bluuebunny/crossref_metadata_2025 huggingface dataset:
Gene set enrichment analysis made simple
Authors: Irizarry Rafael A , Chi Wang  , Yun Zhou  , Speed Terence P
Published: January 2010

Among the many applications of microarray technology, one of the most popular is the identification of genes that are differentially expressed in two conditions. A common statistical approach is to quantify the interest of each gene with a p-value, adjust these p-values for multiple comparisons, choose an appropriate cut-off, and create a list of candidate genes. This approach has been criticised for ignoring biological knowledge regarding how genes work together. Recently a series of methods, that do incorporate biological knowledge, have been proposed. However, the most popular method, gene set enrichment analysis (GSEA), seems overly complicated. Furthermore, GSEA is based on a statistical test known for its lack of sensitivity. In this article we compare the performance of a simple alternative to GSEA. We find that this simple solution clearly outperforms GSEA. We demonstrate this with eight different microarray datasets.
Prior biological knowledge-based approaches for the analysis of genome-wide expression profiles using gene sets and pathways
Authors: Wu Michael C , Xihong Lin
Published: January 2010

An increasing challenge in analysis of microarray data is how to interpret and gain biological insight of profiles of thousands of genes. This article provides a review of statistical methods for analysis of microarray data by incorporating prior biological knowledge using gene sets and biological pathways, which consist of groups of biologically similar genes. We first discuss issues of individual gene analysis. We compare several methods for analysis of gene sets including over-representation anlaysis, gene set enrichment analysis, principal component analysis, global test and kernel machine. We discuss the assumptions of these methods and their pros and cons. We illustrate these methods by application to a type II diabetes data set.
A Hierarchical Object-oriented Functional Modeling Framework for Co-Design of Mechatronic Products
Authors: Wu Jen-Chi , Leu Ming C. , Liu Xiaoqing Frank
Published: January 2010

The existing co-design methods of mechatronic products focus on co-design of mechanical and electronic components or co-design of computer hardware and software components. There exist no effective co-design methods for mechanical, electronic, and software components. This article proposes an integrated object-oriented and functional decomposition framework, developed for co-design and co-analysis of product functions, structures, and their mapping relations in a top-down manner. The framework has three operational models: Function Model, Object Model, and Information Flow Model. The function model is implemented as a function tree (FT), which is a hierarchical structure for the functional decomposition and behavioral analysis of the product under functional domain commonly used in classical engineering design. The object model is a high order object model (HOOM) designed for system and component decomposition for analysis and design of the structure of a system and its components under physical domain. The information flow model is a function and object mapping model, which describes and analyzes implementation parameters and mapping relations between FT functions and HOOM objects. These three models are decomposed and constructed level-by-level and side-by-side to form the concurrent and coordinated design paradigm for the product design team. The components of the resulting design are then carefully reviewed and summarized in a design summary and task assignment table by the product design team, and assigned to their respective disciplinary engineers for detail design or implementation according to their attributes. The proposed methodology enables mechanical, electronic, and software engineers to develop mechatronic products concurrently in a seamlessly integrated fashion.
The Minimum-cost PD Process Planning and Control Methodology with the Consideration of Resource/Time Constraints and Skill Levels
Authors: Chiang Tzu-An
Published: January 2010

This research applies the benchmarking-based concept to propose a minimum-cost product development (PD) process planning and control methodology to consider resource/time constraints and skill levels. The methodology can aid PD project managers to more objectively perceive the relationship among activity times, activity costs, as well as quantities of different skill-level manpower and facilities. Hence, the minimum-cost PD process management approach proposed in this paper can assist project managers to optimize R&D resource allocation of a PD process and estimate activity times and activity costs. In addition, this paper provides the minimum-cost PD process planning and control mechanisms to dynamically modify the PD project process.
Optimal Design of Hierarchic Components Platform under Hybrid Modular Architecture
Authors: Yan Ling Cai  , Nee Andrew Y. C. , Wen Feng Lu
Published: January 2010

Platform-based product family has been proven an effective strategy to economically provide wide market coverage. However, two practical platform design issues need to be properly handled: (1) commonized components require over-design of features that drives capability waste and additional costs with regard to the lower end product variants, and (2) commonization pattern of components is constrained by couplings of the base platform architecture. This research attempts to present a generic approach for the optimal platform design that treats commonization of components in a hierarchic manner under hybrid modular architecture. Three major sections are included: (1) identification of hidden interface costs defined by the architectural couplings, (2) modeling of hierarchic sharing relationship of commonized components across product variants, and (3) configuration of the hierarchic components platform for the lowest total production cost. Finally, a family of cordless drills targeting a series of rated output torques is employed to demonstrate the proposed approach.
On Modular Products Development
Authors: Kong F.B. , Ming X.G. , Wang L. , Wang X.H. , Wang P.P.
Published: January 2010

