silica glasses can be explained by the presence of Al in Q3 species. References : L. Cormier, D.R. Neuville, G. Calas, (2000) J. Non-Cryst. Solids, 274 110-114. NeuvilleD.R. and Mysen B. (1996). Geochim. Cosmochim. Acta., 60, 1727-1737.

  6. Effects of Hydrophile-Lypophile Balance of Emulsifier on Electrooptical Properties and Morphology of Poly(vinylalcohol)/Liquid Crystal Composite

    NASA Astrophysics Data System (ADS)

    Ono, Hiroshi; Kawatsuki, Nobuhiro

    1995-12-01

    We clarified the relationship between the morphology of a poly(vinyl alcohol) (PVA)/liquid crystal (LC) composite film fabricated by an emulsification method and a hydrophile-lypophile balance (HLB) of an emulsifier. The LC domain size was affected by the surface tension of the PVA aqueous solution and of the LC. The surface tension of the PVA aqueous solution and the LC was varied by changing the HLB value. The electrooptical properties, such as threshold voltage and response time, were strongly dependent on the LC droplet size, in good qualitative agreement with results obtained using the equations of Doane et al. [Mol. Cryst. Liq. Cryst. 5 (1989) 1453].

  7. Creativity and Democratic Governance. Adult Learning: A Strategic Choice. Proceedings of the ICAE World Assembly (6th, Ocho Rios, Jamaica, August 9-12, 2001) = Creativite et Gouvernance Democratique. L'apprentissage des Adultes: Un Choix Strategique. Actes de la Assemblee Mondiale du CIEA (6th, Ocho Rios, Jamaique, 9 au 12 aout 2001) = Creatividad y Gobernabilidad Democratica. Educacion de Adultos: Una Eleccion Estrategica. Actas de la Asamblea Mundial del ICAE (6th, Ocho Rios, Jamaica, Agosto 9-12, 2001).

    ERIC Educational Resources Information Center

    Dobson, Stephan, Ed.

    This document contains information from and about a world assembly on creativity and democratic governance in adult learning that was held by the International Council for Adult Education (ICAE) and its partner organizations in the Caribbean. The proceedings begin with English, French, and Spanish translations of the address…

  8. A multi-scale micromechanics framework for shale using the nano-tools

    NASA Astrophysics Data System (ADS)

    Ortega, J.; Ulm, F.; Abousleiman, Y.

    2009-12-01

    . A., Ulm, F.-J., Abousleiman, Y. (2009) ‘The nanogranular acoustic signature of shale.’ Geophysics 74(3), D65-D84. Fig. 1. Comparisons between predicted and experimental elasticity obtained from nanoindentation experiments (left) and acoustic measurements (right) for shale with and without organic content (hollow and solid data points). Nanoindentation elasticity of the porous clay in shale is presented as a function of the clay packing density (one minus the nanoporosity). The x-1, x-3 directions correspond to parallel and normal-to-bedding plane properties, respectively. All nanoindentation data and acoustic measurements for organic-rich shale from [2-3]. Acoustic measurements for organic-free shale were gathered from literature sources compiled in [3].

  9. Properties of thermoplastic starch and TPS/polycaprolactone blend reinforced with sisal whiskers using extrusion processing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sisal whiskers (SW) were prepared by acid hydrolysis for subsequent evaluation as reinforcing material for biodegradable matrices of thermoplastic starch (TPS) and TPS/polycaprolactone (TPS/PCL) blends. The acid hydrolyzed SW had dimensions of 5±2 nm in diameter and 210±60 nm in length and 78% cryst...

  10. Silver catalysts in the partial oxidation of methanol to formaldehyde

    SciTech Connect

    Devochkin, A.N.; Pestryakov, A.N.; Kurina, L.N.; Sakharov, A.A.

    1992-07-20

    A comparative study of the catalytic activity of supported (Ag/pumice, LNKh-M) and bulk (Ag{sub cryst}, SD, KS) catalysts for methanol oxidation was carried out. The effect of technological parameters on the partial oxidation of methanol was studied. The optimum conditions for conducting the process on the catalysts studied were determined. 5 refs., 1 tab.

  11. Arsenic Sorption on TiO2 Nanoparticles: Size And Crystallinity Effects

    EPA Science Inventory

    Single solute As (III) and As (V) sorption on nano-sized amorphous and crystalline TiO2 was investigated to determine: size and crystallinity effects on arsenic sorption capacities, possible As (III) oxidation, and the nature of surface complexes. Amorphous and cryst...

  12. Spectroscopic characterisation of biological vaterite: relations to synthetic and geological vaterites

    NASA Astrophysics Data System (ADS)

    Jacob, D. E.; Wehrmeister, U.; Soldati, A. L.; Hofmeister, W.

    2009-04-01

    band ?1 into three distinct bands, activation and splitting of ?2 and splitting of both, ?3 and ?4 into six distinct Raman bands. FWHMs of the lattice modes are large (8 cm-1- 44 cm-1) compared to those of aragonite, implying that the structure is not well ordered and possibly affected by stacking faults, layer shifts or syntactic intergrowth; irregularities that further complicate the crystal structure determination. Correlation of Mg-contents in vaterite areas in freshwater cultured pearls with Raman spectra obtained at the same spots show that the FWHMs are influenced by the magnesium content. Similarly, the spectra for the vaterite samples synthesized with differing Mg contents show successively increasing FWHM with increasing magnesium content both for the lattice modes and the ?1 - symmetric stretching mode. Wehrmeister et al., 2007. J. Gemmology; 31: 269-276, Falini et al., 2005. Eur. J. Inorg. Chem. 2005(1): 162 -167, Meyer, H. 1969. Angew. Chem. 21: 678-679, Kamhi, S., 1963. Acta Cryst. (1963).16: 770 - 772, Meyer, H., 1969. Z. Kristallographie 128: 183 - 212, Lippmann, F., 1973. New York, Springer, Soldati et al., 2008. Min. Mag. 72: 577- 590, Jacob et al., 2008. Geochim. Cosmochim. Acta 72: 5401- 5415, Loges et al., 2006. Langmuir 22: 3073-3080.

  13. The Vanishing Shakespeare: A Report by the American Council of Trustees and Alumni

    ERIC Educational Resources Information Center

    Neal, Anne D.; Mitchell, Charles

    2007-01-01

    As this report goes to press, the nation's capital is in the midst of a six-moth, city-wide celebration of William Shakespeare. With this celebration as a backdrop, the American Council of Trustees and Alumni (ACTA) researched how Shakespeare fits into English curricula at 70 of the nation's leading colleges and universities. ACTA surveyed English…

  14. Genetics Home Reference: paramyotonia congenita

    MedlinePlus

    ... impact of permanent muscle weakness on quality of life in periodic paralysis: a survey of 66 patients. Acta Myol. 2012 Oct;31(2):126-33. Citation on PubMed or Free article on PubMed Central Finsterer J. Primary periodic paralyses. Acta Neurol Scand. 2008 Mar;117(3):145-58. Epub 2007 Nov 20. ...

  15. Leading the Charge: Governors, Higher Education and Accountability

    ERIC Educational Resources Information Center

    American Council of Trustees and Alumni, 2014

    2014-01-01

    With this new tool, ACTA [American Council of Trustees and Alumni] is working to expand its outreach to governors nationwide on behalf of higher education reform, focusing on key issues of quality, cost, and accountability. ACTA has worked with governors and education leaders from across the country, and that experience has proven that innovative…

  16. NMR Study on Ion Dynamics and Phase Behavior of a Piperidinium-Based Room-Temperature Ionic Liquid: 1-Butyl-1-methylpiperidinium Bis(fluorosulfonyl)amide.

    PubMed

    Shimizu, Yuichi; Wachi, Yuto; Fujii, Kozo; Imanari, Mamoru; Nishikawa, Keiko

    2016-06-30

    By use of pulse NMR methods, the temperature dependences of the longitudinal and transverse relaxation times for (1)H and (19)F were measured for the three phases of 1-butyl-1-methylpiperidinium bis(fluorosulfonyl)amide ([Pip1,4][FSA]), i.e., liquid or supercooled liquid, Cryst-α, and Cryst-β, to investigate the ion dynamics and phase behavior related to the dynamics. Since the cations and anions in the room-temperature ionic liquid have (1)H and (19)F nuclei, respectively, the dynamics of the [Pip1,4] cation and [FSA] anion can be independently observed and the relation between them can be evaluated. The relevant local motions of the ions are fluctuational motion around the chair form of the piperidinium ring, libration or rotation of the alkyl groups, and libration or rotation of the SO2F groups around the N-S axes. Each phase preferentially exhibits these motions. In the Cryst-β phase, it is thought that O atoms in the SO2F groups form strong hydrogen bonds with the H atoms in the piperidinium ring. As a result, the motions of the SO2F groups and the piperidinium ring are restricted. In the liquid or supercooled liquid states and Cryst-α phase, the motion of the anion is more significant than that of the cation and the former works as a trigger for phase changes. Particularly, the motion of the SO2F groups in the Cryst-α phase becomes very significant with rising temperature and is directly related to the melting phase transition. PMID:27281062

  17. High circulating activin A level is associated with tumor progression and predicts poor prognosis in lung adenocarcinoma

    PubMed Central

    Hoda, Mir Alireza; Rozsas, Anita; Lang, Elisabeth; Klikovits, Thomas; Lohinai, Zoltan; Torok, Szilvia; Berta, Judit; Bendek, Matyas; Berger, Walter; Hegedus, Balazs; Klepetko, Walter; Renyi-Vamos, Ferenc; Grusch, Michael; Dome, Balazs; Laszlo, Viktoria

    2016-01-01

    Activin A (ActA)/follistatin (FST) signaling has been shown to be deregulated in different tumor types including lung adenocarcinoma (LADC). Here, we report that serum ActA protein levels are significantly elevated in LADC patients (n=64) as compared to controls (n=46, p=0.015). ActA levels also correlated with more advanced disease stage (p<0.0001) and T (p=0.0035) and N (p=0.0002) factors. M1 patients had significantly higher ActA levels than M0 patients (p<0.001). High serum ActA level was associated with poor overall survival (p<0.0001) and was confirmed as an independent prognostic factor (p=0.004). Serum FST levels were increased only in female LADC patients (vs. female controls, p=0.031). Two out of five LADC cell lines secreted biologically active ActA, while FST was produced in all of them. Transcripts of both type I and II ActA receptors were detected in all five LADC cell lines. In conclusion, our study does not only suggest that measuring blood ActA levels in LADC patients might improve the prediction of prognosis, but also indicates that this parameter might be a novel non-invasive biomarker for identifying LADC patients with organ metastases. PMID:26950277

  18. Serial femtosecond crystallography datasets from G protein-coupled receptors.

    PubMed

    White, Thomas A; Barty, Anton; Liu, Wei; Ishchenko, Andrii; Zhang, Haitao; Gati, Cornelius; Zatsepin, Nadia A; Basu, Shibom; Oberthür, Dominik; Metz, Markus; Beyerlein, Kenneth R; Yoon, Chun Hong; Yefanov, Oleksandr M; James, Daniel; Wang, Dingjie; Messerschmidt, Marc; Koglin, Jason E; Boutet, Sébastien; Weierstall, Uwe; Cherezov, Vadim

    2016-01-01

    We describe the deposition of four datasets consisting of X-ray diffraction images acquired using serial femtosecond crystallography experiments on microcrystals of human G protein-coupled receptors, grown and delivered in lipidic cubic phase, at the Linac Coherent Light Source. The receptors are: the human serotonin receptor 2B in complex with an agonist ergotamine, the human δ-opioid receptor in complex with a bi-functional peptide ligand DIPP-NH2, the human smoothened receptor in complex with an antagonist cyclopamine, and finally the human angiotensin II type 1 receptor in complex with the selective antagonist ZD7155. All four datasets have been deposited, with minimal processing, in an HDF5-based file format, which can be used directly for crystallographic processing with CrystFEL or other software. We have provided processing scripts and supporting files for recent versions of CrystFEL, which can be used to validate the data. PMID:27479354

  19. Crystallographic data processing for free-electron laser sources

    SciTech Connect

    White, Thomas A. Barty, Anton; Stellato, Francesco; Holton, James M.; Kirian, Richard A.; Zatsepin, Nadia A.; Chapman, Henry N.

    2013-07-01

    A processing pipeline for diffraction data acquired using the ‘serial crystallography’ methodology with a free-electron laser source is described with reference to the crystallographic analysis suite CrystFEL and the pre-processing program Cheetah. A processing pipeline for diffraction data acquired using the ‘serial crystallography’ methodology with a free-electron laser source is described with reference to the crystallographic analysis suite CrystFEL and the pre-processing program Cheetah. A detailed analysis of the nature and impact of indexing ambiguities is presented. Simulations of the Monte Carlo integration scheme, which accounts for the partially recorded nature of the diffraction intensities, are presented and show that the integration of partial reflections could be made to converge more quickly if the bandwidth of the X-rays were to be increased by a small amount or if a slight convergence angle were introduced into the incident beam.

  20. Serial femtosecond crystallography datasets from G protein-coupled receptors

    PubMed Central

    White, Thomas A.; Barty, Anton; Liu, Wei; Ishchenko, Andrii; Zhang, Haitao; Gati, Cornelius; Zatsepin, Nadia A.; Basu, Shibom; Oberthür, Dominik; Metz, Markus; Beyerlein, Kenneth R.; Yoon, Chun Hong; Yefanov, Oleksandr M.; James, Daniel; Wang, Dingjie; Messerschmidt, Marc; Koglin, Jason E.; Boutet, Sébastien; Weierstall, Uwe; Cherezov, Vadim

    2016-01-01

    We describe the deposition of four datasets consisting of X-ray diffraction images acquired using serial femtosecond crystallography experiments on microcrystals of human G protein-coupled receptors, grown and delivered in lipidic cubic phase, at the Linac Coherent Light Source. The receptors are: the human serotonin receptor 2B in complex with an agonist ergotamine, the human δ-opioid receptor in complex with a bi-functional peptide ligand DIPP-NH2, the human smoothened receptor in complex with an antagonist cyclopamine, and finally the human angiotensin II type 1 receptor in complex with the selective antagonist ZD7155. All four datasets have been deposited, with minimal processing, in an HDF5-based file format, which can be used directly for crystallographic processing with CrystFEL or other software. We have provided processing scripts and supporting files for recent versions of CrystFEL, which can be used to validate the data. PMID:27479354

  1. tert-Butyl 3-oxo-2-oxa-5-aza­bicyclo­[2.2.1]heptane-5-carboxyl­ate

    PubMed Central

    Lechner, Marie-Charlotte; Aubert, Emmanuel; Guichard, Gilles; Didierjean, Claude

    2008-01-01

    The title compound, C10H15NO4, also known as N-tert-butyl­oxycarbonyl-allohydr­oxy-l-proline lactone, is quite similar to N-acetyl-allohydr­oxy-l-proline lactone [Lenstra, Petit & Geise (1979 ▶). Cryst. Struct. Commun. 8, 1023–1029], whereby both carbonyl groups point roughly in the same direction because of the trans conformation of the peptide bond. PMID:21201231

  2. USING BIOMONITORING DATA TO INFORM EXPOSURE ASSESSMENT IN CHILDREN

    EPA Science Inventory

    Discussing the challenges associated with estimating and interpreting toxicant exposures and health risks from biomonitoring data. Extended abstract will also be translated in Spanish and published in Acta Toxicologica Argentina.

  3. Uso de los Datos de Biomonitoreo para Informar sobre la Evaluacion Infantil (American translation is: USING BIOMONITORING DATA TO INFORM EXPOSURE ASSESSMENT IN CHILDREN)

    EPA Science Inventory

    Discussing the challenges associated with estimating and interpreting toxicant exposures and health risks from biomonitoring data. This extended abstract was translated in Spanish and published in Acta Toxicologica Argentina.

  4. Genetics Home Reference: glucose-galactose malabsorption

    MedlinePlus

    ... mutations in SGLT1 cause glucose-galactose malabsorption by trafficking defects. Biochim Biophys Acta. 1999 Feb 24;1453( ... Accessibility FOIA Viewers & Players U.S. Department of Health & Human Services National Institutes of Health National Library of ...

  5. Genetics Home Reference: myosin storage myopathy

    MedlinePlus

    ... proteins accumulate in type I skeletal muscle fibers, forming the protein clumps characteristic of the disorder. It ... Epub 2007 Mar 2. Citation on PubMed Tajsharghi H, Oldfors A. Myosinopathies: pathology and mechanisms. Acta Neuropathol. ...

  6. Genetics Home Reference: oculopharyngeal muscular dystrophy

    MedlinePlus

    ... advances in the understanding of the molecular pathogenic mechanisms and treatment strategies. Biochim Biophys Acta. 2007 Feb; ... further evidence for unequal recombination as the mutational mechanism. Hum Genet. 2005 Mar;116(4):267-71. ...

  7. VISIÓN GENERAL DE LA EVALUACIÓN DEL RIESGO EN SALUD INFANTIL EMPLEANDO UN ENFOQUE POR ETAPAS DE DESARROLLO (American translation is: Overview of a Life Stage Approach to Children's Health Risk Assessment)

    EPA Science Inventory

    Discussing the challenges associated with estimating and interpreting toxicant exposures and health risks from biomonitoring data. This extended abstract was translated in Spanish and published in Acta Toxicologica Argentina.

  8. 75 FR 79069 - Anti-Counterfeiting Trade Agreement: Request for Comments From the Public

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-17

    ... practices. Together these provisions will help to protect American jobs in innovative and creative... business confidential information, the filer should type ``ACTA Comments--Business Confidential'' in the ``Type Comment & Upload file'' field. Any page containing business confidential information must...

  9. Serial crystallographic analysis of protein isomorphous replacement data from a mixture of native and derivative microcrystals.

    PubMed

    Zhang, Tao; Yao, Deqiang; Wang, Jiawei; Gu, Yuanxin; Fan, Haifu

    2015-12-01

    A post-experimental identification/purification procedure similar to that described in Zhang et al. [(2015), IUCrJ, 2, 322-326] has been proposed for use in the treatment of multiphase protein serial crystallography (SX) diffraction snapshots. As a proof of concept, the procedure was tested using theoretical serial femtosecond crystallography (SFX) data from a mixture containing native and derivatized crystals of a protein. Two known proteins were taken as examples. Multiphase diffraction snapshots were subjected to two rounds of indexing using the program CrystFEL [White et al. (2012). J. Appl. Cryst. 45, 335-341]. In the first round, an ab initio indexing was performed to derive a set of approximate primitive unit-cell parameters, which are roughly the average of those from the native protein and the derivative. These parameters were then used in a second round of indexing as input to CrystFEL. The results were then used to separate the diffraction snapshots into two subsets corresponding to the native and the derivative. For each test sample, integration of the two subsets of snapshots separately led to two sets of three-dimensional diffraction intensities, one belonging to the native and the other to the derivative. Based on these two sets of intensities, a conventional single isomorphous replacement (SIR) procedure solved the structure easily. PMID:26627658

  10. Biocompatibility of core@shell particles: cytotoxicity and genotoxicity in human osteosarcoma cells of colloidal silica spheres coated with crystalline or amorphous zirconia.

    PubMed

    Di Virgilio, A L; Arnal, P M; Maisuls, I

    2014-08-01

    The cytotoxicity and genotoxicity of novel colloidal silica spheres coated with crystalline or amorphous zirconia (SiO2@ZrO2(cryst) or SiO2@ZrO2(am)) have been studied in a human osteosarcoma cell line (MG-63), after 24 h exposure. SiO2@ZrO2(cryst) and SiO2@ZrO2(am) had mean diameters of 782±19 and 891±34 nm, respectively. SiO2@ZrO2(cryst) exposure reduced cell viability, with an increase in reactive oxygen species (ROS) and a decrease of the GSH/GSSG ratio. The comet and micronucleus (MN) assays detected DNA damage at 5 and 25 μg/mL, respectively. SiO2@ZrO2(am) induced genotoxic action only at 10 and 50 μg/mL (comet and MN assays), along with a decrease of the GSH/GSSG ratio at 50 μg/mL. Both particles were found inside the cells, forming vesicles; however, none of them entered the nucleus. Our findings show that crystallization of the shell of the amorphous ZrO2 increases both cytotoxicity and genotoxicity. PMID:25344169

  11. Termochemical Models For Slags and Silicate Melts, Review and Perspectives

    NASA Astrophysics Data System (ADS)

    Ottonello, G.

    R.O. (1983) Contrib. Mineral. Petrol., 84, 107-145. [3] Papale P. (1997) Contrib. Mineral. Petrol., 126, 237-251. [4] Papale P. (1999) Amer. Mineral., 84, 477-492. [5] Nuccio P.M. and Paonita A. (2999) Earth Planet. Sci. Letters., 183, 499-512. [6] Berman R.G. and Brown T.H. (1984) Geochim. Cosmochim. Acta, 48, 661-678. [7] Lin P.L. and Pelton A.D. (1979) Metall. Trans. B., 10B, 667-675. [8] Pelton A.D. and Blander M. (1986) Metall. Trans. B., 17B, 805-15. [9] Kapoor M.L., Mehrotre G.M. and Frohberg M.G. (1975) Proc. Aust. Inst. Mining Metall., 254, 11. [10] Kapoor M.L., Frohberg G.M. (1971) Proc. Symp. "Chemical Metallurgy of Iron and Steel" Sheffield. [11] Taylor J.R. and Dinsdale A.T. (1990] CALPHAD, 14, 71-88. [12] Sastri P. and Lahiri A.K. (1986) Metall. Trans. B., 17B, 105-110. [13] Bjorkman B. (1985) CALPHAD, 9, 271-282. [14] Hastie J.W., Horton W.S., Plante E.R. and Bonnell D.W. (1982) High Temp. High Press., 14, 669-679. [15] Goel R.P., Kellogg H.H. and Larrain J.M. (1980) Metall. Trans. B., 11B, 107-117. [16] Hillert M., Sundman B. and Wang X. (1990) Metall. Trans. B., 21B, 303-12. [17] Hoch M. and Arpshofen I. (1984) Zeits. fur Metallkde., 75, 23-29. [18] Masson C.R. (1965) Proc. Roy. Soc. London, A287, 201-221. [19] Masson C.R. (1968) J. Amer. Ceram. Soc., 51, 134-143. [20] Masson C.R. (1972) Jour. Iron Steel Inst., 210, 89-96. [21] Toop G.W. and Samis C.S. (1962) Can. Met. Quart., 1, 129-52. [22] Toop G.W. and Samis C.S. (1962) Trans. AIME, 224, 878-87. [23] Ottonello G., Moretti R., Marini L. and Vetuschi Zuccolini M. (2000) Chem. Geol., 174, 157-179. [24] Ottonello G. (2001) J. Non-Cryst. Solids, 282, 72-85. [25] Moretti R. and Ottonello G. (2002) , Metall. Trans. (submitted).

  12. Precise detection of L. monocytogenes hitting its highly conserved region possessing several specific antibody binding sites.

    PubMed

    Jahangiri, Abolfazl; Rasooli, Iraj; Reza Rahbar, Mohammad; Khalili, Saeed; Amani, Jafar; Ahmadi Zanoos, Kobra

    2012-07-21

    Listeria monocytogenes, a facultative intracellular fast-growing Gram-positive food-borne pathogen, can infect immunocompromised individuals leading to meningitis, meningoencephalitis and septicaemias. From the pool of virulence factors of the organism, ActA, a membrane protein, has a critical role in the life cycle of L. monocytogenes. High mortality rate of listeriosis necessitates a sensitive and rapid diagnostic test for precise identification of L. monocytogenes. We used bioinformatic tools to locate a specific conserved region of ActA for designing and developing an antibody-antigen based diagnostic test for the detection of L. monocytogenes. A number of databases were looked for ActA related sequences. Sequences were analyzed with several online software to find an appropriate region for our purpose. ActA protein was found specific to Listeria species with no homologs in other organisms. We finally introduced a highly conserved region within ActA sequence that possess several antibody binding sites specific to L. monocytogenes. This protein sequence can serve as an antigen for designing a relatively cheap, sensitive, and specific diagnostic test for detection of L. monocytogenes. PMID:22575546

  13. Quantification and handling of nonlinearity in Raman micro-spectrometry of pharmaceuticals.

    PubMed

    Nagy, Brigitta; Farkas, Attila; Balogh, Attila; Pataki, Hajnalka; Vajna, Balázs; Nagy, Zsombor K; Marosi, György

    2016-09-01

    This work demonstrates how nonlinearity in Raman spectrometry of pharmaceuticals can be handled and accurate quantification can be achieved by applying certain chemometric methods including variable selection. Such approach proved to be successful even if the component spectra are very similar or spectral intensities of the constituents are strongly different. The relevant examples are: blends of two crystalline forms of carvedilol ("CRYST-PM" blend) and a three-component pharmaceutical model system ("PHARM-TM" blend). The widely used classical least squares regression (CLS) and partial least squares regression (PLS) quantification methods provided relatively poor root mean squared error of prediction (RMSEP) values: approximately 2-4% and 4-10% for CRYST-PM and PHARM-TM respectively. The residual plots of these models indicated the nonlinearity of the preprocessed data sets. More accurate quantitative results could be achieved with properly applied variable selection methods. It was observed that variable selection methods discarded the most intensive bands while less intensive ones were retained as the most informative spectral ranges. As a result not only the accuracy of concentration determination was enhanced, but the linearity of models was improved as well. This indicated that nonlinearity occurred especially at the intensive spectral bands. Other methods developed for handling nonlinearity were also capable of adapting to the spectral nature of both data sets. The RMSEP could be decreased this way to 1% in CRYST-PM and 3-6% in PHARM-TM. Raman maps with accurate real concentrations could be prepared this way. All quantitative models were compared by the non-parametric sum of ranking differences (SRD) method, which also proved that models based on variable selection or nonlinear methods provide better quantification. PMID:27281579

  14. Textures on the surface of BSA films with different concentrations of sodium halides and water state in solution

    NASA Astrophysics Data System (ADS)

    Glibitskiy, Gennadiy; Glibitskiy, Dmitriy; Gorobchenko, Olga; Nikolov, Oleg; Roshal, Alexander; Semenov, Mikhail; Gasan, Anatoliy

    2015-03-01

    The formation of the textures on the surface of the films from the solutions of bovine serum albumin (BSA) with sodium halides (NaF, NaCl, and NaBr) of various concentrations was studied. The formation of symmetric zigzag textures on the surface of BSA films (Cryst Eng 3:173-194, 2000) in the presence of sodium halides depends on the conformational state of the protein globule. Thermal denaturation of BSA also did not allow to form zigzag textures on the surface of the films.

  15. A survey of chemical information systems

    NASA Technical Reports Server (NTRS)

    Dominick, Wayne D. (Editor); Shaikh, Aneesa Bashir

    1985-01-01

    A survey of the features, functions, and characteristics of a fairly wide variety of chemical information storage and retrieval systems currently in operation is given. The types of systems (together with an identification of the specific systems) addressed within this survey are as follows: patents and bibliographies (Derwent's Patent System; IFI Comprehensive Database; PULSAR); pharmacology and toxicology (Chemfile; PAGODE; CBF; HEEDA; NAPRALERT; MAACS); the chemical information system (CAS Chemical Registry System; SANSS; MSSS; CSEARCH; GINA; NMRLIT; CRYST; XTAL; PDSM; CAISF; RTECS Search System; AQUATOX; WDROP; OHMTADS; MLAB; Chemlab); spectra (OCETH; ASTM); crystals (CRYSRC); and physical properties (DETHERM). Summary characteristics and current trends in chemical information systems development are also examined.

  16. Pretilt angle effects on critical voltage and dynamic response of pi cell

    NASA Astrophysics Data System (ADS)

    Sun, Yubao; Ma, Hongmei; Li, Zaidong; Zhang, Zhidong; Guan, Ronghua

    2007-02-01

    The critical voltage with an arbitrary pretilt angle is given analytically which is consistent with the numerical results [Acosta et al., Liq. Cryst. 27, 977 (2000)]. The author's results show that the critical voltage is dependent on the parameters of liquid crystal and pretilt angle but is independent of the cell gap. By numerical simulation the authors find that the on time of pi cell decreases with the increasing pretilt at the same voltage, and the off time of the cell driven by the undershoot method is much faster than that of the normal driven method for the cell with nonzero critical voltage.

  17. Modulating myosin restores muscle function in a mouse model of nemaline myopathy

    PubMed Central

    Lindqvist, Johan; Levy, Yotam; Pati‐Alam, Alisha; Hardeman, Edna C.; Gregorevic, Paul

    2016-01-01

    Objective Nemaline myopathy, one of the most common congenital myopathies, is associated with mutations in various genes including ACTA1. This disease is also characterized by various forms/degrees of muscle weakness, with most cases being severe and resulting in death in infancy. Recent findings have provided valuable insight into the underlying pathophysiological mechanisms. Mutations in ACTA1 directly disrupt binding interactions between actin and myosin, and consequently the intrinsic force‐generating capacity of muscle fibers. ACTA1 mutations are also associated with variations in myofiber size, the mechanisms of which have been unclear. In the present study, we sought to test the hypotheses that the compromised functional and morphological attributes of skeletal muscles bearing ACTA1 mutations (1) would be directly due to the inefficient actomyosin complex and (2) could be restored by manipulating myosin expression. Methods We used a knockin mouse model expressing the ACTA1 His40Tyr actin mutation found in human patients. We then performed in vivo intramuscular injections of recombinant adeno‐associated viral vectors harboring a myosin transgene known to facilitate muscle contraction. Results We observed that in the presence of the transgene, the intrinsic force‐generating capacity was restored and myofiber size was normal. Interpretation This demonstrates a direct link between disrupted attachment of myosin molecules to actin monomers and muscle fiber atrophy. These data also suggest that further therapeutic interventions should primarily target myosin dysfunction to alleviate the pathology of ACTA1‐related nemaline myopathy. Ann Neurol 2016;79:717–725 PMID:26891371

  18. Scientometric Analysis of the Journals of the Academy of Medical Sciences in Bosnia and Herzegovina

    PubMed Central

    Masic, Izet; Begic, Edin; Zunic, Lejla

    2016-01-01

    Introduction: Currently in Bosnia and Herzegovina there are 25 journals in the field of biomedicine, 6 of them are indexed in Medline/PubMed base (Medical Archives, Materia Socio-Medica, Acta Informatica Medica, Acta Medica Academica, Bosnian Journal of Basic Medical Sciences (BJBMS) and Medical Glasnik), and one (BJBMS) is indexed in Science Citation Index Expanded (SCIE)/Web of Science base. Aim: The aim of this study was to show the scope of work of the journals that were published by Academy of Medical Sciences of Bosnia and Herzegovina - Medical Archives, Materia Socio-Medica and Acta Informatica Medica. Material and Methods: The research presents a meta-analysis of three journals, or their issues, during the calendar year 2015 (retrospective and descriptive character). Results: During 2015 calendar year a total of 286 articles were published (in Medical Archives 104 (36.3%), in Materia Socio-Medica 99 (34.6%), and in Acta Informatica Medica 83 (29%)). Original articles are present in the highest number in all three journals (in Medical Archives 80.7%, in Materia Socio Medica 77.7%, and in Acta Informatica Medica 68.6%). In Medical Archives, 90.3% of the articles were related to the field of clinical medicine. In Materia Socio-Medica, the domain of clinical medicine and public health was the most represented. Preclinical areas are most frequent in Acta Informatica Medica. The period of 50-60 days for a decision on the admission of article is most common in all three journals, with trend of shortening of that period. Articles came from 19 countries, mostly from Bosnia and Herzegovina, then from Iran, Kosovo, Saudi Arabia and Greece. Conclusion: In Medical Archives original articles in the field of clinical medicine (usually internal and surgical disciplines) are most often present, and that is the case in last four years. The number of articles in Materia Socio-Medica and Acta Informatica Medica is growing from year to year. In Materia Socio-Medica there is a

  19. An In Vivo Selection Identifies Listeria monocytogenes Genes Required to Sense the Intracellular Environment and Activate Virulence Factor Expression

    PubMed Central

    Portnoy, Daniel A.

