bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hydrography shapes bacterial biogeography of the deep Arctic Ocean
Authors: Galand Pierre E , Potvin Marianne , Casamayor Emilio O , Lovejoy Connie 
Published: December 2009

Abstract
It has been long debated as to whether marine microorganisms have a ubiquitous distribution or patterns of biogeography, but recently a consensus for the existence of microbial biogeography is emerging. However, the factors controlling the distribution of marine bacteria remain poorly understood. In this study, we combine pyrosequencing and traditional Sanger sequencing of the 16S rRNA gene to describe in detail bacterial communities from the deep Arctic Ocean. We targeted three separate water masses, from three oceanic basins and show that bacteria in the Arctic Ocean have a biogeography. The biogeographical distribution of bacteria was explained by the hydrography of the Arctic Ocean and subsequent circulation of its water masses. Overall, this first taxonomic description of deep Arctic bacteria communities revealed an abundant presence of SAR11 (Alphaproteobacteria), SAR406, SAR202 (Chloroflexi) and SAR324 (Deltaproteobacteria) clusters. Within each cluster, the abundance of specific phylotypes significantly varied among water masses. Water masses probably act as physical barriers limiting the dispersal and controlling the diversity of bacteria in the ocean. Consequently, marine microbial biogeography involves more than geographical distances, as it is also dynamically associated with oceanic processes. Our ocean scale study suggests that it is essential to consider the coupling between microbial and physical oceanography to fully understand the diversity and function of marine microbes.
Significant roles of bacteriochlorophylla supplemental to chlorophylla in the ocean
Authors: Jiao Nianzhi , Zhang Fan , Hong Ning 
Published: December 2009

Abstract
Bacteriochlorophylla (BChla)-based phototrophy cannot be ignored in understanding of carbon cycle in the ocean. However, the role of BChla relative to chlorophylla (Chla) along environmental gradients remains unclear. On the basis of the investigations in the Pacific, Indian Oceans and the China Seas, we show that the average contribution of BChla relative to Chla is higher in open-ocean compared with shelf environments, the estimated BChla-based phototrophy could reduce respiratory organic carbon consumption of 2.4% and 5.4% of the primary productions in the shelf and oceanic waters, respectively. This suggests that BChla-based phototrophy has an important role supplemental to Chla-based photosynthesis in the ocean's carbon cycle and would be critical for a marine region to be a sink or a source of atmospheric CO2.
EYA1 mutations associated with the branchio‐oto‐renal syndrome result in defective otic development in Xenopus laevis
Authors: Li Youe , Manaligod Jose M. , Weeks Daniel L. 
Published: December 2009

Background information. The BOR (branchio‐oto‐renal) syndrome is a dominant disorder most commonly caused by mutations in the EYA1 (Eyes Absent 1) gene. Symptoms commonly include deafness and renal anomalies.Results. We have used the embryos of the frog Xenopus laevis as an animal model for early ear development to examine the effects of different EYA1 mutations. Four eya1 mRNAs encoding proteins correlated with congenital anomalies in human were injected into early stage embryos. We show that the expression of mutations associated with BOR, even in the presence of normal levels of endogenous eya1 mRNA, leads to morphologically abnormal ear development as measured by overall otic vesicle size, establishment of sensory tissue and otic innervation. The molecular consequences of mutant eya1 expression were assessed by QPCR (quantitative PCR) analysis and in situ hybridization. Embryos expressing mutant eya1 showed altered levels of multiple genes (six1, dach, neuroD, ngnr‐1 and nt3) important for normal ear development.Conclusions. These studies lend support to the hypothesis that dominant‐negative effects of EYA1 mutations may have a role in the pathogenesis of BOR.
Rapid turnover of mitochondrial uncoupling protein 3
Authors: Azzu Vian , Mookerjee Shona A. , Brand Martin D. 
Published: December 2009

