bluuebunny/crossref_metadata_2025 huggingface dataset:
Managing multiple actions through multimodality: Doctors' involvement in interpreter-mediated interactions
Authors: Pasquandrea Sergio
Published: September 2011

Many studies (Heath 1984b, 1986; Robinson 1998; Robinson & Stivers 2001; Greatbach 2006; Frers 2009) have shown that, while interacting with their patients, doctors fulfill several tasks (speaking, reading, writing prescriptions, reporting data on the computer, etc.) through an interplay of diverse multimodal resources (speech, gesture, body posture, gaze, object manipulation, etc.). In comparison, multimodality in interpreter-mediated medical encounters has received scant attention. This contribution examines a corpus of interactions involving Italian doctors, Chinese patients, and an interpreter. Having to manage multiparty and multitask conversations with patients with whom no direct communication is possible, doctors are forced to rely heavily on multimodality. The analysis here shows how the simultaneous actions performed by the doctors are coordinated through the use of multiple modalities. The outcomes on the global organization of interpreter-mediated interaction are also discussed. (Conversation analysis, doctor-patient interaction, interpreting, multitasking, multimodality)*
Density of hyperbolicity for rational maps with Cantor Julia sets
Authors: PENG WENJUAN , YIN YONGCHENG , ZHAI YU
Published: September 2011

In this paper, taking advantage of quasi-conformal surgery, we prove that each non-hyperbolic rational map with a Cantor Julia set can be approximated by hyperbolic rational maps with Cantor Julia sets of the same degree.
A FEAST OF THE ARTS: JOANNA OF CASTILE IN BRUSSELS, 1496
Authors: Tammen Björn R.
Published: September 2011

As the only late fifteenth-century picture book devoted to a ‘joyous entry’, inv. 78.D.5 of the Staatliche Museen zu Berlin – Kupferstichkabinett is a source of singular importance, conveying a total of twenty-seventableaux vivantsstaged for Joanna of Castile (‘the Mad’) on the occasion of her entry into Brussels, 15 December 1496, as duchess of Brabant. The present contribution focuses on two tableaux with musical subject matter, consciously displayed at the very beginning and at the very end: Jubal and Tubalcain, the biblical inventors of music, on the one hand, and St Luke portraying the Virgin Mary with Child, enriched by the means of angelic musicians, on the other. Besides iconographic issues, special emphasis is placed on Joanna, her musical inclinations, and the respective institutional background: whereas the St Luke tableau contributes to the corporate identity of Brussels's painters' guild, the biblical inventor of music allows for the self-presentation of the rhetoricians, who were in charge of ‘programming’ the joyous entry and its festive apparatus. In sum, political messages have been musically disguised; uncommon biblical or even extra-biblical subjects become vehicles for a complex layer of meaning that permeates the public space.
THE HIDDEN ADAM SMITH IN HIS ALLEGED THEOLOGY
Authors: KENNEDY GAVIN
Published: September 2011

The paper examines assertions that Adam Smith was in some sense a Christian, and examines how much current opinion ignores his biography and the dangerous religious context of eighteenth-century Scotland. Zealots regularly intervened against suspected heresy, which created an atmosphere of intimidation. Adam Smith’s biography shows that he too was intimidated, and avoided scandals that would upset his very religious mother, for whom he felt a special protective bond, and that he hid his private skepticism to ensure that nothing he published would provoke the zealots. A close reading of hisWorksshows how he amended them consistently as he grew older to modify their religious content, particularly after his mother died in 1784, and up to just before he died in 1790.
Minerals and Aligned Collagen Fibrils in Tilapia Fish Scales: Structural Analysis Using Dark-Field and Energy-Filtered Transmission Electron Microscopy and Electron Tomography
Authors: Okuda Mitsuhiro , Ogawa Nobuhiro , Takeguchi Masaki , Hashimoto Ayako , Tagaya Motohiro , Chen Song , Hanagata Nobutaka , Ikoma Toshiyuki
Published: September 2011

The mineralized structure of aligned collagen fibrils in a tilapia fish scale was investigated using transmission electron microscopy (TEM) techniques after a thin sample was prepared using aqueous techniques. Electron diffraction and electron energy loss spectroscopy data indicated that a mineralized internal layer consisting of aligned collagen fibrils contains hydroxyapatite crystals. Bright-field imaging, dark-field imaging, and energy-filtered TEM showed that the hydroxyapatite was mainly distributed in the hole zones of the aligned collagen fibrils structure, while needle-like materials composed of calcium compounds including hydroxyapatite existed in the mineralized internal layer. Dark-field imaging and three-dimensional observation using electron tomography revealed that hydroxyapatite and needle-like materials were mainly found in the matrix between the collagen fibrils. It was observed that hydroxyapatite and needle-like materials were preferentially distributed on the surface of the hole zones in the aligned collagen fibrils structure and in the matrix between the collagen fibrils in the mineralized internal layer of the scale.
The Irish Legal System: An Introduction
Authors: Binchy William
Published: September 2011

Professor William Binchy provides a summary of the legal system in the Republic of Ireland and reflects on constitutional developments and challenges facing the country, particularly in the light of the recent economic collapse.
Law Reform in Northern Ireland
Authors: Dickson Brice
Published: September 2011

Professor Brice Dickson offers forthright views relating to law reform issues in Northern Ireland against the background of the peace process.
From Law Library Society to Law Library: the First 180 Years, 1816–1996
Authors: Aston Jennefer
Published: September 2011

This article, by Jennefer Aston, outlines the origins of The Law Library, focusing on its librarians and the services that were provided for members in the first 180 years.
The Judges' Library, Dublin
Authors: Donnelly Joe
Published: September 2011

Joseph Donnelly's article describes the Judges' Library and its role, and some of the issues relating to the library's users, collection, staff activities and use of print and digital material.
On the Use of the Rorschach in the Assessment of Psychological Functioning Following Sexual Abuse in Adolescent Girls: A Research Note
Authors: Rojas Breedy Ana Lorena
Published: September 2011

Le développement de la recherche concernant les caractéristiques psychométriques des victimes d’abus sexuels se justifie par la dynamique psychique qui accompagne fréquemment l’abus, ainsi que par la pression occasionnée par le secret et les états internes douloureux.