    2016-01-01

    Listeria monocytogenes is an environmental saprophyte and facultative intracellular bacterial pathogen with a well-defined life-cycle that involves escape from a phagosome, rapid cytosolic growth, and ActA-dependent cell-to-cell spread, all of which are dependent on the master transcriptional regulator PrfA. The environmental cues that lead to temporal and spatial control of L. monocytogenes virulence gene expression are poorly understood. In this study, we took advantage of the robust up-regulation of ActA that occurs intracellularly and expressed Cre recombinase from the actA promoter and 5’ untranslated region in a strain in which loxP sites flanked essential genes, so that activation of actA led to bacterial death. Upon screening for transposon mutants that survived intracellularly, six genes were identified as necessary for ActA expression. Strikingly, most of the genes, including gshF, spxA1, yjbH, and ohrA, are predicted to play important roles in bacterial redox regulation. The mutants identified in the genetic selection fell into three broad categories: (1) those that failed to reach the cytosolic compartment; (2) mutants that entered the cytosol, but failed to activate the master virulence regulator PrfA; and (3) mutants that entered the cytosol and activated transcription of actA, but failed to synthesize it. The identification of mutants defective in vacuolar escape suggests that up-regulation of ActA occurs in the host cytosol and not the vacuole. Moreover, these results provide evidence for two non-redundant cytosolic cues; the first results in allosteric activation of PrfA via increased glutathione levels and transcriptional activation of actA while the second results in translational activation of actA and requires yjbH. Although the precise host cues have not yet been identified, we suggest that intracellular redox stress occurs as a consequence of both host and pathogen remodeling their metabolism upon infection. PMID:27414028

  20. An In Vivo Selection Identifies Listeria monocytogenes Genes Required to Sense the Intracellular Environment and Activate Virulence Factor Expression.

    PubMed

    Reniere, Michelle L; Whiteley, Aaron T; Portnoy, Daniel A

    2016-07-01

    Listeria monocytogenes is an environmental saprophyte and facultative intracellular bacterial pathogen with a well-defined life-cycle that involves escape from a phagosome, rapid cytosolic growth, and ActA-dependent cell-to-cell spread, all of which are dependent on the master transcriptional regulator PrfA. The environmental cues that lead to temporal and spatial control of L. monocytogenes virulence gene expression are poorly understood. In this study, we took advantage of the robust up-regulation of ActA that occurs intracellularly and expressed Cre recombinase from the actA promoter and 5' untranslated region in a strain in which loxP sites flanked essential genes, so that activation of actA led to bacterial death. Upon screening for transposon mutants that survived intracellularly, six genes were identified as necessary for ActA expression. Strikingly, most of the genes, including gshF, spxA1, yjbH, and ohrA, are predicted to play important roles in bacterial redox regulation. The mutants identified in the genetic selection fell into three broad categories: (1) those that failed to reach the cytosolic compartment; (2) mutants that entered the cytosol, but failed to activate the master virulence regulator PrfA; and (3) mutants that entered the cytosol and activated transcription of actA, but failed to synthesize it. The identification of mutants defective in vacuolar escape suggests that up-regulation of ActA occurs in the host cytosol and not the vacuole. Moreover, these results provide evidence for two non-redundant cytosolic cues; the first results in allosteric activation of PrfA via increased glutathione levels and transcriptional activation of actA while the second results in translational activation of actA and requires yjbH. Although the precise host cues have not yet been identified, we suggest that intracellular redox stress occurs as a consequence of both host and pathogen remodeling their metabolism upon infection. PMID:27414028

  1. Structures of complexes of octahaem cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens with sulfite and cyanide.

    PubMed

    Trofimov, Anton A; Polyakov, Konstantin M; Boyko, Konstantin M; Tikhonova, Tamara V; Safonova, Tatyana N; Tikhonov, Alexey V; Popov, Alexandre N; Popov, Vladimir O

    2010-10-01

    The structures of complexes of octahaem cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens (TvNiR) with the substrate sulfite (1.4 Å resolution; R(cryst) = 0.126) and the inhibitor cyanide (1.55 Å resolution; R(cryst) = 0.148) have been established. The complex with sulfite was prepared by the reduction of the protein crystal with sodium dithionite. The sulfite ion is bound to the iron ion of the catalytic haem through the S atom. The Fe-S distance is 2.24 Å. The structure of the cyanide complex with full occupancy of the ligand site was established for the first time for cytochrome c nitrite reductases. The cyanide ion is bound to the catalytic haem iron through the C atom. The Fe-C distance is 1.91 Å and the Fe-C-N angle is 171°. The sulfite reductase activity of TvNiR was measured at different pH values. The activity is 0.02 µmol of HS(-) per minute per milligram at pH 7.0; it decreases with increasing pH and is absent at pH 9.0. PMID:20944237

  2. Education or Reputation? A Look at America's Top-Ranked Liberal Arts Colleges

    ERIC Educational Resources Information Center

    Poliakoff, Michael; Alacbay, Armand

    2014-01-01

    ACTA [American Council of Trustees and Alumni] today released a report that examines the country's most prestigious liberal arts colleges. Despite endowments soaring as high as $1.8 billion, nearly all institutions increased tuition during the Great Recession to finance bloated administrative spending, with many college presidents enjoying…

  3. Experiences of a local arrangement committee for a large scientific conference

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This paper is an an invited condensation of a paper that appeared in Acta. Hort. 745: 513-532 last year. It describes the history and organization of the combined meeting of the 90th Annual Meeting of the Potato Association of America, the VI International Solanaceae Conference, and the III Solanace...

  4. Erratum to: Vascular endothelial growth factor induces contralesional corticobulbar plasticity and functional neurological recovery in the ischemic brain.

    PubMed

    Reitmeir, Raluca; Kilic, Ertugrul; Reinboth, Barbara S; Guo, Zeyun; ElAli, Ayman; Zechariah, Anil; Kilic, Ülkan; Hermann, Dirk M

    2015-10-01

    Erratum to: Acta Neuropathol (2012) 123:273–284. DOI 10.1007/s00401‑011‑0914‑z. The authors would like to correct Fig. 3 of the original manuscript, since the image in Fig. 3b does not correspond to a VEGF treated animal. Corrected Fig. 3 is shown below. We apologize for this mistake. PMID:26341346

  5. Extension of working range in Zeeman graphite furnace atomic absorption spectrometry by nonlinear calibration with prior correction for stray light

    NASA Astrophysics Data System (ADS)

    Lonardo, Robert F.; Yuzefovsky, Alexander I.; Zhou, Jack X.; McCaffrey, John T.; Michel, Robert G.

    1996-09-01

    The nonlinear working range of a Perkin-Elmer 4100Zl atomic absorption spectrometer was improved in three steps. Firstly, each absorbance datum within the transient profile was corrected for the presence of stray light by an algorithm originally developed by L'vov and co-workers (Spectrochim. Acta Part B, 47 (1992) 889-895 and 1187-1202), but with the incorporation of the Newton method of successive approximations (Spectrochim. Acta Part B, 49 (1994) 1643-1656. Secondly, a dip correction procedure was performed on temporal signal profiles that exhibited a dip due to rollover. In the final step, an analytically useful working curve was generated by the nonlinear calibration routine of Barnett (Spectrochim. Acta Part B, 39 (1984) 829). Goodness of fit between the resultant calibration curve and the data was measured by the method suggested by Miller-Ihli et al. (Spectrochim. Acta Part B, 39 (1984) 1603) that is based on the sum of squares of the percentage deviation (SSPD) and the root mean square (RMS) percentage deviation. For lead, silver, copper, thallium, and cadmium, the analytical nonlinear working range was increased by as much as one and a half orders of magnitude, without any significant effect on the RMS. For chromium and manganese, no significant improvement in the nonlinear working range was observed, while the RMS improved by 50%. In the case of nickel, neither the working range nor the RMS was improved.

  6. Eventos de Agosto (August Events).

    ERIC Educational Resources Information Center

    Toro, Leonor; Pla, Myrna

    Written in Spanish, this booklet contains brief information on seven August events celebrated by Puerto Ricans: Herbert Hoover's birthdate (August 10); Acta del Seguro Social (Social Security Act, August 14); Julian E. Blanco (August 14), Enmienda 19 Sufragia de la Mujer (Amendment 19, Women's Suffrage, August 26); Benjamin Harrison (August 20);…

  7. Intradistrict Resource Allocation: Key Findings and Policy Implications

    ERIC Educational Resources Information Center

    Houck, Eric A.

    2011-01-01

    The focus on school-level performance brought about by the No Child Left Behind Act--as well as recent court cases challenging the use of race in student assignment policies--has brought greater attention to the need to for careful study of the allocation of resources within school districts. This paper describes the policy context, reviews key…

  8. Nebraska Swims Hard against Testing's Tides

    ERIC Educational Resources Information Center

    Borja, Rhea R.

    2007-01-01

    Sometimes assessments that work in theory fall apart in reality. This article discusses the unique learning-measurement system in Nebraska. Instead of relying on statewide standardized tests to comply with the accountability requirements of the federal No Child Left Behind Act--as is the case in the other 49 states--districts in Nebraska use their…

  9. Antimicrobial resistance of Listeria monocytogenes isolated from a poultry further processing plant

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to compare antimicrobial resistance profiles of distinct types of Listeria monocytogenes isolated from a commercial poultry cooking plant. One hundred fifty seven L. monocytogenes isolates representing 14 different ActA types were tested for susceptibility to 19 ant...

  10. The Cost of Chaos in the Curriculum. Perspectives on Higher Education

    ERIC Educational Resources Information Center

    Capaldi Phillips, Elizabeth D.; Poliakoff, Michael B.

    2015-01-01

    ACTA's report "The Cost of Chaos in the Curriculum" reveals that the vast array of course choices given to college students is a cause of exploding costs and poor academic outcomes. And a bloated undergraduate curriculum is particularly detrimental to the success of students from lower socioeconomic backgrounds. The report documents how…

  11. Diffusive Insights: On the Disagreement of Christian Bohr and August Krogh at the Centennial of the Seven Little Devils

    ERIC Educational Resources Information Center

    Gjedde, Albert

    2010-01-01

    The year 2010 is the centennial of the publication of the "Seven Little Devils" in the predecessor of "Acta Physiologica". In these seven papers, August and Marie Krogh sought to refute Christian Bohr's theory that oxygen diffusion from the lungs to the circulation is not entirely passive but rather facilitated by a specific cellular activity…

  12. Investigating Multitasking in High-Functioning Adolescents with Autism Spectrum Disorders Using the Virtual Errands Task

    ERIC Educational Resources Information Center

    Rajendran, Gnanathusharan; Law, Anna S.; Logie, Robert H.; van der Meulen, Marian; Fraser, Diane; Corley, Martin

    2011-01-01

    Using a modified version of the Virtual Errands Task (VET; McGeorge et al. in "Presence-Teleop Virtual Environ" 10(4):375-383, 2001), we investigated the executive ability of multitasking in 18 high-functioning adolescents with ASD and 18 typically developing adolescents. The VET requires multitasking (Law et al. in "Acta Psychol" 122(1):27-44,…

  13. Prepared in Mind and Resources? A Report on Public Higher Education in South Carolina

    ERIC Educational Resources Information Center

    Alacbay, Armand; Poliakoff, Michael

    2011-01-01

    In 2011, South Carolina Governor Nikki Haley signed into law the South Carolina Higher Education Efficiency and Administrative Policies Act, maintaining the transparency and accountability that lead to increased academic quality and affordability at colleges and universities. It is in this context that ACTA (American Council of Trustees and…

  14. Measures of Muscular Strength in U.S. Children and Adolescents, 2012

    MedlinePlus

    ... performance and DXA-derived lean body mass and fat mass in pre-pubertal children. Acta Pædiatr 100(10):1359–67. 2011. Suggested citation Ervin RB, Wang C-Y, Fryar CD, et al. Measures of ...

  15. SPR Biosensor for the Detection of L. monocytogenes using Phage Displayed Antibody

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Whole cells of Listeria monocytogenes were detected with a compact, surface plasmon resonance (SPR) sensor using a phage-displayed scFv antibody to the virulence factor ActA for biorecognition. Phage Lm P4:A8, expressing the scFv antibody fused to the pIII surface protein was immobilized to the se...

  16. Governance for a New Era: A Blueprint for Higher Education Trustees

    ERIC Educational Resources Information Center

    Schmidt, Benno C.

    2014-01-01

    "Governance for a New Era: A Blueprint for Higher Education Governance," is the product of a summit facilitated by ACTA [American Council of Trustees and Alumni] and chaired by Benno Schmidt, City University of New York Board chairman. Signatories to the statement, a diverse group of 22 distinguished national leaders, include college…

  17. Bold Leadership Real Reform [Annual Report, 2014

    ERIC Educational Resources Information Center

    American Council of Trustees and Alumni, 2015

    2015-01-01

    Higher education has never been more "front and center"--almost daily we hear about spiraling costs, the lack of academic rigor, and the stifling political correctness on our college campuses. Long before such issues were hot, ACTA [American Council of Trustees and Alumni] was already pointing out these worrisome trends and calling on…

  18. BIOGEOCHEMICAL CONTROLS ON REACTION OF SEDIMENTARY ORGANIC MATTER AND AQUEOUS SULFIDES IN HOLOCENE SEDIMENTS OF MUD LAKE FLORIDA: JOURNAL ARTICLE

    EPA Science Inventory

    JOURNAL NRMRL-ADA-00133 Filley,T.R., Freeman, K.H., Wilkin*, R.T., and Hatcher, P.G. Biogeochemical Controls on Reaction of Sedimentary Organic Matter and Aqueous Sulfides in Holocene Sediments of Mud Lake Florida. Geochimica et Cosmochimica Acta 66 (6):937-954...

  19. Development of Guidance for States Transitioning to New Safety Analysis Tools

    ERIC Educational Resources Information Center

    Alluri, Priyanka

    2010-01-01

    With about 125 people dying on US roads each day, the US Department of Transportation heightened the awareness of critical safety issues with the passage of SAFETEA-LU (Safe Accountable Flexible Efficient Transportation Equity Act--A Legacy for Users) legislation in 2005. The legislation required each of the states to develop a Strategic Highway…

  20. Activity Scale.

    ERIC Educational Resources Information Center

    Kerpelman, Larry C.; Weiner, Michael J.

    This twenty-four item scale assesses students' actual and desired political-social activism in terms of physical participation, communication activities, and information-gathering activities. About ten minutes are required to complete the instrument. The scale is divided into two subscales. The first twelve items (ACT-A) question respondents on…

  1. Higher: Setting a Higher Bar for Higher Ed. 2013 Annual Report

    ERIC Educational Resources Information Center

    American Council of Trustees and Alumni, 2014

    2014-01-01

    The American Council of Trustees and Alumni (ACTA) is leading the charge to return "higher" to higher education. We are challenging the status quo to restore academic freedom, academic rigor, and real accountability to higher education. And, we are doing so with an ever-widening network of supporters and partners.

  2. Magnus Strandqvist: 50th anniversary of his doctoral thesis.

    PubMed

    Kajanti, M J

    1994-01-01

    This article is dedicated to Magnus Strandqvist's famous doctoral thesis "Studien über die kumulative Wirkung der Röntgenstrahlen bei Fraktionierung. Erfahrungen aus dem Radiumhemmet an 280 Haut- und Lippenkarzinomen" published in Acta Radiologica in 1944. After a short biography of Strandqvist some central points of his work and their influence on future development of modern radiotherapy are presented. PMID:7993639

  3. Effects of space flights on human allergic status (IgE-mediated sensitivity)

    NASA Astrophysics Data System (ADS)

    Buravkova, L. B.; Rykova, M. P.; Gertsik, Y. G.; Antropova, E. N.

    2007-02-01

    Suppression of the immune system after space flights of different duration has been reported earlier by Konstantinova [Immune system in extreme conditions, Space immunology. B. 59. M. Science 1988. 289p. (in Russian) [4]; Immunoresistance of man in space flight, Acta Astronautica 23 (1991) 123-127 [5

  4. The Metalloprotease Mpl Supports Listeria monocytogenes Dissemination through Resolution of Membrane Protrusions into Vacuoles.

    PubMed

    Alvarez, Diego E; Agaisse, Hervé

    2016-06-01

    Listeria monocytogenes is an intracellular pathogen that disseminates within the intestinal epithelium through acquisition of actin-based motility and formation of plasma membrane protrusions that project into adjacent cells. The resolution of membrane protrusions into vacuoles from which the pathogen escapes results in bacterial spread from cell to cell. This dissemination process relies on the mlp-actA-plcB operon, which encodes ActA, a bacterial nucleation-promoting factor that mediates actin-based motility, and PlcB, a phospholipase that mediates vacuole escape. Here we investigated the role of the metalloprotease Mpl in the dissemination process. In agreement with previous findings showing that Mpl is required for PlcB activation, infection of epithelial cells with the ΔplcB or Δmpl strains resulted in the formation of small infection foci. As expected, the ΔplcB strain displayed a strong defect in vacuole escape. However, the Δmpl strain showed an unexpected defect in the resolution of protrusions into vacuoles, in addition to the expected but mild defect in vacuole escape. The Δmpl strain displayed increased levels of ActA on the bacterial surface in protrusions. We mapped an Mpl-dependent processing site in ActA between amino acid residues 207 to 238. Similar to the Δmpl strain, the ΔactA207-238 strain displayed increased levels of ActA on the bacterial surface in protrusions. Although the ΔactA207-238 strain displayed wild-type actin-based motility, it formed small infection foci and failed to resolve protrusions into vacuoles. We propose that, in addition to its role in PlcB processing and vacuole escape, the metalloprotease Mpl is required for ActA processing and protrusion resolution. PMID:27068088

  5. Comment on 'New Brans-Dicke wormholes'

    SciTech Connect

    Bhadra, Arunava; Simaciu, Ion; Nandi, Kamal Kanti; Zhang Yuanzhong

    2005-06-15

    It is shown that the recently claimed two new Brans-Dicke wormhole solutions [F. He and S-W. Kim, Phys. Rev. D 65, 084022 (2002)] are not really new solutions. They are just the well known Brans-Dicke solutions of Class I and II in a different conformal gauge.

  6. Streptomyces alni sp. nov., a daidzein-producing endophyte isolated from a root of Alnus nepalensis D. Don.

    PubMed

    Liu, Ning; Wang, Haibin; Liu, Mei; Gu, Qiang; Zheng, Wen; Huang, Ying

    2009-02-01

    A filamentous actinomycete, designated strain D65(T), was isolated from a root of a wild tree, Alnus nepalensis D. Don (Nepalese Alder), collected in Xishuangbanna, China. It produced the bioactive agents daidzein and N-acetyltyramine and had morphological and chemical properties characteristic of streptomycetes. Pink to brownish red diffusible pigments were produced on several ISP media. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain D65(T) formed a distinct phyletic line that was most closely, albeit loosely, associated with Streptomyces hebeiensis YIM 001(T), Streptomyces aurantiogriseus NRRL B-5416(T), Streptomyces griseoviridis NBRC 12874(T), Streptomyces niveoruber NBRC 15428(T) and Streptomyces thermovulgaris NBRC 13473. A number of phenotypic properties allowed differentiation of the strain from related Streptomyces species. Therefore strain D65(T) represents a novel species of the genus Streptomyces, for which the name Streptomyces alni sp. nov. is proposed. The type strain is D65(T) (=CGMCC 4.3510(T)=NRRL B-24611(T)). PMID:19196762

  7. 77 FR 29692 - Segun M. Rasaki, M.D.; Decision and Order

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-18

    ...'s action at which he may ultimately prevail.'' Kamal Tiwari, M.D., 76 FR 71604, 71606 (2011); see also Bourne Pharmacy, Inc., 72 FR 18273, 18274 (2007); Anne Lazar Thorn, 62 FR 12847 (1997...., 67 FR 35,582 (DEA 2002); Michael G. Dolin, M.D., 65 Fed. Reg. 5661 (DEA 2000); see also Philip...

  8. 23 CFR Appendix to Subpart F of... - Alternate Method of Determining the Color of Retroreflective Sign Materials and Pavement Marking...

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ...-fluorescent retroreflective materials may be measured in accordance with ASTM Test Method E1349, “Standard... colorimetric coordinates shall be D65 and the 2 Degree Standard CIE observer shall be used. 3. For fluorescent... measured. The fluorescent luminous factor must be determined using bispectral fluorescent...

  9. 40 CFR Appendix 1 to Part 3 - Priority Reports

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    .... 1 Appendix 1 to Part 3—Priority Reports Category Description 40 CFR Citation Required Reports State... in 40 CFR 65.6(c) 65.5(d), 65.5(e). Continuous Emissions Monitoring Quarterly emissions monitoring... hazardous waste that was placed in hazardous waste management units in noncompliance with 40 CFR...

  10. 40 CFR Appendix 1 to Part 3 - Priority Reports

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    .... 1 Appendix 1 to Part 3—Priority Reports Category Description 40 CFR Citation Required Reports State... in 40 CFR 65.6(c) 65.5(d), 65.5(e). Continuous Emissions Monitoring Quarterly emissions monitoring... hazardous waste that was placed in hazardous waste management units in noncompliance with 40 CFR...

  11. 40 CFR Appendix 1 to Part 3 - Priority Reports

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... by units subject to acid rain emissions limitations 72.90. Annual Compliance Certification Report.... 1 Appendix 1 to Part 3—Priority Reports Category Description 40 CFR Citation Required Reports State... in 40 CFR 65.6(c) 65.5(d), 65.5(e). Continuous Emissions Monitoring Quarterly emissions...

  12. 40 CFR Appendix 1 to Part 3 - Priority Reports

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... by units subject to acid rain emissions limitations 72.90. Annual Compliance Certification Report.... 1 Appendix 1 to Part 3—Priority Reports Category Description 40 CFR Citation Required Reports State... in 40 CFR 65.6(c) 65.5(d), 65.5(e). Continuous Emissions Monitoring Quarterly emissions...

  13. 40 CFR Appendix 1 to Part 3 - Priority Reports

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... by units subject to acid rain emissions limitations 72.90. Annual Compliance Certification Report.... 1 Appendix 1 to Part 3—Priority Reports Category Description 40 CFR Citation Required Reports State... in 40 CFR 65.6(c) 65.5(d), 65.5(e). Continuous Emissions Monitoring Quarterly emissions...

  14. Metameric effect between natural teeth and the shade tabs of a shade guide.

    PubMed

    Corcodel, Nicoleta; Helling, Stephan; Rammelsberg, Peter; Hassel, Alexander J

    2010-06-01

    The objective of this study was to evaluate metameric effects, that is, the dependence of the colours of teeth and shade tabs on the illuminant used. The colours of 49 teeth of 37 participants and of the corresponding shade tabs of the 3D-Master (VITA Zahnfabrik; colour match DeltaE(ab)< 2) were measured using an intra-oral spectrophotometer (VITA Easyshade). Spectral reflectance data (from 400 to 700 nm) were recorded. Commission Internationale de l'Eclairage (CIE) L*a*b* values were calculated for D65 (reference daylight), A (incandescent light), and TL84 (store/office light) as reference illuminants. A modified metamerism index (Mod-M) and hue-angle ratios were calculated to express differences between tooth and tab colour relative to the difference observed under D65 illumination. The Mod-M for teeth and tabs was greater than unity (indicating a greater colour difference relative to D65) by 57.1% for A and by 49.3% for TL84. Hue-angle ratios of teeth and tabs using the test illuminants were different from those obtained using the standard illuminant D65. If teeth and shade tab matching is conducted using daylight illumination, the colour difference may not be the same under other lighting conditions, leading to perceptible, or even unacceptable, colour differences under these conditions. PMID:20572867

  15. PCDDB: the protein circular dichroism data bank, a repository for circular dichroism spectral and metadata

    PubMed Central

    Whitmore, Lee; Woollett, Benjamin; Miles, Andrew John; Klose, D. P.; Janes, Robert W.; Wallace, B. A.

    2011-01-01

    The Protein Circular Dichroism Data Bank (PCDDB) is a public repository that archives and freely distributes circular dichroism (CD) and synchrotron radiation CD (SRCD) spectral data and their associated experimental metadata. All entries undergo validation and curation procedures to ensure completeness, consistency and quality of the data included. A web-based interface enables users to browse and query sample types, sample conditions, experimental parameters and provides spectra in both graphical display format and as downloadable text files. The entries are linked, when appropriate, to primary sequence (UniProt) and structural (PDB) databases, as well as to secondary databases such as the Enzyme Commission functional classification database and the CATH fold classification database, as well as to literature citations. The PCDDB is available at: http://pcddb.cryst.bbk.ac.uk. PMID:21071417

  16. Three-dimensional structure of Erwinia carotovora L-asparaginase

    SciTech Connect

    Kislitsyn, Yu. A. Kravchenko, O. V.; Nikonov, S. V. Kuranova, I. P.

    2006-10-15

    Three-dimensional structure of Erwinia carotovora L-asparaginase, which has antitumor activity and is used for the treatment of acute lymphoblastic leukemia, was solved at 3 A resolution and refined to R{sub cryst} = 20% and R{sub free} = 28%. Crystals of recombinant Erwinia carotovora L-asparaginase were grown by the hanging-drop vapor-diffusion method from protein solutions in a HEPES buffer (pH 6.5) and PEG MME 5000 solutions in a cacodylate buffer (pH 6.5) as the precipitant. Three-dimensional X-ray diffraction data were collected up to 3 A resolution from one crystal at room temperature. The structure was solved by the molecular replacement method using the coordinates of Erwinia chrysanthemi L-asparaginase as the starting model. The coordinates refined with the use of the CNS program package were deposited in the Protein Data Bank (PDB code 1ZCF)

  17. Superheated liquid fragility and thermodynamic refinement for evaluation of metallic glass-forming ability

    NASA Astrophysics Data System (ADS)

    Meng, Q. G.; Zhang, S. G.; Xia, M. X.; Li, J. G.; Zhou, J. K.

    2007-01-01

    Based on the super-Arrhenius equation and Angell's fragility concept [J. Non-Cryst. Solids 131, 13 (1991)], the expression of the fragility parameter for superheated liquid is deduced as M =E∞/kBTl, where E∞ is the activation energy, kB the Boltzmann constant, and Tl the liquidus temperature. It exhibits a negative correlation with the glass-forming ability (GFA) of the referenced metallic glasses in the same system rather than in the different systems, while the parameter ɛ based on order-disorder competition is just the opposite. The refined fragility parameter M* (=M/ɛ) gives a much better reflection of the GFA for the metallic glasses.

  18. Backscattering at a pulsed neutron source, the MUSICAL instrument

    NASA Astrophysics Data System (ADS)

    Alefeld, B.

    1995-02-01

    In the first part the principles of the neutron backscattering method are described and some simple considerations about the energy resolution and the intensity are presented. A prototype of a backscattering instrument, the first Jülich instrument, is explained in some detail and a representative measurement is shown which was performed on the backscattering instrument IN10 at the ILL in Grenoble. In the second part a backscattering instrument designed for a pulsed neutron source is proposed. It is shown that a rather simple modification, which consists in the replacement of the Doppler drive of the conventional backscattering instrument by a multi silicon monochromator cryst al (MUSICAL) leads to a very effective instrument, benefitting from the peak flux of the pulsed source.

  19. Crystal structure of ribosomal protein L1 from the bacterium Aquifex aeolicus

    NASA Astrophysics Data System (ADS)

    Nikonova, E. Yu.; Tishchenko, S. V.; Gabdulkhakov, A. G.; Shklyaeva, A. A.; Garber, M. B.; Nikonov, S. V.; Nevskaya, N. A.

    2011-07-01

    The crystal structure of ribosomal protein L1 from the bacterium Aquifex aeolicus was solved by the molecular-replacement method and refined to R cryst = 19.4% and R free = 25.1% at 2.1 Å protein consists of two domains linked together by a flexible hinge region. In the structure under consideration, the domains are in close proximity and adopt a closed conformation. Earlier, this conformation has been found in the structure of protein L1 from the bacterium Thermus thermophilus, whereas the structures of archaeal L1 proteins and the structures of all L1 proteins in the RNA-bound form have an open conformation. The fact that a closed conformation was found in the structures of two L1 proteins which crystallize in different space groups and belong to different bacteria suggests that this conformation is a characteristic feature of L1 bacterial proteins in the free form.

  20. Examination of methods to determine free-ion diffusivity and number density from analysis of electrode polarization.

    PubMed

    Wang, Yangyang; Sun, Che-Nan; Fan, Fei; Sangoro, Joshua R; Berman, Marc B; Greenbaum, Steve G; Zawodzinski, Thomas A; Sokolov, Alexei P

    2013-04-01

    Electrode polarization analysis is frequently used to determine free-ion diffusivity and number density in ionic conductors. In the present study, this approach is critically examined in a wide variety of electrolytes, including aqueous and nonaqueous solutions, polymer electrolytes, and ionic liquids. It is shown that the electrode polarization analysis based on the Macdonald-Trukhan model [J. Chem. Phys. 124, 144903 (2006); J. Non-Cryst. Solids 357, 3064 (2011)] progressively fails to give reasonable values of free-ion diffusivity and number density with increasing salt concentration. This should be expected because the original model of electrode polarization is designed for dilute electrolytes. An empirical correction method which yields ion diffusivities in reasonable agreement with pulsed-field gradient nuclear magnetic resonance measurements is proposed. However, the analysis of free-ion diffusivity and number density from electrode polarization should still be exercised with great caution because there is no solid theoretical justification for the proposed corrections. PMID:23679415

  1. Examination of methods to determine free-ion diffusivity and number density from analysis of electrode polarization

    SciTech Connect

    Wang, Yangyang; Sun, Che-Nan; Fan, Fei; Sangoro, Joshua R; Berman, Marc; Greenbaum, Steve; Zawodzinski, Thomas; Sokolov, Alexei P

    2013-01-01

    Electrode polarization analysis is frequently used to determine free-ion diffusivity and number density in ionic conductors. In the present study, this approach is critically examined in a wide variety of electrolytes, including aqueous and nonaqueous solutions, polymer electrolytes, and ionic liquids. It is shown that the electrode polarization analysis based on theMacdonald-Trukhan model [J. Chem. Phys. 124, 144903 (2006); J. Non-Cryst. Solids 357, 3064 (2011)] progressively fails to give reasonable values of free-ion diffusivity and number density with increasing salt concentration. This should be expected because the original model of electrode polarization is designed for dilute electrolytes. An empirical correction method which yields ion diffusivities in reasonable agreement with pulsed-field gradient nuclear magnetic resonance measurements is proposed. However, the analysis of free-ion diffusivity and number density from electrode polarization should still be exercised with great caution because there is no solid theoretical justification for the proposed corrections.

  2. Epitaxial Growth of High-Resistivity CdTe Thick Films Grown Using a Modified Close Space Sublimation Method

    NASA Astrophysics Data System (ADS)

    Jiang, Quanzhong; Brinkman, Andy W.; Veeramani, Perumal; Sellin, Paul. J.

    2010-02-01

    This paper reports the growth of high-resistivity CdTe thick epitaxial films of single crystal nature using a modified close space sublimation method (MCSS) in a Te-rich environment. We propose that the high Te2 partial pressure results in an increased concentration of TeCd antisites acting as deep donors to produce the high-resistivity CdTe, as well as improved quality of thick films. This is in agreement with the deep-donor model introduced by Fiderele et al. [Cryst. Res. Technol. 38 (2003) 588]. The thick films have a µeτe value in the order 10-4 cm2 V-1 and as expected, the TeCd antisites appeared not to act as electron traps.