UCP3 (uncoupling protein 3) and its homologues UCP2 and UCP1 are regulators of mitochondrial function. UCP2 is known to have a short half-life of approx. 1 h, owing to its rapid degradation by the cytosolic 26S proteasome, whereas UCP1 is turned over much more slowly by mitochondrial autophagy. In the present study we investigate whether UCP3 also has a short half-life, and whether the proteasome is involved in UCP3 degradation. UCP3 half-life was examined in the mouse C2C12 myoblast cell line by inhibiting protein synthesis with cycloheximide and monitoring UCP3 protein levels by immunoblot analysis. We show that UCP3 has a short half-life of 0.5–4 h. Rapid degradation was prevented by a cocktail of proteasome inhibitors, supporting a proteasomal mechanism for turnover. In addition, this phenotype is recapitulated in vitro: UCP3 was degraded in mitochondria isolated from rat skeletal muscle or brown adipose tissue with a half-life of 0.5–4 h, but only in the presence of a purified 26S proteasomal fraction. This in vitro proteolysis was also sensitive to proteasome inhibition. This phenotype is in direct contrast with the related proteins UCP1 and the adenine nucleotide translocase, which have long half-lives. Therefore UCP3 is turned over rapidly in multiple cell types in a proteasome-dependent manner.
Worthy the Name of a Grammar
Authors: Fountain Catherine 
Published: December 2009

SummaryThis article compares two missionary grammars written in the middle of the 17th century, Horacio Carochi’s (1579–1662)Arte de la Lengua Mexicana con la declaración de los adverbios della(1645) and John Eliot’s (1604–1690)The Indian Grammar Begun: or, an Essay to Bring the Indian Language into Rules(1666). Although published only 21 years apart, the two works differ in both context and theoretical underpinnings. These differences are manifested both in the type and depth of analysis undertaken by each author. Indeed, Carochi’s analysis goes much deeper and offers a more complete description of the language treated. While this can be attributed in part to Carochi’s own linguistic ability, the quality and completeness of his grammar is due in large part to the existence of a tradition of scholarship concerning Nahuatl in New Spain, a tradition that is strikingly absent in New England of the time.
Léxico purépecha en tiempos de la Ilustración
Authors: Villavicencio Frida 
Published: December 2009

ResumenEn 1756 Joseph Zepherino Botello Movellan (1734–c.1785) terminó de componer unCathecismo breve en lengua tarasca. Dicha obra fue escrita en purépecha o tarasco, una lengua indígena que aún hoy es hablada por cerca de 100,000 personas que radican en la parte noroccidental del estado de Michoacán, México. Éste es, hasta donde sabemos, el único documento de corte religioso escrito en esta lengua durante el siglo XVIII En esta obra el autor incluyó cuatro listas de palabras que en conjunto constituyen un breve vocabulario de la lengua de Michoacán. Sin tener la extensión ni la importancia de los trabajos lexicográficos que fueron realizados durante el siglo XVI, el valor de este documento consiste en ser el único testimonio de este tipo con el que contamos para conocer uno de los períodos menos documentados en la historia de la lengua.En este artículo se describen las características generales del catecismo de Botello incluyendo las cuatro secciones lexicográficas prestando especial atención a la lista de partes del cuerpo. Como punto de referencia para el análisis se utiliza la lista de partes del cuerpo que aparece en el Diccionario de Lagunas (editado en 1574), así como información proveniente de diversos diccionarios actuales. El material lingüístico que encontramos en la obra de Botello nos permite hacernos una buena idea del el purépecha del siglo XVIII y nos ayuda a entender más sobre el desarrollo que ha experimentado esta lengua en casi cinco siglos de historia. También nos provee interesantes datos sobre diversos tópicos, entre ellos: la representación ortográfica, la variación dialectal, los procesos de gramaticalización y derivación, la introducción de préstamos y algunas relaciones semánticas. Por último, en el texto de Botello también encontramos algunos datos interesantes para el español utilizado en México durante esa época.
Australian Young People's Awareness of Headspace, Beyondblue and other Mental Health Organizations
Authors: Jorm Anthony F. 
Published: December 2009

