bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Importance and Challenges of Assessing Cognition in Indigenous Australians
Authors: Dingwall Kylie , Cairney Sheree 
Published: July 2009

Objectives: The aim of this paper was to investigate the importance and challenges involved in conducting serial cognitive assessments among healthy Indigenous adolescents. Method: Cognitive assessments were conducted at fortnightly intervals for 2 months and again at 6 and 12 months among a group of Indigenous students from a boarding school in the Northern Territory. These students were to be the healthy control group in a long-term study of substance abuse. Recruitment and attrition rates were reviewed and related challenges for assessing participants were identified. Results: From the recruited sample (n=49), 18% reported heavy or frequent use of alcohol, cannabis or petrol. Males were more likely to have used these substances compared to females. Attrition increased as the follow-up interval increased with 49 recruits reducing to 32 in the first 2 months and only 15 and 13 of the initial group remaining for the 6 and 12 month follow-ups respectively. Conclusions: Main challenges included (i) appropriateness of tests and assessment processes, (ii) high rates of substance abuse and other illness in the control group and (iii) high attrition rates. The importance of assessing cognition appropriately is highlighted by a lack of information regarding mental health issues in Indigenous populations.
Listening, Sharing Understanding and Facilitating Consumer, Family and Community Empowerment Through a Priority Driven Partnership in Far North Queensland
Authors: Haswell-Elkins Melissa , Reilly Lyndon , Fagan Ruth , Ypinazar Valmae , Hunter Ernest , Tsey Komla , Gibson Victor , Connolly Brian , Laliberte Arlene , Wargent Rachael , Gibson Teresa , Saunders Vicki , McCalman Janya , Kavanagh David 
Published: July 2009

Objectives: This paper provides an example of a mental health research partnership underpinned by empowerment principles that seeks to foster strength among community organizations to support better outcomes for consumers, families and communities. It aims to raise awareness among researchers and service providers that empowerment approaches to assist communities to address mental health problems are not too difficult to be practical but require long-term commitment and appropriate support. Methods: A collaborative research strategy that has become known as the Priority Driven Research (PDR) Partnership emerged through literature review, consultations, Family Wellbeing Program delivery with community groups and activities in two discrete Indigenous communities. Progress to date on three of the four components of the strategy is described. Results: The following key needs were identified in a pilot study and are now being addressed in a research-based implementation phase: (i) gaining two-way understanding of perspectives on mental health and promoting universal awareness; (ii) supporting the empowerment of carers, families, consumers and at-risk groups through existing community organizations to gain greater understanding and control of their situation; (iii) developing pathways of care at the primary health centre level to enable support of social and emotional wellbeing as well as more integrated mental health care; (iv) accessing data to enable an ongoing process of analysis/sharing/planning and monitoring to inform future activity. Conclusion: One of the key learnings to emerge in this project so far is that empowerment through partnership becomes possible when there is a concerted effort to strengthen grassroots community organizations. These include social health teams and men's and women's groups that can engage local people in an action orientation.
The Insidious Problem Inside: Mental Health Problems of Aboriginal and Torres Strait Islander People in Custody
Authors: Heffernan Edward , Andersen Kimina , Kinner Stuart 
Published: July 2009

Objective: Despite recognition of the extremely high rates of mental illness among custodial populations and the fact that Indigenous people represent around one-quarter of Australia's custodial population, little is known about the mental health of Aboriginal and Torres Strait Islander people in custody. Mental health is an important component of social and emotional wellbeing for Indigenous people and this paper considers current evidence regarding the mental health status of Indigenous Australians in custody. Method: A systematic review was undertaken of the quantitative literature relating to the mental health problems of Indigenous people in custody in Australia. Results: Despite high incarceration rates for Indigenous people and evidence that both mental health problems and rates of mental illness are extremely high in this group, studies in this area are few and limited in scope. Conclusion: The first step toward addressing the marked social and mental health problems for Indigenous people in custody is to systematically identify the nature and extent of these problems.
The Healing Journey: Empowering Aboriginal Communities to Close the Health Gap
Authors: Laliberté Arlene , Haswell-Elkins Melissa , Reilly Lyndon 
Published: July 2009

