bluuebunny/crossref_metadata_2025_split huggingface dataset:
Matrix metalloproteinase-9 and matrix metalloproteinase-2 as biomarkers of various courses in multiple sclerosis
Authors: Benešová Y , Vašků A , Novotná H , Litzman J , Štourač P , Beránek M , Kadaňka Z , Bednařík J 
Published: January 2009

Background Matrix metalloproteinases are notable contributors to neuroinflammation and blood-brain barrier disruption in multiple sclerosis (MS). Objective The goal of this study was to determine the serum levels of matrix metalloproteinase-9 (MMP-9), matrix metalloproteinase-2 (MMP-2), and their tissue inhibitors (TIMP-1) and (TIMP-2), and to investigate their possible relations to type, disability, and severity of MS. Materials and methods Eighty-seven patients with definite MS according to the McDonald criteria and 50 healthy controls were enrolled in the study. Their clinical status was evaluated with the Expanded Disability Status Scale. Serum levels were analyzed by enzyme-linked immunoassay. Results A significant elevation in MMP-9 serum levels and in the MMP-9/TIMP-1 ratio was found in the whole MS group ( P < 0.001), in the relapsing–remitting MS (RRMS) ( P < 0.001), and secondary-progressive MS (SPMS) ( P < 0.001) groups when compared with the controls. A significant elevation in MMP-2 serum levels and in the MMP-2/TIMP-2 ratio was observed in the primary progressive ( P < 0.001) and the SPMS ( P < 0.002) groups when compared with the RRMS group, and this increase was also associated with the disability ( P < 0.001) and severity ( P < 0.05) of the disease. Conclusion We confirmed that metalloproteinases are useful biological markers in MS, providing information about the clinical type, disability, and severity of the disease.
Reduced cerebrospinal fluid BACE1 activity in multiple sclerosis
Authors: Mattsson N , Axelsson M , Haghighi S , Malmeström C , Wu G , Anckarsäter R , Sankaranarayanan S , Andreasson U , Fredrikson S , Gundersen A , Johnsen L , Fladby T , Tarkowski A , Trysberg E , Wallin A , Anckarsäter H , Lycke J , Andersen O , Simon AJ , Blennow K , Zetterberg H 
Published: January 2009

Background Cell and animal experiments have shown that β-site APP-cleaving enzyme 1 (BACE1) may be involved in myelination. Objective Here, we assess the association of cerebrospinal fluid (CSF) BACE1 activity with multiple sclerosis (MS). Methods BACE1 activity and levels of secreted amyloid precursor protein (APP) and amyloid-β (Aβ) isoforms were analyzed in CSF from 100 patients with MS and 114 neurologically healthy controls. Patients with systemic lupus erythematosus (SLE), 26 with and 41 without cerebral engagement, were also included to enable comparisons with regards to another autoimmune disease. A subset of patients with MS and controls underwent a second lumbar puncture after 10 years. Results MS patients had lower CSF BACE1 activity than controls ( P = 0.03) and patients with cerebral SLE ( P < 0.001). Patients with cerebral SLE had higher BACE1 activity than any other group ( P < 0.05 for all comparisons). BACE1 activity correlated with the different amyloid markers in all study groups. BACE1 activity decreased over 10 years in the MS group ( P = 0.039) and correlated weakly with clinical disease severity scores in an inverse manner. Conclusions These results suggest an involvement of BACE1 in the MS disease process.
An innovative approach for testing bioinformatics programs using metamorphic testing
Authors: Chen Tsong Yueh , Ho Joshua WK , Liu Huai , Xie Xiaoyuan 
Published: January 2009