Quite a few investigations have been carried out on modularity in product development. However, the presence of various perspectives, representations, and different problems hamper a holistic comprehension of modular products development (MPD) or modularity. This article is developed to give a deeper understanding of MPD. An evolutionary history of modularity, consisting of five stages, is introduced. The relationships among the benefits of modularity, such as cost-reduction, diversity, and innovation ability are then discussed in detail along with their relationships to related research issues. The implementation aspect of MPD is explained in three tiers: central, mediate, and peripheral. It shows that former theories and methods can hardly meet the needs of MPD application in real practice, and that metrics and measurement cannot take into account the degree of modularity, and cost-reduction becomes unclear and more complex. Based on this, a new powerful approach with 15 convenient steps for MPD is presented and compared with former reported research results. Also, recommendations for future research have been suggested.
Reconciling Competing Discourses of Diversity? The UK Non-Profit Sector Between Social Justice and the Business Case
Authors: Tomlinson Frances , Schwabenland Christina
Published: January 2010

The tension between the business case and social justice approaches forms a crucial point of debate in the diversity and equality field. However, their presentation as essentially oppositional is brought into question when the ‘business’ of the organization itself concerns social justice. This article draws on research in UK voluntary (non-profit) organizations to reveal the ambiguities and variations found in local constructions of equality and diversity. Managers and diversity specialists reconciled moral and business rationales through re-inscribing utilitarian arguments within an organizational commitment to social justice; however, significant dilemmas associated with doing diversity remained. The article argues for a shift in the research agenda away from competing ‘cases’ and towards investigating how the challenges that diversity presents can be worked through in day-to-day organizational practice.
The Case of Vanishing Borders: Theorizing Diversity Management as Internal Border Control
Authors: Kalonaityte Viktorija
Published: January 2010

This article adopts a postcolonial lens to contribute to the theorizing of diversity management. It draws on an empirical study of a Swedish municipal school for adults in order to theorize how construction of privileged and disadvantaged ethnic identities is an integral diversity management practice, situated in the Swedish context. Further, the article looks not only at limiting identity construction effects, but also at the traces of ongoing resistance. The contribution of the postcolonial lens in the study of workplace diversity lies in the conceptual space it provides for rendering visible, and legitimizing, non-traditional forms of resistance to hierarchical differentiation of cultural identities.
A ‘healthy baby’: The double imperative of preimplantation genetic diagnosis
Authors: Ehrich Kathryn , Williams Clare
Published: January 2010

This article reports from a study exploring the social processes, meanings and institutions that frame and produce ‘ethical problems’ and clinical dilemmas for practitioners, scientists and others working in the specialty of preimplantation genetic diagnosis (PGD). A major topic in the data was that, in contrast to IVF, the aim of PGD is to transfer to the woman’s womb only those embryos likely to be unaffected by serious genetic disorders; that is, to produce ‘healthy babies’. Staff described the complex processes through which embryos in each treatment cycle must meet a double imperative: they must be judged viable by embryologists and ‘unaffected’ by geneticists. In this article, we focus on some of the ethical, social and occupational issues for staff ensuing from PGD’s double imperative.
The impact of early stroke on identity: A discourse analytic study
Authors: Guise Jennifer , McKinlay Andy , Widdicombe Sue
Published: January 2010

This article examines the ways in which sufferers talk about early stroke and the effects this chronic condition has on identity. Traditional research into chronic illness has largely used medical, psychiatric or cognitive models. We adopt a social constructionist perspective and use a discourse analytic methodology to study data collected via focus group interaction. Analysis of the data collected shows that participants displayed sensitivity about having acquired a potentially ‘damaged’ sense of self by mitigating negative features of their experiences. Participants also attended to the issue of whether their accounts were persuasive or believable. Some carers were present in these discussions. As a consequence, participants who had suffered a stroke displayed sensitivity to the way that carers might respond to mitigation of the negative aspects of stroke.
Introduction to Special Issue: Human Trafficking
Authors: Winterdyk John , Reichel Philip
Published: January 2010

This special issue focuses on a crime that has been classified by the United Nations as the third most profitable crime in the world — human trafficking (Fichtelberg 2008). 1 The international contributions in this issue cover a range of key social, economic, political and legal issues as they relate to human trafficking. The genesis for this collection evolved out of a major project led by Philip Reichel which was completed in 2007. Reichel and an international team examined Canadian and US practices of combating human trafficking. In addition, the project explored a range of initiatives used in Europe and proposed by the United Nations.2 Before presenting an overview of the articles, we thought it instructive to provide a synopsis of some of the fundamental issues involved in human trafficking. Our thinking was that a brief discussion of these more general, descriptive, theoretical and practical issues would provide some context for readers unfamiliar with the subject of human trafficking.
Corruption and Human Trafficking in Brazil: Findings from a Multi-Modal Approach
Authors: Sacco Studnicka Andrea Cirineo
Published: January 2010