Objectives: This paper presents two arguments relevant to both past and present efforts to improve Indigenous health. It advocates for ways of thinking about and doing health promotion that begin with empowerment to help people gain a greater level of control over their lives and circumstances. Conclusion: A combination of the strengths of different approaches is in fact an empowering, dialectical view that can be achieved by considering Aboriginal people not as children in need, but as capable and efficacious individuals.
Reflections on a Community and University Research Collaboration
Authors: Mayo Kevin , Tsey Komla ,   Empowerment Research Team
Published: July 2009

Objective: This paper reflects on the collaborative research relationship between university and community researchers. It identifies emergent themes expressed in the words of researchers and recommends strategies to assist with other research collaborations. Conclusions: Emergent themes included: Initial reticence by community members followed by positive experiences; the value of empowerment frameworks in research; building trust between community and university researchers; capacity building, management, and workloads; and community politics, misunderstandings and wealth disparity. The paper recommends strategies for successful research collaborations and identifies challenges to research collaborations.
‘Bringing Back Respect’: The Role of Participatory Action Research in Transferring Knowledge from an Aboriginal Men's Group to Youth Programs
Authors: McCalman Janya , Tsey Komla , Baird Bradley , Connolly Brian , Baird Leslie , Jackson Rita 
Published: July 2009

Objective: This case study describes the efforts of an Aboriginal men's group to facilitate and support the empowerment of young people in their community. It is part of a broader participatory action research (PAR) study of men's groups. Method: Data was derived from quarterly reflective PAR sessions with men's and youth workers and steering committee members, interviews with workers, and focus groups with young people. The data was coded and categorized, with five themes identified. Results: Key opportunities and challenges related to building staff capacity, engaging young people, giving voice to young people and reconciling diverse community views. Emerging outcomes included young people's definition of vision and values, social cohesion, personal achievements and recognition. The youth projects also resulted in local employment, improvements in workforce capacity and proposals to extend the empowerment model in Yarrabah and transfer it to another community. Conclusion: PAR frameworks provide a useful tool for facilitating and sustaining empowerment outcomes. They can be used to support the transfer of knowledge and skills from one Aboriginal community group to another.
Ethical Research in Partnership with an Indigenous Community
Authors: Weston Richard , Brooks Robert , Gladman Justin , Senior Kate , Denley Louise , Silove Derrick , Whyman Nola , Kickett Mark , Bryant Richard , Files Justin ,   Aboriginal Community Advisory Committee
Published: July 2009

Objective: The aim of this paper is to describe the implementation of the Community Safety Research Project (CSRP) focusing on violence prevention among Aboriginal communities in western NSW in order to examine how practice converges with contemporary ethical guidelines. Method: A comparison was made of key project elements with the principles outlined in existing ethical guidelines, outlining the concrete issues that need to be confronted in practice. Results: The approach being pursued is consonant with the principles of contemporary guidelines; the results of the first phase qualitative study inquiring into workers’ perceptions of violence revealed some differences in the understanding of violence between Aboriginal and non-Aboriginal workers, with some ethical implications. Conclusions: Ethical approaches to research among Aboriginal communities include, but extend well beyond, the principle of avoiding harm. A comprehensive approach to ethical research requires significant ongoing expenditure of effort and resources with implications for project development, management and funding.
A Psychoanalytic Exploration of Collective Trauma Among Indigenous Australians and a Suggestion for Intervention
Authors: O'Loughlin Michael 
Published: July 2009

Objective: Psychoanalysis is used to explore the effects of the annihilation of culture and how this leads to a loss of identification with a collective subjectivity and triggers catastrophic symptoms including loss of collective hope, the rise of addictive and self-destructive behaviours, and the intergenerational transmission of trauma among Indigenous Australian communities. Conclusions: I propose restorative educational interventions for young Indigenous children that seek to engage them with ancestral memory, cultural narratives, and a sense of purpose so that healing from historically transmitted trauma may be initiated and a grounded sense of subjectivity restored.
Efficient stochastic simulation of reaction–diffusion processes via direct compilation
Authors: Lis Mieszko , Artyomov Maxim N. , Devadas Srinivas , Chakraborty Arup K. 
Published: July 2009

