bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ontology and diversity of transcript-associated microsatellites mined from a globe artichoke EST database
Authors: Scaglione Davide , Acquadro Alberto , Portis Ezio , Taylor Christopher A , Lanteri Sergio , Knapp Steven J 
Published: September 2009

AbstractBackgroundThe globe artichoke (Cynara cardunculusvar.scolymusL.) is a significant crop in the Mediterranean basin. Despite its commercial importance and its both dietary and pharmaceutical value, knowledge of its genetics and genomics remains scant. Microsatellite markers have become a key tool in genetic and genomic analysis, and we have exploited recently acquired EST (expressed sequence tag) sequence data (Composite Genome Project - CGP) to develop an extensive set of microsatellite markers.ResultsA unigene assembly was created from over 36,000 globe artichoke EST sequences, containing 6,621 contigs and 12,434 singletons. Over 12,000 of these unigenes were functionally assigned on the basis of homology withArabidopsis thalianareference proteins. A total of 4,219 perfect repeats, located within 3,308 unigenes was identified and the gene ontology (GO) analysis highlighted some GO term's enrichments among different classes of microsatellites with respect to their position. Sufficient flanking sequence was available to enable the design of primers to amplify 2,311 of these microsatellites, and a set of 300 was tested against a DNA panel derived from 28C. cardunculusgenotypes. Consistent amplification and polymorphism was obtained from 236 of these assays. Their polymorphic information content (PIC) ranged from 0.04 to 0.90 (mean 0.66). Between 176 and 198 of the assays were informative in at least one of the three available mapping populations.ConclusionEST-based microsatellites have provided a large set ofde novogenetic markers, which show significant amounts of polymorphism both between and within the three taxa ofC. cardunculus. They are thus well suited as assays for phylogenetic analysis, the construction of genetic maps, marker-assisted breeding, transcript mapping and other genomic applications in the species.
Enrichment of a set of microRNAs during the cotton fiber development
Authors: Kwak Pieter Bas , Wang Qin Qin , Chen Xu Sheng , Qiu Cheng Xiang , Yang Zhi Min 
Published: September 2009

Abstract

Background
Cotton (Gossypium hirsutum) is one of the most important economic crops and provides excellent fibers for textile manufacture. In addition to its industrial and agricultural importance, the fiber cell (plant trichome) also is a biological model system for exploring gene expression and regulation. Small RNAs regulate many aspects of plant growth and development. However, whether small RNAs are involved in regulation of fiber cell development is unknown.

Results
We adopted a deep sequencing approach developed by Solexa (Illumina Inc.) to investigate global expression and complexity of small RNAs during cotton fiber initiation and development. We constructed two small RNA libraries prepared from wild type (WT) and fuzz/lintless (fl Mutant in the WT background) cotton ovules, respectively. Each library was sequenced individually and generated more than 6-7 million short sequences, resulting in a total of over 13 million sequence reads. At least 22 conserved candidate miRNA families including 111 members were identified. Seven families make up the vast majority of expressed miRNAs in developing cotton ovules. In total 120 unique target genes were predicted for most of conserved miRNAs. In addition, we identified 2 cell-type-specific novel miRNA candidates in cotton ovules. Our study has demonstrated significant differences in expression abundance of miRNAs between the wild-type and mutant, and suggests that these differentially expressed miRNAs potentially regulate transcripts distinctly involved in cotton fiber development.

Conclusion
The present study is the first to deep sequence the small RNA population of G. hirsutum ovules where cotton fibers initiate and develop. Millions of unique miRNA sequences ranging from 18~28 nt in length were detected. Our results support the importance of miRNAs in regulating the development of different cell types and indicate that identification of a comprehensive set of miRNAs in cotton fiber cells would facilitate our understanding of the regulatory mechanisms for fiber cell initiation and elongation.
Evaluation of putative reference genes for gene expression normalization in soybean by quantitative real-time RT-PCR
Authors: Hu Ruibo , Fan Chengming , Li Hongyu , Zhang Qingzhu , Fu Yong-Fu 
Published: September 2009

Abstract

Background
Real-time quantitative reverse transcription PCR (RT-qPCR) data needs to be normalized for its proper interpretation. Housekeeping genes are routinely employed for this purpose, but their expression level cannot be assumed to remain constant under all possible experimental conditions. Thus, a systematic validation of reference genes is required to ensure proper normalization. For soybean, only a small number of validated reference genes are available to date.