AbstractBackgroundRecent advances in experimental and computational technologies have fueled the development of many sophisticated bioinformatics programs. The correctness of such programs is crucial as incorrectly computed results may lead to wrong biological conclusion or misguide downstream experimentation. Common software testing procedures involve executing the target program with a set of test inputs and then verifying the correctness of the test outputs. However, due to the complexity of many bioinformatics programs, it is often difficult to verify the correctness of the test outputs. Therefore our ability to perform systematic software testing is greatly hindered.ResultsWe propose to use a novel software testing technique, metamorphic testing (MT), to test a range of bioinformatics programs. Instead of requiring a mechanism to verify whether an individual test output is correct, the MT technique verifies whether a pair of test outputs conform to a set of domain specific properties, called metamorphic relations (MRs), thus greatly increases the number and variety of test cases that can be applied. To demonstrate how MT is used in practice, we applied MT to test two open-source bioinformatics programs, namely GNLab and SeqMap. In particular we show that MT is simple to implement, and is effective in detecting faults in a real-life program and some artificially fault-seeded programs. Further, we discuss how MT can be applied to test programs from various domains of bioinformatics.ConclusionThis paper describes the application of a simple, effective and automated technique to systematically test a range of bioinformatics programs. We show how MT can be implemented in practice through two real-life case studies. Since many bioinformatics programs, particularly those for large scale simulation and data analysis, are hard to test systematically, their developers may benefit from using MT as part of the testing strategy. Therefore our work represents a significant step towards software reliability in bioinformatics.
Simultaneous analysis of distinct Omics data sets with integration of biological knowledge: Multiple Factor Analysis approach
Authors: de Tayrac Marie , Lê Sébastien , Aubry Marc , Mosser Jean , Husson François 
Published: January 2009

Abstract

Background
Genomic analysis will greatly benefit from considering in a global way various sources of molecular data with the related biological knowledge. It is thus of great importance to provide useful integrative approaches dedicated to ease the interpretation of microarray data.

Results
Here, we introduce a data-mining approach, Multiple Factor Analysis (MFA), to combine multiple data sets and to add formalized knowledge. MFA is used to jointly analyse the structure emerging from genomic and transcriptomic data sets. The common structures are underlined and graphical outputs are provided such that biological meaning becomes easily retrievable. Gene Ontology terms are used to build gene modules that are superimposed on the experimentally interpreted plots. Functional interpretations are then supported by a step-by-step sequence of graphical representations.

Conclusion
When applied to genomic and transcriptomic data and associated Gene Ontology annotations, our method prioritize the biological processes linked to the experimental settings. Furthermore, it reduces the time and effort to analyze large amounts of 'Omics' data.
Transcriptomic and metabolomic profiling of Zymomonas mobilis during aerobic and anaerobic fermentations
Authors: Yang Shihui , Tschaplinski Timothy J , Engle Nancy L , Carroll Sue L , Martin Stanton L , Davison Brian H , Palumbo Anthony V , Rodriguez Miguel , Brown Steven D 
Published: January 2009

Abstract

Background

Zymomonas mobilis ZM4 (ZM4) produces near theoretical yields of ethanol with high specific productivity and recombinant strains are able to ferment both C-5 and C-6 sugars. Z. mobilis performs best under anaerobic conditions, but is an aerotolerant organism. However, the genetic and physiological basis of ZM4's response to various stresses is understood poorly.

Results
In this study, transcriptomic and metabolomic profiles for ZM4 aerobic and anaerobic fermentations were elucidated by microarray analysis and by high-performance liquid chromatography (HPLC), gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS) analyses. In the absence of oxygen, ZM4 consumed glucose more rapidly, had a higher growth rate, and ethanol was the major end-product. Greater amounts of other end-products such as acetate, lactate, and acetoin were detected under aerobic conditions and at 26 h there was only 1.7% of the amount of ethanol present aerobically as there was anaerobically. In the early exponential growth phase, significant differences in gene expression were not observed between aerobic and anaerobic conditions via microarray analysis. HPLC and GC analyses revealed minor differences in extracellular metabolite profiles at the corresponding early exponential phase time point.
Differences in extracellular metabolite profiles between conditions became greater as the fermentations progressed. GC-MS analysis of stationary phase intracellular metabolites indicated that ZM4 contained lower levels of amino acids such as alanine, valine and lysine, and other metabolites like lactate, ribitol, and 4-hydroxybutanoate under anaerobic conditions relative to aerobic conditions. Stationary phase microarray analysis revealed that 166 genes were significantly differentially expressed by more than two-fold. Transcripts for Entner-Doudoroff (ED) pathway genes (glk, zwf, pgl, pgk, and eno) and gene pdc, encoding a key enzyme leading to ethanol production, were at least 30-fold more abundant under anaerobic conditions in the stationary phase based on quantitative-PCR results. We also identified differentially expressed ZM4 genes predicted by The Institute for Genomic Research (TIGR) that were not predicted in the primary annotation.