Because both corruption and trafficking are very complex phenomena, a multivariate approach was used to analyse the relationship between corruption and trafficking. The results of the analysis show that, in Brazil, corruption is a causal factor in human trafficking. The paper offers a number of suggestions to help researchers and policy makers better understand where, how and when corruption facilitates trafficking in human beings in order to combat both crimes more effectively.
Protection and Assistance to Victims of Human Trafficking in Serbia: Recent Developments
Authors: Simeunovic-Patic Biljana , Copic Sanja
Published: January 2010

The paper reviews recent developments in the system of protection, assistance and support of victims of human trafficking in Serbia. The establishment of the Agency for Co-ordination of Protection of Victims of Trafficking in Human Beings in 2003, the issuing of the Instruction on Conditions for Obtaining Temporary Residence Permit for Foreign Citizens — Victims of Trafficking in Human Beings by the Minister of Interior in 2004, and the adoption of the Strategy to Combat Trafficking in Human Beings in the Republic of Serbia in 2006 are important steps forward. Notable improvement has been achieved in the protection of victims as injured parties/witnesses in criminal proceedings. However, despite the respectable efforts made so far, further improvements to the system and mechanisms of victim protection in Serbia are still needed, particularly in terms of developing support for and protection of child victims.
Human Trafficking for Sexual Exploitation and Organized Procuring in Finland
Authors: Viuhko Minna
Published: January 2010

A joint Finnish—Swedish—Estonian study, completed in 2008, analysed the connections between human trafficking for the purposes of sexual exploitation and organized crime. This article deals with prostitution-related human trafficking and organized procuring in Finland in the 21st century. Finland is studied as a country of destination where foreign women, mainly from the adjacent eastern and southern regions, are brought to sell sexual services. The article concentrates on the perpetrators, their modi operandi and the structure of the criminal organizations. In particular, the control measures that are imposed on the procured women are examined; such measures comprise different sets of rules, violence and the threat of violence, and the so-called debt bondage.
Epilogue: Human Trafficking Seen from the Future
Authors: Parmentier Stephan
Published: January 2010

The phenomenon of human trafficking cannot be separated from a number of important changes that have taken place in society - at both a local and global level - over the last few decades. In addition, there have been a number of important theoretical developments, as well as the emergence of several law enforcement models directed to combat the growing problem of trafficking in humans. Some of these topics will be dealt with in the following paragraphs that take the form of an epilogue to a very rich special issue.
An Analysis of Racial/Ethnic Pay Disparities Among Hospital Nurses in New York City
Authors: McGinnis Sandra L. , Moore Jean
Published: January 2010

Despite growing concern over cultural competence and diversity in the registered nursing (RN) workforce, minority RNs working in hospitals in New York City who were surveyed in 2007 earned less on average than their non-Hispanic White counterparts. Regression decomposition was applied to these data to investigate how much of the differential could be attributed to different characteristics of different racial/ethnic groups and how much could be attributed to differential valuation of characteristics between racial/ethnic groups. The earnings differential between Black/African American and non-Hispanic White RNs was about equally due to different characteristics and differential valuation of characteristics, but the earnings differentials between Hispanic/Latino RNs and non-Hispanic White RNs and between Asian/Pacific Islander RNs and non-Hispanic White RNs were about two-thirds due to different characteristics and one-third due to differential valuation of their characteristics. In particular, years of nursing experience did not translate into the same earnings advantages for minority RNs.
Justice and Impoverished Women: The Ethical Implications of Work-Based Welfare
Authors: Hildebrandt  , Ford Sandra L.
Published: January 2010

Current U.S. welfare policy, Temporary Assistance for Needy Families, requires impoverished people to work in order to receive welfare, and it limits cash support to 5 years. Most of the people who have used this program are single-parent women, and a disturbing number have been terminated at 5 years, not having made a successful transition to work. The purpose of this longitudinal study was to explore the barriers to success and the social justice of the program from the perspective of single-parent women who were terminated. In all, 41 women were recruited through community-based purposive sampling, and the primary research methods were a qualitative, narrative interview approach and narrative analysis. Data from the semistructured interview guide are reported here. Findings describe health and socioeconomic burdens, and barriers that lie within the social policy. The study has ethical implications for nursing advocacy, and it informs nursing interventions for impoverished women and their families.
Analyzing Ethics in the Administration of Interscholastic Sports
Authors: Whisenant Warren A. , Pedersen Paul M. , Clavio Galen
Published: January 2010

Athletic administrators and decision makers within interscholastic athletics are expected to embrace a code of ethics that serves as a set of rules to guide their professional behavior. Included within this code are areas of controversy that present gender-related ethical dilemmas for administrators. Three specific ethical dilemmas involve (1) providing equitable participation opportunities for students, (2) instituting ethical hiring practices for coaches, athletic administrators and educational leaders and (3) creating an environment and organizational culture that embraces fairness. This article examines these three critical dilemmas.
Management of School Attendance in the UK
Authors: Reid Ken
Published: January 2010

