bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)
Authors: Lorenz W Walter , Alba Rob , Yu Yuan-Sheng , Bordeaux John M , Simões Marta , Dean Jeffrey FD 
Published: May 2011

Abstract
Background
Global transcriptional analysis of loblolly pine (Pinus taeda L.) is challenging due to limited molecular tools. PtGen2, a 26,496 feature cDNA microarray, was fabricated and used to assess drought-induced gene expression in loblolly pine propagule roots. Statistical analysis of differential expression and weighted gene correlation network analysis were used to identify drought-responsive genes and further characterize the molecular basis of drought tolerance in loblolly pine.

Results
Microarrays were used to interrogate root cDNA populations obtained from 12 genotype × treatment combinations (four genotypes, three watering regimes). Comparison of drought-stressed roots with roots from the control treatment identified 2445 genes displaying at least a 1.5-fold expression difference (false discovery rate = 0.01). Genes commonly associated with drought response in pine and other plant species, as well as a number of abiotic and biotic stress-related genes, were up-regulated in drought-stressed roots. Only 76 genes were identified as differentially expressed in drought-recovered roots, indicating that the transcript population can return to the pre-drought state within 48 hours. Gene correlation analysis predicts a scale-free network topology and identifies eleven co-expression modules that ranged in size from 34 to 938 members. Network topological parameters identified a number of central nodes (hubs) including those with significant homology (E-values ≤ 2 × 10-30) to 9-cis-epoxycarotenoid dioxygenase, zeatin O-glucosyltransferase, and ABA-responsive protein. Identified hubs also include genes that have been associated previously with osmotic stress, phytohormones, enzymes that detoxify reactive oxygen species, and several genes of unknown function.

Conclusion
PtGen2 was used to evaluate transcriptome responses in loblolly pine and was leveraged to identify 2445 differentially expressed genes responding to severe drought stress in roots. Many of the genes identified are known to be up-regulated in response to osmotic stress in pine and other plant species and encode proteins involved in both signal transduction and stress tolerance. Gene expression levels returned to control values within a 48-hour recovery period in all but 76 transcripts. Correlation network analysis indicates a scale-free network topology for the pine root transcriptome and identifies central nodes that may serve as drivers of drought-responsive transcriptome dynamics in the roots of loblolly pine.
A genome scan for quantitative trait loci affecting cyanogenic potential of cassava root in an outbred population
Authors: Whankaew Sukhuman , Poopear Supannee , Kanjanawattanawong Supanath , Tangphatsornruang Sithichoke , Boonseng Opas , Lightfoot David A , Triwitayakorn Kanokporn 
Published: May 2011

Abstract

Background
Cassava (Manihot esculenta Crantz) can produce cyanide, a toxic compound, without self-injury. That ability was called the cyanogenic potential (CN). This project aimed to identify quantitative trait loci (QTL) associated with the CN in an outbred population derived from 'Hanatee' × 'Huay Bong 60', two contrasting cultivars. CN was evaluated in 2008 and in 2009 at Rayong province, and in 2009 at Lop Buri province, Thailand. CN was measured using a picrate paper kit. QTL analysis affecting CN was performed with 303 SSR markers.

Results
The phenotypic values showed continuous variation with transgressive segregation events with more (115 ppm) and less CN (15 ppm) than either parent ('Hanatee' had 33 ppm and 'Huay Bong 60' had 95 ppm). The linkage map consisted of 303 SSR markers, on 27 linkage groups with a map that encompassed 1,328 cM. The average marker interval was 5.8 cM. Five QTL underlying CN were detected. CN08R1 from 2008 at Rayong, CN09R1 and CN09R2 from 2009 at Rayong, and CN09L1 and CN09L2 from 2009 at Lop Buri were mapped on linkage group 2, 5, 10 and 11, respectively. Among all the identified QTL, CN09R1 was the most significantly associated with the CN trait with LOD score 5.75 and explained the greatest percentage of phenotypic variation (%Expl.) of 26%.