Conclusion
High oxygen concentrations present during Z. mobilis fermentations negatively influence fermentation performance. The maximum specific growth rates were not dramatically different between aerobic and anaerobic conditions, yet oxygen did affect the physiology of the cells leading to the buildup of metabolic byproducts that ultimately led to greater differences in transcriptomic profiles in stationary phase.
Effective carbon partitioning driven by exotic phloem-specific regulatory elements fused to the Arabidopsis thaliana AtSUC2 sucrose-proton symporter gene
Authors: Srivastava Avinash C , Ganesan Savita , Ismail Ihab O , Ayre Brian G 
Published: January 2009

Abstract

Background

AtSUC2 (At1g22710) from Arabidopsis thaliana encodes a phloem-localized sucrose/proton symporter required for efficient photoassimilate transport from source tissues to sink tissues. AtSUC2 plays a key role in coordinating the demands of sink tissues with the output capacity of source leaves, and in maintaining phloem hydrostatic pressure during changes in plant-water balance. Expression and activity are regulated, both positively and negatively, by developmental (sink to source transition) and environmental cues, including light, diurnal changes, photoassimilate levels, turgor pressure, drought and osmotic stress, and hormones.

Results
To assess the importance of this regulation to whole-plant growth and carbon partitioning, AtSUC2 cDNA was expressed from two exotic, phloem-specific promoters in a mutant background debilitated for AtSUC2 function. The first was a promoter element from Commelina Yellow Mottle Virus (CoYMV), and the second was the rolC promoter from Agrobacterium rhizogenes. CoYMVp::AtSUC2 cDNA restored growth and carbon partitioning to near wild-type levels, whereas plants harboring rolCp::AtSUC2 cDNA showed only partial complementation.

Conclusion
Expressing AtSUC2 cDNA from exotic, phloem-specific promoters argues that strong, phloem-localized expression is sufficient for efficient transport. Expressing AtSUC2 from promoters that foster efficient phloem transport but are subject to regulatory cascades different from the endogenous sucrose/proton symporter genes has implications for biotechnology.
Quantifying the profile and progression of impairments, activity, participation, and quality of life in people with Parkinson disease: protocol for a prospective cohort study
Authors: Morris Meg E , Watts Jennifer J , Iansek Robert , Jolley Damien , Campbell Donald , Murphy Anna T , Martin Clarissa L 
Published: January 2009

Abstract

Background
Despite the finding that Parkinson disease (PD) occurs in more than one in every 1000 people older than 60 years, there have been few attempts to quantify how deficits in impairments, activity, participation, and quality of life progress in this debilitating condition. It is unclear which tools are most appropriate for measuring change over time in PD.

Methods and design
This protocol describes a prospective analysis of changes in impairments, activity, participation, and quality of life over a 12 month period together with an economic analysis of costs associated with PD. One-hundred participants will be included, provided they have idiopathic PD rated I-IV on the modified Hoehn & Yahr (1967) scale and fulfil the inclusion criteria. The study aims to determine which clinical and economic measures best quantify the natural history and progression of PD in a sample of people receiving services from the Victorian Comprehensive Parkinson's Program, Australia. When the data become available, the results will be expressed as baseline scores and changes over 3 months and 12 months for impairment, activity, participation, and quality of life together with a cost analysis.