Objective: The aim of this paper is to assess young people's awareness of mental health organizations supporting their age group. Of particular interest was awareness of headspace, which was created in 2006 to provide youth-oriented mental health services, and of beyondblue, which aims to raise community awareness of depression, anxiety and related disorders. Method: A telephone survey was carried out on a national sample of young people who were part of a 2-year follow-up study of youth mental health literacy. Data were analysed for those aged 13–25 years. Results: Awareness was highest for beyondblue and telephone helplines; headspace had established some awareness, particularly in areas where its services operate. However, awareness was unrelated to the participant's psychological symptoms in the past year. Conclusions: If youth-oriented services are to be successful, young people need to know about them. Awareness campaigns need to be targeted at the sub-group who have greatest need for these services, namely those with mental health problems.
Challenges in Psychiatric Classification: The Case of Generalized Anxiety Disorder
Authors: Ash David , Galletly Cherrie 
Published: December 2009

Objective: This paper aims to describe some of the challenges in psychiatric classification, using generalized anxiety disorder (GAD) as an example. A range of different conceptualizations of GAD are presented. Some are based on theoretical formulations, while others draw on epidemiological data. Each has merit, but also deficiencies. The evolution of diagnostic criteria is not simply a theoretical exercise, but reflects assumptions about the nature of the underlying pathology and the relationships between different disorders. Furthermore, these criteria determine which subjects are included in research and in clinical trials, so they shape the further development of psychiatric classification systems. Conclusion: The controversies about the classification of GAD illustrate the complexities and challenges of developing a valid classification system for psychiatric disorders.
Pearl in the Oyster: Climate Change as a Mental Health Opportunity
Authors: Berry Helen 
Published: December 2009

Objective: Our world faces potentially catastrophic climate change and we have limited capacity to adapt to rapid or extreme climatic changes. As a result, we can expect significant adverse impacts on health. This includes mental health, a major and growing global concern. It is essential to understand how to respond quickly, effectively and within a manageable budget. The aim of this paper is to propose that the adverse consequences of climate change might offer a subtle but important mental health promotion opportunity which meets these criteria. Conclusions: Climate change will affect mental health directly through increasing exposure to trauma, and indirectly through harming physical health and damaging the physical environment on which economic opportunity depends. Disadvantaged people and communities, especially in rural and remote Australia, will be hardest hit. Seminal work by Alexander Leighton demonstrated how profound disadvantage and associated elevated psychiatric morbidity could be addressed by building community capacity. His methods might be adapted, using the need to address adverse climate change as an opportunity to build social capital. Social capital is associated with a wide range of socioeconomic and health advantages, particularly decreased psychiatric morbidity.
‘Radical Hope’ and Rain: Climate Change and the Mental Health of Indigenous Residents of Northern Australia
Authors: Hunter Ernest 
Published: December 2009

Objective: This paper considers the short, intermediate and longer term effects of climate change in relation to the mental health of Indigenous residents of northern Australia, and what these effects mean in terms of supporting adaptation and resilience. Conclusions: Indigenous Australians have contended with change for millennia, with the drivers shifting from ecological to social pressures since European colonization. Climate change resulting from human activities introduces a new set of change forces which will in the short term be mediated by economic and social effects internationally.
Expanding Psychiatry Training: Australian Specialists’ and Trainees’ Perceived Gaps in Experiences and Settings
Authors: O'Connor Daniel , Schweizer Yolanda , Spratt Christine 
Published: December 2009