  3. Kimberlite and related rocks from Garnet Lake, West Greenland, including their mantle constituents, diamond occurrence, age and provenance

    NASA Astrophysics Data System (ADS)

    Hutchison, Mark T.; Frei, Dirk

    2009-11-01

    Observations of thickness, orientation and morphology and mineral chemistry of the principal diamondiferous intrusive sheet and associated bodies in the vicinity of Garnet Lake, Sarfartoq, West Greenland are reported. The principal body dips to the east on a NE/SW (true) trend and reaches a maximum thickness of 4.25 m. Multiple intrusive events are identified within the main sheet including sub-parallel bands occasionally exhibiting grain size sorting, cross-cutting layers and late-stage carbonate-rich emplacement, particularly at the contacts with country rock. Phenocrystic mineral assemblages and compositional measurements reveal two principal petrological types. The dominant type is an aillikite and the second rock type is a kimberlite. The kimberlite exhibits thin Ba-rich rims (towards kinoshitalite) on Al-rich phlogopite crysts, and an abundance of perovskite. Compositional zonation in groundmass spinels suggest a later transition towards an aillikite component. The aillikite is characterised by abundant phlogopite, heavily zoned with tetraferriphlogopite rims, transitional Type 1-Type 2 spinel compositions, rare Al,Ti-rich groundmass clinopyroxene and occasional exotic Sr-carbonate phases such as olekminskite. The Garnet Lake main sheet is characterised by mantle phases occurring as individual grains, most strikingly as garnet xenocrysts up to 5 mm and disaggregated mantle olivine crysts. Xenoliths occur rarely and are typically garnet dunites and garnet lherzolites. Heavy mineral separation reveals an abundance of G10D garnets and, whilst peridotitic garnets dominate, eclogitic G3D and G4D garnets also occur. Trace element compositions of garnet crysts reveal sinusoidal REE patterns in harzburgitic garnets however a component of flat and REE-enriched G11 garnets is apparent, reflecting significant mantle refertilisation. Thermorbarometric calculations on assemblages in Garnet Lake main sheet garnet lherzolites reveal equilibrium conditions clustering closely

  4. X-ray diffraction study of GaSb/AlSb strained-layer-superlattices grown on miscut (100) substrates

    SciTech Connect

    Macrander, A.T. ); Schwartz, G.P.; Guiltieri, G.J.; Gilmer, G. )

    1991-07-01

    A series of superlattices were grown by molecular beam epitaxy on (100) GaSb substrates which had been miscut by 2, 3, and 4 degrees toward the <011> direction. These superlattices were then studied by scanning all possible (444) or (511) (asymmetric) reflections with high resolution multiple-crystal x-ray diffractometry. In addition, the (400) (quasi-symmetric) reflection was scanned. From peak splittings we extracted mismatch and tilt parameters for the epitaxial unit cell. We compared our results for the non-tetragonal component of the distortion ot calculations based on the coherent strain model of Hornstra and Bartels (J. Cryst. Growth 44,513 (1978)). We find that this model which was developed for epitaxial growth on a general (hkl) plane also describes our results for growth on vicinal (100) planes. The resolution of our data is sufficient to establish that the distortion was not purely tetragonal. A monoclinic unit cell symmetry adequately describes our results.

  5. X-ray diffraction study of GaSb/AlSb strained-layer-superlattices grown on miscut (100) substrates

    SciTech Connect

    Macrander, A.T.; Schwartz, G.P.; Guiltieri, G.J.; Gilmer, G.

    1991-07-01

    A series of superlattices were grown by molecular beam epitaxy on (100) GaSb substrates which had been miscut by 2, 3, and 4 degrees toward the <011> direction. These superlattices were then studied by scanning all possible [444] or [511] (asymmetric) reflections with high resolution multiple-crystal x-ray diffractometry. In addition, the (400) (quasi-symmetric) reflection was scanned. From peak splittings we extracted mismatch and tilt parameters for the epitaxial unit cell. We compared our results for the non-tetragonal component of the distortion ot calculations based on the coherent strain model of Hornstra and Bartels (J. Cryst. Growth 44,513 (1978)). We find that this model which was developed for epitaxial growth on a general (hkl) plane also describes our results for growth on vicinal (100) planes. The resolution of our data is sufficient to establish that the distortion was not purely tetragonal. A monoclinic unit cell symmetry adequately describes our results.

  6. Effects of water on the primary and secondary relaxation of xylitol and sorbitol: Implication on the origin of the Johari-Goldstein relaxation

    NASA Astrophysics Data System (ADS)

    Psurek, T.; Maslanka, S.; Paluch, M.; Nozaki, R.; Ngai, K. L.

    2004-07-01

    Dielectric spectroscopy was employed to study the effects of water on the primary α -relaxation and the secondary β -relaxation of xylitol. The measurements were made on anhydrous xylitol and mixtures of xylitol with water with three different water concentrations over a temperature range from 173K to 293K . The α -relaxation speeds up with increasing concentration of water in xylitol, whereas the rate of the β -relaxation is essentially unchanged. Some systematic differences in the behavior of α -relaxation for anhydrous xylitol and the mixtures were observed. Our findings confirm all the observations of Nozaki [R. Nozaki, H. Zenitani, A. Minoguchi, and K. Kitai, J. Non-Cryst. Solids 307, 349 (2002)] in sorbitol/water mixtures. Effects of water on both the α - and β -relaxation dynamics in xylitol and sorbitol are explained by using the coupling model.

  7. Crystallographic data processing for free-electron laser sources.

    PubMed

    White, Thomas A; Barty, Anton; Stellato, Francesco; Holton, James M; Kirian, Richard A; Zatsepin, Nadia A; Chapman, Henry N

    2013-07-01

    A processing pipeline for diffraction data acquired using the `serial crystallography' methodology with a free-electron laser source is described with reference to the crystallographic analysis suite CrystFEL and the pre-processing program Cheetah. A detailed analysis of the nature and impact of indexing ambiguities is presented. Simulations of the Monte Carlo integration scheme, which accounts for the partially recorded nature of the diffraction intensities, are presented and show that the integration of partial reflections could be made to converge more quickly if the bandwidth of the X-rays were to be increased by a small amount or if a slight convergence angle were introduced into the incident beam. PMID:23793149

  8. Twist transition of nematic hyperbolic hedgehogs.

    PubMed

    James, Richard; Fukuda, Jun-ichi

    2014-04-01

    Stability of an idealized hyperbolic hedgehog in a nematic liquid crystal against a twist transition is investigated by extending the methodology of Rüdinger and Stark [Liq. Cryst. 26, 753 (1999)], where the hedgehog is confined between two concentric spheres. In the ideal hyperbolic-hedgehog the molecular orientation is assumed to rotate proportionally with respect to the inclination angle, θ (and in the opposite sense). However, when splay, k11, and bend, k33, moduli differ this proportionality is lost and the liquid crystal deforms relative to the ideal with bend and splay. Although slight, these deformations are shown to significantly shift the transition if k11/k33 is small. By increasing the degree of confinement the twist transition can be inhibited, a characteristic both hyperbolic and radial hedgehogs have in common. The twist transition of a hyperbolic defect that accompanies a particle is found to be well predicted by the earlier stability analysis of a thick shell. PMID:24827263

  9. Bilbao Crystallographic Server. II. Representations of crystallographic point groups and space groups.

    PubMed

    Aroyo, Mois I; Kirov, Asen; Capillas, Cesar; Perez-Mato, J M; Wondratschek, Hans

    2006-03-01

    The Bilbao Crystallographic Server is a web site with crystallographic programs and databases freely available on-line (http://www.cryst.ehu.es). The server gives access to general information related to crystallographic symmetry groups (generators, general and special positions, maximal subgroups, Brillouin zones etc.). Apart from the simple tools for retrieving the stored data, there are programs for the analysis of group-subgroup relations between space groups (subgroups and supergroups, Wyckoff-position splitting schemes etc.). There are also software packages studying specific problems of solid-state physics, structural chemistry and crystallography. This article reports on the programs treating representations of point and space groups. There are tools for the construction of irreducible representations, for the study of the correlations between representations of group-subgroup pairs of space groups and for the decompositions of Kronecker products of representations. PMID:16489249

  10. Redetermination of [Pr(NO3)3(H2O)4]·2H2O

    PubMed Central

    Decadt, Roel; Van Der Voort, Pascal; Van Driessche, Isabel; Van Deun, Rik; Van Hecke, Kristof

    2012-01-01

    The structure of the title compound, tetra­aqua­tris­(nitrato-κ2 O,O′)praseodymium(III) dihydrate, was redetermined. The structure models derived from the previous determinations [Rumanova et al. (1964 ▶). Kristallografiya, 9, 642–654; Fuller & Jacobson (1976 ▶). Cryst. Struct. Commun. 5, 349–352] were confirmed, but now with all H atoms unambiguously located, revealing a complex O—H⋯O hydrogen-bonding network, extending throughout the whole structure. In the title compound, the coordination environment of the PrIII atom can best be described as a distorted bicapped square anti­prism defined by three bidentate nitrate anions and four water mol­ecules. Additionally, two lattice water mol­ecules are observed in the crystal packing. The title compound is isotypic with several other lanthanide-containing nitrate analogues. PMID:22807700

  11. The protein circular dichroism data bank, a Web-based site for access to circular dichroism spectroscopic data.

    PubMed

    Whitmore, Lee; Woollett, Benjamin; Miles, Andrew J; Janes, Robert W; Wallace, B A

    2010-10-13

    The Protein Circular Dichroism Data Bank (PCDDB) is a newly released resource for structural biology. It is a web-accessible (http://pcddb.cryst.bbk.ac.uk) data bank for circular dichroism (CD) and synchrotron radiation circular dichroism (SRCD) spectra and their associated experimental and secondary metadata, with links to protein sequence and structure data banks. It is designed to provide a public repository for CD spectroscopic data on macromolecules, to parallel the Protein Data Bank (PDB) for crystallographic, electron microscopic, and nuclear magnetic resonance spectroscopic data. Similarly to the PDB, it includes validation checking procedures to ensure good practice and the integrity of the deposited data. This paper reports on the first public release of the PCDDB, which provides access to spectral data that comprise standard reference datasets. PMID:20947015

  12. Two surfaces of cytochrome b5 with major and minor contributions to CYP3A4-catalyzed steroid and nifedipine oxygenation chemistries

    PubMed Central

    Peng, Hwei-Ming; Auchus, Richard J.

    2014-01-01

    Conserved human cytochrome b5 (b5) residues D58 and D65 are critical for interactions with CYP2E1 and CYP2C19, whereas E48 and E49 are essential for stimulating the 17,20-lyase activity of CYP17A1. Here, we show that b5 mutations E48G, E49G, D58G, and D65G have reduced capacity to stimulate CYP3A4-catalyzed progesterone and testosterone 6β-hydroxylation or nifedipine oxidation. The b5 double mutation D58G/D65G fails to stimulate these reactions, similar to CYP2E1 and CYP2C19, whereas mutation E48G/E49G retains 23–42% of wild-type stimulation. Neither mutation impairs the activity stimulation of wild-type b5, nor does mutation D58G/D65G impair the partial stimulation of mutations E48G or E48G/E49G. For assays reconstituted with a single phospholipid, phosphatidyl serine afforded the highest testosterone 6β-hydroxylase activity with wild-type b5 but the poorest activity with b5 mutation E48G/E49G, and the activity stimulation of mutation E48G/E49G was lost at [NaCl] > 50 mM. Cross-linking of CYP3A4 and b5 decreased in the order wild-type > E48G/E49G > D58G/D65G and varied with phospholipid. We conclude that two b5 acidic surfaces, primarily the domain including residues D58-D65, participate in the stimulation of CYP3A4 activities. Our data suggest that a minor population of CYP3A4 molecules remains sensitive to b5 mutation E48G/E49G, consistent with phospholipid-dependent conformational heterogeneity of CYP3A4. PMID:24256945

  13. Two surfaces of cytochrome b5 with major and minor contributions to CYP3A4-catalyzed steroid and nifedipine oxygenation chemistries.

    PubMed

    Peng, Hwei-Ming; Auchus, Richard J

    2014-01-01

    Conserved human cytochrome b5 (b5) residues D58 and D65 are critical for interactions with CYP2E1 and CYP2C19, whereas E48 and E49 are essential for stimulating the 17,20-lyase activity of CYP17A1. Here, we show that b5 mutations E48G, E49G, D58G, and D65G have reduced capacity to stimulate CYP3A4-catalyzed progesterone and testosterone 6β-hydroxylation or nifedipine oxidation. The b5 double mutation D58G/D65G fails to stimulate these reactions, similar to CYP2E1 and CYP2C19, whereas mutation E48G/E49G retains 23-42% of wild-type stimulation. Neither mutation impairs the activity stimulation of wild-type b5, nor does mutation D58G/D65G impair the partial stimulation of mutations E48G or E48G/E49G. For assays reconstituted with a single phospholipid, phosphatidyl serine afforded the highest testosterone 6β-hydroxylase activity with wild-type b5 but the poorest activity with b5 mutation E48G/E49G, and the activity stimulation of mutation E48G/E49G was lost at [NaCl]>50mM. Cross-linking of CYP3A4 and b5 decreased in the order wild-type>E48G/E49G>D58G/D65G and varied with phospholipid. We conclude that two b5 acidic surfaces, primarily the domain including residues D58-D65, participate in the stimulation of CYP3A4 activities. Our data suggest that a minor population of CYP3A4 molecules remains sensitive to b5 mutation E48G/E49G, consistent with phospholipid-dependent conformational heterogeneity of CYP3A4. PMID:24256945

  14. Selectivity Principles in Anion Separation by Crystallization of Hydrogen-Bonding Capsules

    SciTech Connect

    Custelcean, Radu; Bock, Aurelien; Moyer, Bruce A

    2010-01-01

    The fundamental factors controlling anion selectivity in the crystallization of hydrogen-bonding capsules [Mg(H2O)6][X L2] (X = SO42-, 1a; SeO42-, 1b; SO32-, 1c; CO32-, 1d; L = tris[2-(3-pyridylurea)ethyl]-amine) from water have been investigated by solution and solid-state thermodynamic measurements, anion competition experiments, and X-ray structural analysis. The crystal structures of 1a-d are isomorphous, thereby simplifying the interpretation of the observed selectivities based on differences in anion coordination geometries. The solubilities of 1a-d in water follow the order: 1a < 1b < 1c < 1d, which is consistent with the selectivity for the tetrahedral sulfate and selenate anions observed in competitive crystallization experiments. Crystallization of the capsules is highly exothermic, with the most favorable {Delta}H{sub cryst}{sup o} of -99.1 and -108.5 kJ/mol corresponding to SO42- and SeO42-, respectively, in agreement with the X-ray structural data showing shape complementarity between these tetrahedral anions and the urea-lined cavities of the capsules. Sulfite, on the other hand, has a significantly less negative {Delta}H{sub cryst}{sup o} of -64.6 kJ/mol, which may be attributed to its poor fit inside the capsules, involving repulsive interactions. The more favorable entropy of crystallization for this anion, however, partly offsets the enthalpic disadvantage, resulting in a solubility product very similar to that of the selenate complex. Because of their very similar shape and size, SO42- and SeO42- have a propensity to form solid solutions, which limits the selectivity between these two anions in competitive crystallizations. In the end, a comprehensive picture of contributing factors to anion selectivity in crystalline hydrogen-bonding capsules emerges.

  15. A Short History of Medical Informatics in Bosnia and Herzegovina

    PubMed Central

    Masic, Izet

    2014-01-01

    The health informatics profession in Bosnia and Herzegovina has relatively long history. Thirty five years from the introduction of the first automatic manipulation of data, thirty years from the establishment of Society for Medical Informatics BiH, twenty years from the establishment of the Scientific journal “Acta Informatica Medica (Acta Inform Med”, indexed in PubMed, PubMed Central Scopus, Embase, etc.), twenty years on from the establishment of the first Cathedra for Medical Informatics on Biomedical Faculties in Bosnia and Herzegovina, ten years on from the introduction of the method of “Distance learning” in medical curriculum. The author of this article is eager to mark the importance of the above mentioned Anniversaries in the development of Health informatics in Bosnia and Herzegovina and have attempted, very briefly, to present the most significant events and persons with essential roles throughout this period. PMID:24648621

  16. The spectral sensitivity of the human short-wavelength sensitive cones derived from thresholds and color matches.

    PubMed

    Stockman, A; Sharpe, L T; Fach, C

    1999-08-01

    We used two methods to estimate short-wave (S) cone spectral sensitivity. Firstly, we measured S-cone thresholds centrally and peripherally in five trichromats, and in three blue-cone monochromats, who lack functioning middle-wave (M) and long-wave (L) cones. Secondly, we analyzed standard color-matching data. Both methods yielded equivalent results, on the basis of which we propose new S-cone spectral sensitivity functions. At short and middle-wavelengths, our measurements are consistent with the color matching data of Stiles and Burch (1955, Optica Acta, 2, 168-181; 1959, Optica Acta, 6, 1-26), and other psychophysically measured functions, such as pi 3 (Stiles, 1953, Coloquio sobre problemas opticos de la vision, 1, 65-103). At longer wavelengths, S-cone sensitivity has previously been over-estimated. PMID:10492818

  17. Autosomal dominant nemaline myopathy caused by a novel alpha-tropomyosin 3 mutation.

    PubMed

    Kiphuth, I C; Krause, S; Huttner, H B; Dekomien, G; Struffert, T; Schröder, R

    2010-04-01

    Nemaline myopathy (NM) is a genetically and clinically heterogenous muscle disorder, which is myopathologically characterized by nemaline bodies. Mutations in six genes have been reported to cause NM: Nebulin (NEB Pelin 1999), alpha-skeletal muscle actin (ACTA1 Nowak 1999), alpha-slow tropomyosin (TPM3 Laing 1995), beta-tropomyosin (TPM2 Donner 2002), slow troponin T (TNNT1 Johnston 2000) and cofilin 2 (CFL2 Agrawal 2007). The majority of cases are due to mutation in NEB and ACTA1. We report on the clinical, myopathological and muscle MRI findings in a German family with autosomal dominant NM due to a novel pathogenic TPM3 mutation (p.Ala156Thr). PMID:20012312

  18. Meeting Report: 7th World Congress on Itch

    PubMed Central

    Azimi, Ehsan; Lerner, Ethan A.

    2014-01-01

    The 7th World Congress on Itch was held in Boston in September 2013. This is the biennial meeting of the International Forum for the Study of Itch (IFSI), www.itchforum.net, There were 240 attendees from 17 countries. They spanned clinical practice, academics and patient advocacy while the opportunity for translation was demonstrated as 80 attendees were from industry. A large academic neuroscience contingent was present. There were plenary sessions, basic and clinical tracts, and sixty posters during the 2½ day meeting. The meeting program and 160 abstracts are available at www.itchboston.org and the open access journal, Acta Dermato-Venereologica, www.medicaljournals.se/acta/. This report highlights selected aspects of the congress and the latest advances in the field. PMID:24924756

  19. Chinese duo fired for scientific fraud

    NASA Astrophysics Data System (ADS)

    Jiao, Li

    2010-02-01

    A major case of academic fraud in China has led to calls for the country to adopt a new system of academic evaluation that steers away from heavily supporting scientists who publish the most papers. The calls have been made after some 70 papers published by Chinese scientists in Acta Crystallographica Section E were retracted from the journal late last year. The authors acknowledged that their analysis had been fabricated.

  20. Measurement of radon gas on major faults in California, USA

    USGS Publications Warehouse

    Zhang, W.; King, C.-Y.

    1994-01-01

    Abundant data have been gathered through measurements of radon gas emission in the soil on several major active faults, such as San Andreas and Calaveras, in California, U.S.A.. They show radon emissions and their spatial variations at the unlocked, locked, and creeping sections of faults with different tectonic movements. The characteristics of these variations and the role of fault gases in the research on earthquake prediction are discussed in this paper. ?? 1994 Acta Seismologica Sinica.

  1. Congenital Heart Defects Are Rarely Caused by Mutations in Cardiac and Smooth Muscle Actin Genes

    PubMed Central

    Khodyuchenko, Tatiana; Zlotina, Anna; Pervunina, Tatiana; Zverev, Dmitry; Malashicheva, Anna; Kostareva, Anna

    2015-01-01

    Background. Congenital heart defects (CHDs) often have genetic background due to missense mutations in cardiomyocyte-specific genes. For example, cardiac actin was shown to be involved in pathogenesis of cardiac septum defects and smooth muscle actin in pathogenesis of aortic aneurysm in combination with patent ductus arteriosus (PDA). In the present study, we further searched for mutations in human α-cardiac actin (ACTC1) and smooth muscle α-actin (ACTA2) genes as a possible cause of atrial septum defect type II (ASDII) and PDA. Findings. Total genomic DNA was extracted from peripheral blood of 86 individuals with ASDs and 100 individuals with PDA. Coding exons and flanking intron regions of ACTC1 (NM_005159.4) and ACTA2 (NM_001613) were amplified by PCR with specific primers designed according to the corresponding gene reference sequences. PCR fragments were directly sequenced and analyzed. Sequence analysis of ACTC1 and ACTA2 did not identify any nucleotide changes that altered the coding sense of the genes. In ACTC1 gene, we were able to detect one previously described nucleotide polymorphism (rs2307493) resulting in a synonymous substitution. The frequency of this SNP was similar in the study and control group, thus excluding it from the possible disease-associated variants. Conclusions. Our results confirmed that the mutations in ACTC1 gene are rare (at least <1%) cause of ASDII. Mutations in ACTA2 gene were not detected in patients with PDA, thus being excluded from the list of frequent PDA-associated genetic defects. PMID:25861618

  2. National Registry of Genetically Triggered Thoracic Aortic Aneurysms and Cardiovascular Conditions

    ClinicalTrials.gov

    2015-12-08

    Marfan Syndrome; Turner Syndrome; Ehlers-Danlos Syndrome; Loeys-Dietz Syndrome; FBN1, TGFBR1, TGFBR2, ACTA2 or MYH11 Genetic Mutation; Bicuspid Aortic Valve Without Known Family History; Bicuspid Aortic Valve With Family History; Bicuspid Aortic Valve With Coarctation; Familial Thoracic Aortic Aneurysm and Dissections; Shprintzen-Goldberg Syndrome; Other Aneur/Diss of Thoracic Aorta Not Due to Trauma, <50yo; Other Congenital Heart Disease

  3. What Will They Learn? A Survey of Core Requirements at Our Nation's Colleges and Universities. 2011-12

    ERIC Educational Resources Information Center

    Kempson, Lauri; Bako, Tom; Markley, Eric

    2012-01-01

    What does it mean to be a college graduate? One knows about the time and ever-increasing amount of money that a diploma demands. But when it comes down to what matters--the skills and knowledge acquired--what does a college degree mean? That is the question the American Council of Trustees and Alumni (ACTA) answers in this book. Inside one will…

  4. Characterization of a Cartilage-Like Engineered Biomass Using a Self-Aggregating Suspension Culture Model: Molecular Composition Using FT-IRIS

    PubMed Central

    Kim, Minwook; Kraft, Jeffrey J.; Volk, Andrew C.; Pugarelli, Joan; Pleshko, Nancy; Dodge, George R.

    2011-01-01

    Maintenance of chondrocyte phenotype and robust expression and organization of macromolecular components with suitable cartilaginous properties is an ultimate goal in cartilage tissue engineering. We used a self-aggregating suspension culture (SASC) method to produce an engineered cartilage, “cartilage tissue analog” (CTA). With an objective of understanding the stability of phenotype of the CTA over long periods, we cultured chondrocytes up to 4 years and analyzed the matrix. Both early (eCTAs) (6 months) and aged (aCTAs) (4 years) showed type II collagen throughout with higher concentrations near the edge. Using Fourier transform-infrared imaging spectroscopy (FT-IRIS), proteoglycan/collagen ratio of eCTA was 2.8 times greater than native cartilage at 1 week, but the ratio was balanced to native level (p = 0.017) by 36 weeks. Surprisingly, aCTAs maintained the hyaline characteristics, but there was evidence of calcification within the tissue with a distinct range of intensities. Mineral/matrix ratio of those aCTA with “intensive” calcification was significantly higher (p = 0.017) than the “partial,” but when compared to native bone the ratio of “intensive” aCTAs was 2.4 times lower. In this study we utilized the imaging approach of FT-IRIS and have shown that a biomaterial formed is compositionally closely related to natural cartilage for long periods in culture. We show that this culture platform can maintain a CTA for extended periods of time (4 years) and under those conditions signs of mineralization can be found. This method of cartilage tissue engineering is a promising method to generate cartilaginous biomaterial and may have potential to be utilized in both cartilage and boney repairs. PMID:21630329

  5. Cosmochemistry and Mineralogy of Primitive Meteorites

    NASA Technical Reports Server (NTRS)

    Buseck, Peter R.

    2003-01-01

    We have produced significant research results during the grant period. These have been reported in five papers published in Geochimica et Cosmochimica Acta and Meteoritics and Planetary Science and several others are in review. We also presented 17 abstracted talks at professional meetings. The citations are given in section 2, and abstracts of the papers are provided in section 3. The full papers are available on request.

  6. Parameter-free exchange potential for excitation in the density-functional theory: Application to excitation energies within the fractional-occupation approach

    NASA Astrophysics Data System (ADS)

    Nagy, Á.

    1990-10-01

    The density-functional theory for ensembles of fractional occupation formulated by Gross, Oliveira, and Kohn [Phys. Rev. A 37, 2821 (1988)] has been applied. The excitation energies of several atoms have been determined using a parameter-free exchange potential of Gáspár [Acta Phys. Hung. 35, 213 (1974)]. The calculated excitation energies are in good agreement with the experimental values.

  7. Thin film adhesion by nanoindentation-induced superlayers. Final report

    SciTech Connect

    Gerberich, William W.; Volinsky, A.A.

    2001-06-01

    This work has analyzed the key variables of indentation tip radius, contact radius, delamination radius, residual stress and superlayer/film/interlayer properties on nanoindentation measurements of adhesion. The goal to connect practical works of adhesion for very thin films to true works of adhesion has been achieved. A review of this work titled ''Interfacial toughness measurements of thin metal films,'' which has been submitted to Acta Materialia, is included.

  8. Finite gradient elasticity and plasticity: a constitutive mechanical framework

    NASA Astrophysics Data System (ADS)

    Bertram, Albrecht

    2015-11-01

    Following a suggestion by Forest and Sievert (Acta Mech 160:71-111, 2003), a constitutive frame for a general gradient elastoplasticity for finite deformations is established. The basic assumptions are the principle of Euclidean invariance and the isomorphy of the elastic ranges. Both the elastic and the plastic laws include the first and the second deformation gradient. The starting point is an objective expression for the stress power.

  9. A survey of recently published papers on orthopedics in the Brazilian scientific press

    PubMed Central

    Rocha-e-Silva, Mauricio; Gomes, Ariane Maris

    2012-01-01

    This paper is a review of articles published in Brazilian scientific periodicals in recent years. Its main purpose is to bring to the attention of the readership of Acta Ortopedica Brasileira original contributions to the field published in non-specialized journals. We hope that this will serve as a general scientific update for readers. The review includes works published in six ISI indexed non-orthopedic journals, following a literature search conducted in fourteen such journals. PMID:24453633

  10. MicroRNA-208b Alleviates Post-Infarction Myocardial Fibrosis in a Rat Model by Inhibiting GATA4

    PubMed Central

    Zhou, Chaoyuan; Cui, Qintao; Su, Guobao; Guo, Xiaoliang; Liu, Xiaochen; Zhang, Jie

    2016-01-01

    Background Myocardial infarction affects the health of many people. Post-infarction myocardial fibrosis has attracted much attention, but details of the mechanism remain elusive. In this study, the role of microRNA-208b (miR-208b) in modulating post-infarction myocardial fibrosis and the related mechanism were investigated. Material/Methods A rat model of myocardial infarction induced by ligating the left anterior descending artery was used to analyze the expression and roles of miR-208b by overexpression with the lentivirus vector of pre-miR-208b. Myocardial function was assessed and the expression of fibrosis-related factors type I collagen (COL1) and ACTA2 (alias αSMA) was detected. Myocardial fibroblasts isolated from newborn rats were transfected with luciferase reporter vectors containing wild-type or mutant Gata4 3′ UTR to verify the relationship between Gata4 and miR-208b. We then transfected the specific small interference RNA of Gata4 to detect changes in COL1 and ACTA2. Results miR-208b was down-regulated in hearts of model rats (P<0.01). Overexpressing miR-208b improved myocardial functions, such as reducing the infarction area (P<0.05) and promoting LVEF and LVFS (P<0.01), and inhibited COL1 and ACTA2 (P<0.01). Luciferase reporter assay proved Gata4 to be the direct target of miR-208b, with the target sequence in the 3′UTR. Inhibiting GATA4 resulted in the down-regulation of COL1 and ACTA2, suggesting that the role of miR-208b was achieved via regulating GATA4. Conclusions This study demonstrates the protective function of miR-208b via GATA4 in post-infarction myocardial fibrosis, providing a potential therapeutic target for treating myocardial fibrosis. PMID:27236543

  11. Growth of Mouse Oocytes to Maturity from Premeiotic Germ Cells In Vitro

    PubMed Central

    Zhang, Zhi-Peng; Liang, Gui-Jin; Zhang, Xi-Feng; Zhang, Guo-Liang; Chao, Hu-He; Li, Lan; Sun, Xiao-Feng; Min, Ling-Jiang; Pan, Qing-Jie; Shi, Qing-Hua; Sun, Qing-Yuan; De Felici, Massimo; Shen, Wei

    2012-01-01

    In the present study, we established an in vitro culture system suitable for generating fertilizable oocytes from premeiotic mouse female germ cells. These results were achieved after first establishing an in vitro culture system allowing immature oocytes from 12–14 day- old mice to reach meiotic maturation through culture onto preantral granulosa cell (PAGC) monolayers in the presence of Activin A (ActA). To generate mature oocytes from premeiotic germ cells, pieces of ovaries from 12.5 days post coitum (dpc) embryos were cultured in medium supplemented with ActA for 28 days and the oocytes formed within the explants were isolated and cocultured onto PAGC monolayers in the presence of ActA for 6–7 days. The oocytes were then subjected to a final meiotic maturation assay to evaluate their capability to undergo germinal vesicle break down (GVBD) and reach the metaphase II (MII) stage. We found that during the first 28 days of culture, a significant number of oocytes within the ovarian explants reached nearly full growth and formed preantral follicle-like structures with the surrounding somatic cells. GSH level and Cx37 expression in the oocytes within the explants were indicative of proper developmental conditions. Moreover, the imprinting of Igf2r and Peg3 genes in these oocytes was correctly established. Further culture onto PAGCs in the presence of ActA allowed about 16% of the oocytes to undergo GVBD, among which 17% reached the MII stage during the final 16–18 hr maturation culture. These MII oocytes showed normal spindle and chromosome assembly and a correct ERK1/2 activity. About 35% of the in vitro matured oocytes were fertilized and 53.44% of them were able to reach the 2-cell stage. Finally, around 7% of the 2-cell embryos developed to the morula/blastocyst stage. PMID:22848595

  12. Clinical, pathological, and genetic analysis of a Korean family with thoracic aortic aneurysms and dissections carrying a novel Asp26Tyr mutation.

    PubMed

    Yoo, Eun-Hyung; Choi, Seung Hyuk; Jang, Shin Yi; Suh, Yeon-Lim; Lee, Inchul; Song, Jae-Kwan; Choe, Yeon Hyeon; Kim, Jong-Won; Ki, Chang-Seok; Kim, Duk-Kyung

    2010-01-01

    Non-syndromic familial thoracic aortic aneurysms and dissections (TAADs), inherited in an autosomal dominant manner in up to 19% of patients, are genetically heterogeneous. The ACTA2 gene, which encodes the vascular smooth muscle cell (SMC)-specific isoform of alpha-actin, is known to cause TAADs and occlusive vascular diseases, including coronary artery disease and premature ischemic stroke. We have investigated a Korean family with DeBakey type I aortic dissection related to pregnancy and a strong family history of TAADs. All affected family members underwent surgical repair of the ascending aorta. Other clinical features of familial TAAD, including inguinal hernias, iris flocculi, and livedo reticularis, were not observed. Histologic studies of aortic tissues showed medial degeneration and SMC hyperplasia in the aorta, consistent with previous observations. Molecular analyses of the ACTA2 gene showed a novel heterozygous missense mutation (c.76G>T; p.Asp26Tyr). Further analysis of a female patient and members of her family revealed that two affected sisters and her asymptomatic son had the same mutation. The novel Asp26Tyr mutation resides in SM alpha-actin subdomain 1 and is linked to TAAD with hypertrophy and disarray of SMCs and severe migraine, but not to livedo reticularis or iris flocculi. This study expands the spectrum of mutations of the ACTA2 gene by identifying a novel missense mutation. This is the first report of a pathologically- and genetically-confirmed family with TAAD in Korea. PMID:20689142

  13. Mutations of the Act Promoter in Myxococcus xanthus▿ †

    PubMed Central

    Gronewold, Thomas M. A.; Kaiser, Dale

    2007-01-01

    Mutations within the −12 and −24 elements provide evidence that the act promoter is recognized by sigma-54 RNA polymerase. Deletion of the −20 base pair, which lies between the two conserved elements of sigma-54 promoters, decreased expression by 90%. In addition, mutation of a potential enhancer sequence, around −120, led to an 80% reduction in act gene expression. actB, the second gene in the act operon, encodes a sigma-54 activator protein that is proposed to be an enhancer-binding protein for the act operon. All act genes, actA to actE, are expressed together and constitute an operon, because an in-frame deletion of actB decreased expression of actA and actE to the same extent. After an initially slow phase of act operon expression, which depends on FruA, there is a rapid phase. The rapid phase is shown to be due to the activation of the operon expression by ActB, which completes a positive feedback loop. That loop appears to be nested within a larger positive loop in which ActB is activated by the C signal via ActA, and the act operon activates transcription of the csgA gene. We propose that, as cells engage in more C signaling, positive feedback raises the number of C-signal molecules per cell and drives the process of fruiting body development forward. PMID:17189369

  14. Chromite alteration processes within Vourinos ophiolite

    NASA Astrophysics Data System (ADS)

    Grieco, Giovanni; Merlini, Anna

    2012-09-01

    The renewed interest in chromite ore deposits is directly related to the increase in Cr price ruled by international market trends. Chromite, an accessory mineral in peridotites, is considered to be a petrogenetic indicator because its composition reflects the degree of partial melting that the mantle experienced while producing the chromium spinel-bearing rock (Burkhard in Geochim Cosmochim Acta 57:1297-1306, 1993). However, the understanding of chromite alteration and metamorphic modification is still controversial (e.g. Evans and Frost in Geochim Cosmochim Acta 39:959-972, 1975; Burkhard in Geochim Cosmochim Acta 57:1297-1306, 1993; Oze et al. in Am J Sci 304:67-101, 2004). Metamorphic alteration leads to major changes in chromite chemistry and to the growth of secondary phases such as ferritchromite and chlorite. In this study, we investigate the Vourinos complex chromitites (from the mines of Rizo, Aetoraches, Xerolivado and Potamia) with respect to textural and chemical analyses in order to highlight the most important trend of alteration related to chromite transformation. The present study has been partially funded by the Aliakmon project in collaboration between the Public Power Corporation of Greece and Institute of Geology and Mineral Exploration of Kozani.