Dans cette étude, le Rorschach fut administré à dix-huit adolescentes qui avaient été victimes d’abus sexuels et qui suivaient une psychothérapie de groupe dans la Clinique pour Adolescents de l’Hôpital National des Enfants de Costa Rica. Le but était d’évaluer l’impact psychologique des abus sexuels. On procéda à l’analyse des contenus et du matériel verbal, et on trouva une élévation inhabituelle des contenus tels que Sang (Bl), Anatomie (An) et Sexe (Sx). Ces contenus, ainsi que le matériel verbal, indiquent la présence d’un stress post-traumatique (images intrusives des scènes traumatiques avec contenus sexuels violents); les relations interpersonnelles sont perçues comme intrinsèquement liées à la sexualité et/ou l’agressivité; on observe une sexualisation traumatique, dans laquelle la sexualité est associée à l’agressivité et à des affects de douleur, et où prédominent les questions sexuelles et la confusion dans l’identité sexuelle; un sentiment d’impuissance, qui indique que le sujet se perçoit comme une victime, incapable de se défendre et persuadé de son inefficacité; et la stigmatisation, qui reflète de forts sentiments d’être abîmé et endommagé.

Tout au long de cette recherche, le Rorschach est apparu comme un instrument tout à fait pertinent pour mieux comprendre les caractéristiques de l’impact psychologique de l’abus sexuel chez les victimes, facilitant ensuite la formulation des objectifs de traitement, et permettant d’alerter sur la possibilité d’un abus chez des victimes silencieuses.
Location Tables, Form Quality, and Popular Responses in a Spanish Sample of 470 Subjects
Authors: Sangro Fátima Miralles
Published: September 2011

La necesidad de establecer datos normativos para la población española a fin de guiar la codificación del Rorschach condujo al estudio de tres criterios importantes: Localización, Calidad Formal y Populares. Una muestra de 485 protocolos fué reducida a 470 luego de descartar 15 sujetos que no cumplían con los criterios de validez requeridos. Ninguno de los protocolos incluídos presentaba menos de 14 respuestas con un valor Lambda inferior a .80. Los 470 sujetos dieron un total de 10562 respuestas a las 10 láminas. La muestra española mostró varias diferencias respecto de la muestra norteamericana usada por Exner en el desarrollo del Sistema Comprehensivo.

En cuanto a la Localización, la muestra española presentó un número mayor de detalles Inusuales y un número menor de Detalles Comunes, manteniendo una proporción equivalente de respuestas de Espacio. Los resultados obtenidos se acercan más a los de Exner que a los de Beck. Nuestros 470 sujetos dieron 6192 respuestas de Detalle Común (58.62% del total de respuestas) y 1463 respuestas de Detalle Inusual (13.85%).

En cuanto a la Calidad Formal, la muestra española, en comparación con la muestra norteamericana, dió un porcentaje significativamente menor de respuestas de Calidad Formal Ordinaria y una proporción significativamente mayor de respuestas de Calidad Formal Negativa. En consecuencia, la muestra española parece traducir los estímulos de una manera más atípica.

En cuanto a las respuestas Populares, la muestra española percibió la realidad de manera menos convencional que la muestra de Exner. Solo nueve de sus respuestas pudieron ser categorizadas como Populares en virtud de aparecer en al menos un tercio de los protocolos. Este hallazgo apoya nuestra conclusión respecto de la Calidad Formal, en cuanto a que en algunas situaciones simple y claramente definidas nuestros sujetos responden de una manera menos convencional.

Comparamos nuestros resultados con los obtenidos por Sendín en una muestra española, los cuales también parecen confirmar la menor convencionalidad de la población española. Se requieren investigaciones adicionales a fin de mejorar la calidad de nuestro trabajo con el Rorschach en España.
The SCZI Index and the Normative Sample of Barcelona (1993)
Authors: Campo Vera
Published: September 2011

Ayant constaté de nombreux indices SCZI faux-positifs et faux-négatifs, je tente ici d’illustrer les difficultés d’utilisation de cet indice du Système Intégré, en relation avec les données normatives produites par l’échantillon de Barcelone (1993). Le but de cette étude est de proposer différents seuils de signification pour cet index (à Barcelone), centrés sur les X+%, X–% et le nombre de reponses M–.

Nous avons sélectionné 60 protocoles de patients d’une consultation privée présentant des indices SCZI positifs à 5 ou 6 sans signe clinique manifeste de psychose (Groupe A), et nous les avons comparés avec un groupe de 60 patients psychiatriques dûment diagnostiqués comme schizophrènes (Groupe B).

Outre l’index SCZI lui-même detaillé dans tous ses critères, nous avons tenu compte des indices DEPI, CDI, S-Con et HVI lorsqu’ils étaient positifs, ainsi que les Scores D, quelques variables des processus de Médiation (P, X+%, F+% et X–%), le nombre de reponses M–, le nombre de réponses “état-limite,” et les données de l’Indice d’Atteinte du Moi (EII)

Nous donnons les statistiques descriptives pour les deux groupes, ainsi que les résultats des tests paramétriques et non paramétriques réalisés.