Objective: The Royal Australian and New Zealand College of Psychiatrists (RANZCP) is working together with the Australian Federal Government to expand the range of training experiences and settings with the object of producing better equipped and better distributed psychiatrists to address the rising prevalence of mental disorder. To assist in this process, the College sought the views of its Fellows (psychiatrists) and trainees concerning important gaps in clinical experience and the settings best suited to filling them. Method: An electronic survey was sent to all Australian RANZCP psychiatrists and trainees in June 2008. Results: Only 15% of psychiatrists and 28% of trainees responded to the survey. There was striking concordance, however, that psychological therapies required much greater emphasis and that this experience would best be acquired in the private healthcare system. Conclusions: These findings support the recommendations of the Medical Specialist Training Steering Committee's report on expanded settings, suggesting that RANZCP members are likely to engage enthusiastically in the expanded specialist training program. It will be important to ensure that trainees are well supervised in their treatment of anxiety, affective and substance abuse disorders.
Patient Aggression Perceived by Community Support Workers
Authors: Gale Christopher , Hannah Annette , Swain Nicola , Gray Andrew , Coverdale John , Oud Nico 
Published: December 2009

Objective: Aggression by patients is a known risk factor for hospital workers. Within New Zealand, the bulk of ongoing care for physical and mental disabilities and health issues is not hospital based, but contracted to various non-governmental agencies. The rate of client aggression towards care workers from these organizations, to our knowledge, has not been assessed. Method: Two hundred and forty-two support workers in non-governmental agencies caring for people with disabilities responded to an anonymous mailed survey on client aggression, personal distress, and communication style. Results: Most support workers did experience verbal forms of aggression or destructive behaviour, fewer experienced physical aggression, and a minority were injured, sexually harassed, stalked or harassed by means of formal complaint. The median total violence score was five (interquartile range 12.25). A higher total violence score (using the POPAS-NZ) was associated with age and gender, the primary disability of clients, and the numbers of hours worked. The length of time worked was not associated with total violence risk. Communication style, after correcting for other factors, was a predictor of aggression. Almost 6% of care workers reported distress symptoms at a level associated with clinically significant stress reactions. Conclusions: Patient aggression is common among care workers, and can cause distress in the minority. We suggest that further research to clarify risk factors and develop interventions for care workers is needed.
The solution of a coupled system of nonlinear physical problems using the homotopy analysis method
Authors: El-Wakil S A , Abdou M A 
Published: December 2009

In this article, the homotopy analysis method (HAM) has been applied to solve coupled nonlinear evolution equations in physics. The validity of this method has been successfully demonstrated by applying it to two nonlinear evolution equations, namely coupled nonlinear diffusion reaction equations and the (2+1)-dimensional Nizhnik–Novikov Veselov system. The results obtained by this method show good agreement with the ones obtained by other methods.
The proposed method is a powerful and easy to use analytic tool for nonlinear problems and does not need small parameters in the equations. The HAM solutions contain an auxiliary parameter that provides a convenient way of controlling the convergence region of series solutions. The results obtained here reveal that the proposed method is very effective and simple for solving nonlinear evolution equations. The basic ideas of this approach can be widely employed to solve other strongly nonlinear problems.
Dynamically weighted clustering with noise set
Authors: Shen Yijing , Sun Wei , Li Ker-Chau 
Published: December 2009

Abstract
Motivation: Various clustering methods have been applied to microarray gene expression data for identifying genes with similar expression profiles. As the biological annotation data accumulated, more and more genes have been organized into functional categories. Functionally related genes may be regulated by common cellular signals, thus likely to be co-expressed. Consequently, utilizing the rapidly increasing functional annotation resources such as Gene Ontology (GO) to improve the performance of clustering methods is of great interest. On the opposite side of clustering, there are genes that have distinct expression profiles and do not co-express with other genes. Identification of these scattered genes could enhance the performance of clustering methods.
Results: We developed a new clustering algorithm, Dynamically Weighted Clustering with Noise set (DWCN), which makes use of gene annotation information and allows for a set of scattered genes, the noise set, to be left out of the main clusters. We tested the DWCN method and contrasted its results with those obtained using several common clustering techniques on a simulated dataset as well as on two public datasets: the Stanford yeast cell-cycle gene expression data, and a gene expression dataset for a group of genetically different yeast segregants.
Conclusion: Our method produces clusters with more consistent functional annotations and more coherent expression patterns than existing clustering techniques.
Contact: yshen@stat.ucla.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
SEUSSandSEUSS-LIKETranscriptional Adaptors Regulate Floral and Embryonic Development in Arabidopsis
Authors: Bao Fang , Azhakanandam Sridevi , Franks Robert G. 
Published: December 2009