Abstract
We present the Stochastic Simulator Compiler (SSC), a tool for exact stochastic simulations of well-mixed and spatially heterogeneous systems. SSC is the first tool to allow a readable high-level description with spatially heterogeneous simulation algorithms and complex geometries; this permits large systems to be expressed concisely. Meanwhile, direct native-code compilation allows SSC to generate very fast simulations.
Availability: SSC currently runs on Linux and Mac OS X, and is freely available at http://web.mit.edu/irc/ssc/.
Contact: mieszko@csail.mit.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Antimony: a modular model definition language
Authors: Smith Lucian P. , Bergmann Frank T. , Chandran Deepak , Sauro Herbert M. 
Published: July 2009

Abstract
Motivation: Model exchange in systems and synthetic biology has been standardized for computers with the Systems Biology Markup Language (SBML) and CellML, but specialized software is needed for the generation of models in these formats. Text-based model definition languages allow researchers to create models simply, and then export them to a common exchange format. Modular languages allow researchers to create and combine complex models more easily. We saw a use for a modular text-based language, together with a translation library to allow other programs to read the models as well.
Summary: The Antimony language provides a way for a researcher to use simple text statements to create, import, and combine biological models, allowing complex models to be built from simpler models, and provides a special syntax for the creation of modular genetic networks. The libAntimony library allows other software packages to import these models and convert them either to SBML or their own internal format.
Availability: The Antimony language specification and the libAntimony library are available under a BSD license from http://antimony.sourceforge.net/
Contact: lpsmith@u.washington.edu
TTA Lynx: a web-based service for analysis of actinomycete genes containing rare TTA codon
Authors: Zaburannyy Nestor , Ostash Bohdan , Fedorenko Victor 
Published: July 2009

Abstract
Motivation: TTA Lynx is a web-based service for finding, assessing and comparing coding sequences that contain TTA codons. This codon is most notable for being a regulatory switch that governs different aspects of the physiology of several GC-rich, Gram-positive bacteria belonging to genus Streptomyces, prolific producers of clinically important natural products. The ever-increasing pace of genome sequencing is creating a huge volume of data that could be utilized to improve our understanding of rare codons in actinomycete biology (and other biological systems.) The service described here is designed to facilitate analysis of TTA-containing genes and to assess the importance of TTA-mediated regulation in an organism of interest. This service and its database of organisms with well-known or hypothetical TTA-based regulation provides an opportunity for the identification of such regulation on a genome-wide scale.
Availability: http://ttalynx.bio.lnu.edu.ua
Contact: ttas@franko.lviv.ua
Supplementary information: Supplementary data are available at Bioinformatics online.
SNP-o-matic
Authors: Manske Heinrich Magnus , Kwiatkowski Dominic P. 
Published: July 2009

Abstract
Motivation: High throughput sequencing technologies generate large amounts of short reads. Mapping these to a reference sequence consumes large amounts of processing time and memory, and read mapping errors can lead to noisy or incorrect alignments. SNP-o-matic is a fast, memory-efficient and stringent read mapping tool offering a variety of analytical output functions, with an emphasis on genotyping.
Availability: http://snpomatic.sourceforge.net
Contact: mm6@sanger.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
FBA-SimVis: interactive visualization of constraint-based metabolic models
Authors: Grafahrend-Belau Eva , Klukas Christian , Junker Björn H. , Schreiber Falk 
Published: July 2009

Abstract
Summary: FBA-SimVis is a VANTED plug-in for the constraint-based analysis of metabolic models with special focus on the visual exploration of metabolic flux data resulting from model analysis. The program provides a user-friendly environment for model reconstruction, constraint-based model analysis, and interactive visualization of the simulation results. With the ability to quantitatively analyse metabolic fluxes in an interactive and visual manner, FBA-SimVis supports a comprehensive understanding of constraint-based metabolic flux models in both overview and detail.
Availability: Software with manual and tutorials are freely available at http://fbasimvis.ipk-gatersleben.de/
Contact: grafahr@ipk-gatersleben.de
Supplementary information: Examples and supplementary data are available at http://fbasimvis.ipk-gatersleben.de/
Statistical lower bounds on protein copy number from fluorescence expression images
Authors: Zamparo Lee , Perkins Theodore J. 
Published: July 2009