  15. Retraction statement: Dynamics of Cytochrome C Oxidase Activity in Acute Ischemic Stroke' by Selaković, V.M., Jovanović, M.D., Mihajlović, R.R. and Radenović, L.L.J.

    PubMed

    2016-10-01

    The above article from Acta Neurologica Scandinavica, published online on 7 April 2005 in Wiley Online Library (wileyonlinelibrary.com) and in Volume 111, pp. 329-332, has been retracted by agreement between the journal Editor in Chief, Professor Elinor Ben-Menachem, and John Wiley & Sons Ltd. The article has been retracted because a similar article had previously been published in the Jugoslovenska medicinska biohemija in 2003. The authors presumed that since the journal was no longer existing, they felt the need to re-publish their work in Acta Neuorologica Scandinavica. However, in the consideration of the Journal, this constitutes dual publication. References SelakovićVM, JovanovićMD, MihajlovićR, RadenovićLLJ. Cytochrome c oxidase in patients with acute ischaemic brain disease. Jugoslovenska medicinska biohemija. 2003;22:329-334. SelakovićVM, JovanovićMD, MihajlovićRR, RadenovićLLJ. Dynamics of cytochrome c oxidase activity in acute ischemic stroke. Acta Neurol Scand. 2005;111:329-332. PMID:27592845

  16. Determination of Structural and Vibrational Properties of 5-QUINOLINECARBOXALDEHYDE Using Experimental Ft-Ir Ft-Raman Techniques and Theoretical HF and DFT Methods

    NASA Astrophysics Data System (ADS)

    Kumru, Mustafa; Kocademir, Mustafa; Bardakci, Tayyibe

    2013-06-01

    Quinoline derivatives have been used in several pharmaceuticals. They have vital roles in regulating the functions of DNA and cancerous cells. It's necessary to determine the structures and spectroscopic properties of quinoline derivates. In this study, the FT-IR (including mid and far regions) and FT-Raman spectra of 5-quinolinecarboxaldehyde have been investigated. Hartree-Fock (HF) and density functional B3LYP calculations have also been employed with the 6-311++G(d,p) basis set for investigating the structural and spectroscopic properties of the cis and trans conformers of 5-quinolinecarboxaldehyde. Experimental and theoretical results have been compared and the results are in good agreement with each other. Keywords: 5-quinolinecarboxaldehyde; Vibrational Spectroscopy; FT-IR spectra; FT-Raman spectra; Vibrational Modes; HF; DFT [1] V. Kucuk, A. Altun, M. Kumru, Spectrochim. Acta Part A 85(2012)92-98 [2] M. Kumru, V. Kucuk, T. Bardakci, Spectrochim. Acta Part A 90(2012)28-34 [3] M. Kumru, V. Kucuk, M. Kocademir, Spectrochim. Acta Part A, 96 (2012) 242-251 We thank the Turkish Scientific and Technical Research Council (TUBITAK) for their financial support through National Postdoctoral Research Scholarship Programme and Scientific Research Fund of Fatih University under the project number P50011001 G (1457).

  17. 78 FR 19009 - Gary Alfred Shearer, M.D.; Decision And Order

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-28

    ... proceeding under section 304, 21 U.S.C. 824, of the CSA.'' Zhiwei Lin, 77 FR 18862, 18864 (2012) (citing... Kentucky, not Florida.) \\16\\ See Michael G. Dolin, M.D., 65 FR 5661 (2000); see also Philip E. Kirk, M.D., 48 FR 32887 (1983), aff'd sub nom. Kirk v. Mullen, 749 F.2d 297 (6th Cir. 1984). \\17\\ See 28...

  18. 77 FR 63419 - Unblocking of Specially Designated Nationals and Blocked Persons Pursuant to the Foreign...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-16

    ... the Kingpin Act: Individuals 1. ROMERO BARRERA, Benedicto, c/o AGROFUTURO R.H. Y CIA. S.C.S., Medellin...) (individual) . Entities 1. AGROFUTURO R.H. Y CIA. S.C.S., Calle 80 Sur No. 47D-65 Bod. 114, Medellin, Colombia..., Carlos Arturo, c/o AGROFUTURO R.H. Y CIA. S.C.S., Medellin, Colombia; c/o COMERCIALIZADORA...

  19. A photometric and radial velocity study of six southern Cepheids. I - The data

    NASA Astrophysics Data System (ADS)

    Coulson, I. M.; Caldwell, J. A. R.; Gieren, W. P.

    1985-03-01

    New observations of the galactic Cepheids AQ Car (period = 9d.77), XX Cen (10d.95), XY Car (12d.44), TT Aql (13d.75), XX Car (15d.71), and XZ Car (16d.65) are presented. 365 photometric measures in the UBVRIc system and 297 radial velocities are combined with previous data to produce light, color, and velocity curves of almost total phase coverage.

  20. New functional aspects of the atypical protein tyrosine phosphatase VHZ

    PubMed Central

    Kuznetsov, Vyacheslav I.; Hengge, Alvan C.

    2013-01-01

    LDP3 (VHZ) is the smallest classical protein tyrosine phosphatase (PTP) known to date, and was originally misclassified as an atypical dual specificity phosphatase (DSP). Kinetic isotope effects with steady state and pre-steady state kinetics of VHZ and mutants with para-nitrophenol phosphate (pNPP) have revealed several unusual properties. VHZ is significantly more active than previously reported, but remains one of the least active PTPs. Highly unusual for a PTP, VHZ possesses two acidic residues (E134 and D65) in the active site. D65 occupies the position corresponding to the typical general acid in the PTP family. However, VHZ primarily utilizes E134 as the general acid, with D65 taking over this role when E134 is mutated. This unusual behavior is facilitated by two coexisting, but unequally populated, substrate binding modes. Unlike most classical PTPs, VHZ exhibits phosphotransferase activity. Despite the presence of the Q-loop that normally prevents alcoholysis of the phosphoenzyme intermediate in other classical PTPs, VHZ readily phosphorylates ethylene glycol. Although mutations to Q-loop residues affect this phosphotransferase activity, mutations on the IPD-loop that contains the general acid exert more control over this process. A single P68V substitution on this loop completely abolishes phosphotransferase activity. The ability of native VHZ to catalyze transphosphorylation may lead to an imbalance of intracellular phosphorylation, which could explain the correlation of its overexpression with several types of cancer. PMID:24073992

  1. Illuminating light-dependent color shifts in core and veneer layers of dental all-ceramics

    NASA Astrophysics Data System (ADS)

    Lee, Yong-Keun; Cha, Hyun-Suk; Yu, Bin

    2014-09-01

    The color of an object is perceived differently depending on the ambient light conditions. Since dental all-ceramic restorations are fabricated by building up several layers to reproduce the tooth shade, the optical properties of each layer should be optimized for successful shade reproduction. This study aimed to determine the separate contributions of the color shifts in each of the core and veneer layers of all-ceramics by switching the illuminating lights on the color shifts of layered ceramics. Specimens of seven kinds of core ceramics and the corresponding veneer ceramics for each core were fabricated with a layered thickness of 1.5 mm. A sintering ceramic was used as a reference core material. The Commission Internationale de l'Eclairage (CIE) color coordinates of core, veneer, and layered specimens were measured with a spectroradiometer under the CIE illuminant D65 (daylight), A (incandescent lamp), and F9 (fluorescent lamp) simulating lights. Color shifts of the layered specimens were primarily determined by the CIE a* shifts (D65 to A switch) or by the CIE b* shifts (D65 to F9 switch) of the veneer layer. The color coordinates shifts in the constituent layers differentially influenced those of the layered specimens by the kind of switched lights. Therefore, the optical properties of the constituent layers of all-ceramics should be controlled to reflect these findings.

  2. Illuminating light-dependent color shifts in core and veneer layers of dental all-ceramics.

    PubMed

    Lee, Yong-Keun; Cha, Hyun-Suk; Yu, Bin

    2014-09-01

    The color of an object is perceived differently depending on the ambient light conditions. Since dental all-ceramic restorations are fabricated by building up several layers to reproduce the tooth shade, the optical properties of each layer should be optimized for successful shade reproduction. This study aimed to determine the separate contributions of the color shifts in each of the core and veneer layers of all-ceramics by switching the illuminating lights on the color shifts of layered ceramics. Specimens of seven kinds of core ceramics and the corresponding veneer ceramics for each core were fabricated with a layered thickness of 1.5 mm. A sintering ceramic was used as a reference core material. The Commission Internationale de l’Eclairage (CIE) color coordinates of core, veneer, and layered specimens were measured with a spectroradiometer under the CIE illuminant D65 (daylight), A (incandescent lamp), and F9 (fluorescent lamp) simulating lights. Color shifts of the layered specimens were primarily determined by the CIE a shifts (D65 to A switch) or by the CIE b shifts (D65 to F9 switch) of the veneer layer. The color coordinates shifts in the constituent layers differentially influenced those of the layered specimens by the kind of switched lights. Therefore, the optical properties of the constituent layers of all-ceramics should be controlled to reflect these findings. PMID:25247394

  3. Bidirectional reflectance spectroscopy of carbonaceous chondrites: Implications for water quantification and primary composition

    NASA Astrophysics Data System (ADS)

    Garenne, A.; Beck, P.; Montes-Hernandez, G.; Brissaud, O.; Schmitt, B.; Quirico, E.; Bonal, L.; Beck, C.; Howard, K. T.

    2016-01-01

    In this study, we measured bidirectional reflectance spectra (0.5-4.0 μm) of 24 CMs, five CRs, one CI, one CV, and one C2 carbonaceous chondrites. These meteorites are known to have experienced an important variability in their relative degrees of aqueous alteration degree (Rubin et al. [2007]. Geochim. Cosmochim. Acta 71, 2361-2382; Howard et al. [2009]. Geochim. Cosmochim. Acta 73, 4576-4589; Howard et al. [2011]. Geochim. Cosmochim. Acta 75, 2735-2751; Alexander et al. [2013]. Geochim. Cosmochim. Acta 123, 244-260). These measurements were performed on meteorite powders inside an environmental cell under a primary vacuum and heated at 60 °C in order to minimize adsorbed terrestrial water. This protocol allows controlling of atmospheric conditions (i.e. humidity) in order to avoid contamination by terrestrial water. We discuss various spectral metrics (e.g. reflectance, band depth, single-scattering albedo, …) in the light of recent bulk composition characterization (Howard et al. [2009]. Geochim. Cosmochim. Acta 73, 4576-4589; Howard et al. [2015]. Geochim. Cosmochim. Acta 149, 206-222; Alexander et al. [2012]. Science 337, 721; Beck et al. [2014]. Icarus 229, 263-277; Garenne et al. [2014]. Geochim. Cosmochim. Acta 137, 93-112). This study reveals variability of reflectance among meteorite groups. The reflectance is not correlated with carbon or hydrogen abundance neither with measured grain size distribution. We suggest that it is rather controlled by the nature of accreted components, in particular the initial matrix/chondrule proportion. Band depth, integrated band depth, mean optical path length, normalized optical path length, effective single-particle absorption thickness were calculated on the so called 3-μm band for reflectance spectra and for single scattering albedo spectra. They were compared with hydrated phase proportions from previous study on the same meteorites by thermogravimetric analyses and infrared spectroscopy in transmission. We find

  4. Cuticular Biominerals of the Terrestrial Crustacean Oniscus asellus (Isopoda, Linnaeus 1758)

    NASA Astrophysics Data System (ADS)

    Mergelsberg, S. T.; Mukhopadhyay, B.; Dove, P. M.

    2013-12-01

    F, Westbroek P et al., 1996, Proc Nat Acad Sci 93:1554-1559 Auzou G, 1953, L Ann Sci Nat 15:71-98 Ziegler A, 1997, Zoomorphology 117:181-187 Ziegler A et al., 2012, Cryst Growth Des 12:646-655 Keene EC et al., 2010, Cryst Growth Des 10:1383-1389

  5. Nanoscale Structure at Mineral-Fluid Interfaces

    NASA Astrophysics Data System (ADS)

    Sturchio, N. C.; Sturchio, N. C.; Fenter, P.; Cheng, L.; Park, C.; Zhang, Z.; Zhang, Z.; Nagy, K. L.; Schlegel, M. L.

    2001-12-01

    The nature of nanoparticles and their role in the natural environment is currently a subject of renewed interest. The high surface area (and surface area-to-volume ratio) of nanoparticles exerts a widespread influence on geochemical reactions and transport processes. A thorough understanding of the nanoscale world remains largely hypothetical, however, because of the challenges associated with characterizing nanoscale structures and processes. Recent insights gained from high-resolution synchrotron x-ray reflectivity measurements at the solid-fluid interfaces of macroscopic (i.e., mm-scale) mineral particles may provide relevant guidelines for expected nanoparticle surface structures. For example, at calcite-water and barite-water interfaces, undercoordinated surface cations bond with water species of variable protonation, and modest relaxations (to several hundredths of a nanometer) affect the outermost unit cells [1,2]. Undercoordinated tetrahedral ions at aluminosilicate surfaces also bond with water species, whereas interstitial or interlayer alkali or alkaline earth ions at the surface may readily exchange with hydronium or other ions; modest relaxations also affect the outermost unit cells [3,4]. Modulation of liquid water structure out to about one nanometer has been observed at the (001) cleavage surface of muscovite in deionized water, and may be present at other mineral-fluid interfaces [4]. Dissolution mechanisms at the orthoclase-water interface have been clarified by combining x-ray reflectivity and scanning force microscopy measurements [5]. Further progress in understanding nanoscale structures and processes at macroscopic mineral-water interfaces is likely to benefit nanoparticle studies. [1] Fenter et al. (2000) Geochim. Cosmochim. Acta 64, 1221-1228. [2] Fenter et al. (2001) J. Phys. Chem. B 105(34), 8112-8119. [3] Fenter et al. (2000) Geochim. Cosmochim. Acta 64, 3663-3673. [4] Cheng et al. (2001) Phys. Rev. Lett., (in press). [5] Teng et al

  6. Nemaline myopathy caused by mutations in the muscle alpha-skeletal-actin gene.

    PubMed

    Ilkovski, B; Cooper, S T; Nowak, K; Ryan, M M; Yang, N; Schnell, C; Durling, H J; Roddick, L G; Wilkinson, I; Kornberg, A J; Collins, K J; Wallace, G; Gunning, P; Hardeman, E C; Laing, N G; North, K N

    2001-06-01

    Nemaline myopathy (NM) is a clinically and genetically heterogeneous disorder characterized by muscle weakness and the presence of nemaline bodies (rods) in skeletal muscle. Disease-causing mutations have been reported in five genes, each encoding a protein component of the sarcomeric thin filament. Recently, we identified mutations in the muscle alpha-skeletal-actin gene (ACTA1) in a subset of patients with NM. In the present study, we evaluated a new series of 35 patients with NM. We identified five novel missense mutations in ACTA1, which suggested that mutations in muscle alpha-skeletal actin account for the disease in approximately 15% of patients with NM. The mutations appeared de novo and represent new dominant mutations. One proband subsequently had two affected children, a result consistent with autosomal dominant transmission. The seven patients exhibited marked clinical variability, ranging from severe congenital-onset weakness, with death from respiratory failure during the 1st year of life, to a mild childhood-onset myopathy, with survival into adulthood. There was marked variation in both age at onset and clinical severity in the three affected members of one family. Common pathological features included abnormal fiber type differentiation, glycogen accumulation, myofibrillar disruption, and "whorling" of actin thin filaments. The percentage of fibers with rods did not correlate with clinical severity; however, the severe, lethal phenotype was associated with both severe, generalized disorganization of sarcomeric structure and abnormal localization of sarcomeric actin. The marked variability, in clinical phenotype, among patients with different mutations in ACTA1 suggests that both the site of the mutation and the nature of the amino acid change have differential effects on thin-filament formation and protein-protein interactions. The intrafamilial variability suggests that alpha-actin genotype is not the sole determinant of phenotype. PMID:11333380

  7. Myc Potentiates Apoptosis by Stimulating Bax Activity at the Mitochondria†

    PubMed Central

    Soucie, Erinn L.; Annis, Matthew G.; Sedivy, John; Filmus, Jorge; Leber, Brian; Andrews, David W.; Penn, Linda Z.

    2001-01-01

    The ability of the c-Myc oncoprotein to potentiate apoptosis has been well documented; however, the mechanism of action remains ill defined. We have previously identified spatially distinct apoptotic pathways within the same cell that are differentially inhibited by Bcl-2 targeted to either the mitochondria (Bcl-acta) or the endoplasmic reticulum (Bcl-cb5). We show here that in Rat1 cells expressing an exogenous c-myc allele, distinct apoptotic pathways can be inhibited by Bcl-2 or Bcl-acta yet be distinguished by their sensitivity to Bcl-cb5 as either susceptible (serum withdrawal, taxol, and ceramide) or refractory (etoposide and doxorubicin). Myc expression and apoptosis were universally associated with Bcl-acta and not Bcl-cb5, suggesting that Myc acts downstream at a point common to these distinct apoptotic signaling cascades. Analysis of Rat1 c-myc null cells shows these same death stimuli induce apoptosis with characteristic features of nuclear condensation, membrane blebbing, poly (ADP-ribose) polymerase cleavage, and DNA fragmentation; however, this Myc-independent apoptosis is not inhibited by Bcl-2. During apoptosis, Bax translocation to the mitochondria occurs in the presence or absence of Myc expression. Moreover, Bax mRNA and protein expression remain unchanged in the presence or absence of Myc. However, in the absence of Myc, Bax is not activated and cytochrome c is not released into the cytoplasm. Reintroduction of Myc into the c-myc null cells restores Bax activation, cytochrome c release, and inhibition of apoptosis by Bcl-2. These results demonstrate a role for Myc in the regulation of Bax activation during apoptosis. Moreover, apoptosis that can be triggered in the absence of Myc provides evidence that signaling pathways exist which circumvent Bax activation and cytochrome c release to trigger caspase activation. Thus, Myc increases the cellular competence to die by enhancing disparate apoptotic signals at a common mitochondrial amplification

  8. An examination of the regulatory mechanism of Pxdn mutation-induced eye disorders using microarray analysis

    PubMed Central

    YANG, YANG; XING, YIQIAO; LIANG, CHAOQUN; HU, LIYA; XU, FEI; MEI, QI

    2016-01-01

    The present study aimed to identify biomarkers for peroxidasin (Pxdn) mutation-induced eye disorders and study the underlying mechanisms involved in this process. The microarray dataset GSE49704 was used, which encompasses 4 mouse samples from embryos with Pxdn mutation and 4 samples from normal tissues. After data preprocessing, the differentially expressed genes (DEGs) between Pxdn mutation and normal tissues were identified using the t-test in the limma package, followed by functional enrichment analysis. The protein-protein interaction (PPI) network was constructed based on the STRING database, and the transcriptional regulatory (TR) network was established using the GeneCodis database. Subsequently, the overlapping DEGs with high degrees in two networks were identified, as well as the sub-network extracted from the TR network. In total, 121 (75 upregulated and 46 downregulated) DEGs were identified, and these DEGs play important roles in biological processes (BPs), including neuron development and differentiation. A PPI network containing 25 nodes such as actin, alpha 1, skeletal muscle (Acta1) and troponin C type 2 (fast) (Tnnc2), and a TR network including 120 nodes were built. By comparing the two networks, seven crucial genes which overlapped were identified, including cyclin-dependent kinase inhibitor 1B (Cdkn1b), Acta1 and troponin T type 3 (Tnnt3). In the sub-network, Cdkn1b was predicted as the target of miRNAs such as mmu-miR-24 and transcription factors (TFs) including forkhead box O4 (FOXO4) and activating enhancer binding protein 4 (AP4). Thus, we suggest that seven crucial genes, including Cdkn1b, Acta1 and Tnnt3, play important roles in the progression of eye disorders such as glaucoma. We suggest that Cdkn1b exert its effects via the inhibition of proliferation and is mediated by mmu-miR-24 and targeted by the TFs FOXO4 and AP4. PMID:27121343

  9. Meta-analysis as Statistical and Analytical Method of Journal’s Content Scientific Evaluation

    PubMed Central

    Masic, Izet; Begic, Edin

    2015-01-01

    Introduction: A meta-analysis is a statistical and analytical method which combines and synthesizes different independent studies and integrates their results into one common result. Goal: Analysis of the journals “Medical Archives”, “Materia Socio Medica” and “Acta Informatica Medica”, which are located in the most eminent indexed databases of the biomedical milieu. Material and methods: The study has retrospective and descriptive character, and included the period of the calendar year 2014. Study included six editions of all three journals (total of 18 journals). Results: In this period was published a total of 291 articles (in the “Medical Archives” 110, “Materia Socio Medica” 97, and in “Acta Informatica Medica” 84). The largest number of articles was original articles. Small numbers have been published as professional, review articles and case reports. Clinical events were most common in the first two journals, while in the journal “Acta Informatica Medica” belonged to the field of medical informatics, as part of pre-clinical medical disciplines. Articles are usually required period of fifty to fifty nine days for review. Articles were received from four continents, mostly from Europe. The authors are most often from the territory of Bosnia and Herzegovina, then Iran, Kosovo and Macedonia. Conclusion: The number of articles published each year is increasing, with greater participation of authors from different continents and abroad. Clinical medical disciplines are the most common, with the broader spectrum of topics and with a growing number of original articles. Greater support of the wider scientific community is needed for further development of all three of the aforementioned journals. PMID:25870484

  10. Potential Role of Glycogen Synthase Kinase-3β in Regulation of Myocardin Activity in Human Vascular Smooth Muscle Cells.

    PubMed

    Zhou, Yi-Xia; Shi, Zhan; Singh, Pavneet; Yin, Hao; Yu, Yan-Ni; Li, Long; Walsh, Michael P; Gui, Yu; Zheng, Xi-Long

    2016-02-01

    Glycogen synthase kinase (GSK)-3β, a serine/threonine kinase with an inhibitory role in glycogen synthesis in hepatocytes and skeletal muscle, is also expressed in cardiac and smooth muscles. Inhibition of GSK-3β results in cardiac hypertrophy through reducing phosphorylation and increasing transcriptional activity of myocardin, a transcriptional co-activator for serum response factor. Myocardin plays critical roles in differentiation of smooth muscle cells (SMCs). This study, therefore, aimed to examine whether and how inhibition of GSK-3β regulates myocardin activity in human vascular SMCs. Treatment of SMCs with the GSK-3β inhibitors AR-A014418 and TWS 119 significantly reduced endogenous myocardin activity, as indicated by lower expression of myocardin target genes (and gene products), CNN1 (calponin), TAGLN1 (SM22), and ACTA2 (SM α-actin). In human SMCs overexpressing myocardin through the T-REx system, treatment with either GSK-3β inhibitor also inhibited the expression of CNN1, TAGLN1, and ACTA2. These effects of GSK-3β inhibitors were mimicked by transfection with GSK-3β siRNA. Notably, both AR-A014418 and TWS 119 decreased the serine/threonine phosphorylation of myocardin. The chromatin immunoprecipitation assay showed that AR-A014418 treatment reduced myocardin occupancy of the promoter of the myocardin target gene ACTA2. Overexpression of a dominant-negative GSK-3β mutant in myocardin-overexpressing SMCs reduced the expression of calponin, SM22, and SM α-actin. As expected, overexpression of constitutively active or wild-type GSK-3β in SMCs without myocardin overexpression increased expression of these proteins. In summary, our results indicate that inhibition of GSK-3β reduces myocardin transcriptional activity, suggesting a role for GSK-3β in myocardin transcriptional activity and smooth muscle differentiation. PMID:26129946

  11. Autocrine production of TGF-β1 promotes myofibroblastic differentiation of neonatal lung mesenchymal stem cells

    PubMed Central

    Popova, Antonia P.; Bozyk, Paul D.; Goldsmith, Adam M.; Linn, Marisa J.; Lei, Jing; Bentley, J. Kelley

    2010-01-01

    We have isolated mesenchymal stem cells (MSCs) from tracheal aspirates of premature infants with respiratory distress. We examined the capacity of MSCs to differentiate into myofibroblasts, cells that participate in lung development, injury, and repair. Gene expression was measured by array, qPCR, immunoblot, and immunocytochemistry. Unstimulated MSCs expressed mRNAs encoding contractile (e.g., ACTA2, TAGLN), extracellular matrix (COL1A1 and ELN), and actin-binding (DBN1, PXN) proteins, consistent with a myofibroblast phenotype, although there was little translation into immunoreactive protein. Incubation in serum-free medium increased contractile protein (ACTA2, MYH11) gene expression. MSC-conditioned medium showed substantial levels of TGF-β1, and treatment of serum-deprived cells with a type I activin receptor-like kinase inhibitor, SB-431542, attenuated the expression of genes encoding contractile and extracellular matrix proteins. Treatment of MSCs with TGF-β1 further induced the expression of mRNAs encoding contractile (ACTA2, MYH11, TAGLN, DES) and extracellular matrix proteins (FN1, ELN, COL1A1, COL1A2), and increased the protein expression of α-smooth muscle actin, myosin heavy chain, and SM22. In contrast, human bone marrow-derived MSCs failed to undergo TGF-β1-induced myofibroblastic differentiation. Finally, primary cells from tracheal aspirates behaved in an identical manner as later passage cells. We conclude that human neonatal lung MSCs demonstrate an mRNA expression pattern characteristic of myofibroblast progenitor cells. Autocrine production of TGF-β1 further drives myofibroblastic differentiation, suggesting that, in the absence of other signals, fibrosis represents the “default program” for neonatal lung MSC gene expression. These data are consistent with the notion that MSCs play a key role in neonatal lung injury and repair. PMID:20190033

  12. Second-order Optimality Conditions for Optimal Control of the Primitive Equations of the Ocean with Periodic Inputs

    SciTech Connect

    Tachim Medjo, T.

    2011-02-15

    We investigate in this article the Pontryagin's maximum principle for control problem associated with the primitive equations (PEs) of the ocean with periodic inputs. We also derive a second-order sufficient condition for optimality. This work is closely related to Wang (SIAM J. Control Optim. 41(2):583-606, 2002) and He (Acta Math. Sci. Ser. B Engl. Ed. 26(4):729-734, 2006), in which the authors proved similar results for the three-dimensional Navier-Stokes (NS) systems.

  13. Discovery of a meta-stable Al–Sm phase with unknown stoichiometry using a genetic algorithm

    SciTech Connect

    Zhang, Feng; McBrearty, Ian; Ott, R T; Park, E; Mendelev, Mikhail I; Kramer, M J; Wang, Cai-Zhuang; Ho, Kai-Ming

    2014-06-01

    Unknown crystalline phases observed during the devitrification process of glassy metal alloys significantly limit our ability to understand and control phase selection in these systems driven far from equilibrium. Here, we report a new meta-stable Al5Sm phase identified by simultaneously searching Al-rich compositions of the Al-Sm system, using an efficient genetic algorithm. The excellent match between calculated and experimental X-ray diffraction patterns confirms that this new phase appeared in the crystallization of melt-spun Al90Sm10 alloys. Published by Elsevier Ltd. on behalf of Acta Materialia Inc.

  14. The Local Orthogonality Between Quantum States and Entanglement Decomposition

    NASA Astrophysics Data System (ADS)

    Kim, Sunho; Wu, Junde; Zhang, Lin; Cho, Minhyung

    2016-06-01

    In the paper, we show that when a quantum state can be decomposed as a convex combination of locally orthogonal mixed states, its entanglement can be decomposed into the entanglement of these mixed states without losing them. The obtained result generalizes a corresponding one proved by Horodecki (Acta Phys. Slov. 48, 141 1998). But, for the entanglement cost it requires certain conditions for holding the decomposition, and the distillable entanglement only has a week result as inequality. Finally, we presented an example to show that the conditions of our conclusions are existence.

  15. Aortic Aneurysm: Etiopathogenesis and Clinicopathologic Correlations

    PubMed Central

    2016-01-01

    Aortic aneurysm (AA) is one of the life-threatening aortic diseases, leading to aortic rupture of any cause including atherosclerotic and non-atherosclerotic diseases. AA is diagnosed in a variable proportion of patients with dilated aorta by imaging modality. The etiopathogenesis of AA remains unclear in many aortic diseases. Furthermore, although it may be difficult to explain all phenotypes of patients even if genetic mutation could be identified in some proteins such as smooth muscle cell α-actin (ACTA2), myosin heavy chain 11 (MYH11) or SMAD3, individualized consideration of these factors in each patient is essential on the basis of clinicopathological characteristics. PMID:27375798

  16. Comparison of beetroot extracts originating from several sites using time-resolved laser-induced fluorescence spectroscopy

    NASA Astrophysics Data System (ADS)

    Rabasović, M. S.; Šević, D.; Terzić, M.; Marinković, B. P.

    2012-05-01

    Beetroot (Beta vulgaris) juice contains a large number of fluorophores which can fluoresce. There is a growing interest in beetroot extracts analysis. In contrast, there is only limited information about beetroot obtained without sample preparation and/or extraction of components from the sample. In this work, we continue our previous study (Rabasović et al 2009 Acta Phys. Pol. A 116 570-2), analyzing and comparing beetroot extracts from several sites, using the time-resolved laser-induced fluorescence technique to measure the fluorescence of samples at different excitation wavelengths (340-470 nm) and for different sample dilutions.

  17. GENERAL: Efficient quantum secure communication with a publicly known key

    NASA Astrophysics Data System (ADS)

    Li, Chun-Yan; Li, Xi-Han; Deng, Fu-Guo; Zhou, Hong-Yu

    2008-07-01

    This paper presents a simple way for an eavesdropper to eavesdrop freely the secret message in the experimental realization of quantum communication protocol proposed by Beige et al (2002 Acta Phys. Pol. A 101 357). Moreover, it introduces an efficient quantum secure communication protocol based on a publicly known key with decoy photons and two biased bases by modifying the original protocol. The total efficiency of this new protocol is double that of the original one. With a low noise quantum channel, this protocol can be used for transmitting a secret message. At present, this protocol is good for generating a private key efficiently.

  18. The analysis of protein conformation by infrared spectroscopy: An introduction of the editor to a scientific dispute

    NASA Astrophysics Data System (ADS)

    Mäntele, Werner

    2015-03-01

    Spectrochimica Acta A is open for a vivid exchange among scientists and fosters the open discussion of published papers. This may proceed in the form of a "Comment on a published paper", submitted to our journal as a short communication. Typically, this comment will be sent to the authors of the original article to give them a chance for rebuttal in a "Reply to Comment". Both the Comment and the Reply will be published together in one issue after review by experts. In the interest of a fair discussion, both contributions will eventually have to undergo some editing before publication can be made.