Results
A systematic comparison of 14 potential reference genes for soybean is presented. These included seven commonly used (ACT2, ACT11, TUB4, TUA5, CYP, UBQ10, EF1b) and seven new candidates (SKIP16, MTP, PEPKR1, HDC, TIP41, UKN1, UKN2). Expression stability was examined by RT-qPCR across 116 biological samples, representing tissues at various developmental stages, varied photoperiodic treatments, and a range of soybean cultivars. Expression of all 14 genes was variable to some extent, but that of SKIP16, UKN1 and UKN2 was overall the most stable. A combination of ACT11, UKN1 and UKN2 would be appropriate as a reference panel for normalizing gene expression data among different tissues, whereas the combination SKIP16, UKN1 and MTP was most suitable for developmental stages. ACT11, TUA5 and TIP41 were the most stably expressed when the photoperiod was altered, and TIP41, UKN1 and UKN2 when the light quality was changed. For six different cultivars in long day (LD) and short day (SD), their expression stability did not vary significantly with ACT11, UKN2 and TUB4 being the most stable genes. The relative gene expression level of GmFTL3, an ortholog of Arabidopsis FT (FLOWERING LOCUS T) was detected to validate the reference genes selected in this study.

Conclusion
None of the candidate reference genes was uniformly expressed across all experimental conditions, and the most suitable reference genes are conditional-, tissue-specific-, developmental-, and cultivar-dependent. Most of the new reference genes performed better than the conventional housekeeping genes. These results should guide the selection of reference genes for gene expression studies in soybean.
A transcription-dependent increase in miniature EPSC frequency accompanies late-phase plasticity in cultured hippocampal neurons
Authors: Wiegert J Simon , Hofmann Frank , Bading Hilmar , Bengtson C Peter 
Published: September 2009

Abstract

Background
The magnitude and longevity of synaptic activity-induced changes in synaptic efficacy is quantified by measuring evoked responses whose potentiation requires gene transcription to persist for more than 2-3 hours. While miniature EPSCs (mEPSCs) are also increased in amplitude and/or frequency during long-term potentiation (LTP), it is not known how long such changes persist or whether gene transcription is required.

Results
We use whole-cell patch clamp recordings from dissociated hippocampal cultures to characterise for the first time the persistence and transcription dependency of mEPSC upregulation during synaptic potentiation. The persistence of recurrent action potential bursting in these cultures is transcription-, translation- and NMDA receptor-dependent thus providing an accessible model for long-lasting plasticity. Blockade of GABAA-receptors with bicuculline for 15 minutes induced action potential bursting in all neurons and was maintained in 50-60% of neurons for more than 6 hours. Throughout this period, the frequency but neither the amplitude of mEPSCs nor whole-cell AMPA currents was markedly increased. The transcription blocker actinomycin D abrogated, within 2 hours of burst induction, both action potential bursting and the increase in mEPSCs. Reversible blockade of action potentials during, but not after this 2 hour transcription period suppressed the increase in mEPSC frequency and the recovery of burst activity at a time point 6 hours after induction.

Conclusion
These results indicate that increased mEPSC frequency persists well beyond the 2 hour transcription-independent phase of plasticity in this model. This long-lasting mEPSC upregulation is transcription-dependent and requires ongoing action potential activity during the initial 2 hour period but not thereafter. Thus mEPSC upregulation may underlie the long term, transcription-dependent persistence of action potential bursting. This provides mechanistic insight to link gene candidates already identified by gene chip analysis to long lasting plasticity in this in vitro model.
Identification of flowering genes in strawberry, a perennial SD plant
Authors: Mouhu Katriina , Hytönen Timo , Folta Kevin , Rantanen Marja , Paulin Lars , Auvinen Petri , Elomaa Paula 
Published: September 2009

AbstractBackgroundWe are studying the regulation of flowering in perennial plants by using diploid wild strawberry (Fragaria vescaL.) as a model. Wild strawberry is a facultative short-day plant with an obligatory short-day requirement at temperatures above 15°C. At lower temperatures, however, flowering induction occurs irrespective of photoperiod. In addition to short-day genotypes, everbearing forms of wild strawberry are known. In 'Baron Solemacher' recessive alleles of an unknown repressor,SEASONAL FLOWERING LOCUS(SFL), are responsible for continuous flowering habit. Although flower induction has a central effect on the cropping potential, the molecular control of flowering in strawberries has not been studied and the genetic flowering pathways are still poorly understood. The comparison of everbearing and short-day genotypes of wild strawberry could facilitate our understanding of fundamental molecular mechanisms regulating perennial growth cycle in plants.ResultsWe have searched homologs for 118Arabidopsisflowering time genes fromFragariaby EST sequencing and bioinformatics analysis and identified 66 gene homologs that by sequence similarity, putatively correspond to genes of all known genetic flowering pathways. The expression analysis of 25 selected genes representing various flowering pathways did not reveal large differences between the everbearing and the short-day genotypes. However, putative floral identity and floral integrator genesAP1andLFYwere co-regulated during early floral development.AP1mRNA was specifically accumulating in the shoot apices of the everbearing genotype, indicating its usability as a marker for floral initiation. Moreover, we showed that flowering induction in everbearing 'Baron Solemacher' and 'Hawaii-4' was inhibited by short-day and low temperature, in contrast to short-day genotypes.ConclusionWe have shown that many central genetic components of the flowering pathways inArabidopsiscan be identified from strawberry. However, novel regulatory mechanisms exist, likeSFLthat functions as a switch between short-day/low temperature and long-day/high temperature flowering responses between the short-day genotype and the everbearing 'Baron Solemacher'. The identification of putative flowering gene homologs andAP1as potential marker gene for floral initiation will strongly facilitate the exploration of strawberry flowering pathways.
Small islands and pandemic influenza: Potential benefits and limitations of travel volume reduction as a border control measure
Authors: Eichner Martin , Schwehm Markus , Wilson Nick , Baker Michael G 
Published: September 2009