Abstract
Motivation: Fluorescence imaging has become a commonplace for quantitatively measuring mRNA or protein expression in cells and tissues. However, such expression data are usually relative—absolute concentrations or molecular copy numbers are typically not known. While this is satisfactory for many applications, for certain kinds of quantitative network modeling and analysis of expression noise, absolute measures of expression are necessary.
Results: We propose two methods for estimating molecular copy numbers from single uncalibrated expression images of tissues. These methods rely on expression variability between cells, due either to steady-state fluctuations or unequal distribution of molecules during cell division, to make their estimates. We apply these methods to 152 protein fluorescence expression images of Drosophila melanogaster embryos during early development, generating copy number estimates for 14 genes in the segmentation network. We also analyze the effects of noise on our estimators and compare with empirical findings. Finally, we confirm an observation of Bar-Even et al., made in the much different setting of Saccharomyces cerevisiae, that steady-state expression variance tends to scale with mean expression.
Availability: The data are all drawn from FlyEx (explained within), and is available at http://flyex.ams.sunysb.edu/FlyEx/. Data and MATLAB codes for all algorithms described in this article are available at http://www.perkinslab.ca/pubs/ZP2009.html.
Contact: tperkins@ohri.ca
TreeTime: an extensible C++ software package for Bayesian phylogeny reconstruction with time-calibration
Authors: Himmelmann Lin , Metzler Dirk 
Published: July 2009

Abstract
Motivation: For the estimation of phylogenetic trees from molecular data, it is worthwhile to take prior paleontologic knowledge into account, if available. To calibrate the branch lengths of the tree with times assigned to geo-historical events or fossils, it is necessary to select a relaxed molecular clock model to specify how mutation rates can change along the phylogeny.
Results: We present the software TreeTime for Bayesian phylogeny estimation. It can take prior information about the topology of the tree and about branching times into account. Several relaxed molecular clock models are implemented in TreeTime. TreeTime is written in C++ and designed to be efficient and extensible.
Availability: TreeTime is freely available from http://evol.bio.lmu.de/statgen/software/treetime under the terms of the GNU General Public Licence (GPL, version 3 or later).
Contact: lin@linhi.de; metzler@bio.lmu.de
Endothelium‐dependent and ‐independent vasodilation is more attenuated in ischaemic than in non‐ischaemic heart failure
Authors: Klosinska Magdalena , Rudzinski Tomasz , Grzelak Piotr , Stefanczyk Ludomir , Drozdz Jaroslaw , Krzeminska‐Pakula Maria 
Published: July 2009

AimsEndothelial dysfunction in chronic heart failure (CHF) contributes to vasoconstriction. Underlying atherosclerosis may increase vascular abnormalities in ischaemic CHF. We aimed to compare flow‐mediated dilation (FMD) and nitroglycerin‐mediated dilation (NMD) of the brachial artery between patients with ischaemic and non‐ischaemic CHF.Methods and resultsA total of 57 patients with systolic CHF participated in the study (mean age 59 ± 8 years, 81% male). Patients were in stable NYHA class II (40 patients, 70%) and III (17 patients, 30%). Ischaemic aetiology of CHF was confirmed by coronary angiography in 34 (60%) patients and ruled out in 23 (40%). Flow‐mediated dilation and NMD of the brachial artery was assessed by high‐resolution ultrasound. Endothelium‐dependent vasodilation was markedly reduced in patients with ischaemic CHF compared with those with non‐ischaemic aetiology of CHF—mean absolute change in artery diameter (Δd) 0.09 ± 0.07 mm in ischaemic group vs. 0.18 ± 0.07 mm in non‐ischaemic (P < 0.0001). Nitroglycerin‐mediated vasodilation was also significantly different—Δd = 0.14 ± 0.06 mm in ischaemic vs. 0.31 ± 0.10 mm in non‐ischaemic CHF (P < 0.0001).ConclusionEndothelium‐dependent and ‐independent vascular response is more attenuated in ischaemic than in non‐ischaemic CHF.
Identification and Characterization of Maize and Barley Lsi2-Like Silicon Efflux Transporters Reveals a Distinct Silicon Uptake System from That in Rice
Authors: Mitani Namiki , Chiba Yukako , Yamaji Naoki , Ma Jian Feng 
Published: July 2009