Prior to 1997, managing school attendance was the sole responsibility of the Department for Education and Skills (DfES). Since devolution, responsibility for school attendance has resided with each of the four UK-wide administrations. These are the Department for Children, Schools and Families (DCSF) in England; the Scottish Executive Education Department (SEED); the Northern Irish Department for Education (NIDE); and in Wales, the Department for Children, Education, Lifelong Learning and Skills (DCELLS). Since then, each of the four administrations has begun to develop different policy directions over the management of education in England, Scotland, Northern Ireland and Wales. Within each of the four countries, different management approaches to school attendance has evolved between 1997 and 2007. The focus of this article is on describing these four different approaches until 2007, the present position post 2007, while attempting to compare, contrast and evaluate some of the potential outcomes of these strategies. It also seems increasingly likely that the future educational policy directions of the four national governments will continue to diverge, possibly leading to new legislation which will mean that policies on school attendance will differ significantly in the years ahead.
Impact of parents’ involvement and engagement in a learning readiness programme for children with severe and profound intellectual disability and complex needs in India
Authors: Kurani D. , Nerurka A. , Miranda L. , Jawadwala F. , Prabhulkar D.
Published: January 2010

Cognitive, social, motor and language skills are key factors that contribute to the quality of life for people with learning disabilities and for their carers. Development of these skills for children with severe learning disabilities who have other complex needs however remains a challenge. A pilot study was undertaken by the staff from The Jai Vakeel School for Children in Need of Special Care, Mumbai, with a view to examining the effects of training offered by parents of children with severe learning disabilities and complex needs on their emotional, social, language, cognitive and motor skill development. Using a Parental Involvement/Engagement Scale it was seen that children with lower parental involvement had less improvement in the above areas whilst children with higher parental involvement showed greater improvement. The findings are discussed in relation to the hypothesis that the pre-clinical condition of the child will affect the outcome of therapy.
Genome size differentiates co-occurring populations of the planktonic diatom Ditylum brightwellii(Bacillariophyta)
Authors: Koester Julie A , Swalwell Jarred E , von Dassow Peter , Armbrust E Virginia
Published: January 2010

Background

Diatoms are one of the most species-rich groups of eukaryotic microbes known. Diatoms are also the only group of eukaryotic micro-algae with a diplontic life history, suggesting that the ancestral diatom switched to a life history dominated by a duplicated genome. A key mechanism of speciation among diatoms could be a propensity for additional stable genome duplications. Across eukaryotic taxa, genome size is directly correlated to cell size and inversely correlated to physiological rates. Differences in relative genome size, cell size, and acclimated growth rates were analyzed in isolates of the diatom Ditylum brightwellii. Ditylum brightwellii consists of two main populations with identical 18s rDNA sequences; one population is distributed globally at temperate latitudes and the second appears to be localized to the Pacific Northwest coast of the USA. These two populations co-occur within the Puget Sound estuary of WA, USA, although their peak abundances differ depending on local conditions.

Results

All isolates from the more regionally-localized population (population 2) possessed 1.94 ± 0.74 times the amount of DNA, grew more slowly, and were generally larger than isolates from the more globally distributed population (population 1). The ITS1 sequences, cell sizes, and genome sizes of isolates from New Zealand were the same as population 1 isolates from Puget Sound, but their growth rates were within the range of the slower-growing population 2 isolates. Importantly, the observed genome size difference between isolates from the two populations was stable regardless of time in culture or the changes in cell size that accompany the diatom life history.

Conclusions

The observed two-fold difference in genome size between the D. brightwellii populations suggests that whole genome duplication occurred within cells of population 1 ultimately giving rise to population 2 cells. The apparent regional localization of population 2 is consistent with a recent divergence between the populations, which are likely cryptic species. Genome size variation is known to occur in other diatom genera; we hypothesize that genome duplication may be an active and important mechanism of genetic and physiological diversification and speciation in diatoms.
Adaptation of Hansenula polymorpha to methanol: a transcriptome analysis
Authors: van Zutphen Tim , Baerends Richard JS , Susanna Kim A , de Jong Anne , Kuipers Oscar P , Veenhuis Marten , van der Klei Ida J
Published: January 2010

Background

Methylotrophic yeast species (e.g. Hansenula polymorpha, Pichia pastoris) can grow on methanol as sole source of carbon and energy. These organisms are important cell factories for the production of recombinant proteins, but are also used in fundamental research as model organisms to study peroxisome biology. During exponential growth on glucose, cells of H. polymorpha typically contain a single, small peroxisome that is redundant for growth while on methanol multiple, enlarged peroxisomes are present. These organelles are crucial to support growth on methanol, as they contain key enzymes of methanol metabolism.

