bluuebunny/crossref_metadata_2025_split huggingface dataset:
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.
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

Abstract
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

AbstractIntroduction 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

AbstractThe 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

AbstractLibSBGN 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.
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.
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

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.
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

Abstract
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

Abstract
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

Abstract
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.
On homology
Authors: Nixon Kevin C. , Carpenter James M. 
Published: September 2011

AbstractHomology in cladistics is reviewed. The definition of important terms is explicated in historical context. Homology is not synonymous with synapomorphy: it includes symplesiomorphy, and Hennig clearly included both plesiomorphy and synapomorphy as types of homology. Homoplasy is error, in coding, and is analogous to residual error in simple regression. If parallelism and convergence are to be distinguished, homoplasy would be evidence of the former and analogy evidence of the latter. We discuss whether there is a difference between molecular homology and morphological homology, character state homology, nested homology (additive characters), and serial homology. We conclude by proposing a global definition of homology.©The Will Henning Society 2011.
Nanostructured hydroxyapatite as filler for methacrylate‐based root canal sealers
Authors: Collares F. M. , Leitune V. C. B. , Rostirolla F. V. , Trommer R. M. , Bergmann C. P. , Samuel S. M. W. 
Published: September 2011

Collares FM, Leitune VCB, Rostirolla FV, Trommer RM, Bergmann CP, Samuel SMW. Nanostructured hydroxyapatite as filler for methacrylate‐based root canal sealers. International Endodontic Journal, 45, 63–67, 2012.AbstractAim  To evaluate the effect of different concentrations of nanostructured hydroxyapatite on the radiopacity, flow and film thickness of an experimental root canal sealer.Methodology  An experimental dual‐cured root canal sealer was produced with a methacrylate‐based comonomer blend. Nanostructured hydroxyapatite/calcium tungstate solutions (ratios 10 : 90, 20 : 80, 30 : 70 and 40 : 60) were added to produce the sealer. Radiopacity was evaluated using a digital system and an aluminium step wedge (n = 5). Flow and thickness tests were conducted in accordance with ISO 6876 (n = 3). The data were analysed using one‐way anova and Tukey’s test (α = 0.05).Results  All groups had levels of radiopacity in accordance with ISO 6876. The flow of the experimental sealers was not significantly different (P = 0.204). All groups had a film thickness in accordance with ISO 6876 and with no statistical difference (P = 0.654).Conclusion  The addition of up to 40% HAnano to root canal sealers did not alter their radiopacity and film thickness.
Effect of heat stress on the expression levels of receptor activator of NF‐κB ligand and osteoprotegerin in human periodontal ligament cells
Authors: Zhang L. , Zhou X. , Wang Q. , Wang Y. , Tang L. , Huang D. 
Published: September 2011

Zhang L, Zhou X, Wang Q, Wang Y, Tang L, Huang D. Effect of heat stress on the expression levels of receptor activator of NF‐κB ligand and osteoprotegerin in human periodontal ligament cells. International Endodontic Journal, 45, 68–75, 2012.AbstractAim  To investigate the expression levels of the receptor activator of NF‐κB ligand (RANKL) and osteoprotegerin (OPG) in human periodontal ligament fibroblasts (PDLs) when stimulated with heat.Methodology  Periodontal ligament fibroblasts were subjected to various temperature increases for 5 min and then maintained at 37 °C. After that, cell viability was determined using an MTT assay. The expression levels of RANKL and OPG were investigated using real‐time RT‐PCR and ELISA. As a control, the cells were cultured at 37 °C. Data were analysed using one‐way anova at a significant level of P = 0.05.Results  Cell viability was reduced significantly in the heated groups (P < 0.05). Heat stress downregulated the mRNA expression levels of RANKL and OPG (P < 0.05). When the cells were heated at 39 °C, the protein release of OPG was increased (P < 0.05). There were no significant differences between the heated groups and the control in the release of soluble RANKL (P > 0.05). The relative RANKL/OPG expression ratios were decreased at 39, 43 and 50 °C (P < 0.05), but increased at 47 °C (P < 0.05).Conclusions  Heat influenced the balance between RANKL and OPG in PDLs. Low heat downregulated their relative ratio, whilst high heat upregulated it.