Conclusions
Five new QTL affecting CN were successfully identified from 4 linkage groups. Discovery of these QTL can provide useful markers to assist in cassava breeding and studying genes affecting the trait.
Differential distribution of a SINE element in the Entamoeba histolytica and Entamoeba dispar genomes: Role of the LINE-encoded endonuclease
Authors: Kumari Vandana , Sharma Rahul , Yadav Vijay P , Gupta Abhishek K , Bhattacharya Alok , Bhattacharya Sudha 
Published: May 2011

Abstract

Background

Entamoeba histolytica and Entamoeba dispar are closely related protistan parasites but while E. histolytica can be invasive, E. dispar is completely non pathogenic. Transposable elements constitute a significant portion of the genome in these species; there being three families of LINEs and SINEs. These elements can profoundly influence the expression of neighboring genes. Thus their genomic location can have important phenotypic consequences. A genome-wide comparison of the location of these elements in the E. histolytica and E. dispar genomes has not been carried out. It is also not known whether the retrotransposition machinery works similarly in both species. The present study was undertaken to address these issues.

Results
Here we extracted all genomic occurrences of full-length copies of EhSINE1 in the E. histolytica genome and matched them with the homologous regions in E. dispar, and vice versa, wherever it was possible to establish synteny. We found that only about 20% of syntenic sites were occupied by SINE1 in both species. We checked whether the different genomic location in the two species was due to differences in the activity of the LINE-encoded endonuclease which is required for nicking the target site. We found that the endonucleases of both species were essentially very similar, both in their kinetic properties and in their substrate sequence specificity. Hence the differential distribution of SINEs in these species is not likely to be influenced by the endonuclease. Further we found that the physical properties of the DNA sequences adjoining the insertion sites were similar in both species.

Conclusions
Our data shows that the basic retrotransposition machinery is conserved in these sibling species. SINEs may indeed have occupied all of the insertion sites in the genome of the common ancestor of E. histolytica and E. dispar but these may have been subsequently lost from some locations. Alternatively, SINE expansion took place after the divergence of the two species. The absence of SINE1 in 80% of syntenic loci could affect the phenotype of the two species, including their pathogenic properties, which needs to be explored.
Retest reliability of measuring hip extensor muscle strength in different testing positions in young people with cerebral palsy
Authors: Dyball Kate M , Taylor Nicholas F , Dodd Karen J 
Published: May 2011

AbstractBackgroundIn young people with spastic diplegic cerebral palsy weakness of the hip extensor muscles are associated with limitations in activity. It is important that clinicians can reliably measure hip extensor muscle strength to monitor changes over time and the effects of any interventions. Previous research has demonstrated high reliability for measuring strength of all muscles of the lower limb, with the exception of the hip extensors. Therefore the aim of this study was to examine the retest reliability of measuring hip extensor strength in young people with cerebral palsy.MethodsUsing a test-retest reliability research design, 19 participants with spastic diplegic cerebral palsy (Gross Motor Function Classification System Levels II and III) (mean 19 y 2 mo [S D 2 y 5 mo]) attended two testing sessions held 12 weeks apart. Three trials with a hand-held dynamometer were taken at each testing session in supine, prone and standing. Retest reliability was calculated with Intraclass Correlation Coefficients (ICC(2,1)) and with units of measurement (kilograms) converted to a percentage strength change.ResultsICC values ranged from .74 to .78 in supine, .75 to .80 in prone, and .73 to .75 in standing. To be 95% confident that real change had occurred, an individual's strength would need to increase 55 to 60% in supine, 86 to 102% in prone, and 102 to 105% in standing. To be 95% confident that real change had occurred across groups, strength would need to increase 4 to 8% in supine, 22 to 31% in prone, and 32% to 34% in standing. Higher ICC values were observed when three trials were used for testing.ConclusionsThe supine testing position was more reliable than the prone or standing testing positions. It is possible to measure hip extensor strength with sufficient reliability to be able monitor change within groups using the supine position provided three trials are used during testing. However, there is insufficient reliability to monitor changes in hip extensor strength in individuals with cerebral palsy unless they exhibit very large strength increases.
An association between Helicobacter pylori infection and cognitive function in children at early school age: a community-based study
Authors: Muhsen Khitam , Ornoy Asher , Akawi Ashraf , Alpert Gershon , Cohen Dani 
Published: May 2011

Abstract

Background

H. pylori infection has been linked to iron deficiency anemia, a risk factor of diminished cognitive development. The hypothesis on an association between H. pylori infection and cognitive function was examined in healthy children, independently of socioeconomic and nutritional factors.