Les résultats montrent qu’il n’y a pas de différence significative pour M– et les variables de la Médiation (sauf pour le F+%), alors que des différences fortement significatives apparaissent pour les items 4, 5 et 6 de l’indice SCZI. Nous avons donc dû abandonner notre premier objectif. Les éléments qui différenciaient vraiment les deux groupes étaient ceux liés aux affects: DEPI, S-Con, D et EII étaient significativement plus élevés dans le groupe A, tandis que le CDI, Lambda et F+% étaient significativement plus élevés dans le groupe B, indiquant par là que le groupe A apparaît comme beaucoup plus “fou” que le groupe des patients schizophrènes.

Nous discutons de ces résultats en élargissant le débat sur des questions plus générales touchant à la perception, la structure de la personnalité, l’“adaptation” à la realité, et le diagnostic basé sur 1’indice SCZI au Rorschach.
Mg/Ca ratios of single planktonic foraminifer shells and the potential to reconstruct the thermal seasonality of the water column
Authors: Haarmann Tim , Hathorne Ed C. , Mohtadi Mahyar , Groeneveld Jeroen , Kölling Martin , Bickert Torsten
Published: September 2011

Mg/Ca ratios of surface and subsurface dwelling foraminifera provide valuable information about the past temperature of the water column. Planktonic foraminifera calcify over a period of weeks to months. Therefore, the range of Mg/Ca temperatures obtained from single specimens potentially records seasonal temperature changes. We present solution‐derived Mg/Ca ratios for single specimens of the planktonic foraminifera species Globigerinoides ruber (pink), Globigerinoides ruber (white), and Globorotalia inflata from a sediment trap off northwest Africa (20°45.6′N, 18°41.9′W). Cleaning of single specimens was achieved using a flow‐through system in order to prevent sample loss. Mg/Ca ratios of surface dwelling G. ruber (pink) show strong seasonality linked to sea surface temperature. Mg/Ca ratios of G. ruber (white) do not show such seasonality. Subsurface dwelling G. inflata flux is largest during the main upwelling season, but Mg/Ca ratios reflect annual temperatures at intermediate water depths. The sediment trap time series suggests that changes in the range of Mg/Ca ratios exhibited by single specimens of G. ruber (pink) and G. inflata from the sedimentary record should provide information on the past temperature range under which these species calcified. Statistical analysis suggests detectable changes in the Mg/Ca range are ≥0.80 mmol/mol (G. ruber (pink)) and ≥0.34 mmol/mol (G. inflata). For G. ruber (pink), such changes would indicate changes in the seasonal sea surface temperature range >4°C or a shift in the main calcification and reproductive period. For G. inflata, such changes would indicate >1.7°C changes in the thermocline temperature or a change in the depth habitat.
An investigation into changes in climate characteristics causing the recent very low runoff in the southern Murray‐Darling Basin using rainfall‐runoff models
Authors: Potter N. J. , Chiew F. H. S.
Published: September 2011

The recent drought in the southern Murray‐Darling Basin has seen a larger reduction in annual runoff in many places compared to historical droughts with similar annual rainfall reductions. Several reasons have been suggested for this, including proportionally less autumn and winter rainfall, fewer high rainfall years, and increased temperatures. Using the SIMHYD daily rainfall‐runoff model and scenarios of rainfall and potential evapotranspiration, we investigate the causes of the observed runoff reduction over 1997–2008 in the Campaspe river basin, an area representative of the southern Murray‐Darling Basin. This method accounts for 83% of the runoff reduction, with the reduction in annual rainfall accounting for 52%. The remainder is not explained by any single hydroclimatic feature but is mostly accounted for by the combination of changes in rainfall variability outside monthly and annual time scales (15%), changed seasonality of rainfall (11%), and increased potential evapotranspiration (5%).
Quorum sensing control of phosphorus acquisition in Trichodesmium consortia
Authors: Van Mooy Benjamin A S , Hmelo Laura R , Sofen Laura E , Campagna Shawn R , May Amanda L , Dyhrman Sonya T , Heithoff Abigail , Webb Eric A , Momper Lily , Mincer Tracy J
Published: September 2011

Colonies of the cyanobacterium Trichodesmium are abundant in the oligotrophic ocean, and through their ability to fix both CO2 and N2, have pivotal roles in the cycling of carbon and nitrogen in these highly nutrient-depleted environments. Trichodesmium colonies host complex consortia of epibiotic heterotrophic bacteria, and yet, the regulation of nutrient acquisition by these epibionts is poorly understood. We present evidence that epibiotic bacteria in Trichodesmium consortia use quorum sensing (QS) to regulate the activity of alkaline phosphatases (APases), enzymes used by epibionts in the acquisition of phosphate from dissolved-organic phosphorus molecules. A class of QS molecules, acylated homoserine lactones (AHLs), were produced by cultivated epibionts, and adding these AHLs to wild Trichodesmium colonies collected at sea led to a consistent doubling of APase activity. By contrast, amendments of (S)-4,5-dihydroxy-2,3-pentanedione (DPD)—the precursor to the autoinducer-2 (AI-2) family of universal interspecies signaling molecules—led to the attenuation of APase activity. In addition, colonies collected at sea were found by high performance liquid chromatography/mass spectrometry to contain both AHLs and AI-2. Both types of molecules turned over rapidly, an observation we ascribe to quorum quenching. Our results reveal a complex chemical interplay among epibionts using AHLs and AI-2 to control access to phosphate in dissolved-organic phosphorus.
LibSBGN: Electronic Processing of SBGN maps
Authors: Demir Emek , Dogrusoz Ugur , Le Novère Nicolas , Matsuoka Yukiko , Sorokin Anatoly , Funahashi Akira , Mi Huaiyu , Kitano Hiroaki , Aladjem Mirit , van Iersel Martijn , Blinov Michael , Boyd Sarah , Villéger Alice , Bergmann Frank , Moodie Stuart , Schreiber Falk , Luna Augustin , Czauderna Tobias
Published: September 2011