Abstract

Background
Some island nations have explicit components of their influenza pandemic plans for providing travel warnings and restricting incoming travellers. But the potential value of such restrictions has not been quantified.

Methods
We developed a probabilistic model and used parameters from a published model (i.e., InfluSim) and travel data from Pacific Island Countries and Territories (PICTs).

Results
The results indicate that of the 17 PICTs with travel data, only six would be likely to escape a major pandemic with a viral strain of relatively low contagiousness (i.e., for R
0 = 1.5) even when imposing very tight travel volume reductions of 99% throughout the course of the pandemic. For a more contagious viral strain (R
0 = 2.25) only five PICTs would have a probability of over 50% to escape. The total number of travellers during the pandemic must not exceed 115 (for R
0 = 3.0) or 380 (for R
0 = 1.5) if a PICT aims to keep the probability of pandemic arrival below 50%.

Conclusion
These results suggest that relatively few island nations could successfully rely on intensive travel volume restrictions alone to avoid the arrival of pandemic influenza (or subsequent waves). Therefore most island nations may need to plan for multiple additional interventions (e.g., screening and quarantine) to raise the probability of remaining pandemic free or achieving substantial delay in pandemic arrival.
Gastric cancer mortality trends in Spain, 1976-2005, differences by autonomous region and sex
Authors: García-Esquinas Esther , Pérez-Gómez Beatriz , Pollán Marina , Boldo Elena , Fernández-Navarro Pablo , Lope Virginia , Vidal Enrique , López-Abente Gonzalo , Aragonés Nuria 
Published: September 2009

Abstract

Background
Gastric cancer is the second leading cause of oncologic death worldwide. One of the most noteworthy characteristics of this tumor's epidemiology is the marked decline reported in its incidence and mortality in almost every part of the globe in recent decades. This study sought to describe gastric cancer mortality time trends in Spain's regions for both sexes.

Methods
Mortality data for the period 1976 through 2005 were obtained from the Spanish National Statistics Institute. Cases were identified using the International Classification of Diseases 9th and 10th revision (codes 151 and C16, respectively). Crude and standardized mortality rates were calculated by geographic area, sex, and five-year period. Joinpoint regression analyses were performed to ascertain whether changes in gastric cancer mortality trends had occurred, and to estimate the annual percent change by sex and geographic area.

Results
Gastric cancer mortality decreased across the study period, with the downward trend being most pronounced in women and in certain regions situated in the interior and north of mainland Spain. Across the study period, there was an overall decrease of 2.90% per annum among men and 3.65% per annum among women. Generally, regions in which the rate of decline was sharpest were those that had initially registered the highest rates. However, the rate of decline was not constant throughout the study period: joinpoint analysis detected a shift in trend for both sexes in the early 1980s.

Conclusion
Gastric cancer mortality displayed in both sexes a downward trend during the study period, both nationally and regionally. The different trend in rates in the respective geographic areas translated as greater regional homogeneity in gastric cancer mortality by the end of the study period. In contrast, rates in women fell more than did those in men. The increasing differences between the sexes could indicate that some risk factors may be modifying the sex-specific pattern of this tumor.
Diagonal ear lobe crease in diabetic south Indian population: Is it associated with Diabetic Retinopathy?. Sankara Nethralaya Diabetic Retinopathy Epidemiology And Molecular-genetics Study (SN-DREAMS, Report no. 3)
Authors: Raman Rajiv , Rani Padmaja Kumari , Kulothungan Vaitheeswaran , Sharma Tarun 
Published: September 2009