In this study, changes in the transcriptional profiles during adaptation of H. polymorpha cells from glucose- to methanol-containing media were investigated using DNA-microarray analyses.

Results

Two hours after the shift of cells from glucose to methanol nearly 20% (1184 genes) of the approximately 6000 annotated H. polymorpha genes were significantly upregulated with at least a two-fold differential expression. Highest upregulation (> 300-fold) was observed for the genes encoding the transcription factor Mpp1 and formate dehydrogenase, an enzyme of the methanol dissimilation pathway. Upregulated genes also included genes encoding other enzymes of methanol metabolism as well as of peroxisomal ?-oxidation.

A moderate increase in transcriptional levels (up to 4-fold) was observed for several PEX genes, which are involved in peroxisome biogenesis. Only PEX11 and PEX32 were higher upregulated. In addition, an increase was observed in expression of the several ATG genes, which encode proteins involved in autophagy and autophagy processes. The strongest upregulation was observed for ATG8 and ATG11.

Approximately 20% (1246 genes) of the genes were downregulated. These included glycolytic genes as well as genes involved in transcription and translation.

Conclusion

Transcriptional profiling of H. polymorpha cells shifted from glucose to methanol showed the expected downregulation of glycolytic genes together with upregulation of the methanol utilisation pathway. This serves as a confirmation and validation of the array data obtained. Consistent with this, also various PEX genes were upregulated. The strong upregulation of ATG genes is possibly due to induction of autophagy processes related to remodeling of the cell architecture required to support growth on methanol. These processes may also be responsible for the enhanced peroxisomal ?-oxidation, as autophagy leads to recycling of membrane lipids. The prominent downregulation of transcription and translation may be explained by the reduced growth rate on methanol (td glucose 1 h vs td methanol 4.5 h).
Extensive analysis of D-J-C arrangements allows the identification of different mechanisms enhancing the diversity in sheep T cell receptor β-chain repertoire
Authors: Di Tommaso Silvia , Antonacci Rachele , Ciccarese Salvatrice , Massari Serafina
Published: January 2010

Background

In most species of mammals, theTRBlocus has the common feature of a library ofTRBVgenes positioned at the 5'- end of two in tandem aligned D-J-C gene clusters, each composed of a singleTRBDgene, 6-7TRBJgenes and oneTRBCgene. An enhancer located at the 3'end of the lastTRBCand a well-defined promoter situated at the 5'end of theTRBDgene and/or a undefined promoter situated at the 5'end of theTRBD2are sufficient to generate the full recombinase accessibility at the locus. In ruminant species, the 3'end of theTRBlocus is characterized by the presence of three D-J-C clusters, each constituted by a singleTRBD, 5-7TRBJand oneTRBCgenes with the center cluster showing a structure combined with the clusters upstream and downstream, suggesting that a unequal crossover occurred in the duplication. An enhancer downstream the lastTRBC, and a promoter at the 5'-end of eachTRBDgene are also present.

Results

In this paper we focused our attention on the analysis of a large number of sheep TR β-chain transcripts derived from four different lymphoid tissues of three diverse sheep breed animals to certify the use and frequency of the three gene clusters in the β-chain repertoire. As the sheepTRBlocus genomic organization is known, the exact interpretation of the V-D-J rearrangements was fully determined. Our results clearly demonstrate that sheep β-chain constitutes a level of variability that is substantially larger than that described in other mammalian species. This is due not only to the increase of the number of D and J genes available to the somatic recombination, but also to the presence of the trans-rearrangement process. Moreover, the functional complexity of β-chain repertoire is resolved by other mechanisms such as alternative cis- and trans-splicing and recombinational diversification that seems to affect the variety of the constant region.

Conclusion

All together our data demonstrate that a disparate set of molecular mechanisms operate to perform a diversified repertoire in the sheep β-chain and this could confer some special biological properties to the corresponding αβ T cells in the ruminant lineage.
aes, the gene encoding the esterase B in Escherichia coli, is a powerful phylogenetic marker of the species
Authors: Lescat Mathilde , Hoede Claire , Clermont Olivier , Garry Louis , Darlu Pierre , Tuffery Pierre , Denamur Erick , Picard Bertrand
Published: January 2010

Background

Previous studies have established a correlation between electrophoretic polymorphism of esterase B, and virulence and phylogeny ofEscherichia coli. Strains belonging to the phylogenetic group B2 are more frequently implicated in extraintestinal infections and include esterase B2variants, whereas phylogenetic groups A, B1 and D contain less virulent strains and include esterase B1variants. We investigated esterase B as a marker of phylogeny and/or virulence, in a thorough analysis of the esterase B-encoding gene.