  19. A Multiparty Controlled Bidirectional Quantum Secure Direct Communication and Authentication Protocol Based on EPR Pairs

    NASA Astrophysics Data System (ADS)

    Chang, Yan; Zhang, Shi-Bin; Yan, Li-Li; Sheng, Zhi-Wei

    2013-06-01

    A multiparty controlled bidirectional quantum secure direct communication and authentication protocol is proposed based on EPR pair and entanglement swapping. The legitimate identities of communicating parties are encoded to Bell states which act as a detection sequence. Secret messages are transmitted by using the classical XOR operation, which serves as a one-time-pad. No photon with secret information transmits in the quantum channel. Compared with the protocols proposed by Wang et al. [Acta Phys. Sin. 56 (2007) 673; Opt. Commun. 266 (2006) 732], the protocol in this study implements bidirectional communication and authentication, which defends most attacks including the ‘man-in-the-middle’ attack efficiently.

  20. Critical analysis and extension of the Hirshfeld atoms in molecules.

    PubMed

    Bultinck, Patrick; Van Alsenoy, Christian; Ayers, Paul W; Carbó-Dorca, Ramon

    2007-04-14

    The computational approach to the Hirshfeld [Theor. Chim. Acta 44, 129 (1977)] atom in a molecule is critically investigated, and several difficulties are highlighted. It is shown that these difficulties are mitigated by an alternative, iterative version, of the Hirshfeld partitioning procedure. The iterative scheme ensures that the Hirshfeld definition represents a mathematically proper information entropy, allows the Hirshfeld approach to be used for charged molecules, eliminates arbitrariness in the choice of the promolecule, and increases the magnitudes of the charges. The resulting "Hirshfeld-I charges" correlate well with electrostatic potential derived atomic charges. PMID:17444705

  1. Critical analysis and extension of the Hirshfeld atoms in molecules

    NASA Astrophysics Data System (ADS)

    Bultinck, Patrick; Van Alsenoy, Christian; Ayers, Paul W.; Carbó-Dorca, Ramon

    2007-04-01

    The computational approach to the Hirshfeld [Theor. Chim. Acta 44, 129 (1977)] atom in a molecule is critically investigated, and several difficulties are highlighted. It is shown that these difficulties are mitigated by an alternative, iterative version, of the Hirshfeld partitioning procedure. The iterative scheme ensures that the Hirshfeld definition represents a mathematically proper information entropy, allows the Hirshfeld approach to be used for charged molecules, eliminates arbitrariness in the choice of the promolecule, and increases the magnitudes of the charges. The resulting "Hirshfeld-I charges" correlate well with electrostatic potential derived atomic charges.

  2. Reinvestigation of growth of urea thiosemicarbazone monohydrate crystal

    NASA Astrophysics Data System (ADS)

    Srinivasan, Bikshandarkoil R.; Raghavaiah, Pallepogu; Nadkarni, V. S.

    2013-08-01

    The reaction of urea with thiosemicarbazide in 1:1 mole ratio in aqueous solution does not result in the formation of urea thiosemicarbazone monohydrate crystal, as reported by Hanumantharao, Kalainathan and Bhagavannarayana [Spectrochim. Acta A91 (2012) 345-351]. A reinvestigation of the reported reaction reveals that the crystal obtained is the starting material namely thiosemicarbazide, which has been unambiguously confirmed with the aid of infrared and 1H NMR spectra and single crystal X-ray structure determination. Analysis of 1H NMR spectrum reveals that thiosemicarbazide exhibits thione-thiol tautomerism in solution. In contrast, thiosemicarbazide exists as the thione tautomer in the solid state.

  3. On the mathematical and geometrical structure of the determining equations for shear waves in nonlinear isotropic incompressible elastodynamics

    NASA Astrophysics Data System (ADS)

    Saccomandi, Giuseppe; Vitolo, Raffaele

    2014-08-01

    Using the theory of 1 + 1 hyperbolic systems we put in perspective the mathematical and geometrical structure of the celebrated circularly polarized waves solutions for isotropic hyperelastic materials determined by Carroll [Acta Mechanica 3, 167-181 (1967)]. We show that a natural generalization of this class of solutions yields an infinite family of linear solutions for the equations of isotropic elastodynamics. Moreover, we determine a huge class of hyperbolic partial differential equations having the same property of the shear wave system. Restricting the attention to the usual first order asymptotic approximation of the equations determining transverse waves we provide the complete integration of this system using generalized symmetries.

  4. Use of an alumina column in estimating total iron-binding capacity.

    PubMed

    Starr, R T

    1980-01-01

    I describe a simple, rapid technique for saturating the transferrin in serum and then removing unbound (excess) iron. This technique involves use of an easily prepared column of basic chromatographic alumina and a saturating solution of ferric chloride in citric acid. This method, when compared with the magnesium carbonate method of Ramsay (Clin. Chim. Acta 2: 221, 1957) by regression analysis and tests of precision, showed a negative bias for results by the alumina technique with respect to the magnesium carbonate method. PMID:7356553

  5. Reaustenitization in Fe-C steels revisited

    SciTech Connect

    Mancini, R.; Budde, C.

    1999-08-10

    A finite difference method used in order to model the reaustenitization from a ferrite/cementite mixture in Fe-C steels is presented in this paper. The numerical results obtained are compared with the exact solution of the diffusion equion that describes the process for the planar geometry. The agreement between both methods is excellent in a large range of temperatures. Incidentally, the authors consider worth noting that the second moment of mass condition used by Akbay et al. [Acta Metallurgica et Materialia 47, 1649 (1994)] does not seem to be necessary in the framework of the numerical method. Finally, they compare their results with available experimental values finding good agreement.

  6. Comment on "Density functional theory studies on molecular structure, vibrational spectra and electronic properties of cyanuric acid".

    PubMed

    Reva, Igor

    2015-12-01

    In a recently published paper [Spectrochim. Acta A: Mol. Biomol. Spect. 138 (2015) 711-722], Prabhaharan, Prabakaran, Srinivasan, and Gunasekaran presented a combined experimental and theoretical study on molecular structure, vibrational spectra and NBO analysis of cyanuric acid, and explain their findings using the tri-hydroxy tautomeric form of the compound. In reality, the compound adopts the tri-oxo tautomeric form, which is by over 100kJmol(-1) more stable comparatively to the tri-hydroxy tautomer discussed and characterized by Prabhaharan et al. PMID:26142656

  7. Infantile hypophosphatasia without bone deformities presenting with severe pyridoxine-resistant seizures.

    PubMed

    de Roo, Marieke G A; Abeling, Nico G G M; Majoie, Charles B; Bosch, Annet M; Koelman, Johannes H T M; Cobben, Jan M; Duran, Marinus; Poll-The, Bwee Tien

    2014-03-01

    An infant carrying a heterozygous c.43_46delACTA and a heterozygous c.668 G>A mutation in the ALPL gene with hypophosphatasia in the absence of bone deformities presented with therapy-resistant seizures. Pyridoxal phosphate was extremely high in CSF and plasma. Pyridoxine treatment had only a transient effect and the severe encephalopathy was fatal. Repeated brain MRIs showed progressive cerebral damage. The precise metabolic cause of the seizures remains unknown and pyridoxine treatment apparently does not cure the epilepsy. PMID:24100244

  8. Spherical nanoindentation stress-strain curves of commercially pure titanium and Ti-6Al-4V

    DOE Data Explorer

    Weaver, Jordan S. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Priddy, Matthew W. [Georgia Inst. of Technology, Atlanta, GA (United States); McDowell, David L. [Georgia Inst. of Technology, Atlanta, GA (United States); Kalidindi, Surya R. [Georgia Inst. of Technology, Atlanta, GA (United States)

    2016-07-27

    Spherical nanoindentation combined with electron back-scattered diffraction was employed to characterize the grain-scale elastic and plastic anisotropy of single crystal alpha-Ti for commercially pure (CP-Ti) and alloyed (Ti-64) titanium. In addition, alpha-beta Ti (single colony) grains were characterized. The data set includes the nanoindentation force, displacement, and contact stiffness, the nanoindentation stress-strain analysis, and the alpha-Ti crystal orientations. Details of the samples and experimental protocols can be found in Weaver et al. (2016) Acta Materialia doi:10.1016/j.actamat.2016.06.053.

  9. Statistical thermodynamics of strain hardening in polycrystalline solids

    NASA Astrophysics Data System (ADS)

    Langer, J. S.

    2015-09-01

    This paper starts with a systematic rederivation of the statistical thermodynamic equations of motion for dislocation-mediated plasticity proposed in 2010 by Langer, Bouchbinder, and Lookman [Acta Mat. 58, 3718 (2010), 10.1016/j.actamat.2010.03.009]. It then uses that theory to explain the anomalous rate-hardening behavior reported in 1988 by Follansbee and Kocks and to explore the relation between hardening rate and grain size reported in 1995 by Meyers et al. A central theme is the need for physics-based, nonequilibrium analyses in developing predictive theories of the strength of polycrystalline materials.

  10. Sediment transport mechanics

    NASA Astrophysics Data System (ADS)

    Ballio, Francesco; Tait, Simon

    2012-12-01

    The Editor of Acta Geophysica and the Guest Editors wish to dedicate this Topical Issue on Sediment Transport Mechanics to the memory of Stephen Coleman, who died recently. During his career, Stephen had made an outstanding scientific contribution to the topic of Sediment Transport. The level of his contribution is demonstrated in the paper by Aberle, Coleman, and Nikora included in this issue, on which he started working before becoming aware of the illness that led to his untimely death. For scholars and colleagues Stephen remains an example of intellectual honesty and scientific insight.

  11. Magmas and their sources: A special issue honoring Frederick A. Frey

    NASA Astrophysics Data System (ADS)

    Garcia, Michael O.; Rhodes, J. Michael; Huang, Shichun; Hickey-Vargas, Rosemary

    2016-07-01

    This special issue is dedicated to Frederick A. Frey (Fig. 1), a pioneer in the use of trace element geochemistry (especially the rare-earth elements, REE) to interpret the origin and evolution of basalts and andesites, peridotites, granites, meteorites, tektites and even sediments. Fred's remarkable career spans more than 5 decades starting in 1964 with his seminal paper with advisor Larry Haskin entitled "rare earths in oceanic basalts" (Frey and Haskin, 1964). Given that Fred was an Associate Editor of Geochimica et Cosmochimica Acta (GCA) for 20 years, GCA is a highly appropriate venue for this collection of twenty-seven new scientific papers in his honor.

  12. PubMed Central

    2011-01-01

    Events for which complete information is available are listed in chronological order. Those taking place in Italy are in bold script. Information, following the style of the present list, should be submitted to the Editorial Secretariat of Acta Otorhinolaryngologica Italica. In accordance with the Regulations of S.I.O. and Ch.C.-F. (Art. 8) Members of the Society organising Courses, Congresses or other scientific events should inform the Secretary of the Association (A.U.O.R.L., A.O.O.I.) within the deadlines set down in the respective Statutes and Regulations.

  13. DBI analog of a decaying vacuum cosmology

    NASA Astrophysics Data System (ADS)

    Bessada, Dennis

    2013-07-01

    In this work I discuss the dynamical and thermodynamical equivalence between a general k-essence scalar field cosmology and an arbitrary cosmological model with a decaying vacuum, thus generalizing the approach proposed by Maia and Lima [Phys. Rev. D 65, 083513 (2002)]. The formalism obtained is quite general and holds for any noncanonical scalar field model. As a special case I derive a Dirac-Born-Infeld model with an exponential potential and constant speed of sound, and show that it is equivalent to a cosmological model with decay law Λ(H)=3βH2.

  14. Retinal image contrast obtained by a model eye with combined correction of chromatic and spherical aberrations

    PubMed Central

    Ohnuma, Kazuhiko; Kayanuma, Hiroyuki; Lawu, Tjundewo; Negishi, Kazuno; Yamaguchi, Takefumi; Noda, Toru

    2011-01-01

    Correcting spherical and chromatic aberrations in vitro in human eyes provides substantial visual acuity and contrast sensitivity improvements. We found the same improvement in the retinal images using a model eye with/without correction of longitudinal chromatic aberrations (LCAs) and spherical aberrations (SAs). The model eye included an intraocular lens (IOL) and artificial cornea with human ocular LCAs and average human SAs. The optotypes were illuminated using a D65 light source, and the images were obtained using two-dimensional luminance colorimeter. The contrast improvement from the SA correction was higher than the LCA correction, indicating the benefit of an aspheric achromatic IOL. PMID:21698008

  15. Target binding to S100B reduces dynamic properties and increases Ca2+-binding affinity for wild type and EF-hand mutant proteins

    PubMed Central

    Liriano, Melissa A.; Varney, Kristen M.; Wright, Nathan T.; Hoffman, Cassandra L.; Toth, Eric A.; Ishima, Rieko; Weber, David J.

    2012-01-01

    Mutations in the second EF-hand (D61N, D63N, D65N, E72A) of S100B were used to study its Ca2+-binding and dynamic properties in the absence and presence of abound target, TRTK-12. With D63NS100B as an exception (D63NKD = 50 ± 9 µM), Ca2+-binding to EF2-hand mutants were reduced by more than 8-fold in the absence of TRTK-12 (D61NKD = 412 ± 67 µM; D65NKD = 968 ± 171 µM; E72AKD = 471 ± 133 µM), when compared to wild-type protein (WTKD = 56 ± 9 µM). For the TRTK-12 complexes, the Ca2+-binding affinity to wild type (WT+TRTKKD = 12 ± 10 µM) and the EF2 mutants were increased by 5- to 19-fold versus in the absence of target (D61N+TRTKKD = 29 ± 1.2 µM; D63N+TRTKKD = 10 ± 2.2 µM; D65N+TRTKKD = 73 ± 4.4 µM; E72A+TRTKKD = 18 ± 3.7 µM). In addition, Rex, as measured using relaxation dispersion for side chain 15N resonances of Asn63 (D63NS100B) was reduced upon TRTK-12 binding when measured by nuclear magnetic resonance (NMR). Likewise, backbone motions on multiple time scales (ps-ms) throughout wild type, D61NS100B D63NS100B, and D65NS100B were lowered upon binding TRTK-12. However, the X-ray structures of Ca2+-bound (2.0 Å) and TRTK-bound (1.2 Å) D63NS100B showed no change in Ca2+ coordination, so these and analogous structural data for the wild-type protein could not be used to explain how target binding increased Ca2+-binding affinity in solution. Thus, a model for how S100B-TRTK12 complex formation increases Ca2+ binding is discussed, which considers changes in protein dynamics upon binding the target TRTK-12. PMID:22824086

  16. Neural network method for characterizing video cameras

    NASA Astrophysics Data System (ADS)

    Zhou, Shuangquan; Zhao, Dazun

    1998-08-01

    This paper presents a neural network method for characterizing color video camera. A multilayer feedforward network with the error back-propagation learning rule for training, is used as a nonlinear transformer to model a camera, which realizes a mapping from the CIELAB color space to RGB color space. With SONY video camera, D65 illuminant, Pritchard Spectroradiometer, 410 JIS color charts as training data and 36 charts as testing data, results show that the mean error of training data is 2.9 and that of testing data is 4.0 in a 2563 RGB space.

  17. Effects of the International Temperature Scale of 1990 (ITS-90) on CIE documentary standards for radiometry, photometry, and colorimetry

    SciTech Connect

    Mielenz, K.D.; Hsia, J.J.

    1990-01-01

    The differences between ITS-90 and IPTS-68 (International Practical Temperature Scale of 1968) above 1235 K are described. It is shown that none of the following CIE (Commission Internationale de l'Eclairage or International Commission on Illumination) definitions or recommendations require revision because of the introduction of the ITS-90: International Lighting Vocabulary definitions; CIE Standard Illuminants A, D(65), other illuminants; and sources for realizing CIE Illuminants. The effect of the ITS-90 on previously calibrated sources for realizing CIE illuminants is negligibly small.

  18. Power analysis of light source in laser projector

    NASA Astrophysics Data System (ADS)

    Duan, Jingyuan; Shi, Ancun; Zhang, Yunfang; Fang, Qing; Liu, Yuliang

    2012-01-01

    In this paper, we design a high power and small volume laser projector using the red laser diode, green laser diode, blue laser diode and green fluorescence as light source, which could improve the performance of the projector significantly with longer lifetime than lamps, higher reliability, and larger color gamut. According to the requirement of CIE Standard Illuminant D65 and light output, the power of red laser diode, green laser diode, blue laser diode and green fluorescence were calculated. The energy efficiency of four base-color optical path was also analyzed. It could be concluded that the blue laser and red laser have higher power requirements.

  19. SDM--a server for predicting effects of mutations on protein stability and malfunction.

    PubMed

    Worth, Catherine L; Preissner, Robert; Blundell, Tom L

    2011-07-01

    The sheer volume of non-synonymous single nucleotide polymorphisms that have been generated in recent years from projects such as the Human Genome Project, the HapMap Project and Genome-Wide Association Studies means that it is not possible to characterize all mutations experimentally on the gene products, i.e. elucidate the effects of mutations on protein structure and function. However, automatic methods that can predict the effects of mutations will allow a reduced set of mutations to be studied. Site Directed Mutator (SDM) is a statistical potential energy function that uses environment-specific amino-acid substitution frequencies within homologous protein families to calculate a stability score, which is analogous to the free energy difference between the wild-type and mutant protein. Here, we present a web server for SDM (http://www-cryst.bioc.cam.ac.uk/~sdm/sdm.php), which has obtained more than 10,000 submissions since being online in April 2008. To run SDM, users must upload a wild-type structure and the position and amino acid type of the mutation. The results returned include information about the local structural environment of the wild-type and mutant residues, a stability score prediction and prediction of disease association. Additionally, the wild-type and mutant structures are displayed in a Jmol applet with the relevant residues highlighted. PMID:21593128

  20. Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams.

    PubMed

    Coquelle, Nicolas; Brewster, Aaron S; Kapp, Ulrike; Shilova, Anastasya; Weinhausen, Britta; Burghammer, Manfred; Colletier, Jacques Philippe

    2015-05-01

    High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Å resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering. PMID:25945583

  1. Correlating Sampling and Intensity Statistics in Nanoparticle Diffraction Experiments

    SciTech Connect

    Ozturk, Hande; Yan, Hanfei; Hill, John P.; Noyan, I. Cevdet

    2015-08-01

    In this article, [Öztürk, Yan, Hill & Noyan (2014). J. Appl. Cryst. 47, 1016-1025] it was shown that the sampling statistics of diffracting particle populations within a polycrystalline ensemble depended on the size of the constituent crystallites: broad X-ray peak breadths enabled some nano-sized particles to contribute more than one diffraction spot to Debye-Scherrer rings. Here it is shown that the equations proposed by Alexander, Klug & Kummer [J. Appl. Phys. (1948), 19, 742-753] (AKK) to link diffracting particle and diffracted intensity statistics are not applicable if the constituent crystallites of the powder are below 10 nm. In this size range, (i) the one-to-one correspondence between diffracting particles and Laue spots assumed in the AKK analysis is not satisfied, and (ii) the crystallographic correlation between Laue spots originating from the same grain invalidates the assumption that all diffracting plane normals are randomly oriented and uncorrelated. Such correlation produces unexpected results in the selection of diffracting grains. Three or more Laue spots from a given grain for a particular reflection can only be observed at certain wavelengths. In addition, correcting the diffracted intensity values by the traditional Lorentz term, 1/cos [theta], to compensate for the variation of particles sampled within a reflection band does not maintain fidelity to the number of poles contributing to the diffracted signal. A new term, cos [theta]B/cos [theta], corrects this problem.

  2. Thermal behavior of water confined in micro porous of clay mineral at additional pressure.

    NASA Astrophysics Data System (ADS)

    Ito, Y.; Takemura, T.; Fujimori, H.; Nagoe, A.; Sugimoto, T.

    2014-12-01

    Water is the most familiar substance. However water has specific properties that has a crystal structure of a dozen and density of that is maximum at 277.15 K. Therefore it understands various natural phenomena to study physical properties of water. Oodo et al study physical properties of water confined in silica gel [1]. They indicate that melting point of water confined in silica gel decrease with decreasing pore size of silica gel. Also in case that pore size is less than 2 nm, water confined in silica gel is unfreezing water at low temperature. It is considered that effect of pore size prevent crystal growth of water. Therefore we are interested in water confined in clay minerals. Clay minerals have a number of water conditions. Also it is thought that water confined in clay minerals show different physical behavior to exist the domain where change with various effect. Therefore we studied a thermal properties and phase behavior of absorption water in clay minerals. In addition, we analyzed the changes in the thermal behavior of absorption water due to the effect of earth pressure that was an environmental factor in the ground. [1] Oodo & Fujimori, J. Non-Cryst. Solids, 357 (2011) 683.

  3. Influence of strain rates on the mechanical behaviors of shape memory polymer

    NASA Astrophysics Data System (ADS)

    Guo, Xiaogang; Liu, Liwu; Zhou, Bo; Liu, Yanju; Leng, Jinsong

    2015-09-01

    In the last few decades, shape memory polymers have demonstrated their major advantages of extremely high recovery strain, low density and low cost. Generally, the mechanical behavior of shape memory polymers is strongly dependent on the loading strain rates. Uniaxial tensile experiments were conducted on one kind of typical shape memory polymer (epoxy) at several different temperatures (348 K, 358 K, 368 K and 378 K) and true strain rates (0.25% s-1, 1.25% s-1 and 2.5% s-1). Thus, the influence of strain rate and temperature on the mechanical behavior of epoxy, in particular on the post yield stresses and the strain hardening behavior, were investigated through this experimental study. Based on our previous work Guo (2014 Smart Mater. Struct. 23 105019), a simplified model which can explain the shape memory effect of epoxy was proposed to predict the strain hardening behavior of the shape memory polymer. Based on the suggestion of Rault (1998 J. Non-Cryst. Solids 235-7 737-41), a linear compensation model was introduced to indicate the change in yield stresses with the increase of strain rate and temperature. Finally, the new model predictions for the true strain and stress behavior of epoxy were compared with the experimental results.

  4. Carbon Dioxide "Trapped" in a β-Carbonic Anhydrase.

    PubMed

    Aggarwal, Mayank; Chua, Teck Khiang; Pinard, Melissa A; Szebenyi, Doletha M; McKenna, Robert

    2015-11-01

    Carbonic anhydrases (CAs) are enzymes that catalyze the hydration/dehydration of CO2/HCO3(-) with rates approaching diffusion-controlled limits (kcat/KM ∼ 10(8) M(-1) s(-1)). This family of enzymes has evolved disparate protein folds that all perform the same reaction at near catalytic perfection. Presented here is a structural study of a β-CA (psCA3) expressed in Pseudomonas aeruginosa, in complex with CO2, using pressurized cryo-cooled crystallography. The structure has been refined to 1.6 Å resolution with R(cryst) and R(free) values of 17.3 and 19.9%, respectively, and is compared with the α-CA, human CA isoform II (hCA II), the only other CA to have CO2 captured in its active site. Despite the lack of structural similarity between psCA3 and hCA II, the CO2 binding orientation relative to the zinc-bound solvent is identical. In addition, a second CO2 binding site was located at the dimer interface of psCA3. Interestingly, all β-CAs function as dimers or higher-order oligomeric states, and the CO2 bound at the interface may contribute to the allosteric nature of this family of enzymes or may be a convenient alternative binding site as this pocket has been previously shown to be a promiscuous site for a variety of ligands, including bicarbonate, sulfate, and phosphate ions. PMID:26457866

  5. Nano confinement effects on dynamic and viscoelastic properties of Selenium Films

    NASA Astrophysics Data System (ADS)

    Yoon, Heedong; McKenna, Gregory

    2015-03-01

    In current study, we use a novel nano bubble inflation technique to study nano confinement effects on the dynamic and viscoelastic properties of physical vapor deposited Selenium films. Film thicknesses ranged from 60 to 260 nm. Creep experiments were performed for the temperatures ranging from Tg,macroscopic-14 °C to Tg,\\ macroscopic + 19 °C. Time temperature superposition and time thickness superposition were applied to create reduced creep curves, and those were compared with macroscopic data [J. Non-Cryst. Solids. 2002, 307, 790-801]. The results showed that the time temperature superposition was applicable in the glassy relaxation regime to the steady-state plateau regime. However in the long time response of the creep compliance, time thickness superposition failed due to the thickness dependence on the steady-state plateau. It was observed that the steady state compliance increased with film thickness. The thickness dependence on the plateau stiffening followed a power law of DPlateau ~ h2.46, which is greater than observed in organic polymers where the exponents observed range from 0.83 to 2.0 [Macromolecules. 2012, 45 (5), 2453-2459]. National Science Foundation Grant No. CHE 1112416 and John R. Bradford Endowment at Texas Tech

  6. Probing of structural relaxation times in the glassy state of sucrose and trehalose based on dynamical properties of two secondary relaxation processes

    SciTech Connect

    Kaminski, K.; Adrjanowicz, K.; Paluch, M.; Kaminska, E.

    2011-06-15

    Time-dependent isothermal dielectric measurements were carried out deeply in the glassy state on two very important saccharides: sucrose and trehalose. In both compounds two prominent secondary relaxation processes were identified. The faster one is an inherent feature of the whole family of carbohydrates. The slower one can also be detected in oligo- and polysaccharides. It was shown earlier that the {beta} process is the Johari-Goldstein (JG) relaxation coupled to motions of the glycosidic linkage, while the {gamma} relaxation originates from motions of the exocyclic hydroxymethyl unit. Recently, it was shown that the JG relaxation process can be used to determine structural relaxation times in the glassy state [R. Casalini and C. M. Roland, Phys. Rev. Lett. 102, 035701 (2009)]. In this paper we present the results of an analysis of the data obtained during aging using two independent approaches. The first was proposed by Casalini and Roland, and the second one is based on the variation of the dielectric strength of the secondary relaxation process during aging [J. K. Vij and G. Power, J. Non-Cryst. Solids 357, 783 (2011)]. Surprisingly, we found that the estimated structural relaxation times in the glassy state of both saccharides are almost the same, independent of the type of secondary mode. This finding calls into question the common view that secondary modes of intramolecular origin do not provide information about the dynamics of the glassy state.

  7. Crystal structure of 4-methyl-N-{(E)-meth-yl[(3aR,8aS)-2-oxo-3,3a,8,8a-tetra-hydro-2H-indeno-[1,2-d][1,3]oxazol-3-yl]-λ(4)-sulfanyl-idene}benzene-sulfonamide.

    PubMed

    Pereira, Patrícia A; Noll, Bruce C; Oliver, Allen G; Silveira, Gustavo P

    2015-12-01

    The formulation that the title compound, C18H18N2O4S2, adopts is a zwitterionic core with the charge separated to the sulfilimine S and N atoms and is supported by the two different S-N bond distances about the sulfinimine N atom [1.594 (2) and 1.631 (2) Å, respectively] that are typical for such bonds. The notably unusual bond is S-N(oxazolidinone) [1.692 (2) Å] that is longer than a typical S-N bond [1.603 (18) Å, Mogul analysis; Macrae et al. (2008 ▸). J. Appl. Cryst. 41, 466-470]. The bond-angle sum about sulfilimine sulfur (308.35°) reflects the trigonal-pyramidal geometry of this atom. Two of the angles are less than 100°. Despite the pyramidalization of this sulfur, there are no significant inter-molecular inter-actions, beyond usual van der Waals contacts, in the crystal packing. PMID:26870517

  8. A Hidden Markov model web application for analysing bacterial genomotyping DNA microarray experiments.

    PubMed

    Newton, Richard; Hinds, Jason; Wernisch, Lorenz

    2006-01-01

    Whole genome DNA microarray genomotyping experiments compare the gene content of different species or strains of bacteria. A statistical approach to analysing the results of these experiments was developed, based on a Hidden Markov model (HMM), which takes adjacency of genes along the genome into account when calling genes present or absent. The model was implemented in the statistical language R and applied to three datasets. The method is numerically stable with good convergence properties. Error rates are reduced compared with approaches that ignore spatial information. Moreover, the HMM circumvents a problem encountered in a conventional analysis: determining the cut-off value to use to classify a gene as absent. An Apache Struts web interface for the R script was created for the benefit of users unfamiliar with R. The application may be found at http://hmmgd.cryst.bbk.ac.uk/hmmgd. The source code illustrating how to run R scripts from an Apache Struts-based web application is available from the corresponding author on request. The application is also available for local installation if required. PMID:17140267

  9. Ezetimibe anhydrate, determined from laboratory powder diffraction data.

    PubMed

    Brüning, Jürgen; Alig, Edith; Schmidt, Martin U

    2010-07-01

    Ezetimibe {systematic name: (3R,4S)-1-(4-fluorophenyl)-3-[(3S)-3-(4-fluorophenyl)-3-hydroxypropyl]-4-(4-hydroxyphenyl)azetidin-2-one}, C(24)H(21)F(2)NO(3), is used to lower cholesterol levels by inhibiting cholesterol resorption in the human intestine. The crystal structure of ezetimibe anhydrate was solved from laboratory powder diffraction data by means of real-space methods using the program DASH [David et al. (2006). J. Appl. Cryst. 39, 910-915]. Subsequent Rietveld refinement with TOPAS Academic [Coelho (2007). TOPAS Academic User Manual. Version 4.1. Coelho Software, Brisbane, Australia] led to a final R(wp) value of 8.19% at 1.75 A resolution. The compound crystallizes in the space group P2(1)2(1)2(1) with one molecule in the asymmetric unit. The molecules are closely packed and two intermolecular hydrogen bonds form an extended hydrogen-bond architecture. PMID:20603561

  10. Correlation between low temperature properties and fragility of glasses

    NASA Astrophysics Data System (ADS)

    Zhu, Da-Ming

    1997-03-01

    The nature of glass transition and the nature of low energy excitations that govern the low temperature properties of glasses are the two fundamental problems remain unsolved in the study of glasses. It was recently suggested that several properties governed by the low energy excitations in glasses are correlated to the glass fragility,[1] a parameter used to characterize the temperature variation of relaxation time near glass transitions.[2] A previous examination of the specific heats at T < 1 K and the fragility of a dozen different glasses found a correlation seems to exist.[3] The correlation is also consistent with an interpretation of fragility of glasses in terms of difference in potential energy landscape in configuration space.[2] We recently compared the specific heats and thermal conductivity of several glasses at 1K < T < 20 K and their fragility. We found that a general trend appears to exist that more fragile glasses have lower specific heat bump in the plot of C/T3 versus T or lower step in the plot of C/T versus T. The implication of the correlation and the possible interpretation in terms of potential energy landscape will be discussed. [1] A. P. Sokolov et al, Phys. Rev. Lett. 71, 2062 (1993). [2] C. A. Angell, J. Non-Cryst. Solids 131-133, 13 (1993). [3] Da-Ming Zhu, Phys. Rev. B 54, 6287 (1996).

  11. Tuning Fragility: The Quest for Strong Polymeric Glass Formers

    NASA Astrophysics Data System (ADS)

    Erwin, Brian; Colby, Ralph; Lizotte, Jeremy; Long, Timothy

    2001-03-01

    Angell [1] has defined fragility m from the temperature dependence of relaxation time τ at the glass transition temperature T_g: m≡ [ dlog τ /d( T_g/T) ] _T=T_g. The strongest glass formers (e.g., silica) have m=16-20 and the most fragile glass formers are typically polymers, with m>100. Recent work [2] has reported that the fragility of polystyrene decreases as chain length is lowered, with a range 70Cryst. Solids QTRbf275, 153 (2000). [3] R. H. Colby, Phys. Rev. E QTRbf61, 1783 (2000).

  12. Correlating sampling and intensity statistics in nanoparticle diffraction experiments

    DOE PAGESBeta

    Öztürk, Hande; Yan, Hanfei; Hill, John P.; Noyan, I. Cevdet

    2015-07-28

    It is shown in a previous article [Öztürk, Yan, Hill & Noyan (2014).J. Appl. Cryst.47, 1016–1025] that the sampling statistics of diffracting particle populations within a polycrystalline ensemble depended on the size of the constituent crystallites: broad X-ray peak breadths enabled some nano-sized particles to contribute more than one diffraction spot to Debye–Scherrer rings. Here it is shown that the equations proposed by Alexander, Klug & Kummer [J. Appl. Phys.(1948),19, 742–753] (AKK) to link diffracting particle and diffracted intensity statistics are not applicable if the constituent crystallites of the powder are below 10 nm. In this size range, (i) themore » one-to-one correspondence between diffracting particles and Laue spots assumed in the AKK analysis is not satisfied, and (ii) the crystallographic correlation between Laue spots originating from the same grain invalidates the assumption that all diffracting plane normals are randomly oriented and uncorrelated. Such correlation produces unexpected results in the selection of diffracting grains. For example, three or more Laue spots from a given grain for a particular reflection can only be observed at certain wavelengths. In addition, correcting the diffracted intensity values by the traditional Lorentz term, 1/cos θ, to compensate for the variation of particles sampled within a reflection band does not maintain fidelity to the number of poles contributing to the diffracted signal. A new term, cos θB/cos θ, corrects this problem.« less

  13. The temperature-dependent electrical transport properties of liquid Sn using pseudopotential theory

    NASA Astrophysics Data System (ADS)

    Patel, A. B.; Bhatt, N. K.; Thakore, B. Y.; Vyas, P. R.; Jani, A. R.