Introduction Graphical representations of participants and their relationships are essential for exchanging knowledge about complex biological processes. To convey this information clearly and unambiguously, it is necessary to assign standard meanings to symbols and their connectivity. For this purpose, the System Biology Graphical Notation (SBGN) has been developed.As SBGN is becoming more widely adopted, and used in various software tools, there is an increasing need for a standard file format able to capture the SBGN maps. Exchange using graphics-only file formats (such as SVG) is insufficient, because the biological meaning of elements is lost. There is a need for a toolset that enables diagram exchange while preserving biological meaning and relations.

Results

To meet this need, we are developing an Extensible Markup Language (XML) schema definition. In addition we are developing a software library called LibSBGN. Besides reading and writing files, this library will also be used to validate SBGN maps against the specifications, and convert to and from related systems biology standards, such as SBML and BioPAX.LibSBGN is still under development, but is already being adopted by several tools (See the LibSBGN project page for an up-to-date list of client software). The early adoption of LibSBGN by those tools helps to ensure that LibSBGN is independent of a specific software application, and does not contain artifacts for specific tools. LibSBGN is currently implemented in Java, a parallel C++ version is planned for the future.A test-suite of dozens of LibSBGN documents, covering every possible feature of SBGN maps, was created. This test-suite can be used by developers to check for compliance with the standard, and compare rendering capabilities with other tools.LibSBGN is a community effort, involving people from institutes all around the world, representing a wide selection of pathway tools. The community is organized around a sourceforge project site (http://libsbgn.sourceforge.net), a mailing list and monthly online meetings.A first release of LibSBGN, covering only the Process Description (PD) language, is planned in October 2010. Support for all three languages of SBGN is planned for a later release.
JSBML: a flexible and entirely Java-based library for working with SBML
Authors: Fröhlich Sebastian , Le Novère Nicolas , Zell Andreas , Hucka Michael , Dräger Andreas , Rodriguez Nicolas , Dumousseau Marine , Dörr Alexander , Wrzodek Clemens , Keller Roland
Published: September 2011

The specifications of the Systems Biology Markup Language (SBML) define standards for storing and exchanging computer models of biological processes in text files. In order to perform model simulations, graphical visualizations and other software manipulations, an in-memory representation of SBML is required. We developed JSBML for this purpose. In contrast to prior implementations of SBML APIs, JSBML has been designed from the ground up for the Java™ programming language, and can therefore be used on all platforms supported by a Java Runtime Environment. This offers important benefits for Java users, including the ability to distribute software as Java Web Start applications. JSBML supports all SBML Levels and Versions through Level 3 Version 1, and we have strived to maintain the highest possible degree of compatibility with the popular library libSBML. JSBML also supports modules that can facilitate the development of plugins for end user applications, as well as ease migration from a libSBMLbased backend.Source code, binaries and documentation for JSBML can be freely obtained under the terms of the LGPL 2.1 from the website http://sbml.org/Software/JSBML.
LibSBGN Status Update
Authors: van Iersel Martijn , Czauderna Tobias , Villeger Alice
Published: September 2011

LibSBGN is a library for reading, writing and validating maps that use the Systems Biology Graphical Notation (SBGN). The goals of LibSBGN are to 1) increase interoperability between pathway visualization tools, 2) increase the amount of code re-used, and 3) make it easier for tool developers to adopt the SBGN standard. This presentation is a status update of the project, presented at the COMBINE 2011 meeting.
The spectroscopic characterization of the methoxy radical. III. Rotationally resolved $\skew3\tilde{A}^2A_1\text{–}\skew3\tilde{X}^2E$Ã2A1–X̃2E electronic and $\skew3\tilde{X}^2E$X̃2E submillimeter wave spectra of partially deuterated CH2DO and CHD2O radicals
Authors: Melnik Dmitry G. , Liu Jinjun , Chen Ming-Wei , Miller Terry A. , Curl Robert F.
Published: September 2011

Rotationally resolved laser induced fluorescence and stimulated emission pumping \documentclass[12pt]{minimal}\begin{document}$\tilde{A}^2A_1 - \tilde{X}^2E$\end{document}Ã2A1−X̃2E spectra, along with pure rotational spectra in the 153–263 GHz region within the E3/2 component of the ground state in asymmetrically deuterated methoxy radicals CH2DO and CHD2O have been observed. The combined data set allows for the direct measurement with high precision of the energy separation between the E1/2 and E3/2 components of the ground state and the energy separation between the parity stacks in the E3/2 component of the ground state. The experimentally observed frequencies in both isotopologues are fit to an effective rotational Hamiltonian accounting for rotational and spin-rotational effects arising in a near-prolate asymmetric top molecule with dynamic Jahn-Teller distortion. Isotopic dependencies for the molecular parameters have been successfully implemented to aid the analysis of these very complex spectra. The analysis of the first and second order contributions to the effective values of molecular parameters has been extended to elucidate the physical significance of resulting molecular parameters. Comparisons of measured parameters, e.g., spin-orbit coupling, rotational and spin-rotation constants, are made among the 5 methoxy isotopologues for which data is now available. Comparisons of experimental results, including the derived geometric structure at both the C3v conical intersection and at the Jahn-Teller distorted minima, are made with quantum chemistry calculations.
Data Matter(s): Legitimacy, Coding, and Qualifications-of-Life
Authors: Wilson Matthew W
Published: September 2011