Results

We identified the gene encoding esterase B as the acetyl-esterase gene (aes) using gene disruption. The analysis ofaesnucleotide sequences in a panel of 78 reference strains, including theE. colireference (ECOR) strains, demonstrated that the gene is under purifying selection. The phylogenetic tree reconstructed fromaessequences showed a strong correlation with the species phylogenetic history, based on multi-locus sequence typing using six housekeeping genes. The unambiguous distinction between variants B1and B2by electrophoresis was consistent with Aes amino-acid sequence analysis and protein modelling, which showed that substituted amino acids in the two esterase B variants occurred mostly at different sites on the protein surface. Studies in an experimental mouse model of septicaemia using mutant strains did not reveal a direct link betweenaesand extraintestinal virulence. Moreover, we did not find any genes in the chromosomal region ofaesto be associated with virulence.

Conclusion

Our findings suggest thataesdoes not play a direct role in the virulence ofE. coliextraintestinal infection. However, this gene acts as a powerful marker of phylogeny, illustrating the extensive divergence of B2 phylogenetic group strains from the rest of the species.
Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaeaL.)
Authors: Zhao Chuan-Zhi , Xia Han , Frazier Taylor Price , Yao Ying-Yin , Bi Yu-Ping , Li Ai-Qin , Li Meng-Jun , Li Chang-Sheng , Zhang Bao-Hong , Wang Xing-Jun
Published: January 2010

Background

MicroRNAs (miRNAs) are a new class of small, endogenous RNAs that play a regulatory role in the cell by negatively affecting gene expression at the post-transcriptional level. miRNAs have been shown to control numerous genes involved in various biological and metabolic processes. There have been extensive studies on discovering miRNAs and analyzing their functions in model species, such as Arabidopsis and rice. Increasing investigations have been performed on important agricultural crops including soybean, conifers, and Phaselous vulgaris but no studies have been reported on discovering peanut miRNAs using a cloning strategy.

Results

In this study, we employed the next generation high through-put Solexa sequencing technology to clone and identify both conserved and species-specific miRNAs in peanuts. Next generation high through-put Solexa sequencing showed that peanuts have a complex small RNA population and the length of small RNAs varied, 24-nt being the predominant length for a majority of the small RNAs. Combining the deep sequencing and bioinformatics, we discovered 14 novel miRNA families as well as 75 conserved miRNAs in peanuts. All 14 novel peanut miRNAs are considered to be species-specific because no homologs have been found in other plant species except ahy-miRn1, which has a homolog in soybean. qRT-PCR analysis demonstrated that both conserved and peanut-specific miRNAs are expressed in peanuts.

Conclusions

This study led to the discovery of 14 novel and 22 conserved miRNA families from peanut. These results show that regulatory miRNAs exist in agronomically important peanuts and may play an important role in peanut growth, development, and response to environmental stress.
Apyrase treatment of myocardial infarction according to a clinically applicable protocol fails to reduce myocardial injury in a porcine model
Authors: van der Pals Jesper , Koul Sasha , Götberg Michael I , Olivecrona Göran K , Ugander Martin , Kanski Mikael , Otto Andreas , Götberg Matthias , Arheden Håkan , Erlinge David
Published: January 2010

Background

Ectonucleotidase dependent adenosine generation has been implicated in preconditioning related cardioprotection against ischemia-reperfusion injury, and treatment with a soluble ectonucleotidase has been shown to reduce myocardial infarct size (IS) when applied prior to induction of ischemia. However, ectonucleotidase treatment according to a clinically applicable protocol, with administration only after induction of ischemia, has not previously been evaluated. We therefore investigated if treatment with the ectonucleotidase apyrase, according to a clinically applicable protocol, would reduce IS and microvascular obstruction (MO) in a large animal model.

Methods

A percutaneous coronary intervention balloon was inflated in the left anterior descending artery for 40 min, in 16 anesthetized pigs (40-50 kg). The pigs were randomized to 40 min of 1 ml/min intracoronary infusion of apyrase (10 U/ml, n = 8) or saline (0.9 mg/ml, n = 8), twenty minutes after balloon inflation. Area at risk (AAR) was evaluated byex vivoSPECT. IS and MO were evaluated byex vivoMRI.

Results

No differences were observed between the apyrase group and saline group with respect to IS/AAR (75.7 ± 4.2% vs 69.4 ± 5.0%, p = NS) or MO (10.7 ± 4.8% vs 11.4 ± 4.8%, p = NS), but apyrase prolonged the post-ischemic reactive hyperemia.

Conclusion

Apyrase treatment according to a clinically applicable protocol, with administration of apyrase after induction of ischemia, does not reduce myocardial infarct size or microvascular obstruction.
Predictors of health decline in older adults with pneumonia: findings from the Community Acquired Pneumonia Impact Study
Authors: Fernandez Eduardo , Krueger Paul , Loeb Mark
Published: January 2010

Background

The purpose of this study was to identify predictors of health decline among older adults with clinically diagnosed community acquired pneumonia (CAP). It was hypothesized that older adults with CAP who had lower levels of social support would be more likely to report a decline in health.