    2014-08-01

    We present the calculations of electrical resistivity, thermo-electric power and thermal conductivity based on the self-consistent approximation. The pseudopotential due to Hasegawa et al. [J. Non-Cryst. Solids 117/118, 300 (1990)] for full electron-ion interaction, which is valid for all electrons and contains the repulsive delta function to achieve the necessary s-pseudisation, was used in the calculation. Temperature dependence of structure factor is achieved through temperature-dependent potential parameter in the pair-potential. The outcome of the present study is discussed in the light of other such results and with predictions of Wiedemann and Franz law up to moderately high temperature. Specially, high-temperature resistivity data necessitates the careful investigation of electron energy dispersion close to the Fermi level and possible metal to non-metal transition while going from dense-fluid to low density-fluid state. In the absence of experimental data at high temperature, these findings may serve as future guideline.

  14. On favorable thermal fields for detached Bridgman growth

    NASA Astrophysics Data System (ADS)

    Stelian, Carmen; Volz, Martin P.; Derby, Jeffrey J.

    2009-06-01

    The thermal fields of two Bridgman-like configurations, representative of real systems used in prior experiments for the detached growth of CdTe and Ge crystals, are studied. These detailed heat transfer computations are performed using the CrysMAS code and expand upon our previous analysis [C. Stelian, A. Yeckel, J.J. Derby, Influence of thermal phenomena on crystal reattachment during the dewetted Bridgman growth, J. Cryst. Growth, in press] that posited a new mechanism involving the thermal field and meniscus position to explain stable conditions for dewetted Bridgman growth. Computational results indicate that heat transfer conditions that led to successful detached growth in both of these systems are in accordance with our prior assertion, namely that the prevention of crystal reattachment to the crucible wall requires the avoidance of any undercooling of the melt meniscus during the growth run. Significantly, relatively simple process modifications that promote favorable thermal conditions for detached growth may overcome detrimental factors associated with meniscus shape and crucible wetting. Thus, these ideas may be important to advance the practice of detached growth for many materials.

  15. Ericksen number and Deborah number cascade predictions of a model for liquid crystalline polymers for simple shear flow

    NASA Astrophysics Data System (ADS)

    Klein, D. Harley; Leal, L. Gary; García-Cervera, Carlos J.; Ceniceros, Hector D.

    2007-02-01

    We consider the behavior of the Doi-Marrucci-Greco (DMG) model for nematic liquid crystalline polymers in planar shear flow. We found the DMG model to exhibit dynamics in both qualitative and quantitative agreement with experimental observations reported by Larson and Mead [Liq. Cryst. 15, 151 (1993)] for the Ericksen number and Deborah number cascades. For increasing shear rates within the Ericksen number cascade, the DMG model displays three distinct regimes: stable simple shear, stable roll cells, and irregular structure accompanied by disclination formation. In accordance with experimental observations, the model predicts both ±1 and ±1/2 disclinations. Although ±1 defects form via the ridge-splitting mechanism first identified by Feng, Tao, and Leal [J. Fluid Mech. 449, 179 (2001)], a new mechanism is identified for the formation of ±1/2 defects. Within the Deborah number cascade, with increasing Deborah number, the DMG model exhibits a streamwise banded texture, in the absence of disclinations and roll cells, followed by a monodomain wherein the mean orientation lies within the shear plane throughout the domain.

  16. Numerical study of liquid phase diffusion growth of SiGe subjected to accelerated crucible rotation

    NASA Astrophysics Data System (ADS)

    Sekhon, M.; Lent, B.; Dost, S.

    2016-03-01

    The effect of accelerated crucible rotation technique (ACRT) on liquid phase diffusion (LPD) growth of SixGe1-x crystal has been investigated numerically. Transient, axisymmetric simulations have been carried out for triangular and trapezoidal ACRT cycles. Natural convection driven flow in the early growth hours is found to be modified by the ACRT induced Ekman flow. Results also reveal that a substantial mixing in the solution can be induced by the application of ACRT in the later hours of growth which is otherwise a diffusion dominated growth period for LPD growth technique. A comparison is drawn to the cases of stationary crucible and crucible rotating at a constant speed examined previously for this growth system by Sekhon and Dost (J. Cryst. Growth 430 (2015) 63). It is found that a superior interface flattening effect and radial compositional uniformity along the growth interface can be accomplished by employing ACRT at 12 rpm than that which could be achieved by using steady crucible rotation at 25 rpm, owing to the higher time averaged growth velocity achieved in the former case. Furthermore, minor differences are also predicted in the results obtained for trapezoidal and triangular ACRT cycles.

  17. Powder diffraction from a continuous microjet of submicrometer protein crystals.

    PubMed

    Shapiro, D A; Chapman, H N; Deponte, D; Doak, R B; Fromme, P; Hembree, G; Hunter, M; Marchesini, S; Schmidt, K; Spence, J; Starodub, D; Weierstall, U

    2008-11-01

    Atomic-resolution structures from small proteins have recently been determined from high-quality powder diffraction patterns using a combination of stereochemical restraints and Rietveld refinement [Von Dreele (2007), J. Appl. Cryst. 40, 133-143; Margiolaki et al. (2007), J. Am. Chem. Soc. 129, 11865-11871]. While powder diffraction data have been obtained from batch samples of small crystal-suspensions, which are exposed to X-rays for long periods of time and undergo significant radiation damage, the proof-of-concept that protein powder diffraction data from nanocrystals of a membrane protein can be obtained using a continuous microjet is shown. This flow-focusing aerojet has been developed to deliver a solution of hydrated protein nanocrystals to an X-ray beam for diffraction analysis. This method requires neither the crushing of larger polycrystalline samples nor any techniques to avoid radiation damage such as cryocooling. Apparatus to record protein powder diffraction in this manner has been commissioned, and in this paper the first powder diffraction patterns from a membrane protein, photosystem I, with crystallite sizes of less than 500 nm are presented. These preliminary patterns show the lowest-order reflections, which agree quantitatively with theoretical calculations of the powder profile. The results also serve to test our aerojet injector system, with future application to femtosecond diffraction in free-electron X-ray laser schemes, and for serial crystallography using a single-file beam of aligned hydrated molecules. PMID:18955765

  18. Rapid automated superposition of shapes and macromolecular models using spherical harmonics

    PubMed Central

    Konarev, Petr V.; Petoukhov, Maxim V.; Svergun, Dmitri I.

    2016-01-01

    A rapid algorithm to superimpose macromolecular models in Fourier space is proposed and implemented (SUPALM). The method uses a normalized integrated cross-term of the scattering amplitudes as a proximity measure between two three-dimensional objects. The reciprocal-space algorithm allows for direct matching of heterogeneous objects including high- and low-resolution models represented by atomic coordinates, beads or dummy residue chains as well as electron microscopy density maps and inhomogeneous multi-phase models (e.g. of protein–nucleic acid complexes). Using spherical harmonics for the computation of the amplitudes, the method is up to an order of magnitude faster than the real-space algorithm implemented in SUPCOMB by Kozin & Svergun [J. Appl. Cryst. (2001 ▸), 34, 33–41]. The utility of the new method is demonstrated in a number of test cases and compared with the results of SUPCOMB. The spherical harmonics algorithm is best suited for low-resolution shape models, e.g. those provided by solution scattering experiments, but also facilitates a rapid cross-validation against structural models obtained by other methods. PMID:27275142

  19. Direct numerical simulation of homogeneous nucleation and growth in a phase-field model using cell dynamics method.

    PubMed

    Iwamatsu, Masao

    2008-02-28

    The homogeneous nucleation and growth in a simplest two-dimensional phase field model is numerically studied using the cell dynamics method. The whole process from nucleation to growth is simulated and is shown to follow closely the Kolmogorov-Johnson-Mehl-Avrami (KJMA) scenario of phase transformation. Specifically the time evolution of the volume fraction of new stable phase is found to follow closely the KJMA formula. By fitting the KJMA formula directly to the simulation data, not only the Avrami exponent but the magnitude of nucleation rate and, in particular, of incubation time are quantitatively studied. The modified Avrami plot is also used to verify the derived KJMA parameters. It is found that the Avrami exponent is close to the ideal theoretical value m=3. The temperature dependence of nucleation rate follows the activation-type behavior expected from the classical nucleation theory. On the other hand, the temperature dependence of incubation time does not follow the exponential activation-type behavior. Rather the incubation time is inversely proportional to the temperature predicted from the theory of Shneidman and Weinberg [J. Non-Cryst. Solids 160, 89 (1993)]. A need to restrict thermal noise in simulation to deduce correct Avrami exponent is also discussed. PMID:18315058

  20. Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

    SciTech Connect

    Coquelle, Nicolas; Brewster, Aaron S.; Kapp, Ulrike; Shilova, Anastasya; Weinhausen, Britta; Burghammer, Manfred; Colletier, Jacques-Philippe

    2015-05-01

    A raster scanning serial protein crystallography approach is presented, that consumes as low ∼200–700 nl of sedimented crystals. New serial data pre-analysis software, NanoPeakCell, is introduced. High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Å resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.

  1. Dislocations in mismatched layers of GaAsxP1 - x in between GaP as observed by low-temperature cathodoluminescence: Part II. Grown on (111) oriented substrates

    NASA Astrophysics Data System (ADS)

    Gustafsson, A.; Pistol, M.-E.; Gerling, M.; Samuelson, L.; Titze, H.

    1991-08-01

    Spectrally resolved low-temperature cathodoluminescence (CL) imaging has been performed on thin, 250 Å, mismatched layers of GaAsxP1-x in between bulk GaP. The layers were grown on (111) oriented substrates by metalorganic vapor phase epitaxy, with layers ranging from perfectly strained to totally relaxed. CL imaging has proven to be a very sensitive technique for the study of the onset of the formation of misfit dislocations and is therefore useful for determination of the critical thickness [A. Gustafsson, M.-E. Pistol, M. Gerling, L. Samuelson, M. R. Leys and H. Titze, J. Appl. Phys. 70, 1660 (1991)]. For the use of perfectly strained layers, growth on (111) oriented substrates can be of interest since the critical thickness predicted by the mechanical equilibrium theory [J. W. Matthews and A. E. Blakeslee, J. Cryst. Growth 27, 118 (1974)] is about twice that for growth on (001) oriented substrates. In this work we show that the dislocations involved in the strain relief for the growth of mismatched layers on (111) oriented substrates are of the perfect 60° type and that the experimental critical thickness agrees well with the value expected from the mechanical equilibrium theory.

  2. Slow dynamics in a primitive tetrahedral network model.

    PubMed

    De Michele, Cristiano; Tartaglia, Piero; Sciortino, Francesco

    2006-11-28

    We report extensive Monte Carlo and event-driven molecular dynamics simulations of the fluid and liquid phase of a primitive model for silica recently introduced by Ford et al. [J. Chem. Phys. 121, 8415 (2004)]. We evaluate the isodiffusivity lines in the temperature-density plane to provide an indication of the shape of the glass transition line. Except for large densities, arrest is driven by the onset of the tetrahedral bonding pattern and the resulting dynamics is strong in Angell's classification scheme [J. Non-Cryst. Solids 131-133, 13 (1991)]. We compare structural and dynamic properties with corresponding results of two recently studied primitive models of network forming liquids-a primitive model for water and an angular-constraint-free model of four-coordinated particles-to pin down the role of the geometric constraints associated with bonding. Eventually we discuss the similarities between "glass" formation in network forming liquids and "gel" formation in colloidal dispersions of patchy particles. PMID:17144726

  3. Density scaling of the transport properties of molecular and ionic liquids.

    PubMed

    López, Enriqueta R; Pensado, Alfonso S; Comuñas, María J P; Pádua, Agílio A H; Fernández, Josefa; Harris, Kenneth R

    2011-04-14

    Casalini and Roland [Phys. Rev. E 69, 062501 (2004); J. Non-Cryst. Solids 353, 3936 (2007)] and other authors have found that both the dielectric relaxation times and the viscosity, η, of liquids can be expressed solely as functions of the group (TV (γ)), where T is the temperature, V is the molar volume, and γ a state-independent scaling exponent. Here we report scaling exponents γ, for the viscosities of 46 compounds, including 11 ionic liquids. A generalization of this thermodynamic scaling to other transport properties, namely, the self-diffusion coefficients for ionic and molecular liquids and the electrical conductivity for ionic liquids is examined. Scaling exponents, γ, for the electrical conductivities of six ionic liquids for which viscosity data are available, are found to be quite close to those obtained from viscosities. Using the scaling exponents obtained from viscosities it was possible to correlate molar conductivity over broad ranges of temperature and pressure. However, application of the same procedures to the self-diffusion coefficients, D, of six ionic and 13 molecular liquids leads to superpositioning of poorer quality, as the scaling yields different exponents from those obtained with viscosities and, in the case of the ionic liquids, slightly different values for the anion and the cation. This situation can be improved by using the ratio (D∕T), consistent with the Stokes-Einstein relation, yielding γ values closer to those of viscosity. PMID:21495764

  4. Wave packet dynamics in doubly excited states of He

    NASA Astrophysics Data System (ADS)

    Feist, Johannes; Nagele, Stefan; Persson, Emil; Burgdörfer, Joachim; Schneider, Barry

    2007-06-01

    We have developed a method for the ab initio simulation of the interaction of ultrashort laser pulses with helium atoms. We expand the two-electron Schr"odinger equation in coupled spherical harmonics and perform direct time integration utilizing either the Arnoldi-Lanczos or the Leapfrog method. The spatial discretization is performed in an FEDVR basis [1]. This allows for a numerically accurate description while possessing desirable computational features, e.g. a block-diagonal form of the kinetic energy matrix. We will present results on electron-electron correlation and wave packet dynamics in He. By using a suitable combination of attosecond XUV/EUV pulses, we prepare a wave packet in the doubly excited states of helium. The motion of this wave packet can be observed by using a probe pulse to induce ionization. We aim for a detailed understanding of the process by a careful study of the ionized electrons, e.g. by investigating doubly differential momentum spectra. [enumi] *B. I. Schneider and L. A. Collins. J. Non-Cryst. Solids 351, 1551.

  5. DFT Ab initio Calculation of Vibrational Frequencies in AsSe glass

    NASA Astrophysics Data System (ADS)

    Shrivastava, Keshav; Kassim, Hasan; Nazrul Rosli, Ahmad

    2008-03-01

    By using DFT double zeta wave functions, we calculated the structure, bond length (picometer, pm), frequencies(intensities)[degeneracy] for various clusters of arsenic selenide. Our results are as follows. (i) AsSe(diatomic) bond length 216pm, 244.0(1/cm). (ii) As2Se(linear) bond length 228.5 pm, frequencies 27.6(1.9) and 387.6(4.3). (iii) As2Se(triangular) As-Se 243.4 pm, As-As 223.3 pm, frequencies 237.3(2.4) and 332.4(0.05)(1/cm). (iv) As3Se (triangular) bond length 238.4 pm, frequencies 107.5 and 296(weak)(1/cm). (v) As4Se (square) bond length 250.2 pm, 58.5(0.04), 241.3(5.9)(1/cm). (vi) AsSe3 (triangular), bond length 231.2 pm, 75.9(0.003), 103.5(1.26)[2], 350.9(33.2)[2]. From this study we identify that linear As-Se-As for which the calculated frequency is 27.6(1/cm) is in agreement with the data of Nemanich, Phys. Rev. B 16, 1655(1977), J. C. Phillips et al Phys. Rev B 21, 5724(1980). We have successfully calculated several vibrational frequencies accurately which agree with the Raman data. *V. R. Devi et al J. Non-Cryst. Solids 351, 489(2005);353,111(2007)

  6. Large and high-quality single-crystal growth of cuprate superconductor Bi-2223 using the traveling-solvent floating-zone (TSFZ) method

    NASA Astrophysics Data System (ADS)

    Adachi, Shintaro; Usui, Tomohiro; Kosugi, Kenta; Sasaki, Nae; Sato, Kentaro; Fujita, Masaki; Yamada, Kazuyoshi; Fujii, Takenori; Watanabe, Takao

    In high superconducting transition temperature (high-Tc) cuprates, it is empirically known that Tc increases on increasing the number of CuO2 planes in a unit cell n from 1 to 3. Bi-family cuprates are ideal for investigating the microscopic mechanism involved. However, it is difficult to grow tri-layered Bi-2223, probably owing to its narrow crystallization field. Here, we report improved crystal growth of this compound using the TSFZ method under conditions slightly different from those in an earlier report [J. Cryst. Growth 223, 175 (2001)]. A Bi-rich feed-rod composition of Bi2.2Sr1.9Ca2Cu3Oy and a slightly oxygen-reduced atmosphere (mixed gas flow of O2 (10%) and Ar (90%)) were adopted for the crystal growth. In addition, to increase the supersaturation of the melts, we applied a large temperature gradient along the solid-liquid interface by shielding a high-angle light beam using Al foil around the quartz tube. In this way, we succeeded in preparing large (2 × 2 × 0 . 05 mm3) and high-quality (almost 100% pure) Bi-2223 single crystals. Hirosaki University Grant for Exploratory Research by Young Scientists and Newly-appointed Scientists.

  7. Molecular organization of nematic liquid crystals between concentric cylinders: Role of the elastic anisotropy

    NASA Astrophysics Data System (ADS)

    Chiccoli, C.; Pasini, P.; Evangelista, L. R.; Teixeira-Souza, R. T.; Zannoni, C.

    2015-02-01

    The orientational order in a nematic liquid crystal sample confined to an annular region between two concentric cylinders is investigated by means of lattice Monte Carlo simulations. Strong anchoring and homeotropic orientations, parallel to the radial direction, are implemented at the confining surfaces. The elastic anisotropy is taken into account in the bulk interactions by using the pair potential introduced by Gruhn and Hess [T. Gruhn and S. Hess, Z. Naturforsch. A 51, 1 (1996)] and parametrized by Romano and Luckhurst [S. Romano, Int. J. Mod. Phys. B 12, 2305 (1998), 10.1142/S0217979298001344; Phys. Lett. A 302, 203 (2002), 10.1016/S0375-9601(02)01042-3; G. R. Luckhurst and S. Romano, Liq. Cryst. 26, 871 (1999), 10.1080/026782999204561], i.e., the so-called GHRL potential. In the case of equal elastic constants, a small but appreciable deformation along the cylinder axis direction is observed, whereas when the values of K11/K33 if K22=K33 are low enough, all the spins in the bulk follow the orientation imposed by the surfaces. For larger values of K11/K33 , spontaneous deformations, perpendicular to the polar plane, increase significantly. Our findings indicate that the onset of these deformations also depends on the ratio K22/K33 and on the radius of the cylindrical surfaces. Although expected from the elastic theory, no tangential component of the deformations was observed in the simulations for the set of parameters analyzed.

  8. Twist transition of nematic hyperbolic hedgehogs

    NASA Astrophysics Data System (ADS)

    James, Richard; Fukuda, Jun-ichi

    2014-04-01

    Stability of an idealized hyperbolic hedgehog in a nematic liquid crystal against a twist transition is investigated by extending the methodology of Rüdinger and Stark [Liq. Cryst. 26, 753 (1999), 10.1080/026782999204840], where the hedgehog is confined between two concentric spheres. In the ideal hyperbolic-hedgehog the molecular orientation is assumed to rotate proportionally with respect to the inclination angle, θ (and in the opposite sense). However, when splay, k11, and bend, k33, moduli differ this proportionality is lost and the liquid crystal deforms relative to the ideal with bend and splay. Although slight, these deformations are shown to significantly shift the transition if k11/k33 is small. By increasing the degree of confinement the twist transition can be inhibited, a characteristic both hyperbolic and radial hedgehogs have in common. The twist transition of a hyperbolic defect that accompanies a particle is found to be well predicted by the earlier stability analysis of a thick shell.

  9. Redetermination of 1-carboxy­cyclo­hexan-1-aminium chloride

    PubMed Central

    Belandria, Lusbely M.; Delgado, Gerzon E.; Mora, Asiloé J.; Seijas, Luis E.; González, Teresa

    2009-01-01

    The crystal structure of the title compound, C7H14NO2 +·Cl−, was reported previously [Chacko, Srinivasan & Zand (1975 ▶). J. Cryst. Mol. Struct. 5, 353–357] from Weissenberg photographic data with R = 0.113. It has now been redetermined, providing a significant increase in the precision of the derived geometric parameters, viz. mean σ(C—C) = 0.003 Å in the present work compared with 0.021 Å for the previous work. The complete cation is generated by crystallographic mirrror symmetry, with three C atoms, two O atoms and the N atom lying on the reflecting plane; the chloride anion also has m site symmetry. The crystal structure is established by a two-dimensional network of O—H⋯Cl and N—H⋯Cl hydrogen bonds, generating C 1 2(4) and C 1 2(7) chains, and R 2 4(8) and R 2 4(14) rings. PMID:21581862

  10. Redetermination of 1-carboxy-cyclo-hexan-1-aminium chloride.

    PubMed

    Belandria, Lusbely M; Delgado, Gerzon E; Mora, Asiloé J; Seijas, Luis E; González, Teresa

    2009-01-01

    The crystal structure of the title compound, C(7)H(14)NO(2) (+)·Cl(-), was reported previously [Chacko, Srinivasan & Zand (1975 ▶). J. Cryst. Mol. Struct.5, 353-357] from Weissenberg photographic data with R = 0.113. It has now been redetermined, providing a significant increase in the precision of the derived geometric parameters, viz. mean σ(C-C) = 0.003 Å in the present work compared with 0.021 Å for the previous work. The complete cation is generated by crystallographic mirrror symmetry, with three C atoms, two O atoms and the N atom lying on the reflecting plane; the chloride anion also has m site symmetry. The crystal structure is established by a two-dimensional network of O-H⋯Cl and N-H⋯Cl hydrogen bonds, generating C(1) (2)(4) and C(1) (2)(7) chains, and R(2) (4)(8) and R(2) (4)(14) rings. PMID:21581862

  11. Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

    PubMed Central

    Coquelle, Nicolas; Brewster, Aaron S.; Kapp, Ulrike; Shilova, Anastasya; Weinhausen, Britta; Burghammer, Manfred; Colletier, Jacques-Philippe

    2015-01-01

    High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Å resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering. PMID:25945583

  12. Facilitating model reconstruction for single-particle scattering using small-angle X-ray scattering methods1

    PubMed Central

    Ma, Shufen; Liu, Haiguang

    2016-01-01

    X-ray free-electron lasers generate intense femtosecond X-ray pulses, so that high-resolution structure determination becomes feasible from noncrystalline samples, such as single particles or single molecules. At the moment, the orientation of sample particles cannot be precisely controlled, and consequently the unknown orientation needs to be recovered using computational algorithms. This delays the model reconstruction until all the scattering patterns have been re-oriented, which often entails a long elapse of time and until the completion of the experiment. The scattering patterns from single particles or multiple particles can be summed to form a virtual powder diffraction pattern, and the low-resolution region, corresponding to the small-angle X-ray scattering (SAXS) regime, can be analysed using existing SAXS methods. This work presents a pipeline that converts single-particle data sets into SAXS data, from which real-time model reconstruction is achieved using the model retrieval approach implemented in the software package SASTBX [Liu, Hexemer & Zwart (2012). J. Appl. Cryst.45, 587–593]. To illustrate the applications, two case studies are presented with real experimental data sets collected at the Linac Coherent Light Source. PMID:27047310

  13. Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

    DOE PAGESBeta

    Coquelle, Nicolas; Brewster, Aaron S.; Kapp, Ulrike; Shilova, Anastasya; Weinhausen, Britta; Burghammer, Manfred; Colletier, Jacques -Philippe

    2015-04-25

    High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Åmore » resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.« less

  14. Correlation between luminescence and EPR spectroscopy as evidence of ytterbium pair formation in Li6Ln(BO3)3:Yb3+ (Ln=Gd, Y) borate single crystals.

    PubMed

    Jubera, Véronique; Chavoutier, Marie; Artemenko, Alla; Veber, Philippe; Velazquez, Matias; Garcia, Alain

    2011-05-01

    Synthesized powders and grown single crystals of nominal compositions Li(6)Ln(BO(3))(3):Yb(3+) (Ln=Y, Gd) were investigated by means of powder and single-crystal X-ray diffraction (XRD), as well as optical near-IR spectroscopy in conjunction with electron paramagnetic resonance (EPR) spectroscopy. The appearance of two distinct zero-phonon lines suggests the existence of two kinds of Yb(3+) ions in the single crystals. The XRD results exclude the possibility of a phase transition occurring between room and low temperatures. EPR spectra of single crystals show the presence of both isolated ions and pairs of ytterbium ions substituted for Y(3+). A strong temperature dependence of the intensity of Yb-Yb pairs resonance lines coincides with temperature dependence of emission peak at 978 nm, confirming a common origin of the defect giving rise to these spectra. Calculated from EPR spectra, the distance between pairs of Yb(3+) is in good agreement with crystallographic ones: R=3.856 Å, R(cryst) =3.849 Å. PMID:21506236

  15. Data reduction from twinned RNA crystals.

    PubMed

    Lietzke, S E; Carperos, V E; Kundrot, C E

    1996-07-01

    Methods were developed to process diffraction data from epitaxically twinned crystals. Four programs for data reduction and two display programs were developed to augment the data-reduction program XDS [Kabsch (1988). J. Appl. Cryst. 21, 916-924]. The programs can be generalized for use with other data-reduction software that provides the user with a list of the reflections used to determine lattice constants and crystal orientation. LATTICE_VIEW generates a PDB file containing 'water molecules' at the reciprocal-space coordinates of the strong spots found in the initial data frames. The PDB file is visualized to identify spots that belong to the same lattice, obtain unit-cell dimensions for a lattice, and assess data quality. VECTOR_MATCH is used to find additional spots belonging to a lattice. ACCOUNT4 determines which spots have been processed by XDS. COMFORT discards reflections that are too close to a reflection in another lattice. The display programs provide useful visual information on the quality of the crystal orientations used. Data with an R(merge) of 7.1% at 2.4 A resolution were obtained from epitaxically twinned crystals of an RNA dodecamer. The data were of sufficient quality to solve the structure with a combination of molecular replacement and single isomorphous replacement methods. PMID:15299632

  16. Crystal structure of 4-methyl-N-{(E)-meth­yl[(3aR,8aS)-2-oxo-3,3a,8,8a-tetra­hydro-2H-indeno­[1,2-d][1,3]oxazol-3-yl]-λ4-sulfanyl­idene}benzene­sulfonamide

    PubMed Central

    Pereira, Patrícia A.; Noll, Bruce C.; Oliver, Allen G.; Silveira, Gustavo P.

    2015-01-01

    The formulation that the title compound, C18H18N2O4S2, adopts is a zwitterionic core with the charge separated to the sulfilimine S and N atoms and is supported by the two different S—N bond distances about the sulfinimine N atom [1.594 (2) and 1.631 (2) Å, respectively] that are typical for such bonds. The notably unusual bond is S—N(oxazolidinone) [1.692 (2) Å] that is longer than a typical S—N bond [1.603 (18) Å, Mogul analysis; Macrae et al. (2008 ▸). J. Appl. Cryst. 41, 466–470]. The bond-angle sum about sulfilimine sulfur (308.35°) reflects the trigonal–pyramidal geometry of this atom. Two of the angles are less than 100°. Despite the pyramidalization of this sulfur, there are no significant inter­molecular inter­actions, beyond usual van der Waals contacts, in the crystal packing. PMID:26870517

  17. Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

    SciTech Connect

    Coquelle, Nicolas; Brewster, Aaron S.; Kapp, Ulrike; Shilova, Anastasya; Weinhausen, Britta; Burghammer, Manfred; Colletier, Jacques -Philippe

    2015-04-25

    High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Å resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.

  18. Structure of the Unbound Form of HIV-1 Subtype A Protease: Comparison with Unbound Forms of Proteases from other HIV Subtypes

    SciTech Connect

    Robbins, Arthur H.; Coman, Roxana M.; Bracho-Sanchez, Edith; Fernandez, Marty A.; Gilliland, C.Taylor; Li, Mi; Agbandje-McKenna, Mavis; Wlodawer, Alexander; Dunn, Ben M.; McKenna, Robert

    2010-03-12

    The crystal structure of the unbound form of HIV-1 subtype A protease (PR) has been determined to 1.7 {angstrom} resolution and refined as a homodimer in the hexagonal space group P6{sub 1} to an R{sub cryst} of 20.5%. The structure is similar in overall shape and fold to the previously determined subtype B, C and F PRs. The major differences lie in the conformation of the flap region. The flaps in the crystal structures of the unbound subtype B and C PRs, which were crystallized in tetragonal space groups, are either semi-open or wide open. In the present structure of subtype A PR the flaps are found in the closed position, a conformation that would be more anticipated in the structure of HIV protease complexed with an inhibitor. The amino-acid differences between the subtypes and their respective crystal space groups are discussed in terms of the differences in the flap conformations.

  19. Symmetry-Based Computational Tools for Magnetic Crystallography

    NASA Astrophysics Data System (ADS)

    Perez-Mato, J. M.; Gallego, S. V.; Tasci, E. S.; Elcoro, L.; de la Flor, G.; Aroyo, M. I.

    2015-07-01

    In recent years, two important advances have opened new doors for the characterization and determination of magnetic structures. Firstly, researchers have produced computer-readable listings of the magnetic or Shubnikov space groups. Secondly, they have extended and applied the superspace formalism, which is presently the standard approach for the description of nonmagnetic incommensurate structures and their symmetry, to magnetic structures. These breakthroughs have been the basis for the subsequent development of a series of computer tools that allow a more efficient and comprehensive application of magnetic symmetry, both commensurate and incommensurate. Here we briefly review the capabilities of these computation instruments and present the fundamental concepts on which they are based, providing various examples. We show how these tools facilitate the use of symmetry arguments expressed as either a magnetic space group or a magnetic superspace group and allow the exploration of the possible magnetic orderings associated with one or more propagation vectors in a form that complements and goes beyond the traditional representation method. Special focus is placed on the programs available online at the Bilbao Crystallographic Server ( http://www.cryst.ehu.es ).

  20. Phase sensitive small angle neutron scattering

    NASA Astrophysics Data System (ADS)

    Brok, Erik; Majkrzak, Charles F.; Krycka, Kathryn

    It is a well-known problem that information about the scattered wave is lost in scattering experiments because the measured quantity is the modulus squared of the complex wave function. This ''phase problem'' leads to ambiguity in determining the physical properties of the scattering sample. Small angle neutron scattering (SANS) is a useful technique for determining the structure of biomolecules, in particular proteins that cannot be crystallized and studied with x-ray crystallography. However, because the biomolecules are usually suspended in a liquid the observed scattering is an average of all possible orientations, making it difficult to obtain three dimensional structural information. In a proposed method polarized SANS and magnetic nanoparticle references attached to the sample molecules is used to obtain phase sensitive structural information and simultaneously circumvent the problem of orientational averaging (Majkrzak et al. J. Appl. Cryst. 47, 2014) If realized and perfected the technique is very promising for unambiguous determination of the three dimensional structure of biomolecules. We demonstrate the principles of our method and show the first experimental data obtained on a simple test system consisting of core shell magnetic nanoparticles.

  1. Transdifferentiation of human endothelial progenitors into smooth muscle cells.

    PubMed

    Ji, HaYeun; Atchison, Leigh; Chen, Zaozao; Chakraborty, Syandan; Jung, Youngmee; Truskey, George A; Christoforou, Nicolas; Leong, Kam W

    2016-04-01

    Access to smooth muscle cells (SMC) would create opportunities for tissue engineering, drug testing, and disease modeling. Herein we report the direct conversion of human endothelial progenitor cells (EPC) to induced smooth muscle cells (iSMC) by induced expression of MYOCD. The EPC undergo a cytoskeletal rearrangement resembling that of mesenchymal cells within 3 days post initiation of MYOCD expression. By day 7, the reprogrammed cells show upregulation of smooth muscle markers ACTA2, MYH11, and TAGLN by qRT-PCR and ACTA2 and MYH11 expression by immunofluorescence. By two weeks, they resemble umbilical artery SMC in microarray gene expression analysis. The iSMC, in contrast to EPC control, show calcium transients in response to phenylephrine stimulation and a contractility an order of magnitude higher than that of EPC as determined by traction force microscopy. Tissue-engineered blood vessels constructed using iSMC show functionality with respect to flow- and drug-mediated vasodilation and vasoconstriction. PMID:26874281

  2. Lithium isotopes as a probe of weathering processes: Orinoco River

    NASA Astrophysics Data System (ADS)

    Huh, Youngsook; Chan, Lui-Heung; Edmond, John M.