Methods
A community-based study was conducted among 200 children aged 6-9 years, from different socioeconomic background. H. pylori infection was examined by an ELISA kit for detection of H. pylori antigen in stool samples. Cognitive function of the children was blindly assessed using Stanford-Benit test 5th edition, yielding IQ scores. Data on socioeconomic factors and nutritional covariates were collected through maternal interviews and from medical records. Multivariate linear regression analysis was performed to obtain adjusted beta coefficients.

Results

H. pylori infection was associated with lower IQ scores only in children from a relatively higher socioeconomic community; adjusted beta coefficient -6.1 (95% CI -11.4, -0.8) (P = 0.02) for full-scale IQ score, -6.0 (95% CI -11.1, -0.2) (P = 0.04) for non-verbal IQ score and -5.7 (95% CI -10.8, -0.6) (P = 0.02) for verbal IQ score, after controlling for potential confounders.

Conclusions

H. pylori infection might be negatively involved in cognitive development at early school age. Further studies in other populations with larger samples are needed to confirm this novel finding.
From planning to practice: building the national network for the surveillance of severe maternal morbidity
Authors: Haddad Samira M , Cecatti José G , Parpinelli Mary A , Souza João P , Costa Maria L , Sousa Maria H , Surita Fernanda G , Pinto e Silva João L , Pacagnella Rodolfo C , Camargo Rodrigo S , Bahamondes Maria V , Zotareli Vilma , Gurgel Lúcio T , Say Lale , Pattinson Robert C ,   National Network for the Surveillance of Severe Maternal Morbidity Group
Published: May 2011

Abstract

Background
Improving maternal health is one of the Millennium Development Goals for 2015. Recently some progress has been achieved in reducing mortality. On the other hand, in developed regions, maternal death is a relatively rare event compared to the number of cases of morbidity; hence studying maternal morbidity has become more relevant. Electronic surveillance systems may improve research by facilitating complete data reporting and reducing the time required for data collection and analysis. Therefore the purpose of this study was to describe the methods used in elaborating and implementing the National Network for the Surveillance of Severe Maternal Morbidity in Brazil.

Methods
The project consisted of a multicenter, cross-sectional study for the surveillance of severe maternal morbidity including near-miss, in Brazil.

Results
Following the development of a conceptual framework, centers were selected for inclusion in the network, consensus meetings were held among the centers, an electronic data collection system was identified, specific software and hardware tools were developed, research material was prepared, and the implementation process was initiated and analyzed.

Conclusion
The conceptual framework developed for this network was based on the experience acquired in various studies carried out in the area over recent years and encompasses maternal and perinatal health. It is innovative especially in the context of a developing country. The implementation of the project represents the first step towards this planned management. The system online elaborated for this surveillance network may be used in further studies in reproductive and perinatal health.
Using spatial analysis to demonstrate the heterogeneity of the cardiovascular drug-prescribing pattern in Taiwan
Authors: Cheng Ching-Lan , Chen Yi-Chi , Liu Tzu-Ming , Kao Yang Yea-Huei 
Published: May 2011

AbstractBackgroundGeographic Information Systems (GIS) combined with spatial analytical methods could be helpful in examining patterns of drug use. Little attention has been paid to geographic variation of cardiovascular prescription use in Taiwan. The main objective was to use local spatial association statistics to test whether or not the cardiovascular medication-prescribing pattern is homogenous across 352 townships in Taiwan.MethodsThe statistical methods used were the global measures of Moran'sIand Local Indicators of Spatial Association (LISA). While Moran'sIprovides information on the overall spatial distribution of the data, LISA provides information on types of spatial association at the local level. LISA statistics can also be used to identify influential locations in spatial association analysis. The major classes of prescription cardiovascular drugs were taken from Taiwan's National Health Insurance Research Database (NHIRD), which has a coverage rate of over 97%. The dosage of each prescription was converted into defined daily doses to measure the consumption of each class of drugs. Data were analyzed with ArcGIS and GeoDa at the township level.ResultsThe LISA statistics showed an unusual use of cardiovascular medications in the southern townships with high local variation. Patterns of drug use also showed more low-low spatial clusters (cold spots) than high-high spatial clusters (hot spots), and those low-low associations were clustered in the rural areas.ConclusionsThe cardiovascular drug prescribing patterns were heterogeneous across Taiwan. In particular, a clear pattern of north-south disparity exists. Such spatial clustering helps prioritize the target areas that require better education concerning drug use.
The effects of disruption of phosphoglucose isomerase gene on carbon utilisation and cellulase production in Trichoderma reesei Rut-C30
Authors: Carmen Limón M , Pakula Tiina , Saloheimo Markku , Penttilä Merja 
Published: May 2011