AbstractSilicon (Si) uptake has been extensively examined in rice (Oryza sativa), but it is poorly understood in other gramineous crops. We identified Low Silicon Rice 2 (Lsi2)-like Si efflux transporters from two important gramineous crops: maize (Zea mays) and barley (Hordeum vulgare). Both maize and barley Lsi2 expressed in Xenopus laevis oocytes showed Si efflux transport activity. Furthermore, barley Lsi2 was able to recover Si uptake in a rice mutant defective in Si efflux. Maize and barley Lsi2 were only expressed in the roots. Expression of maize and barley Lsi2 was downregulated in response to exogenously applied Si. Moreover, there was a significant positive correlation between the ability of roots to absorb Si and the expression levels of Lsi2 in eight barley cultivars, suggesting that Lsi2 is a key Si transporter in barley. Immunostaining showed that maize and barley Lsi2 localized only at the endodermis, with no polarity. Protein gel blot analysis indicated that maize and barley Lsi2 localized on the plasma membrane. The unique features of maize and barley Si influx and efflux transporters, including their cell-type specificity and the lack of polarity of their localization in Lsi2, indicate that these crops have a different Si uptake system from that in rice.
Analysis of bibliographic references in Zootecnia Tropical
Authors: Chaparro‐Martinez Exio , Ángel Marzal Miguel 
Published: July 2009

PurposeThe purpose of this paper is to analyze the bibliographic references contained in the scientific papers (articles and technical notes) published from 1985 to 2005 in Zootecnia Tropical (ZT), a scientific journal.Design/methodology/approachA retrospective descriptive study is conducted using one‐dimensional bibliometric indicators such as: output, bibliographic density, institutional affiliation, recentness of the documents cited, document typology, self‐citations and scientific collaboration. Univariate descriptive analysis is used to study the indicators.FindingsA total of 349 scientific papers (300 articles and 49 technical notes) are reviewed; output ranged from a maximum of 34 papers in 2001 to a minimum of four in 1990, with a mean of 15 papers per volume. The papers analyzed contain a total of 5,651 bibliographic references, with an average of 19 ± 9 references per paper; the largest number of references (19 ± 33) are found in the articles and the smallest (10.5 ± 13) in the notes. Venezuelan institutions account for 89 per cent of the papers and international institutions for the remain in 11 per cent; of the Venezuelan institutions, most (62 per cent) are National Institute of Agricultural Research (INIA) bodies and the rest universities and other organizations, especially the Universidad Central de Venezuela (UCV) and Universidad de Oriente (UDO). Universities are also among the most frequent international contributors, most prominently Marianga State University in Brazil and Tucumán National University in Argentina. Around 60 per cent of the references were more than ten years old when they were cited; 21 per cent were between five and ten years old and 19 per cent less than five years old. Journal articles, with 57 per cent, are the document type most frequently cited, followed by books, with 23 per cent; the rest consisted in postgraduate theses (3 per cent), undergraduate theses (2 per cent) and congress, conference and seminar proceedings (12 per cent). The self‐citation or endogamy rate in the journal is 4 per cent. Over half (53 per cent) of the papers are written by authors with the same affiliation. Inter‐institutional papers account for the remaining 47 per cent, with 34 per cent involving national collaboration, particularly between the INIA and the UCV; international co‐authorship comes to 13 per cent, primarily involving Brazilian and Argentine universities.Originality/valueThis paper analyzes the use of information in the Venezuelan scientific community from the vantage of a specific journal, ZT. These studies constitute useful and objective tools for evaluating scientific activity.