Discussion
This study has the potential to identify baseline characteristics of PD for different Hoehn & Yahr stages, to determine the influence of disease duration on performance, and to calculate the costs associated with idiopathic PD. Valid clinical and economic measures for quantifying the natural history and progression of PD will also be identified.

Trial Registration
ACTRN12609000008224
Systematic review of effect of community-level interventions to reduce maternal mortality
Authors: Kidney Elaine , Winter Heather R , Khan Khalid S , Gülmezoglu A Metin , Meads Catherine A , Deeks Jonathan J , MacArthur Christine 
Published: January 2009

Abstract

Background
The objective was to provide a systematic review of the effectiveness of community-level interventions to reduce maternal mortality.

Methods
We searched published papers using Medline, Embase, Cochrane library, CINAHL, BNI, CAB ABSTRACTS, IBSS, Web of Science, LILACS and African Index Medicus from inception or at least 1982 to June 2006; searched unpublished works using National Research Register website, metaRegister and the WHO International Trial Registry portal. We hand searched major references.
Selection criteria were maternity or childbearing age women, comparative study designs with concurrent controls, community-level interventions and maternal death as an outcome. We carried out study selection, data abstraction and quality assessment independently in duplicate.

Results
We found five cluster randomised controlled trials (RCT) and eight cohort studies of community-level interventions. We summarised results as odds ratios (OR) and confidence intervals (CI), combined using the Peto method for meta-analysis. Two high quality cluster RCTs, aimed at improving perinatal care practices, showed a reduction in maternal mortality reaching statistical significance (OR 0.62, 95% CI 0.39 to 0.98). Three equivalence RCTs of minimal goal-oriented versus usual antenatal care showed no difference in maternal mortality (1.09, 95% CI 0.53 to 2.25). The cohort studies were of low quality and did not contribute further evidence.

Conclusion
Community-level interventions of improved perinatal care practices can bring about a reduction in maternal mortality. This challenges the view that investment in such interventions is not worthwhile. Programmes to improve maternal mortality should be evaluated using randomised controlled techniques to generate further evidence.
Polymorphism +17 C/G in Matrix Metalloprotease MMP8 decreases lung cancer risk
Authors: González-Arriaga Patricia , López-Cima M Felicitas , Fernández-Somoano Ana , Pascual Teresa , Marrón Manuel G , Puente Xose S , Tardón Adonina 
Published: January 2009

AbstractBackgroundMatrix metalloproteases (MMPs) constitute a family of enzymes capable of degrading different components of the extracellular matrix and are implicated in the invasion of tumor cells through the basement membrane. Polymorphisms in MMP genes may result in changes in the expression of MMPs being associated with the development and progression of cancer. We have investigated the association between three polymorphisms (-1607 1G/2G, +17 C/G and -77 A/G) in the human collagenases MMP1, MMP8 and MMP13 and the risk of development or progression of lung cancer.MethodsA hospital-based case-control study was designed including 501 lung cancer patients and 510 controls matched. Genotypes were determined by PCR-RFLP. Results were analyzed using unconditional logistic regression, Cox's proportional hazard regression, and the Kaplan-Meier method.ResultsThe MMP1 and MMP13 promoter polymorphisms were not associated with lung cancer risk, while the C/G polymorphism in MMP8 was associated with a statistically significant decreased risk of developing lung cancer (ORadj = 0.65; 95%CI = 0.45–0.93). The Kaplan-Meier analysis showed that the polymorphisms in MMP1, MMP8 and MMP13 not seem to modify the overall survival. Multivariate analysis revealed that MMP1, MMP8 and MMP13 polymorphisms are not independent prognostic factors for overall survival.ConclusionThis study suggests that the polymorphism in MMP8 is associated with a decreased lung cancer risk, which can be used as a prognostic marker in lung cancer.
Older cancer patients' information and support needs surrounding treatment: An evaluation through the eyes of patients, relatives and professionals
Authors: Posma Elise R , van Weert Julia CM , Jansen Jesse , Bensing Jozien M 
Published: January 2009

Abstract

Background
Providing cancer patients with adequate treatment information is important for patients' health, well-being and satisfaction. Nurses play an important role in patient education. So far, few studies focused on the specific information needs of older cancer patients surrounding chemotherapy treatment. Given the growing incidence of cancer among older individuals, insight in these needs is crucial. This article describes the views of older cancer patients, their relatives and professionals on older patients' specific communication needs regarding chemotherapy treatment.