    2001-12-01

    Lithium isotopes have the potential to be effective tracers of weathering processes due to their large relative mass difference and therefore fractionation. In this study an attempt is made to fill a major gap in the knowledge of Li isotope fractionation during continental weathering and of the mechanisms involved. Finally the relationship between the suspended and dissolved material is made on a basin-wide scale. The Orinoco basin provides a clear contrast in reaction-limited and transport-limited weathering regimes that has already been documented by a comprehensive study on its fluvial geochemistry (Edmond et al., Geochim. Cosmochim. Acta 60 (1996) 2949-2976; Edmond et al., Geochim. Cosmochim. Acta 59 (1995) 3301-3325). Conspicuous in our new results is the difference in δ6Li of the dissolved load between the Andean (-30 to -22‰) and Shield (-22 to -7‰) tributaries, while the δ6Li of the suspended load is similar between the two. To a first approximation, during superficial weathering in high-relief, tectonically active terrains the dissolved load is high in Li and isotopically heavy (more negative δ6Li), whereas in stable Shield regions the concentrations are low and isotopically light in proportion to the increasing degree of weathering.

  3. Aspherical-atom modeling of coordination compounds by single-crystal X-ray diffraction allows the correct metal atom to be identified.

    PubMed

    Dittrich, Birger; Wandtke, Claudia M; Meents, Alke; Pröpper, Kevin; Mondal, Kartik Chandra; Samuel, Prinson P; Amin Sk, Nurul; Singh, Amit Pratap; Roesky, Herbert W; Sidhu, Navdeep

    2015-02-01

    Single-crystal X-ray diffraction (XRD) is often considered the gold standard in analytical chemistry, as it allows element identification as well as determination of atom connectivity and the solid-state structure of completely unknown samples. Element assignment is based on the number of electrons of an atom, so that a distinction of neighboring heavier elements in the periodic table by XRD is often difficult. A computationally efficient procedure for aspherical-atom least-squares refinement of conventional diffraction data of organometallic compounds is proposed. The iterative procedure is conceptually similar to Hirshfeld-atom refinement (Acta Crystallogr. Sect. A- 2008, 64, 383-393; IUCrJ. 2014, 1,61-79), but it relies on tabulated invariom scattering factors (Acta Crystallogr. Sect. B- 2013, 69, 91-104) and the Hansen/Coppens multipole model; disordered structures can be handled as well. Five linear-coordinate 3d metal complexes, for which the wrong element is found if standard independent-atom model scattering factors are relied upon, are studied, and it is shown that only aspherical-atom scattering factors allow a reliable assignment. The influence of anomalous dispersion in identifying the correct element is investigated and discussed. PMID:25393218

  4. Internalin must be on the bacterial surface to mediate entry of Listeria monocytogenes into epithelial cells.

    PubMed

    Lebrun, M; Mengaud, J; Ohayon, H; Nato, F; Cossart, P

    1996-08-01

    Entry of Listeria monocytogenes into cultured epithelial cells requires production of internalin, a protein with features characteristic of some Gram-positive bacterial surface proteins, in particular an LPXTG motif preceding a hydrophobic sequence and a few basic residues at its C-terminal end. By immunofluorescence and immunogold labelling, we show that in wild-type L. monocytogenes, internalin is present on the cell surface and has a polarized distribution similar to that of ActA, another surface protein of L. monocytogenes involved in actin assembly. Through a genetic analysis, we establish that the C-terminal region of internalin is necessary for cell-surface association, and that although internalin is partially released in the culture medium, its location on the bacterial surface is required to promote entry. Finally, using a 'domain-swapping' strategy-replacement of the cell wall anchor of IniA by the membrane anchor of ActA- we show that the reduced ability to adhere and enter cells of strains expressing IniA-ActA correlates with a lower amount of surface-exposed internalin. Taken together, these results suggest that internalin exposed on the bacterial surface mediates direct contact between the bacterium and the host cell. PMID:8866480

  5. Crystal Structure of the Streptomyces coelicolor TetR-Like Protein ActR Alone and in Complex with Actinorhodin or the Actinorhodin Biosynthetic Precursor (S)-DNPA

    SciTech Connect

    Willems,A.; Tahlan, K.; Taguchi, T.; Zhang, K.; Lee, Z.; Ichinose, K.; Junop, M.; Nodwell, J.

    2008-01-01

    Actinorhodin, an antibiotic produced by Streptomyces coelicolor, is exported from the cell by the ActA efflux pump. actA is divergently transcribed from actR, which encodes a TetR-like transcriptional repressor. We showed previously that ActR represses transcription by binding to an operator from the actA/actR intergenic region. Importantly, actinorhodin itself or various actinorhodin biosynthetic intermediates can cause ActR to dissociate from its operator, leading to derepression. This suggests that ActR may mediate timely self-resistance to an endogenously produced antibiotic by responding to one of its biosynthetic precursors. Here, we report the structural basis for this precursor-mediated derepression with crystal structures of homodimeric ActR by itself and in complex with either actinorhodin or the actinorhodin biosynthetic intermediate (S)-DNPA [4-dihydro-9-hydroxy-1-methyl-10-oxo-3-H-naphtho-[2, 3-c]-pyran-3-(S)-acetic acid]. The ligand-binding tunnel in each ActR monomer has a striking hydrophilic/hydrophobic/hydrophilic arrangement of surface residues that accommodate either one hexacyclic actinorhodin molecule or two back-to-back tricyclic (S)-DNPA molecules. Moreover, our work also reveals the strongest structural evidence to date that TetR-mediated antibiotic resistance may have been acquired from an antibiotic-producer organism.

  6. Task effects, performance levels, features, configurations, and holistic face processing: a reply to Rossion.

    PubMed

    Riesenhuber, Maximilian; Wolff, Brian S

    2009-11-01

    A recent article in Acta Psychologica ("Picture-plane inversion leads to qualitative changes of face perception" by Rossion [Rossion, B. (2008). Picture-plane inversion leads to qualitative changes of face perception. Acta Psychologica (Amst), 128(2), 274-289]) criticized several aspects of an earlier paper of ours [Riesenhuber, M., Jarudi, I., Gilad, S., & Sinha, P. (2004). Face processing in humans is compatible with a simple shape-based model of vision. Proceedings of the Royal Society of London B (Supplements), 271, S448-S450]. We here address Rossion's criticisms and correct some misunderstandings. To frame the discussion, we first review our previously presented computational model of face recognition in cortex [Jiang, X., Rosen, E., Zeffiro, T., Vanmeter, J., Blanz, V., & Riesenhuber, M. (2006). Evaluation of a shape-based model of human face discrimination using FMRI and behavioral techniques. Neuron, 50(1), 159-172] that provides a concrete biologically plausible computational substrate for holistic coding, namely a neural representation learned for upright faces, in the spirit of the original simple-to-complex hierarchical model of vision by Hubel and Wiesel. We show that Rossion's and others' data support the model, and that there is actually a convergence of views on the mechanisms underlying face recognition, in particular regarding holistic processing. PMID:19665104

  7. Enzyme transient state kinetics in crystal and solution from the perspective of a time-resolved crystallographer

    PubMed Central

    Schmidt, Marius; Saldin, Dilano K.

    2014-01-01

    With recent technological advances at synchrotrons [Graber et al., J. Synchrotron Radiat. 18, 658–670 (2011)], it is feasible to rapidly collect time-resolved crystallographic data at multiple temperature settings [Schmidt et al., Acta Crystallogr. D 69, 2534–2542 (2013)], from which barriers of activation can be extracted. With the advent of fourth generation X-ray sources, new opportunities emerge to investigate structure and dynamics of biological macromolecules in real time [M. Schmidt, Adv. Condens. Matter Phys. 2013, 1–10] in crystals and potentially from single molecules in random orientation in solution [Poon et al., Adv. Condens. Matter Phys. 2013, 750371]. Kinetic data from time-resolved experiments on short time-scales must be interpreted in terms of chemical kinetics [Steinfeld et al., Chemical Kinetics and Dynamics, 2nd ed. (Prentience Hall, 1985)] and tied to existing time-resolved experiments on longer time-scales [Schmidt et al., Acta Crystallogr. D 69, 2534–2542 (2013); Jung et al., Nat. Chem. 5, 212–220 (2013)]. With this article, we will review and outline steps that are required to routinely determine the energetics of reactions in biomolecules in crystal and solution with newest X-ray sources. In eight sections, we aim to describe concepts and experimental details that may help to inspire new approaches to collect and interpret these data. PMID:26798774

  8. An assessment of the accuracy of isochore location techniques for H 2O-CO 2-NaCl fluids at granulite facies pressure-temperature conditions

    NASA Astrophysics Data System (ADS)

    Johnson, Eric Lee

    1992-01-01

    Synthetic H 2O-CO 2-NaCl fluid inclusions with XCO2 compositions ranging from 0.10-0.51 and relative salinities ( r-s = wtNaCl/( wt NaCl + wt H 2O )) of 6 to 23.9 wt% have been produced in spontaneously nucleated forsterite, diopside, and orthopyroxene hosts. Molar volumes of the fluids at the pressure and temperature of formation have been calculated using microthermometric data from the fluid inclusions. These P- V- T data are used to compare the accuracy of published methods of isochore location for H 2O-CO 2-NaCl fluids at elevated pressures and temperatures. The results of these analyses show that isochores calculated with the MRK equation of BOWERS and HELGESON ( Geochim. Cosmochim. Acta, vol. 47, 1247-1275, 1983) reproduce the trapping pressures and temperatures well for fluids with XCO2 ≤ 0.3 and up to 23.9 wt% NaCl. For a fluid with XCO2 = 0.49 and relative salinity of 15%, however, the agreement is poor. For these fluid compositions, the observed molar volume is larger than that predicted from the MRK equation of Bowers and Helgeson and, if not corrected, will give isochores that are too low in pressure for a given temperature. The ideal geometric mixing model of BROWN and LAMB ( Geochim. Cosmochim. Acta, vol. 53, 1209-1221, 1989) provides less satisfactory results for the fluid compositions studied.

  9. Diagnosis and epidemiological association of Listeria monocytogenes strains in two outbreaks of listerial encephalitis in small ruminants.

    PubMed Central

    Wiedmann, M; Czajka, J; Bsat, N; Bodis, M; Smith, M C; Divers, T J; Batt, C A

    1994-01-01

    Two outbreaks of epizootic listerial encephalitis, one in sheep and one in goats, were investigated through pathology, microbiology, and DNA amplification-based techniques. Efforts were made to survey the diversity of Listeria monocytogenes strains in the silage consumed by affected animals and to verify the causal relationship between silage and disease outbreak. In both outbreaks, L. monocytogenes was isolated from silage and brain tissue samples. Random amplified polymorphic DNA patterns revealed two distinct L. monocytogenes strains, one of which was identical to the sheep brain isolate, in the silage associated with the outbreak in sheep. Three brain isolates and one silage isolate, all of which had different random amplified polymorphic DNA patterns, were found in the outbreak involving goats. All isolates from both outbreaks were indistinguishable in an in vitro assay for cell-to-cell spread and growth in macrophages. All brain isolates from the goat outbreak had identical intracellular ActA patterns, which were different from the pattern for the silage isolate. While the sheep brain isolate had an ActA pattern different from that of the corresponding silage isolate, the patterns for the brain isolates from the two outbreaks were not identical. This survey demonstrates the diversity of L. monocytogenes in silage and suggests the existence of one or more selective processes by which certain strains are more prone to give rise to disease. Images PMID:8027356

  10. Ultra High-Resolution In vivo Computed Tomography Imaging of Mouse Cerebrovasculature Using a Long Circulating Blood Pool Contrast Agent

    PubMed Central

    Starosolski, Zbigniew; Villamizar, Carlos A.; Rendon, David; Paldino, Michael J.; Milewicz, Dianna M.; Ghaghada, Ketan B.; Annapragada, Ananth V.

    2015-01-01

    Abnormalities in the cerebrovascular system play a central role in many neurologic diseases. The on-going expansion of rodent models of human cerebrovascular diseases and the need to use these models to understand disease progression and treatment has amplified the need for reproducible non-invasive imaging methods for high-resolution visualization of the complete cerebral vasculature. In this study, we present methods for in vivo high-resolution (19 μm isotropic) computed tomography imaging of complete mouse brain vasculature. This technique enabled 3D visualization of large cerebrovascular networks, including the Circle of Willis. Blood vessels as small as 40 μm were clearly delineated. ACTA2 mutations in humans cause cerebrovascular defects, including abnormally straightened arteries and a moyamoya-like arteriopathy characterized by bilateral narrowing of the internal carotid artery and stenosis of many large arteries. In vivo imaging studies performed in a mouse model of Acta2 mutations demonstrated the utility of this method for studying vascular morphometric changes that are practically impossible to identify using current histological methods. Specifically, the technique demonstrated changes in the width of the Circle of Willis, straightening of cerebral arteries and arterial stenoses. We believe the use of imaging methods described here will contribute substantially to the study of rodent cerebrovasculature. PMID:25985192

  11. Symmetry breaking in actin gels - Implications for cellular motility

    NASA Astrophysics Data System (ADS)

    John, Karin; Peyla, Philippe; Misbah, Chaouqi

    2007-03-01

    The physical origin of cell motility is not fully understood. Recently minimal model systems have shown, that polymerizing actin itself can produce a motile force, without the help of motor proteins. Pathogens like Shigella or Listeria use actin to propel themselves forward in their host cell. The same process can be mimicked with polystyrene beads covered with the activating protein ActA, which reside in a solution containing actin monomers. ActA induces the growth of an actin gel at the bead surface. Initially the gel grows symmetrically around the bead until a critical size is reached. Subsequently one observes a symmetry breaking and the gel starts to grow asymmetrically around the bead developing a tail of actin at one side. This symmetry breaking is accompanied by a directed movement of the bead, with the actin tail trailing behind the bead. Force generation relies on the combination of two properties: growth and elasticity of the actin gel. We study this phenomenon theoretically within the framework of a linear elasticity theory and linear flux-force relationships for the evolution of an elastic gel around a hard sphere. Conditions for a parity symmetry breaking are identified analytically and illustrated numerically with the help of a phasefield model.

  12. Monte Carlo simulation of electrothermal atomization on a desktop personal computer

    NASA Astrophysics Data System (ADS)

    Histen, Timothy E.; Güell, Oscar A.; Chavez, Iris A.; Holcombea, James A.

    1996-07-01

    Monte Carlo simulations have been applied to electrothermal atomization (ETA) using a tubular atomizer (e.g. graphite furnace) because of the complexity in the geometry, heating, molecular interactions, etc. The intense computational time needed to accurately model ETA often limited its effective implementation to the use of supercomputers. However, with the advent of more powerful desktop processors, this is no longer the case. A C-based program has been developed and can be used under Windows TM or DOS. With this program, basic parameters such as furnace dimensions, sample placement, furnace heating and kinetic parameters such as activation energies for desorption and adsorption can be varied to show the absorbance profile dependence on these parameters. Even data such as time-dependent spatial distribution of analyte inside the furnace can be collected. The DOS version also permits input of external temperaturetime data to permit comparison of simulated profiles with experimentally obtained absorbance data. The run-time versions are provided along with the source code. This article is an electronic publication in Spectrochimica Acta Electronica (SAE), the electronic section of Spectrochimica Acta Part B (SAB). The hardcopy text is accompanied by a diskette with a program (PC format), data files and text files.

  13. Syntenic assignment of human chromosome 1 homologous loci in the bovine.

    PubMed

    Threadgill, D S; Threadgill, D W; Moll, Y D; Weiss, J A; Zhang, N; Davey, H W; Wildeman, A G; Womack, J E

    1994-08-01

    Three mouse chromosomes (MMU 1, 3, and 4) carry homologs of human chromosome 1 (HSA 1) genes. A similar situation is found in the bovine, where five bovine chromosomes (BTA 2, 3, 5, 16, and unassigned syntenic group U25) contain homologs of HSA 1 loci. To evaluate further the syntenic relationship of HSA 1 homologs in cattle, 10 loci have been physically mapped through segregation analysis in bovine-rodent hybrid somatic cells. These loci, chosen for their location on HSA 1, are antithrombin 3 (AT3), renin (REN), complement component receptor 2 (CR2), phosphofructokinase muscle type (PFKM), Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog (FGR), alpha fucosidase (FUCA1), G-protein beta 1 subunit (GNB1), alpha 1A amylase, (AMY1), the neuroblastoma RAS viral (v-ras) oncogene homolog (NRAS), and alpha skeletal actin (ACTA1). AT3, REN, CR2, and GNB1 mapped to BTA 16, PFKM to BTA 5, AMY1A and NRAS to BTA 3, FGR and FUCA1 to BTA 2, and ACTA1 to BTA 28. PMID:8001974

  14. The Kalman filter approach to inductively coupled plasma atomic emission spectrometry

    NASA Astrophysics Data System (ADS)

    Van Veen, E. H.; Bosch, S.; De Loos-Vollebregt, M. T. C.

    1994-07-01

    This article is an electronic publication in Spectrochimica Acta Electronica (SAE), the electronic section of Spectrochimica Acta Part B (SAB). The hardcopy text, comprising the main article and two appendices, is accompanied by a disk containing the compiled program, a reference manual and data files. The work deals with data handling in inductively coupled plasma atomic emission spectrometry (ICP-AES). With this technique, the analyte signal is superimposed on a background signal. When separating the signals by manual or automated three-point background correction, there are many instances in which the data reduction fails. Based on scans recorded in a fast-scanning mode and on a library of pure-component scans, the Kaiman filter approach models the emission in the spectral window (about 100 pm) of the analyte and mathematically solves the problem of background correction. By using a criterion-based algorithm to correct for optical instability, the uncertainty in the determination of the interferent line signal is eliminated. Therefore, the present filter implementation yields more accurate and precise results, especially in the case of line overlap. The Kalman filter Approach to Atomic Spectrometry (KAAS) software automatically processes Perkin-Elmer Plasma 1000/2000 text files, but can also handle ASCII data files. Practical and comprehensive examples are given to evoke the "Kalman filter feeling" in the crucial step of creating the emission model.

  15. Listeria monocytogenes Exploits Normal Host Cell Processes to Spread from Cell to Cell✪

    PubMed Central

    Robbins, Jennifer R.; Barth, Angela I.; Marquis, Hélène; de Hostos, Eugenio L.; Nelson, W. James; Theriot, Julie A.

    1999-01-01

    The bacterial pathogen, Listeria monocytogenes, grows in the cytoplasm of host cells and spreads intercellularly using a form of actin-based motility mediated by the bacterial protein ActA. Tightly adherent monolayers of MDCK cells that constitutively express GFP-actin were infected with L. monocytogenes, and intercellular spread of bacteria was observed by video microscopy. The probability of formation of membrane-bound protrusions containing bacteria decreased with host cell monolayer age and the establishment of extensive cell-cell contacts. After their extension into a recipient cell, intercellular membrane-bound protrusions underwent a period of bacterium-dependent fitful movement, followed by their collapse into a vacuole and rapid vacuolar lysis. Actin filaments in protrusions exhibited decreased turnover rates compared with bacterially associated cytoplasmic actin comet tails. Recovery of motility in the recipient cell required 1–2 bacterial generations. This delay may be explained by acid-dependent cleavage of ActA by the bacterial metalloprotease, Mpl. Importantly, we have observed that low levels of endocytosis of neighboring MDCK cell surface fragments occurs in the absence of bacteria, implying that intercellular spread of bacteria may exploit an endogenous process of paracytophagy. PMID:10491395

  16. Mutation-Specific Effects on Thin Filament Length in Thin Filament Myopathy

    PubMed Central

    de Winter, Josine M.; Joureau, Barbara; Lee, Eun-Jeong; Kiss, Balázs; Yuen, Michaela; Gupta, Vandana A.; Pappas, Christopher T.; Gregorio, Carol C.; Stienen, Ger J. M.; Edvardson, Simon; Wallgren-Pettersson, Carina; Lehtokari, Vilma-Lotta; Pelin, Katarina; Malfatti, Edoardo; Romero, Norma B.; van Engelen, Baziel G.; Voermans, Nicol C.; Donkervoort, Sandra; Bönnemann, C. G.; Clarke, Nigel F.; Beggs, Alan H.; Granzier, Henk; Ottenheijm, Coen A. C.

    2016-01-01

    Objective Thin filament myopathies are among the most common nondystrophic congenital muscular disorders, and are caused by mutations in genes encoding proteins that are associated with the skeletal muscle thin filament. Mechanisms underlying muscle weakness are poorly understood, but might involve the length of the thin filament, an important determinant of force generation. Methods We investigated the sarcomere length-dependence of force, a functional assay that provides insights into the contractile strength of muscle fibers as well as the length of the thin filaments, in muscle fibers from 51 patients with thin filament myopathy caused by mutations in NEB, ACTA1, TPM2, TPM3, TNNT1, KBTBD13, KLHL40, and KLHL41. Results Lower force generation was observed in muscle fibers from patients of all genotypes. In a subset of patients who harbor mutations in NEB and ACTA1, the lower force was associated with downward shifted force–sarcomere length relations, indicative of shorter thin filaments. Confocal microscopy confirmed shorter thin filaments in muscle fibers of these patients. A conditional Neb knockout mouse model, which recapitulates thin filament myopathy, revealed a compensatory mechanism; the lower force generation that was associated with shorter thin filaments was compensated for by increasing the number of sarcomeres in series. This allowed muscle fibers to operate at a shorter sarcomere length and maintain optimal thin–thick filament overlap. Interpretation These findings might provide a novel direction for the development of therapeutic strategies for thin filament myopathy patients with shortened thin filament lengths. PMID:27074222

  17. Determination of barium, chromium, cadmium, manganese, lead and zinc in atmospheric particulate matter by inductively coupled plasma atomic emission spectrometry (ICP-AES)

    NASA Astrophysics Data System (ADS)

    Boevski, I. V.; Daskalova, N.; Havezov, I.

    2000-11-01

    The present paper has shown that the Q concept, as proposed by P.W.J.M. Boumans, J.J.A.M. Vrakking, Spectrochim. Acta Part B 43 (1988) 69, can be used as a basic methodology in the determination of Ba, Cr, Cd, Mn, Pb and Zn in pairs of atmospheric particles by inductively coupled plasma atomic emission spectrometry (ICP-AES). The data base of Q values for line interference [ QIj(λ a)] and Q values for wing background interference [ QWJ(Δλ a)] were obtained in our former work [N. Daskalova, Iv. Boevski, Spectral interferences in the determination of trace elements in environmental materials by inductively coupled plasma atomic emission spectrometry, Spectrochim. Acta Part B 54 (1999) 1099-1122]. The samples of atmospheric particles were collected by the Bergerhoff method. The ICP-AES determination was performed after sample digestion with aqua regia. Q values were used for the calculation of both the total interfering signal under the analysis lines and the true detection limits, depending on the matrix constituents in the different samples. Comparative data for the concentration of analytes were obtained by flame atomic absorption spectrometry (FAAS) and direct current arc atomic emission spectrographic method (dc arc-AES).

  18. Parameter identification of chaos system based on unknown parameter observer

    NASA Astrophysics Data System (ADS)

    Wang, Shaoming; Luo, Haigeng; Yue, Chaoyuan; Liao, Xiaoxin

    2008-04-01

    Parameter identification of chaos system based on unknown parameter observer is discussed generally. Based on the work of Guan et al. [X.P. Guan, H.P. Peng, L.X. Li, et al., Acta Phys. Sinica 50 (2001) 26], the design of unknown parameter observer is improved. The application of the improved approach is extended greatly. The works in some literatures [X.P. Guan, H.P. Peng, L.X. Li, et al., Acta Phys. Sinica 50 (2001) 26; J.H. Lü, S.C. Zhang, Phys. Lett. A 286 (2001) 148; X.Q. Wu, J.A. Lu, Chaos Solitons Fractals 18 (2003) 721; J. Liu, S.H. Chen, J. Xie, Chaos Solitons Fractals 19 (2004) 533] are only the special cases of our Corollaries 1 and 2. Some observers for Lü system and a new chaos system are designed to test our improved method, and simulations results demonstrate the effectiveness and feasibility of the improved approach.

  19. Influence of static magnetic fields combined with human insulin-like growth factor 1 on human satellite cell cultures.

    PubMed

    Birk, Richard; Sommer, J Ulrich; Haas, Dominik; Faber, Anne; Aderhold, Christoph; Schultz, Johannes D; Hoermann, Karl; Stern-Straeter, Jens

    2014-01-01

    Tissue engineering represents a promising research field, targeting the creation of new functional muscle tissue in vitro. The aim of the present study was to show the influence of static magnetic fields (SMF) and insulin-like growth factor-1 (IGF1), as enhancing stimuli on human satellite cell cultures, which are preferred sources of stem cells in engineering skeletal muscle tissue. To detect effects on myogenic maturation and proliferation, AlamarBlue® proliferation, assay and semi-quantitative reverse transcription-polymerase chain reaction of following markers was performed: desmin (DES), myogenic factor-5 (MYF5), myogenic differentiation antigen-1 (MYOD1), myogenin (MYOG), myosin heavy chain (MYH) and α1 actin (ACTA1). As a distinct marker of differentiation, immunohistochemical staining and fusion index determination was performed on satellite cell cultures stimulated with IGF1 and IGF1-plus-SMF with an intensity of 80 mT. Proliferation was increased by additional SMF application to IGF1-stimulated cell cultures on the first day of myogenesis. Relative gene expression of measured markers was increased by IGF1 application in the first days of myogenesis except for ACTA1. Additional SMF application enhanced this effect. Nevertheless we were unable to demonstrate the formation of contractile muscle tissue. Immunhistochemical staining verified muscle origin and all markers were displayed. PMID:25189891

  20. Relevance of feline interferon omega for clinical improvement and reduction of concurrent viral excretion in retrovirus infected cats from a rescue shelter.

    PubMed

    Gil, Solange; Leal, Rodolfo O; Duarte, Ana; McGahie, David; Sepúlveda, Nuno; Siborro, Inês; Cravo, Joana; Cartaxeiro, Clara; Tavares, Luís M

    2013-06-01

    Feline Immnunodeficiency (FIV) and Feline Leukemia (FeLV) viruses are common infectious agents in stray cats and shelter environments. Recombinant feline interferon-ω (rFeIFNω) has shown an antiviral action not only against FIV and FeLV but also against herpesvirus (FHV-1) and calicivirus (FCV). Sixteen naturally infected FIV/FeLV cats were followed during rFeIFNω therapy in order to monitor clinical signs and to correlate with excretion of concomitant viruses (FCV, FHV-1, feline coronavirus (FCoV) and parvovirus (FPV)). Cats were submitted to clinical evaluations and concomitant virus excretion assessement. Comparing D0-D65, 10/16 cats improved clinical scores. Of the 10 cats positive for FHV-1 on D0, 4 were negative and 6 reduced viral loads. Of the 11 FCoV positive cats, 9 reduced viral loads. The 13 FCV positive cats and the FPV positive cat were negative on D65. In conclusion, rFeIFNω improves clinical signs and reduces concurrent viral excretion in naturally infected retroviral cats. PMID:23122808

  1. Critical view to ``IGEX 76Ge neutrinoless double-beta decay experiment: Prospects for next generation experiments''

    NASA Astrophysics Data System (ADS)

    Klapdor-Kleingrothaus, H. V.; Dietz, A.; Krivosheina, I. V.

    2004-10-01

    Recently, a paper entitled “The IGEX 76Ge neutrinoless double-beta decay experiment: Prospects for next generation experiments” has been published [

    Phys. Rev. D 65, 092007 (2002)PRVDAQ0556-282110.1103/PhysRevD.65.092007
    ]. In view of the recently reported evidence for neutrinoless double-beta decay [
    Mod. Phys. Lett. A 16, 2409 (2001).MPLAEQ0217-732310.1142/S0217732301005825
    ;
    Found. Phys.FNDPA40015-9018 31, 1181 (2002)
    ;
    Phys. Lett. BPYLBAJ0370-2693 586, 198 (2004).10.1016/j.physletb.2004.02.025
    ], it is particularly unfortunate that the IGEX paper is rather incomplete in its presentation. We would like to point out in this Comment that and why it would be highly desirable to make more details about the experimental conditions and the analysis of IGEX available. We list some of the main points, which require further explanation. We also point to an arithmetic mistake in the analysis of the IGEX data, the consequence of which are too high half-life limits given in that paper.