Methods

A telephone survey was used to collect detailed information from older adults about their experiences with CAP. A broader determinants of health framework was used to guide data collection. This was a community wide study with participants being recruited from all radiology clinics in one Ontario community.

Results

The most important predictors of a health decline included: two symptoms (no energy; diaphoresis), two lifestyle variables (being very active; allowing people to smoke in their home), one quality of life variable (little difficulty in doing usual daily activities) and one social support variable (having siblings).

Conclusions

A multiplicity of factors was found to be associated with a decline in health among older adults with clinically diagnosed CAP. These findings may be useful to physicians, family caregivers and others for screening older adults and providing interventions to help ensure positive health outcomes.
A randomised controlled trial and cost-effectiveness evaluation of "booster" interventions to sustain increases in physical activity in middle-aged adults in deprived urban neighbourhoods
Authors: Hind Daniel , Scott Emma J , Copeland Robert , Breckon Jeff D , Crank Helen , Walters Stephen J , Brazier John E , Nicholl Jon , Cooper Cindy , Goyder Elizabeth
Published: January 2010

Background

Systematic reviews have identified a range of brief interventions which increase physical activity in previously sedentary people. There is an absence of evidence about whether follow up beyond three months can maintain long term physical activity. This study assesses whether it is worth providing motivational interviews, three months after giving initial advice, to those who have become more active.

Methods/Design

Study candidates (n = 1500) will initially be given an interactive DVD and receive two telephone follow ups at monthly intervals checking on receipt and use of the DVD. Only those that have increased their physical activity after three months (n = 600) will be randomised into the study. These participants will receive either a "mini booster" (n = 200), "full booster" (n = 200) or no booster (n = 200). The "mini booster" consists of two telephone calls one month apart to discuss physical activity and maintenance strategies. The "full booster" consists of a face-to-face meeting with the facilitator at the same intervals. The purpose of these booster sessions is to help the individual maintain their increase in physical activity. Differences in physical activity, quality of life and costs associated with the booster interventions, will be measured three and nine months from randomisation. The research will be conducted in 20 of the most deprived neighbourhoods in Sheffield, which have large, ethnically diverse populations, high levels of economic deprivation, low levels of physical activity, poorer health and shorter life expectancy. Participants will be recruited through general practices and community groups, as well as by postal invitation, to ensure the participation of minority ethnic groups and those with lower levels of literacy. Sheffield City Council and Primary Care Trust fund a range of facilities and activities to promote physical activity and variations in access to these between neighbourhoods will make it possible to examine whether the effectiveness of the intervention is modified by access to community facilities. A one-year integrated feasibility study will confirm that recruitment targets are achievable based on a 10% sample.

Discussion

The choice of study population, study interventions, brief intervention preceding the study, and outcome measure are discussed.

Trial Registration

Current Controlled Trials: ISRCTN56495859; ClinicalTrials.gov: NCT00836459.
Health-related quality of life among individuals with long-standing spinal cord injury: a comparative study of veterans and non-veterans
Authors: Saadat Soheil , Javadi Masoud , Divshali Baharak Sabet , Tavakoli Amir Hussein , Ghodsi Seyed Mohammad , Montazeri Ali , Rahimi-Movaghar Vafa
Published: January 2010

Background

Spinal cord-injured (SCI) patients experience poor health-related quality of life (HRQOL) and they usually report lower HRQOL than the general population or population subgroups in Iran and elsewhere. The aim of this study was to compare HRQOL between veterans and non-veterans with SCI in Iran.

Methods

This was a cross-sectional study. HRQOL was measured using the 36-item Short Form Health Survey (SF-36). Thirty-nine male veterans and 63 non-veteran males with SCI were included in the study. Regression analyses were applied to determine the variables affecting physical and mental health-related quality of life among the patients.

Results

The male veterans had a lower HRQOL than the non-veterans with SCI. The differences were significant for all measures except for physical and social functioning. The greatest difference was observed for bodily pain (P = 0.001). The regression analysis results indicated that a longer time since injury was associated (P = 0.01) with better physical health-related quality of life (PCS), while being a veteran (P < 0.001) and having a spinal lesion in the cervical region (P = 0.001) were associated with poorer PCS. Older age (P < 0.001) and higher education (P = 0.01) were associated with better mental health-related quality of life (MCS), while being a veteran and having a spinal lesion in the cervical region (P = 0.02) were associated with poorer MCS.