Methods
A qualitative design was used. Five focus group interviews were held with older cancer patients and their partners (two groups) and professionals with a background in nursing, oncology, gerontology and/or patient-provider communication (three groups). In addition, face to face in-depth interviews were conducted with older cancer patients. A total number of 38 patients and relatives participated, with a mean age of 67.6 years. The focus groups and interviews were audio-recorded for subsequent transcription and analysis.

Results
Older people have more difficulties processing and remembering information than younger ones. A trustful environment appears to be a prerequisite for reflection of older patients on the information provided and individualized information is essential to enhance memory of information. However, the results show that both patients and professionals experienced insufficient exploration of the patients' personal situation and individual information needs. Patients also strengthened the importance of sensitive communication, e.g. showing empathy en emotional support, throughout the continuum of cancer care. Moreover, potential areas of improvement were identified, including engaging the patients' relatives and encouraging patients and relatives to ask questions.

Conclusion
Patient education should be more tailored to older cancer patients' individual information and support needs and abilities by exploring the required amount and content of information, treatment goals and expectations. Nurses can establish a trustful environment by showing empathy and emotional support. Recommendations are given to enhance recall of information in older patients; information giving should be more structured by summarizing and repeating the most important, personally relevant information. To adapt to specific information needs, communication training for nurses and the use of aids such as a question prompt sheet could be useful tools.
Malaria transmission in two localities in north-western Argentina
Authors: Dantur Juri María J , Zaidenberg Mario , Claps Guillermo L , Santana Mirta , Almirón Walter R 
Published: January 2009

Abstract

Background
Malaria is one of the most important tropical diseases that affects people globally. The influence of environmental conditions in the patterns of temporal distribution of malaria vectors and the disease has been studied in different countries. In the present study, ecological aspects of the malaria vector Anopheles (Anopheles) pseudopunctipennis and their relationship with climatic variables, as well as the seasonality of malaria cases, were studied in two localities, El Oculto and Aguas Blancas, in north-western Argentina.

Methods
The fluctuation of An. pseudopunctipennis and the malaria cases distribution was analysed with Random Effect Poisson Regression. This analysis takes into account the effect of each climatic variable on the abundance of both vector and malaria cases, giving as results predicted values named Incidence Rate Radio.

Results
The number of specimens collected in El Oculto and Aguas Blancas was 4224 (88.07%) and 572 (11.93%), respectively. In El Oculto no marked seasonality was found, different from Aguas Blancas, where high abundance was detected at the end of spring and the beginning of summer. The maximum mean temperature affected the An. pseudopunctipennis fluctuation in El Oculto and Aguas Blancas. When considering the relationship between the number of malaria cases and the climatic variables in El Oculto, maximum mean temperature and accumulated rainfall were significant, in contrast with Aguas Blancas, where mean temperature and humidity showed a closer relationship to the fluctuation in the disease.

Conclusion
The temporal distribution patterns of An. pseudopunctipennis vary in both localities, but spring appears as the season with better conditions for mosquito development. Maximum mean temperature was the most important variable in both localities. Malaria cases were influenced by the maximum mean temperature in El Oculto, while the mean temperature and humidity were significant in Aguas Blancas. In Aguas Blancas peaks of mosquito abundance and three months later, peaks of malaria cases were observed. The study reported here will help to increase knowledge about not only vectors and malaria seasonality but also their relationships with the climatic variables that influence their appearances and abundances.