AbstractMultimeric protein complexes are required during development to regulate transcription and orchestrate cellular proliferation and differentiation. The Arabidopsis (Arabidopsis thaliana) SEUSS (SEU) gene encodes a transcriptional adaptor that shares sequence similarity with metazoan Lim domain-binding transcriptional adaptors. In Arabidopsis, SEU forms a physical complex with the LEUNIG transcriptional coregulator. This complex regulates a number of diverse developmental events, including proper specification of floral organ identity and number and the development of female reproductive tissues derived from the carpel margin meristem. In addition to SEU, there are three Arabidopsis SEUSS-LIKE (SLK) genes that encode putative transcriptional adaptors. To determine the functions of the SLK genes and to investigate the degree of functional redundancy between SEU and SLK genes, we characterized available slk mutant lines in Arabidopsis. Here, we show that mutations in any single SLK gene failed to condition an obvious morphological abnormality. However, by generating higher order mutant plants, we uncovered a degree of redundancy between the SLK genes and between SLK genes and SEU. We report a novel role for SEU and the SLK genes during embryonic development and show that the concomitant loss of both SEU and SLK2 activities conditions severe embryonic and seedling defects characterized by a loss of the shoot apical meristem. Furthermore, we demonstrate that SLK gene function is required for proper development of vital female reproductive tissues derived from the carpel margin. We propose a model that posits that SEU and SLK genes support organ development from meristematic regions through two different pathways: one that facilitates auxin response and thus organ initiation and a second that sustains meristematic potential through the maintenance of SHOOTMERISTEM-LESS and PHABULOSA expression.
WallGen, Software to Construct Layered Cellulose-Hemicellulose Networks and Predict Their Small Deformation Mechanics
Authors: Kha Hung , Tuble Sigrid C. , Kalyanasundaram Shankar , Williamson Richard E. 
Published: December 2009

Abstract
We understand few details about how the arrangement and interactions of cell wall polymers produce the mechanical properties of primary cell walls. Consequently, we cannot quantitatively assess if proposed wall structures are mechanically reasonable or assess the effectiveness of proposed mechanisms to change mechanical properties. As a step to remedying this, we developed WallGen, a Fortran program (available on request) building virtual cellulose-hemicellulose networks by stochastic self-assembly whose mechanical properties can be predicted by finite element analysis. The thousands of mechanical elements in the virtual wall are intended to have one-to-one spatial and mechanical correspondence with their real wall counterparts of cellulose microfibrils and hemicellulose chains. User-defined inputs set the properties of the two polymer types (elastic moduli, dimensions of microfibrils and hemicellulose chains, hemicellulose molecular weight) and their population properties (microfibril alignment and volume fraction, polymer weight percentages in the network). This allows exploration of the mechanical consequences of variations in nanostructure that might occur in vivo and provides estimates of how uncertainties regarding certain inputs will affect WallGen's mechanical predictions. We summarize WallGen's operation and the choice of values for user-defined inputs and show that predicted values for the elastic moduli of multinet walls subject to small displacements overlap measured values. “Design of experiment” methods provide systematic exploration of how changed input values affect mechanical properties and suggest that changing microfibril orientation and/or the number of hemicellulose cross-bridges could change wall mechanical anisotropy.