Data are central to geographical technologies and provide the pathways in which geographic investigations are forwarded. The mattering of data is therefore important to those engaging in participatory use of these technologies. This paper understands ‘mattering’ both in the material sense, that data are products resulting from specific practices, and in the affective sense, that data are imaginative, generative, and evocative. I examine these senses of mattering, of both presence and significance, in a discussion of a community survey project held in Seattle, USA. During this four-year project, residents in ten neighborhoods were asked to collect data about their community streets using handheld computers. Residents tracked ‘assets’ and ‘deficits’ by locating objects such as damaged sidewalks and graffiti on telephone booths. These data records were then uploaded to a central server administered by a local nonprofit organization. The nonprofit worked with community residents to help link these data about their changing neighborhoods to agencies in the municipal government. Here, I argue that the legitimacy of these data practices is constructed through processes of standardization and objectification and that these processes transduct urban space. I ask, as participatory mapping practices target governing agencies with their data products, what are the implications for the kinds of knowledge produced and for its legitimacy? In other words, how does data come to matter?
Pulsed quantum optomechanics
Authors: Vanner M. R. , Pikovski I. , Cole G. D. , Kim M. S. , Brukner Č. , Hammerer K. , Milburn G. J. , Aspelmeyer M.
Published: September 2011

Studying mechanical resonators via radiation pressure offers a rich avenue for the exploration of quantum mechanical behavior in a macroscopic regime. However, quantum state preparation and especially quantum state reconstruction of mechanical oscillators remains a significant challenge. Here we propose a scheme to realize quantum state tomography, squeezing, and state purification of a mechanical resonator using short optical pulses. The scheme presented allows observation of mechanical quantum features despite preparation from a thermal state and is shown to be experimentally feasible using optical microcavities. Our framework thus provides a promising means to explore the quantum nature of massive mechanical oscillators and can be applied to other systems such as trapped ions.
Carbon monoxide poisoning is prevented by the energy costs of conformational changes in gas-binding haemproteins
Authors: Antonyuk Svetlana V. , Rustage Neil , Petersen Christine A. , Arnst Jamie L. , Heyes Derren J. , Sharma Raman , Berry Neil G. , Scrutton Nigel S. , Eady Robert R. , Andrew Colin R. , Hasnain S. Samar
Published: September 2011

Carbon monoxide (CO) is a product of haem metabolism and organisms must evolve strategies to prevent endogenous CO poisoning of haemoproteins. We show that energy costs associated with conformational changes play a key role in preventing irreversible CO binding.
Ax
CYTcp is a member of a family of haem proteins that form stable 5c–NO and 6c–CO complexes but do not form O
2
complexes. Structure of the
Ax
CYTcp–CO complex at 1.25 Å resolution shows that CO binds in two conformations moderated by the extent of displacement of the distal residue Leu16 toward the haem 7-propionate. The presence of two CO conformations is confirmed by cryogenic resonance Raman data. The preferred linear Fe–C–O arrangement (170 ± 8°) is accompanied by a flip of the propionate from the distal to proximal face of the haem. In the second conformation, the Fe–C–O unit is bent (158 ± 8°) with no flip of propionate. The energetic cost of the CO-induced Leu-propionate movements is reflected in a 600 mV (57.9 kJmol
-1
) decrease in haem potential, a value in good agreement with density functional theory calculations. Substitution of Leu by Ala or Gly (structures determined at 1.03 and 1.04 Å resolutions) resulted in a haem site that binds CO in the linear mode only and where no significant change in redox potential is observed. Remarkably, these variants were isolated as ferrous 6c–CO complexes, attributable to the observed eight orders of magnitude increase in affinity for CO, including an approximately 10,000-fold decrease in the rate of dissociation. These new findings have wide implications for preventing CO poisoning of gas-binding haem proteins.
A critical look at the current gillnet regulations meant to protect the Nile Perch stocks in Lake Victoria
Authors: Msuku B. S. , Mrosso H. D. J. , Nsinda P. E.
Published: September 2011

Nile Perch fishing in Lake Victoria is done using gillnets and long lines. These gears have been deployed in the lake indiscriminately to the extent that in early 2000s the species showed signs of over-fishing. To address this situation, a slot size of 50–85 cm total length (TL) was instituted by the partner states to protect immature fish, and large adults to replenish the stocks while at the same time harvesting mature individuals. Catch Assessment Surveys, have been conducted regularly by the partner states between July 2005 and December 2008 to generate data for setting policies, development planning, and management intervention. A study involving two-stage stratified sampling on the Tanzanian side of the lake showed that Nile Perch caught in the minimum legal 5” gillnets were immature by more than 80%. In contrast Nile Perch of ≥85 cm total length, targeted by long-lines, were seldom encountered to validate the upper limit of the slot size. We advise to abolish the upper slot size limit and introduce a lower legal limit of 7” for gillnets.
Chevalley restriction theorem for vector-valued functions on quantum groups
Authors: Balagović Martina
Published: September 2011