Abstract

Background
Cellulase and hemicellulase genes in the fungus Trichoderma reesei are repressed by glucose and induced by lactose. Regulation of the cellulase genes is mediated by the repressor CRE1 and the activator XYR1. T. reesei strain Rut-C30 is a hypercellulolytic mutant, obtained from the natural strain QM6a, that has a truncated version of the catabolite repressor gene, cre1. It has been previously shown that bacterial mutants lacking phosphoglucose isomerase (PGI) produce more nucleotide precursors and amino acids. PGI catalyzes the second step of glycolysis, the formation of fructose-6-P from glucose-6-P.

Results
We deleted the gene pgi1, encoding PGI, in the T. reesei strain Rut-C30 and we introduced the cre1 gene in a Δpgi1 mutant. Both Δpgi1 and cre1

+
Δpgi1 mutants showed a pellet-like and growth as well as morphological alterations compared with Rut-C30. None of the mutants grew in media with fructose, galactose, xylose, glycerol or lactose but they grew in media with glucose, with fructose and glucose, with galactose and fructose or with lactose and fructose. No growth was observed in media with xylose and glucose. On glucose, Δpgi1 and cre1

+
Δpgi1 mutants showed higher cellulase activity than Rut-C30 and QM6a, respectively. But in media with lactose, none of the mutants improved the production of the reference strains. The increase in the activity did not correlate with the expression of mRNA of the xylanase regulator gene, xyr1. Δpgi1 mutants were also affected in the extracellular β-galactosidase activity. Levels of mRNA of the glucose 6-phosphate dehydrogenase did not increase in Δpgi1 during growth on glucose.

Conclusions
The ability to grow in media with glucose as the sole carbon source indicated that Trichoderma Δpgi1 mutants were able to use the pentose phosphate pathway. But, they did not increase the expression of gpdh. Morphological characteristics were the result of the pgi1 deletion. Deletion of pgi1 in Rut-C30 increased cellulase production, but only under repressing conditions. This increase resulted partly from the deletion itself and partly from a genetic interaction with the cre1-1 mutation. The lower cellulase activity of these mutants in media with lactose could be attributed to a reduced ability to hydrolyse this sugar but not to an effect on the expression of xyr1.
Decreased expression of BRCA1 in SK-BR-3 cells is the result of aberrant activation of the GABP Beta promoter by an NRF-1-containing complex
Authors: Thompson Crista , MacDonald Gwen , Mueller Christopher R 
Published: May 2011

Abstract

Background
BRCA1 has recently been identified as a potential regulator of mammary stem/progenitor cell differentiation, and this function may explain the high prevalence of breast cancer in BRCA1 mutation carriers, as well as the downregulation of BRCA1 in a large proportion of sporadic breast cancers. That is, loss of BRCA1 function results in blocked differentiation with expansion of the mammary stem/progenitor cells. Because BRCA1 also maintains genomic integrity, its loss could produce a pool of genetically unstable stem/progenitor cells that are prime targets for further transforming events. Thus, elucidating the regulatory mechanisms of BRCA1 expression is important to our understanding of normal and malignant breast differentiation.