Conclusion

The study findings showed that veterans with SCI experienced lower HRQOL than their non-veteran counterparts. A qualitative study is recommended to evaluate why HRQOL was lower in veterans than in non-veterans with SCI although veterans had higher incomes as a result of their pensions and increased access to equipment, and medications. To improve quality of life in both veterans and non-veterans with spinal cord injuries, policy changes or implementation of new interventions may be essential so that veterans could receive additional support (e.g. counseling, recreation therapy, vocational therapy, etc.) and non-veterans could meet their basic needs.
Assessing a risk tailored intervention to prevent disabling low back pain - protocol of a cluster randomized controlled trial
Authors: Schmidt Carsten Oliver , Chenot Jean-François , Pfingsten Michael , Fahland Ruth Anja , Lindena Gabriele , Marnitz Ulf , Pfeifer Klaus , Kohlmann Thomas
Published: January 2010

Background

Although most patients with low back pain (LBP) recover within a few weeks a significant proportion has recurrent episodes or will develop chronic low back pain. Several mainly psychosocial risk factors for developing chronic LBP have been identified. However, effects of preventive interventions aiming at behavioural risk factors and unfavourable cognitions have yielded inconsistent results. Risk tailored interventions may provide a cost efficient and effective means to take systematic account of the individual risk factors but evidence is lacking.

Methods/Design

This study will be a cluster-randomised controlled trial comparing screening and a subsequent risk tailored intervention for patients with low back pain to prevent chronic low back pain compared to treatment as usual in primary care. A total of 600 patients from 20 practices in each study arm will be recruited in Berlin and Goettingen. The intervention comprises the following elements: Patients will be assigned to one of four risk groups based on a screening questionnaire. Subsequently they receive an educational intervention including information and counselling tailored to the risk group. A telephone/email consulting service for back pain related problems are offered independent of risk group assignment. The primary outcomes will be functional capacity and sick leave.

Discussion

This trial will evaluate the effectiveness of screening for risk factors for chronic low back pain followed by a risk tailored intervention to prevent chronic low back pain. This trial will contribute new evidence regarding the flexible use of individual physical and psychosocial risk factors in general practice.

Trial registration

ISRCTN 68205910
Plexin-B1, glycodelin and MMP7 expression in the human fallopian tube and in the endometrium
Authors: Amir Michal , Romano Shabtai , Goldman Shlomit , Shalev Eliezer
Published: January 2010

Background

To study the expression of Plexin-B1, Glycodelin, and MMP7 during the menstrual cycle in the endometrium and in the fallopian tube.

Methods

The research included women undergoing hysterectomy, tubal sterilization or salpingo-oophoerectomy. Total RNA from endometrial and fallopian tube tissues was extracted using a total RNA isolation kit. Semi-quantitative RT-PCR was performed to examine mRNA relative expression.

Results

Plexin-B1 expression in the endometrium was significantly higher on days 19 - 23 compared to days 12 - 14 (1.166 +/- 0.42 versus 0.523 +/- 0.299), P < 0.005. In the fallopian tube the level of plexin-B1 did not change significantly throughout the menstrual cycle. Glycodelin expression was significantly higher on days 19 - 23 compared with days 12-14, both in the endometrium (0.819 +/- 0.564 versus 0.072 +/- 0.343, P < 0.05) and the fallopian tube (0.796 +/- 0.196 versus 0.329 +/- 0.398, P < 0.05). Although the level of MMP7 secretion was the highest in the secretory phase the difference from the proliferative phase did not reach statistical significance, neither in the endometrium nor in the fallopian tube. This could result from a lack of power.

Conclusions

In the endometrium, both Glycodelin and Plexin-B1 are exhibiting a cyclic pattern suggesting a possible steroid regulation and a role in endometrial receptivity.
Evaluation of ammonia fibre expansion (AFEX) pretreatment for enzymatic hydrolysis of switchgrass harvested in different seasons and locations
Authors: Bals Bryan , Rogers Chad , Jin Mingjie , Balan Venkatesh , Dale Bruce
Published: January 2010

Background

When producing biofuels from dedicated feedstock, agronomic factors such as harvest time and location can impact the downstream production. Thus, this paper studies the effectiveness of ammonia fibre expansion (AFEX) pretreatment on two harvest times (July and October) and ecotypes/locations (Cave-in-Rock (CIR) harvested in Michigan and Alamo harvested in Alabama) for switchgrass (Panicum virgatum).

Results

Both harvest date and ecotype/location determine the pretreatment conditions that produce maximum sugar yields. There was a high degree of correlation between glucose and xylose released regardless of the harvest, pretreatment conditions, or enzyme formulation. Enzyme formulation that produced maximum sugar yields was the same across all harvests except for the CIR October harvest. The least mature sample, the July harvest of CIR switchgrass, released the most sugars (520 g/kg biomass) during enzymatic hydrolysis while requiring the least severe pretreatment conditions. In contrast, the most mature harvest released the least amount of sugars (410 g/kg biomass). All hydrolysates were highly fermentable, although xylose utilisation in the July CIR hydrolysate was poor.

Conclusions

Each harvest type and location responded differently to AFEX pretreatment, although all harvests successfully produced fermentable sugars. Thus, it is necessary to consider an integrated approach between agricultural production and biochemical processing in order to insure optimal productivity.