We generalize Chevalley’s theorem about restriction

Res
:

C

[

g

]

g

→

C

[

h

]
W

\operatorname {Res}: \mathbb {C}[\mathfrak {g}]^{\mathfrak {g}} \to \mathbb {C}[\mathfrak {h}]^W

to the case when a semisimple Lie algebra

g

\mathfrak {g}

is replaced by a quantum group and the target space

C

\mathbb {C}

of the polynomial maps is replaced by a finite dimensional representation

V
V

of this quantum group. We prove that the restriction map
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="upper R e s colon left-parenthesis upper O Subscript q Baseline left-parenthesis upper G right-parenthesis circled-times upper V right-parenthesis Superscript upper U Super Subscript q Superscript left-parenthesis German g right-parenthesis Baseline right-arrow upper O left-parenthesis upper H right-parenthesis circled-times upper V">

Res
:
(

O

q

(
G
)
⊗
V

)

U

q

(

g

)

→
O
(
H
)
⊗
V

\operatorname {Res}:(O_{q}(G)\otimes V)^{U_{q}(\mathfrak {g})}\to O(H)\otimes V

is injective and describe the image.
The chromatin remodeler ISWI regulates the cellular response to hypoxia: role of FIH
Authors: Melvin Andrew , Mudie Sharon , Rocha Sonia
Published: September 2011

The hypoxia-inducible factor (HIF) is a master regulator of the cellular response to hypoxia. Its levels and activity are controlled by dioxygenases called prolyl-hydroxylases and factor inhibiting HIF (FIH). To activate genes, HIF has to access sequences in DNA that are integrated in chromatin. It is known that the chromatin-remodeling complex switch/sucrose nonfermentable (SWI/SNF) is essential for HIF activity. However, no additional information exists about the role of other chromatin-remodeling enzymes in hypoxia. Here we describe the role of imitation switch (ISWI) in the cellular response to hypoxia. We find that unlike SWI/SNF, ISWI depletion enhances HIF activity without altering its levels. Furthermore, ISWI knockdown only alters a subset of HIF target genes. Mechanistically, we find that ISWI is required for full expression of FIH mRNA and protein levels by changing RNA polymerase II loading to the FIH promoter. Of interest, exogenous FIH can rescue the ISWI-mediated upregulation of CA9 but not BNIP3, suggesting that FIH-independent mechanisms are also involved. Of importance, ISWI depletion alters the cellular response to hypoxia by reducing autophagy and increasing apoptosis. These results demonstrate a novel role for ISWI as a survival factor during the cellular response to hypoxia.
Cholesterol transport from late endosomes to the Golgi regulates t-SNARE trafficking, assembly, and function
Authors: Reverter Meritxell , Rentero Carles , de Muga Sandra Vilà , Alvarez-Guaita Anna , Mulay Vishwaroop , Cairns Rose , Wood Peta , Monastyrskaya Katia , Pol Albert , Tebar Francesc , Blasi Joan , Grewal Thomas , Enrich Carlos
Published: September 2011

Cholesterol regulates plasma membrane (PM) association and functioning of syntaxin-4 and soluble N-ethylmaleimide-sensitive fusion protein 23 (SNAP23) in the secretory pathway. However, the molecular mechanism and cellular cholesterol pools that determine the localization and assembly of these target membrane SNAP receptors (t-SNAREs) are largely unknown. We recently demonstrated that high levels of annexin A6 (AnxA6) induce accumulation of cholesterol in late endosomes, thereby reducing cholesterol in the Golgi and PM. This leads to an impaired supply of cholesterol needed for cytosolic phospholipase A2(cPLA2) to drive Golgi vesiculation and caveolin transport to the cell surface. Using AnxA6-overexpressing cells as a model for cellular cholesterol imbalance, we identify impaired cholesterol egress from late endosomes and diminution of Golgi cholesterol as correlating with the sequestration of SNAP23/syntaxin-4 in Golgi membranes. Pharmacological accumulation of late endosomal cholesterol and cPLA2inhibition induces a similar phenotype in control cells with low AnxA6 levels. Ectopic expression of Niemann-Pick C1 (NPC1) or exogenous cholesterol restores the location of SNAP23 and syntaxin-4 within the PM. Importantly, AnxA6-mediated mislocalization of these t-SNAREs correlates with reduced secretion of cargo via the SNAP23/syntaxin-4–dependent constitutive exocytic pathway. We thus conclude that inhibition of late endosomal export and Golgi cholesterol depletion modulate t-SNARE localization and functioning along the exocytic pathway.
STARD4 abundance regulates sterol transport and sensing
Authors: Mesmin Bruno , Pipalia Nina H. , Lund Frederik W. , Ramlall Trudy F. , Sokolov Anna , Eliezer David , Maxfield Frederick R.
Published: September 2011

Nonvesicular transport of cholesterol plays an essential role in the distribution and regulation of cholesterol within cells, but it has been difficult to identify the key intracellular cholesterol transporters. The steroidogenic acute regulatory-related lipid-transfer (START) family of proteins is involved in several pathways of nonvesicular trafficking of sterols. Among them, STARD4 has been shown to increase intracellular cholesteryl ester formation and is controlled at the transcriptional level by sterol levels in cells. We found that STARD4 is very efficient in transporting sterol between membranes in vitro. Cholesterol levels are increased in STARD4-silenced cells, while sterol transport to the endocytic recycling compartment (ERC) and to the endoplasmic reticulum (ER) are enhanced upon STARD4 overexpression. STARD4 silencing attenuates cholesterol-mediated regulation of SREBP-2 activation, while its overexpression amplifies sterol sensing by SCAP/SREBP-2. To analyze STARD4's mode of action, we compared sterol transport mediated by STARD4 with that of a simple sterol carrier, methyl-β-cyclodextrin (MCD), when STARD4 and MCD were overexpressed or injected into cells. Interestingly, STARD4 and cytosolic MCD act similarly by increasing the rate of transfer of sterol to the ERC and to the ER. Our results suggest that cholesterol transport mediated by STARD4 is an important component of the cholesterol homeostasis regulatory machinery.
Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast
Authors: Hickman Mark J. , Petti Allegra A. , Ho-Shing Olivia , Silverman Sanford J. , McIsaac R. Scott , Lee Traci A. , Botstein David
Published: September 2011