  2. Expression and Function of Water Channels (Aquaporins) in Migrating Malignant Astrocytes

    PubMed Central

    McCOY, ERIC; SONTHEIMER, HARALD

    2008-01-01

    Aquaporins (AQP) constitute the principal pathway for water movement across biological membranes. Consequently, their expression and function is important for cell volume regulation. Glioma cells quickly adjust their cell volume in response to osmotic challenges or spontaneously as they invade into the narrow and tortuous extracellular spaces of the brain. These cell volume changes are likely to engage water movements across the cell membrane through AQP. AQP expression in glioma cells is poorly understood. In this study, we examined the expression of AQP in several commonly used human glioma cell lines (D54, D65, STTG1, U87, U251) and in numerous acute patient biopsies by PCR, Western blot, and immunocytochemistry and compared them to nonmalignant astrocytes and normal brain. All glioma patient biopsies expressed AQP1, AQP4 and some expressed AQP5. However, when isolated and grown as cell lines they lose all AQP proteins except a few cell lines that maintain expression of AQP1 (D65, U251, GBM62). Reintroducing either AQP1 or AQP4 stably into glioma cell lines allowed us to show that each AQP is sufficient to restore water permeability. Yet, only the presence of AQP1, but not AQP4, enhanced cell growth and migration, typical properties of gliomas, while AQP4 enhanced cell adhesion suggesting differential biological roles for AQP1 and AQP4 in glioma cell biology. PMID:17549682

  3. Accretion and differentiation of carbon in the early Earth.

    PubMed

    Tingle, T N

    1998-05-15

    The abundance of C in carbonaceous and ordinary chondrites decreases exponentially with increasing shock pressure as inferred from the petrologic shock classification of Scott et al. [Scott, E.R.D., Keil, K., Stoffler, D., 1992. Shock metamorphism of carbonaceous chondrites. Geochim. Cosmochim. Acta 56, 4281-4293] and Stoffler et al. [Stoffler, D., Keil, K., Scott, E.R.D., 1991. Shock metamorphism of ordinary chondrites. Geochim. Cosmochim. Acta 55, 3845-3867]. This confirms the experimental results of Tyburczy et al. [Tyburczy, J.A., Frisch, B., Ahrens, T.J., 1986. Shock-induced volatile loss from a carbonaceous chondrite: implications for planetary accretion. Earth Planet. Sci. Lett. 80, 201-207] on shock-induced devolatization of the Murchison meteorite showing that carbonaceous chondrites appear to be completely devolatilized at impact velocities greater than 2 km s-1. Both of these results suggest that C incorporation would have been most efficient in the early stages of accretion, and that the primordial C content of the Earth was between 10(24) and 10(25) g C (1-10% efficiency of incorporation). This estimate agrees well with the value of 3-7 x 10(24) g C based on the atmospheric abundance of 36Ar and the chondritic C/36Ar (Marty and Jambon, 1987). Several observations suggest that C likely was incorporated into the Earth's core during accretion. (1) Graphite and carbides are commonly present in iron meteorites, and those iron meteorites with Widmanstatten patterns reflecting the slowest cooling rates (mostly Group I and IIIb) contain the highest C abundances. The C abundance-cooling rate correlation is consistent with dissolution of C into Fe-Ni liquids that segregated to form the cores of the iron meteorite parent bodies. (2) The carbon isotopic composition of graphite in iron meteorites exhibits a uniform value of -5% [Deines, P., Wickman, F.E. 1973. The isotopic composition of 'graphitic' carbon from iron meteorites and some remarks on the troilitic

  4. Hydrogeologic uncertainties and policy implications: The Water Consumer Protection Act of Tucson, Arizona, USA

    NASA Astrophysics Data System (ADS)

    Wilson, L. G.; Matlock, W. G.; Jacobs, K. L.

    confusion entre "infiltration" et "recharge". C'est ainsi que la loi laisse entendre que l'infiltration à partir des lits de rivières le long du champ captant central favorise la recharge de cette zone. En réalité, les différences de perméabilité entre les alluvions du lit et les dépôts sous-jacents remplissant le bassin peuvent provoquer un écoulement sous-jacent. En outre, même si une recharge par l'eau de la rivière Colorado se produit dans cette zone, la nappe sera progressivement salifiée. Les restrictions imposées par la loi quant à l'utilisation de l'eau de la station centrale d'Arizona affectent les quatre outils réglementaires du Code des eaux souterraines de l'Arizona de 1980, en ce qu'ils concernent la zone de gestion active de Tucson: (a) l'augmentation de l'approvisionnement (b) les conditions requises pour les prélèvements d'eau souterraine et les autorisations; (c) les conditions requises pour le plan de gestion, en particulier la pérennité du concessionnaire et les résultats en matière de qualité de l'eau et (d) la condition que tous les nouveaux districts aient recours à des ressources en eau renouvelables à la place de l'eau souterraine. Les demandes concernant la mise en oeuvre de la loi ont conduit jusqu'à l'arrêt des activités normales des instances politiques. Resumen El Acta de Protección de los Usuarios de Agua de Tucson, Arizona (EE.UU.) de 1995 (el Acta) se aprobó a raíz de las quejas de los usuarios de agua de Tucson que recibían agua tratada por el Proyecto de Arizona Central (CAP). Las consecuencias del Acta demuestran las incertidumbres y dificultades que se producen cuando se le pide al público que vote sobre temas muy técnicos. Los requerimientos de recarga del Acta desprecian incertidumbres hidrogeológicas al confundir entre "infiltración" y "recarga". Así, el Acta dice que la infiltración en los canales de los arroyos a lo largo del Campo de Producción Central aumentará la recarga a dicho campo. De

  5. Automated CO2 extraction from air for clumped isotope analysis in the atmo- and biosphere

    NASA Astrophysics Data System (ADS)

    Hofmann, Magdalena; Ziegler, Martin; Pons, Thijs; Lourens, Lucas; Röckmann, Thomas

    2015-04-01

    The conventional stable isotope ratios 13C/12C and 18O/16O in atmospheric CO2 are a powerful tool for unraveling the global carbon cycle. In recent years, it has been suggested that the abundance of the very rare isotopologue 13C18O16O on m/z 47 might be a promising tracer to complement conventional stable isotope analysis of atmospheric CO2 [Affek and Eiler, 2006; Affek et al. 2007; Eiler and Schauble, 2004; Yeung et al., 2009]. Here we present an automated analytical system that is designed for clumped isotope analysis of atmo- and biospheric CO2. The carbon dioxide gas is quantitatively extracted from about 1.5L of air (ATP). The automated stainless steel extraction and purification line consists of three main components: (i) a drying unit (a magnesium perchlorate unit and a cryogenic water trap), (ii) two CO2 traps cooled with liquid nitrogen [Werner et al., 2001] and (iii) a GC column packed with Porapak Q that can be cooled with liquid nitrogen to -30°C during purification and heated up to 230°C in-between two extraction runs. After CO2 extraction and purification, the CO2 is automatically transferred to the mass spectrometer. Mass spectrometric analysis of the 13C18O16O abundance is carried out in dual inlet mode on a MAT 253 mass spectrometer. Each analysis generally consists of 80 change-over-cycles. Three additional Faraday cups were added to the mass spectrometer for simultaneous analysis of the mass-to-charge ratios 44, 45, 46, 47, 48 and 49. The reproducibility for δ13C, δ18O and Δ47 for repeated CO2 extractions from air is in the range of 0.11o (SD), 0.18o (SD) and 0.02 (SD)o respectively. This automated CO2 extraction and purification system will be used to analyse the clumped isotopic signature in atmospheric CO2 (tall tower, Cabauw, Netherlands) and to study the clumped isotopic fractionation during photosynthesis (leaf chamber experiments) and soil respiration. References Affek, H. P., Xu, X. & Eiler, J. M., Geochim. Cosmochim. Acta 71, 5033

  6. An examination of the regulatory mechanism of Pxdn mutation-induced eye disorders using microarray analysis.

    PubMed

    Yang, Yang; Xing, Yiqiao; Liang, Chaoqun; Hu, Liya; Xu, Fei; Mei, Qi

    2016-06-01

    The present study aimed to identify biomarkers for peroxidasin (Pxdn) mutation-induced eye disorders and study the underlying mechanisms involved in this process. The microarray dataset GSE49704 was used, which encompasses 4 mouse samples from embryos with Pxdn mutation and 4 samples from normal tissues. After data preprocessing, the differentially expressed genes (DEGs) between Pxdn mutation and normal tissues were identified using the t-test in the limma package, followed by functional enrichment analysis. The protein-protein interaction (PPI) network was constructed based on the STRING database, and the transcriptional regulatory (TR) network was established using the GeneCodis database. Subsequently, the overlapping DEGs with high degrees in two networks were identified, as well as the sub-network extracted from the TR network. In total, 121 (75 upregulated and 46 downregulated) DEGs were identified, and these DEGs play important roles in biological processes (BPs), including neuron development and differentiation. A PPI network containing 25 nodes such as actin, alpha 1, skeletal muscle (Acta1) and troponin C type 2 (fast) (Tnnc2), and a TR network including 120 nodes were built. By comparing the two networks, seven crucial genes which overlapped were identified, including cyclin‑dependent kinase inhibitor 1B (Cdkn1b), Acta1 and troponin T type 3 (Tnnt3). In the sub-network, Cdkn1b was predicted as the target of miRNAs such as mmu-miR-24 and transcription factors (TFs) including forkhead box O4 (FOXO4) and activating enhancer binding protein 4 (AP4). Thus, we suggest that seven crucial genes, including Cdkn1b, Acta1 and Tnnt3, play important roles in the progression of eye disorders such as glaucoma. We suggest that Cdkn1b exert its effects via the inhibition of proliferation and is mediated by mmu-miR-24 and targeted by the TFs FOXO4 and AP4. PMID:27121343

  7. Predictive Framework and Experimental Tests of the Kinetic Isotope Effect at Redox-Active Interfaces

    NASA Astrophysics Data System (ADS)

    Kavner, A.; John, S.; Black, J. R.

    2013-12-01

    Electrochemical reactions provide a compelling framework to study kinetic isotope effects because redox-related processes are important for a wide variety of geological and environmental processes. In the laboratory, electrochemical reaction rates can be electronically controlled and measured in the laboratory using a potentiostat. This enables variation of redox reactions rates independent of changes in chemistry and, and the resulting isotope compositions of reactants and products can be separated and analyzed. In the past years, a series of experimental studies have demonstrated a large, light, and tunable kinetic isotope effect during electrodeposition of metal Fe, Zn, Li, Cu, and Mo from a variety of solutions (e.g. Black et al., 2009, 2010, 2011). A theoretical framework based on Marcus kinetic theory predicts a voltage-dependent kinetic isotope effect (Kavner et al., 2005, 2008), however while this framework was able to predict the tunable nature of the effect, it was not able to simultaneously predict absolute reaction rates and relative isotope rates. Here we present a more complete development of a statistical mechanical framework for simple interfacial redox reactions, which includes isotopic behavior. The framework is able to predict a kinetic isotope effect as a function of temperature and reaction rate, starting with three input parameters: a single reorganization energy which describes the overall kinetics of the electron transfer reaction, and the equilibrium reduced partition function ratios for heavy and light isotopes in the product and reactant phases. We show the framework, elucidate some of the predictions, and show direct comparisons against isotope fractionation data obtained during laboratory and natural environment redox processes. A. Kavner, A. Shahar, F. Bonet, J. Simon and E. Young (2005) Geochim. Cosmochim. Acta, 69(12), 2971-2979. A. Kavner, S. G. John, S. Sass, and E. A. Boyle (2008), Geochim. Cosmochim. Acta, vol 72, pp. 1731

  8. 40Ar/39Ar dating of the Honghuaqiao Formation in SE China

    NASA Astrophysics Data System (ADS)

    Chang, S.; Zhang, H.; Hemming, S. R.; Mesko, G. T.; Fang, Y.

    2010-12-01

    The Jehol Biota, defined as the characteristic Eosestheria-Ephemeropsis-Lycoptera assemblage (Grabau, 1923, Bulletin of the Geological Survey of China), is widely distributed in eastern and central Asia (Li et al., 1982, Acta Geologica Sinica; Chen, 1988, Acta Palaeontologica Sinica). Abundant and varied fossils of the terrestrial Jehol Biota, including plants, insects, dinosaurs, birds, mammals, and freshwater invertebrates, have been discovered from the Dabeigou, the Yixian and the Jiufotang Formations (or their correlative strata) in northeast China from the Liaoning and Hebei Provinces and Inner Mongolia (Chen and Jin, 1999, Acta Palaeontologica Sinica). In addition, strata that may be correlative with the classic Jehol fossil-bearing formations have been identified extensively in central and eastern China, the Korean Peninsula, Mongolia, and Siberia. In the past three decades mollusk, conchostracan, ostracod, insect, fish, and plant fossils from localities in southeastern China, interpreted as related to the Jehol biota of the northeast, have been found (Mateer and Chen, 1986, Cretaceous Research; Li, 2003, Chinese Science Bulletin; Chen, Li and Batten, 2007, Geological Journal). However, a detailed correlation between the classic Jehol outcrops and the more recently found localities to the South and West has yet to emerge. Volcanic rocks from the Honghuaqiao fossil-bearing Formation in Tuzhou City of eastern Anhui Province, southeastern China provide an excellent opportunity to rectify this situation. Preliminary results of a pilot study suggest that the Honghuaqiao Formation is equivalent to the Longwanshan Formation of Anhui Province, southeastern China and the Yixian Formation, northeastern China (Chang et al., 2009, AGU abstract). Initial 40Ar/39Ar results indicate that conchostracans from the upper Honghuaqiao Formation are approximately 130 Ma. Our ongoing work aims to establish a high-resolution chronostratigraphy for Tuzhou City in Anhui Province

  9. Biogeochemistry of Sulfur Intermediates in Marine Sediments - Insights from Laboratory and Field Studies

    NASA Astrophysics Data System (ADS)

    Ferdelman, T. G.; Milucka, J.; Kuypers, M. M. M.; Berg, J.; Buckner, C.; Graf, J.; Holmkvist, L.; Jørgensen, B. B.; Kamyshny, A.; Piepgras, L.

    2014-12-01

    The sulfur cycle in marine sediments exerts a major control on the redox state of the ocean and atmosphere. The overall driver in the sulfur cycle is the microbial mediated sulfate reduction to sulfide (SR), In near-surface sediments, only a small fraction of the sulfide produced becomes permanently buried in the reduced form as pyrite (FeS2) Paradoxically, the deep, reduced, sulfidic zone of marine sediments is often characterized by the presence of zero-valent sulfur compounds, e.g. elemental sulfur and polysulfides [1,2,3]. The presence of oxidized iron and manganese has been suggested as the source of oxidizing power for the formation of elemental S and polysulfides in these deep, anoxic and sulfidic sediment environments, which often lie at or below the sulfate-methane transition [1,3]. The findings of Milucka et al. [4] suggest that anaerobic oxidation of methane coupled to sulfate reduction (AOM) may provide another source of zerovalent sulfur to such environments. AOM is thought to be mediated by a consortium of methanotrophic archaea (ANME) and sulfate-reducing Deltaproteobacteria. Milucka et al. [4] show that zero-valent sulfur compounds (S0) are formed during AOM-coupled SR and conclude that the S0 is a product of a novel pathway for sulfate reduction performed by the ANME. Thus, AOM may not be an obligately syntrophic process. Furthermore, the produced S0, in the form of hydrodisulfide, can serve as a substrate for disproportionation by the Deltaproteobacteria associated with the ANME, and that this disproptionation proceeds under sulfidic conditions. These observations may have significant implications for role of sulfur intermediates in our understanding of the biogeochemical carbon and sulfur cycle in modern and past environments. [1] Holmkvist et al. (2011) Geochim. Cosmochim. Acta 75, 3581-3599. [2] Lichtschlag et al. (2013) Geochim. Cosmochim. Acta 105, 130-145. [3] Holmkvist et al. (2014) Geochim. Cosmochim. Acta, accepted. [4] Milucka et al

  10. An update on 11B,10B fractionation in the fundamental reaction: 10B(OH)3 + 11B(OH)4- = 11B(OH)3 + 10B(OH)4-

    NASA Astrophysics Data System (ADS)

    Klochko, K.; Tossell, J. A.

    2007-12-01

    It has recently been demonstrated experimentally by Byrne, et al. (2006) and Klochko, et al. (2006) that the equilibrium constant for the isotopic exchange reaction: 10B(OH)3 + 11B(OH)4- = 11B(OH)3 + 10B(OH)4- (1) has a value around 1.027 for seawater at 25°C, for total B concentrations from 0.01 to 0.05 molal. These experimental studies involved essentially the accurate determination of the small pKa difference between the 11B and 10B isotopomers of boric acid. This new equilibrium constant value is significantly higher than the traditional value of 1.0194 from Kakihana, et al. (1977). This result has been obscured in recent controversies (Honisch, et al., 2007). The new value agrees well with the ab initio quantum cluster calculated values of Liu and Tossell (2005) and with the ab initio MD harmonic values of Rustad and Bylaska (2007). We will present additional calculations supporting and extending the study of Liu and Tossell (2005) and will discuss the general unsuitability of methods such as Sanchez-Valle, et al. (2005) which employ experimental spectral data. We have also established that polyborate formation in solutions as concentrated as 0.50 molal total B has little effect on the equilibrium constant. A mechanism is also presented for the interaction of B(OH)3 and B(OH)4- with HCO3- species occurring on the calcite surface. References: Byrne, et al. Deep-Sea Research I (2006) 53, 684-688. Honisch, et al. Geochim. Cosmochim. Acta (2007) 71, 1636-1641. Kakihana, et al. Bull. Chem. Soc. Jpn. (1977) 50, 158-163. Klochko, et al. Earth Planet. Sci. Lett. (2006) 248, 276-285. Liu and Tossell Geochim. Cosmochim. Acta (2005) 69, 3995-4006. Rustad and Bylaska J. Am. Chem. Soc. (2007) 129, 2222-2223. Sanchez-Valle, et al. Geochim. Cosmochim. Acta (2005) 69, 4301-4313.

  11. Major Cation, Carbon System and Trace Element Chemistry in Pore Waters from a Depth Transect of Cores on the Iberian Margin: Implications for Paleoproxies.

    NASA Astrophysics Data System (ADS)

    Greaves, M.; Elderfield, H.; Hodell, D. A.; Skinner, L. C.; Sevilgen, D.; Grauel, A. L.; de la Fuente, M.; Misra, S.

    2014-12-01

    A significant body of work exists on the chemistry of pore waters from DSDP and ODP drilling cores (e.g. Gieskes 1975; Sayles 1981) showing large gradients in sea salt cations and anions interpreted in terms of diagenetic reactions such as the formation of Mg-rich clays and dolomite formation (Higgins and Schrag, 2010). Another class of diagenetic reactions involves the breakdown of organic matter and trace element behaviour (Froelich et al., 1979). The translation of chemical gradients into fluxes requires estimates of pore water chemistry across the sea water - sediment surface boundary. Additionally, the use of the chemistry of benthic foraminiferal calcite for seawater paleochemistry requires estimation of the chemistry of pore waters which may differ from that of bottom seawater because of diagenetic reactions. In this work we have collected multi core samples from 10 core sites on cruise RRS James Cook JC089 on the southwest Iberian continental margin. Pore waters were extracted from the core surface and at 1 cm depth intervals down core (typically to ~40 cm depth) using Rhizon samplers and analysed for Alkalinity, DIC, ∂13C and Na, K, Mg, Ca, Li, Mn, Fe, Ba, B, Sr by atomic emission spectrophotometry as well as O2 penetration and pH by microelectrodes. This has allowed us to inspect chemical behavior at the bottom water - sediment interface. Some examples of results are a large gradient in ∂13C of DIC, the similarity of zero O2 penetration followed by an increase in Mn concentration and then decrease to zero, the similarity of Li to Mn and, in contrast to much DSDP/ODP work, Ca2+ and Mg2+both decrease with depth in pore waters near the sediment surface. References: Gieskes J.M. Annu. Rev. Earth Planet. Sci. 3, 433 (1975). Sayles F. L. Geochim. Cosmochim. Acta45, 1061 (1981). Higgins J.A. and D.P. Schrag. Geochim. Cosmochim. Acta.74, 5039 (2010). Froelich, P.N., et al., Geochim. Cosmochim. Acta. 43, 1075 (1979).

  12. Epigenetic and phenotypic changes result from a continuous pre and post natal dietary exposure to phytoestrogens in an experimental population of mice

    PubMed Central

    Guerrero-Bosagna, Carlos M; Sabat, Pablo; Valdovinos, Fernanda S; Valladares, Luis E; Clark, Susan J

    2008-01-01

    Background Developmental effects of exposure to endocrine disruptors can influence adult characters in mammals, but could also have evolutionary consequences. The aim of this study was to simulate an environmental exposure of an experimental population of mice to high amounts of nutritional phytoestrogens and to evaluate parameters of relevance for evolutionary change in the offspring. The effect of a continuous pre- and post-natal exposure to high levels of dietary isoflavones was evaluated on sexual maturity, morphometric parameters and DNA methylation status in mice. Adult mice male/female couples were fed ad libitum either with control diet (standard laboratory chow) or ISF diet (control diet plus a soy isoflavone extract at 2% (w/w) that contained the phytoestrogens genistein and daidzein). In the offspring we measured: i) the onset of vaginal opening (sexual maturation) in females, ii) weight and size in all pups at 7, 14, 21 and 42 days post-natal (dpn) and iii) DNA methylation patterns in skeletal α-actin (Acta1), estrogen receptor-α and c-fos in adults (42 dpn). Results Vaginal opening was advanced in female pups in the ISF group, from 31.6 ± 0.75 dpn to 25.7 ± 0.48. No differences in size or weight at ages 7, 14 or 21 dpn were detected between experimental groups. Nevertheless, at age 42 dpn reduced size and weight were observed in ISF pups, in addition to suppression of normal gender differences in weight seen in the control group (males heavier that females). Also, natural differences seen in DNA methylation at Acta1 promoter in the offspring originated in the control group were suppressed in the ISF group. Acta1 is known to be developmentally regulated and related to morphomotric features. Conclusion This study demonstrates in mammals that individuals from a population subjected to a high consumption of isoflavones can show alterations in characters that may be of importance from an evolutionary perspective, such as epigenetic and morphometric

  13. Detection of multiple virulence-associated genes in Listeria monocytogenes isolated from bovine mastitis cases.

    PubMed

    Rawool, D B; Malik, S V S; Shakuntala, I; Sahare, A M; Barbuddhe, S B

    2007-01-25

    Clinical samples (n=725) were collected from bovines (n=243) which were positive for mastitis using the California mastitis test (CMT) and somatic cell count (SCC). The clinical samples comprising blood (n=239), milk (n=243), and faecal swabs (n=243) were examined for the presence of pathogenic Listeria spp. Isolation of the pathogen was done using selective enrichment in University of Vermont Medium and plating onto Dominguez-Rodriguez isolation agar. Confirmation of the isolates was based on biochemical tests and Christie, Atkins, Munch-Petersen (CAMP) test followed by pathogenicity testing. Pathogenicity of the isolates was tested by phosphatidylinositol-specific phospholipase C (PI-PLC) assay as well as in vivo tests namely, chick embryo and mice inoculation tests. The isolates were subjected to PCR assay for five virulence-associated genes, plcA, prfA, hlyA, actA and iap. Listeria spp. were isolated from 12 (1.66%) samples. Of these 4 (0.55%) and 1 (0.14%) were confirmed as Listeria monocytogenes and Listeria ivanovii, respectively. L. monocytogenes and L. ivanovii were recovered from milk samples (2) and faecal (3) of mastitic cattle (3) and buffaloes (2). L. monocytogenes recovered from the milk of mastitic cattle and L. ivanovii from the faecal swab of buffalo turned out to be pathogenic. However, the remaining three hemolytic isolates exhibiting positive CAMP test turned out to be negative in PI-PLC assay, chick embryo and mice inoculation. L. monocytogenes and L. ivanovii isolates characterized as pathogenic by PI-PLC assay and in vivo pathogenicity tests were found to possess all the five virulence-associated genes and three genes, plcA, prfA and actA respectively. The remaining three hemolytic but non-pathogenic L. monocytogenes isolates were negative for plcA by PCR. It seems that the plcA gene and its expression (in the PI-PLC assay) have an important role as virulence determinants in pathogenic Listeria spp. In conclusion, the PI-PLC assay and

  14. Isolation, identification, and characterization of Listeria spp. from various animal origin foods

    PubMed Central

    Nayak, Deepti N.; Savalia, C. V.; Kalyani, I. H.; Kumar, Rajeev; Kshirsagar, D. P.

    2015-01-01

    Aim: The present study was undertaken with the prime objective of isolating and identifying Listeria spp. from various foods of animal origin sold at retail market outlets in the city of Navsari, Gujarat. Materials and Methods: Total 200 samples comprising of milk, milk products, meat, and fish (50 each) collected aseptically from local market which were subjected first to pre-enrichment in half strength Fraser broth followed by enrichment in full strength Fraser broth and subsequent plating on PALCAM agar. The growth with the typical colony characteristics were further identified up to species level on the basis of their morphological and biochemical characteristics. Cultures identified as Listeria monocytogenes were further subjected to in vitro pathogenicity tests and detection of different virulence-associated genes viz. actA, hlyA, and iap using polymerase chain reaction. Results: Of the total 200 food samples of animal origin; 18 (9%) were found positive for Listeria spp. which were identified as Listeria seeligeri (6, 33.3%), Listeria innocua (5, 27.7%), Listeria welshimeri (4, 22.2%), and L. monocytogenes (3, 16.6%). The highest prevalence was observed in milk samples (8). Species wise, 6 isolates of L. seeligeri which included two each from cow milk, buffalo milk, and meat samples; 5 L. innocua isolates included four recovered from fish and one from meat sample; 4 L. welshimeri comprised of two isolates from ice cream and one each from buffalo milk and meat sample; and 3 isolates of L. monocytogenes recovered from milk (1 cow and 2 buffalo milk). All 3 L. monocytogenes isolates screened for the presence of virulence genes viz. actA, hlyA, and iap using the specific primers revealed the presence of all the genes suggesting the possibility of danger of foodborne listeriosis among raw milk consumers. Conclusion: Listeria spp. was isolated from 9% (18/200) of the animal origin food samples viz.; milk, milk products, meat, and fish with the highest prevalence

  15. Si transfers during Archean weathering processes traced by silicon isotopes and Ge/Si ratios

    NASA Astrophysics Data System (ADS)

    Delvigne, Camille; Opfergelt, Sophie; Hofmann, Axel; Cardinal, Damien; André, Luc

    2015-04-01

    Weathering conditions in the Mesoarchean are poorly constrained. Recent advances in analytical capabilities have added Si isotopes and Ge/Si ratios to the repertoire of tracers used in the study of soil formation processes: neoformation of secondary clay minerals is associated with large Si isotope and Ge/Si fractionation in response to desilication processes and the weathering degree [1, 2, 3, 4]. Here we combine Si isotopes and Ge/Si ratios of a Mesoarchean paleosol (~2.95 Ga) and of nearly coeval but younger shales as proxies of weathering processes and Si mass transfer at the early Earth's surface. The paleosol is developed on andesite and shows a well defined mineralogical and chemical differentiation. In a first step, similar to modern soils, neoformation of secondary clay minerals in the paleosol was associated with fractionation of Si isotopes and Ge/Si ratios in response to chemical weathering degree and soil desilication. In a second step, the loss of Fe(II)-rich minerals, likely Fe-rich smectites, due to low pO2 conditions produced additional control on Si and Ge mobilities. Opposite fractionation behaviors are observed: products of desilication acted as 28Si and Ge sink while the leaching of Fe(II)-rich minerals released 28Si and Ge to soil solutions. Furthermore, the shales deposited immediately after the paleosol display δ30Si and Ge/Si compositions which may be explained as mixtures of the recognized Archean paleosols components. Their recording within the sedimentary pile suggests that the observed weathering-induced desilication might have been widely effective during the Mesoarchean as well as Fe(II)-rich minerals leaching in a lesser extent and pointing out these processes as determinant in the Si transfers from continents to hydrosphere. [1] Kurtz et al., (2002) Geochim. Cosmochim. Acta 66, 1525-1537 [2] Ziegler et al., (2005) Geochim. Cosmochim. Acta 69, 4597-4610. [3] Opfergelt et al., (2010) Geochim. Cosmochim. Acta 74, 225-240. [4

  16. Molybdenum Cycling in Upwelling Sediments: An Example from Namibian Margin Sediments

    NASA Astrophysics Data System (ADS)

    Arnold, G. L.; Goldhammer, T.; Formolo, M.; Brunner, B.; Ferdelman, T.

    2008-12-01

    (1973), Geochim. Cosmochim. Acta 87, 1415. (2)McManus et al. (2006), Geochim. Cosmochim. Acta 70, 4643. (3)Erickson and Helz (2000) Geochim. Cosmochim. Acta 64, 1149.

  17. The proposed icy mineralogy package (XRD/XRF) for TandEM

    NASA Astrophysics Data System (ADS)

    Fortes, Andrew Dominic; Wood, Ian G.; Dobson, David P.; Fewster, Paul F.; Coustenis, Athena; Lebreton, Jean-Pierre

    synthetic diffraction data to estimate detection limits as a function of resolution and count times; and (d) trade-off studies of synthetic multilayer optics versus crystal monochromators. We will also report on environmental factors which affect (both positively and negatively) the likely instrument performance, including sample and atmosphere X-ray attenuation lengths. Summary: The proposed IMPs will be able to identify any crystalline substances (including organic polymers) present on Titan's surface at > 1 wt % levels, and quantify their relative abundance [2,3], as well as, in principle, estimate the abundance of any amorphous material. The focusing geometry maximises the flux and resolution obtainable from radioisotope sources and also has the advantage of illuminating a relatively large sample volume (compared to other mini-XRD designs); this improves the measured powder statistics. Most of the mass, and all of the power use is confined to the detector system (which is cooled passively by Titan's atmosphere) and data rates will be very small. The robustness of the technique renders it the method of choice for unambiguous determination of Titan's surface mineralogy. References: [1] Coustenis, A., et al. (2008) paper in press Astrophys. Instr. Methods. [2] Rietveld, H. (1969) J. Appl. Cryst. 2, 65-71. [3] Hill, R. J. & C. J. Howard (1987) J. Appl. Cryst. 20, 467-474.

  18. Development of a new micro-furnace for "in situ" high-temperature single crystal X-ray diffraction measurements

    NASA Astrophysics Data System (ADS)

    Alvaro, Matteo; Angel, Ross J.; Marciano, Claudio; Zaffiro, Gabriele; Scandolo, Lorenzo; Mazzucchelli, Mattia L.; Milani, Sula; Rustioni, Greta; Domeneghetti, Chiara M.; Nestola, Fabrizio

    2015-04-01

    -position method (King and Finger 1979), and thus maximize precision in unit-cell parameter measurements. The software has been modified to restrict the χ circle movements to between -90° and +90° to reduce chimney effects in the furnace and thus improve stability. Moreover, the temperature stability during the measurements is further improved by optimizing the order of measurements to minimize χ circle movements, and then imposing a waiting time after large angular movements on χ to allow the temperature inside the furnace to re-equilibrate before each measurement. Temperature calibration has been performed iteratively by combining measurements with a standard small diameter thermocouple mounted in the same conditions as the sample together with the lattice parameter determination of materials with known thermal expansion behavior (i.e. silicon, quartz etc…). This procedure has the main advantage that the temperature calibration can obtained with a large number of measurements over a large temperature interval (room-T to 1200°C) and allows the waiting time for the χ movements to be calibrated as a function of temperature. References Angel RJ, Finger LW (2011) JAppCryst, 44:247-251. King HE, Finger LW (1979) JAppCryst,12:374-378

  19. Plant Growth-Promoting Rhizobacteria Inoculation to Enhance Vegetative Growth, Nitrogen Fixation and Nitrogen Remobilisation of Maize under Greenhouse Conditions

    PubMed Central

    Kuan, Khing Boon; Othman, Radziah; Abdul Rahim, Khairuddin; Shamsuddin, Zulkifli H.

    2016-01-01

    Plant growth-promoting rhizobacteria (PGPR) may provide a biological alternative to fix atmospheric N2 and delay N remobilisation in maize plant to increase crop yield, based on an understanding that plant-N remobilisation is directly correlated to its plant senescence. Thus, four PGPR strains were selected from a series of bacterial strains isolated from maize roots at two locations in Malaysia. The PGPR strains were screened in vitro for their biochemical plant growth-promoting (PGP) abilities and plant growth promotion assays. These strains were identified as Klebsiella sp. Br1, Klebsiella pneumoniae Fr1, Bacillus pumilus S1r1 and Acinetobacter sp. S3r2 and a reference strain used was Bacillus subtilis UPMB10. All the PGPR strains were tested positive for N2 fixation, phosphate solubilisation and auxin production by in vitro tests. In a greenhouse experiment with reduced fertiliser-N input (a third of recommended fertiliser-N rate), the N2 fixation abilities of PGPR in association with maize were determined by 15N isotope dilution technique at two harvests, namely, prior to anthesis (D50) and ear harvest (D65). The results indicated that dry biomass of top, root and ear, total N content and bacterial colonisations in non-rhizosphere, rhizosphere and endosphere of maize roots were influenced by PGPR inoculation. In particular, the plants inoculated with B. pumilus S1r1 generally outperformed those with the other treatments. They produced the highest N2 fixing capacity of 30.5% (262 mg N2 fixed plant−1) and 25.5% (304 mg N2 fixed plant−1) of the total N requirement of maize top at D50 and D65, respectively. N remobilisation and plant senescence in maize were delayed by PGPR inoculation, which is an indicative of greater grain production. This is indicated by significant interactions between PGPR strains and time of harvests for parameters on N uptake and at. % 15Ne of tassel. The phenomenon is also supported by the lower N content in tassels of maize treated

  20. Plant Growth-Promoting Rhizobacteria Inoculation to Enhance Vegetative Growth, Nitrogen Fixation and Nitrogen Remobilisation of Maize under Greenhouse Conditions.

    PubMed

    Kuan, Khing Boon; Othman, Radziah; Abdul Rahim, Khairuddin; Shamsuddin, Zulkifli H

    2016-01-01

    Plant growth-promoting rhizobacteria (PGPR) may provide a biological alternative to fix atmospheric N2 and delay N remobilisation in maize plant to increase crop yield, based on an understanding that plant-N remobilisation is directly correlated to its plant senescence. Thus, four PGPR strains were selected from a series of bacterial strains isolated from maize roots at two locations in Malaysia. The PGPR strains were screened in vitro for their biochemical plant growth-promoting (PGP) abilities and plant growth promotion assays. These strains were identified as Klebsiella sp. Br1, Klebsiella pneumoniae Fr1, Bacillus pumilus S1r1 and Acinetobacter sp. S3r2 and a reference strain used was Bacillus subtilis UPMB10. All the PGPR strains were tested positive for N2 fixation, phosphate solubilisation and auxin production by in vitro tests. In a greenhouse experiment with reduced fertiliser-N input (a third of recommended fertiliser-N rate), the N2 fixation abilities of PGPR in association with maize were determined by 15N isotope dilution technique at two harvests, namely, prior to anthesis (D50) and ear harvest (D65). The results indicated that dry biomass of top, root and ear, total N content and bacterial colonisations in non-rhizosphere, rhizosphere and endosphere of maize roots were influenced by PGPR inoculation. In particular, the plants inoculated with B. pumilus S1r1 generally outperformed those with the other treatments. They produced the highest N2 fixing capacity of 30.5% (262 mg N2 fixed plant-1) and 25.5% (304 mg N2 fixed plant-1) of the total N requirement of maize top at D50 and D65, respectively. N remobilisation and plant senescence in maize were delayed by PGPR inoculation, which is an indicative of greater grain production. This is indicated by significant interactions between PGPR strains and time of harvests for parameters on N uptake and at. % 15Ne of tassel. The phenomenon is also supported by the lower N content in tassels of maize treated with