Results
Loss of BRCA1 expression in the ErbB2-amplified SK-BR-3 cell line was found to be the result of loss of activity of the ets transcription factor GABP, a previously characterized regulator of BRCA1 transcription. The expression of the non-DNA binding GABPβ subunit was shown to be deficient, while the DNA binding subunit, GABPα was rendered unstable by the absence of GABPβ. Deletion analysis of the GABPβ proximal promoter identified a potential NRF-1 binding site as being critical for expression. Supershift analysis, the binding of recombinant protein and chromatin immunoprecipitation confirmed the role of NRF-1 in regulating the expression of GABPβ. The siRNA knockdown of NRF-1 resulted in decreased GABPβ and BRCA1 expression in MCF-7 cells indicating that they form a transcriptional network. NRF-1 levels and activity did not differ between SK-BR-3 and MCF-7 cells, however the NRF-1 containing complex on the GABPβ promoter differed between the two lines and appears to be the result of altered coactivator binding.

Conclusions
Both NRF-1 and GABP have been linked to the regulation of nuclear-encoded mitochondrial proteins, and the results of this study suggest their expression is coordinated by NRF-1's activation of the GABPβ promoter. Their linkage to BRCA1, a potential breast stem cell regulator, implies a connection between the induction of mitochondrial metabolism and breast differentiation.
Understanding client satisfaction with a health insurance scheme in Nigeria: factors and enrollees experiences
Authors: Mohammed Shafiu , Sambo Mohammad N , Dong Hengjin 
Published: May 2011

Abstract

Background
Health insurance schemes have been widely introduced during this last decade in many African countries, which have strived for improvements in health service provision and the promotion of health care utilization. Client satisfaction with health service provision during the implementation of health insurance schemes has often been neglected since numerous activities take place concurrently. The satisfaction of enrollees and its influencing factors have been providing evidence which have assisted in policy and decision making. Our objective is to determine the enrollee's satisfaction with health service provision under a health insurance scheme and the factors which influence the satisfaction.

Methods
This retrospective, cross-sectional survey took place between May and September 2008. Two hundred and eighty (280) enrollees insured for more than one year in Zaria-Nigeria were recruited using two stage sampling. Enrollee's satisfaction was categorized into more satisfied and less satisfied based on positive responses obtained. Satisfaction, general knowledge and awareness of contribution were each aggregated and assessed as composite measure. Logistic regression analysis was used to analyze factors that influenced the satisfaction of enrollees.

Results
A high satisfaction rate with the health insurance scheme was observed (42.1%). Marital status (p < .05), general knowledge (p < .001) and awareness of contributions (p < .05) positively influenced clients' satisfaction. Length of employment, salary income, hospital visits and duration of enrolment slightly influenced satisfaction.

Conclusions
This study highlighted the potential effects of general health insurance knowledge and awareness of contributions by end-users (beneficiaries) of such new program on client satisfaction which have significant importance. The findings provided evidence which have assisted the amendment and re-prioritization of the medium term strategic plan of operations for the scheme. Future planning efforts could consider the client satisfaction and the factors which influenced it regularly.
Response to combination therapy of HCV 3a infected Pakistani patients and the role of NS5A protein
Authors: Ali Ijaz , Khan Sanaullah , Attaullah Sobia , Khan Shahid Niaz , Khan Jabbar , Siraj Sami , Iqbal Aqib , Swati Zahoor A , Idrees Muhammad 
Published: May 2011

Abstract

Background
Hepatitis C virus (HCV) genotype 3a is known to show comparatively better response to combination therapy than genotype 1 and 4. Mutations within NS5A gene of HCV have earlier been implicated with response to interferon (IFN) therapies in chronic HCV patients among various populations. As response to therapy are available in different populations because of the ethnic and viral factors and there was no study available on the phenomenon of resistivity to IFN.

Results
Chronic HCV 3a infected Pakistani patients were kept on IFN-α and ribavirin therapy for six months. NS5A gene of HCV was amplified and sequenced in the case of all the patients prior to therapy and the sequences were analysed for mutations. Out of the total 27 patients, 20 (74.07%) were observed with sustained virological response (SVR), 4 (14.81%) patients were non responder (NR) while 3 (11.11%) patients exhibited in end of treatment response (ETR). Three (3/20) (15%) SVR patients and two (2/3) ETR patients had mutations (ranging from I-V amino acids) within the NS5A ISDR regions. While the rest of the SVR patients (85%) and the NR had no mutations at ISDR region when compared with HCV K3a ISDR.

Conclusions
Mutations within the NS5A gene of HCV 3a genotype may not influence the outcome of combination therapy in Pakistani populations.