A yeast strain lacking Met4p, the primary transcriptional regulator of the sulfur assimilation pathway, cannot synthesize methionine. This apparently simple auxotroph did not grow well in rich media containing excess methionine, forming small colonies on yeast extract/peptone/dextrose plates. Faster-growing large colonies were abundant when overnight cultures were plated, suggesting that spontaneous suppressors of the growth defect arise with high frequency. To identify the suppressor mutations, we used genome-wide single-nucleotide polymorphism and standard genetic analyses. The most common suppressors were loss-of-function mutations in OPI1, encoding a transcriptional repressor of phospholipid metabolism. Using a new system that allows rapid and specific degradation of Met4p, we could study the dynamic expression of all genes following loss of Met4p. Experiments using this system with and without Opi1p showed that Met4 activates and Opi1p represses genes that maintain levels of S-adenosylmethionine (SAM), the substrate for most methyltransferase reactions. Cells lacking Met4p grow normally when either SAM is added to the media or one of the SAM synthetase genes is overexpressed. SAM is used as a methyl donor in three Opi1p-regulated reactions to create the abundant membrane phospholipid, phosphatidylcholine. Our results show that rapidly growing cells require significant methylation, likely for the biosynthesis of phospholipids.
β-Actin specifically controls cell growth, migration, and the G-actin pool
Authors: Bunnell Tina M. , Burbach Brandon J. , Shimizu Yoji , Ervasti James M.
Published: September 2011

Ubiquitously expressed β-actin and γ-actin isoforms play critical roles in most cellular processes; however, their unique contributions are not well understood. We generated whole-body β-actin–knockout (Actb−/−) mice and demonstrated that β-actin is required for early embryonic development. Lethality of Actb−/−embryos correlated with severe growth impairment and migration defects in β-actin–knockout primary mouse embryonic fibroblasts (MEFs) that were not observed in γ-actin–null MEFs. Migration defects were associated with reduced membrane protrusion dynamics and increased focal adhesions. We also identified migration defects upon conditional ablation of β-actin in highly motile T cells. Of great interest, ablation of β-actin altered the ratio of globular actin (G-actin) to filamentous actin in MEFs, with corresponding changes in expression of genes that regulate the cell cycle and motility. These data support an essential role for β-actin in regulating cell migration and gene expression through control of the cellular G-actin pool.
Mechanically induced structural changes during dynamic compression of engineered cartilaginous constructs can potentially explain increases in bulk mechanical properties
Authors: Nagel Thomas , Kelly Daniel J.
Published: September 2011

Several studies on chondrocyte-seeded hydrogels in bioreactor culture report increased mechanical properties of mechanically loaded constructs compared with unloaded free swelling controls despite no significant differences in biochemical composition. One possible explanation is that changes in the collagen architecture of dynamically compressed constructs lead to improved mechanical properties. Collagen molecules are incorporated locally into the extracellular matrix with individual stress-free configurations and orientations. In this study, we computationally investigated possible influences of loading on the collagen architecture in chondrocyte-seeded hydrogels and their resulting mechanical properties. Both the collagen orientation and its stress-free configuration were hypothesized to depend on the local mechanical environment. Reorientation of the collagen network alone in response to dynamic compression leads to a prediction of constructs with lower compressive properties. In contrast, remodelling of the stress-free configuration of the collagen fibres was predicted to result in a more compacted tissue with higher swelling pressures and an altered pre-stressed state within the collagen network. Combining both mechanisms resulted in predictions of construct geometry and mechanical properties in agreement with experimental observations. This study provides support for the hypothesis that structural changes to the collagen network contribute to the enhanced mechanical properties of cartilaginous tissues engineered in bioreactors.
Flavivirus-induced antibody cross-reactivity
Authors: Mansfield Karen L. , Horton Daniel L. , Johnson Nicholas , Li Li , Barrett Alan D. T. , Smith Derek J. , Galbraith Sareen E. , Solomon Tom , Fooks Anthony R.
Published: September 2011

Dengue viruses (DENV) cause countless human deaths each year, whilst West Nile virus (WNV) has re-emerged as an important human pathogen. There are currently no WNV or DENV vaccines licensed for human use, yet vaccines exist against other flaviviruses. To investigate flavivirus cross-reactivity, sera from a human cohort with a history of vaccination against tick-borne encephalitis virus (TBEV), Japanese encephalitis virus (JEV) and yellow fever virus (YFV) were tested for antibodies by plaque reduction neutralization test. Neutralization of louping ill virus (LIV) occurred, but no significant neutralization of Murray Valley encephalitis virus was observed. Sera from some individuals vaccinated against TBEV and JEV neutralized WNV, which was enhanced by YFV vaccination in some recipients. Similarly, some individuals neutralized DENV-2, but this was not significantly influenced by YFV vaccination. Antigenic cartography techniques were used to generate a geometric illustration of the neutralization titres of selected sera against WNV, TBEV, JEV, LIV, YFV and DENV-2. This demonstrated the individual variation in antibody responses. Most sera had detectable titres against LIV and some had titres against WNV and DENV-2. Generally, LIV titres were similar to titres against TBEV, confirming the close antigenic relationship between TBEV and LIV. JEV was also antigenically closer to TBEV than WNV, using these sera. The use of sera from individuals vaccinated against multiple pathogens is unique relative to previous applications of antigenic cartography techniques. It is evident from these data that notable differences exist between amino acid sequence identity and mapped antigenic relationships within the familyFlaviviridae.
Arabidopsis Roots and Shoots Show Distinct Temporal Adaptation Patterns toward Nitrogen Starvation
Authors: Krapp Anne , Berthomé Richard , Orsel Mathilde , Mercey-Boutet Stéphanie , Yu Agnes , Castaings Loren , Elftieh Samira , Major Hilary , Renou Jean-Pierre , Daniel-Vedele Françoise
Published: September 2011

Nitrogen (N) is an essential macronutrient for plants. N levels in soil vary widely, and plants have developed strategies to cope with N deficiency. However, the regulation of these adaptive responses and the coordinating signals that underlie them are still poorly understood. The aim of this study was to characterize N starvation in adult Arabidopsis (Arabidopsis thaliana) plants in a spatiotemporal manner by an integrative, multilevel global approach analyzing growth, metabolites, enzyme activities, and transcript levels. We determined that the remobilization of N and carbon compounds to the growing roots occurred long before the internal N stores became depleted. A global metabolite analysis by gas chromatography-mass spectrometry revealed organ-specific differences in the metabolic adaptation to complete N starvation, for example, for several tricarboxylic acid cycle intermediates, but also for carbohydrates, secondary products, and phosphate. The activities of central N metabolism enzymes and the capacity for nitrate uptake adapted to N starvation by favoring N remobilization and by increasing the high-affinity nitrate uptake capacity after long-term starvation. Changes in the transcriptome confirmed earlier studies and added a new dimension by revealing specific spatiotemporal patterns and several unknown N starvation-regulated genes, including new predicted small RNA genes. No global correlation between metabolites, enzyme activities, and transcripts was evident. However, this multilevel spatiotemporal global study revealed numerous new patterns of adaptation mechanisms to N starvation. In the context of a sustainable agriculture, this work will give new insight for the production of crops with increased N use efficiency.
A Role for Protein Kinase Casein Kinase2 α-Subunits in the Arabidopsis Circadian Clock
Authors: Lu Sheen X. , Liu Hongtao , Knowles Stephen M. , Li Jian , Ma Ligeng , Tobin Elaine M. , Lin Chentao
Published: September 2011

Circadian rhythms are autoregulatory, endogenous rhythms with a period of approximately 24 h. A wide variety of physiological and molecular processes are regulated by the circadian clock in organisms ranging from bacteria to humans. Phosphorylation of clock proteins plays a critical role in generating proper circadian rhythms. Casein Kinase2 (CK2) is an evolutionarily conserved serine/threonine protein kinase composed of two catalytic α-subunits and two regulatory β-subunits. Although most of the molecular components responsible for circadian function are not conserved between kingdoms, CK2 is a well-conserved clock component modulating the stability and subcellular localization of essential clock proteins. Here, we examined the effects of a cka1a2a3 triple mutant on the Arabidopsis (Arabidopsis thaliana) circadian clock. Loss-of-function mutations in three nuclear-localized CK2α subunits result in period lengthening of various circadian output rhythms and central clock gene expression, demonstrating that the cka1a2a3 triple mutant affects the pace of the circadian clock. Additionally, the cka1a2a3 triple mutant has reduced levels of CK2 kinase activity and CIRCADIAN CLOCK ASSOCIATED1 phosphorylation in vitro. Finally, we found that the photoperiodic flowering response, which is regulated by circadian rhythms, was reduced in the cka1a2a3 triple mutant and that the plants flowered later under long-day conditions. These data demonstrate that CK2α subunits are important components of the Arabidopsis circadian system and their effects on rhythms are in part due to their phosphorylation of CIRCADIAN CLOCK ASSOCIATED1.
Brush and Spray: A High-Throughput Systemic Acquired Resistance Assay Suitable for Large-Scale Genetic Screening
Authors: Jing Beibei , Xu Shaohua , Xu Mo , Li Yan , Li Shuxin , Ding Jinmei , Zhang Yuelin
Published: September 2011

Systemic acquired resistance (SAR) is a defense mechanism induced in the distal parts of plants after primary infection. It confers long-lasting protection against a broad spectrum of microbial pathogens. Lack of high-throughput assays has hampered the forward genetic analysis of SAR. Here, we report the development of an easy and efficient assay for SAR and its application in a forward genetic screen for SAR-deficient mutants in Arabidopsis (Arabidopsis thaliana). Using the new assay for SAR, we identified six flavin-dependent monooxygenase1, four AGD2-like defense response protein1, three salicylic acid induction-deficient2, one phytoalexin deficient4, and one avrPphB-susceptible3 alleles as well as a gain-of-function mutant of CALMODULIN-BINDING TRANSCRIPTION ACTIVATOR3 designated camta3-3D. Like transgenic plants overexpressing CAMTA3, camta3-3D mutant plants exhibit compromised SAR and enhanced susceptibility to virulent pathogens, suggesting that CAMTA3 is a critical regulator of both basal resistance and SAR.