AbstractBackgroundTo report the prevalence of ear lobe crease (ELC), a sign of coronary heart disease, in subjects (more than 40 years old) with diabetes and find its association with diabetic retinopathy.MethodsSubjects were recruited from the Sankara Nethralaya Diabetic Retinopathy Epidemiology And Molecular-genetics Study (SN-DREAMS), a cross-sectional study between 2003 and 2006; the data were analyzed for the1414 eligible subjects with diabetes. All patients' fundi were photographed using 45° four-field stereoscopic digital photography. The diagnosis of diabetic retinopathy was based on the modified Klein classification. The presence of ELC was evaluated on physical examination.ResultsThe prevalence of ELC, among the subjects with diabetes, was 59.7%. The ELC group were older, had longer duration of diabetes, had poor glycemic control and had a high socio-economic status compared to the group without ELC and the variables were statistically significant. There was no statistical difference in the prevalence of diabetic retinopathy in two groups. On multivariate analysis for any diabetic retinopathy, the adjusted OR for women was 0.69 (95% CI 0.51-0.93) (p = 0.014); for age >70 years, 0.49 (95% CI 0.26-0.89) (p = 0.024); for increasing duration of diabetes (per year increase), 1.11(95% CI 1.09-1.14) (p < 0.0001); and for poor glycemic control (per unit increase in glycosylated heamoglobin), 1.26 (95% CI 1.19-1.35) (p < 0.0001). For sight-threatening diabetic retinopathy, no variable was significant on multivariable analysis. In predicting any diabetic retinopathy, the presence of ELC had sensitivity of 60.4%, and specificity, 40.5%. The area under the ROC curve was 0.50 (95% CI 0.46-0.54) (p 0.02).ConclusionThe ELC was observed in nearly 60% of the urban south Indian population. However, the present study does not support the use of ELC as a screening tool for both any diabetic retinopathy and sight-threatening retinopathy.
Self-Rated Health in middle-aged and elderly Chinese: distribution, determinants and associations with cardio-metabolic risk factors
Authors: Haseli-Mashhadi Nazanin , Pan An , Ye Xingwang , Wang Jing , Qi Qibin , Liu Yong , Li Huaixing , Yu Zhijie , Lin Xu , Franco Oscar H 
Published: September 2009

Abstract

Background
Self-rated health (SRH) has been demonstrated to be an accurate reflection of a person's health and a valid predictor of incident mortality and chronic morbidity. We aimed to evaluate the distribution and factors associated with SRH and its association with biomarkers of cardio-metabolic diseases among middle-aged and elderly Chinese.

Methods
Survey of 1,458 men and 1,831 women aged 50 to 70 years, conducted in one urban and two rural areas of Beijing and Shanghai in 2005. SRH status was measured and categorized as good (very good and good) vs. not good (fair, poor and very poor). Determinants of SRH and associations with biomarkers of cardio-metabolic diseases were evaluated using logistic regression.

Results
Thirty two percent of participants reported good SRH. Males and rural residents tended to report good SRH. After adjusting for potential confounders, residence, physical activity, employment status, sleep quality and presence of diabetes, cardiovascular disease, and depression were the main determinants of SRH. Those free from cardiovascular disease (OR 3.68; 95%CI 2.39; 5.66), rural residents (OR 1.89; 95% CI 1.47; 2.43), non-depressed participants (OR 2.50; 95% CI 1.67; 3.73) and those with good sleep quality (OR 2.95; 95% CI 2.22; 3.91) had almost twice or over the chance of reporting good SRH compared to their counterparts. There were significant associations -and trend- between SRH and levels of inflammatory markers, insulin levels and insulin resistance.

Conclusion
Only one third of middle-aged and elderly Chinese assessed their health status as good or very good. Although further longitudinal studies are required to confirm our findings, interventions targeting social inequalities, lifestyle patterns might not only contribute to prevent chronic morbidity but as well to improve populations' perceived health.
Structural and functional characteristics of xenavidin, the first frog avidin from Xenopus tropicalis
Authors: Määttä Juha AE , Helppolainen Satu H , Hytönen Vesa P , Johnson Mark S , Kulomaa Markku S , Airenne Tomi T , Nordlund Henri R 
Published: September 2009

AbstractBackgroundAvidins are proteins with extraordinarily high ligand-binding affinity, a property which is used in a wide array of life science applications. Even though useful for biotechnology and nanotechnology, the biological function of avidins is not fully understood. Here we structurally and functionally characterise a novel avidin named xenavidin, which is to our knowledge the first reported avidin from a frog.ResultsXenavidin was identified from an EST sequence database forXenopus tropicalisand produced in insect cells using a baculovirus expression system. The recombinant xenavidin was found to be homotetrameric based on gel filtration analysis. Biacore sensor analysis, fluorescently labelled biotin and radioactive biotin were used to evaluate the biotin-binding properties of xenavidin - it binds biotin with high affinity though less tightly than do chicken avidin and bacterial streptavidin. X-ray crystallography revealed structural conservation around the ligand-binding site, while some of the loop regions have a unique design. The location of structural water molecules at the entrance and/or within the ligand-binding site may have a role in determining the characteristic biotin-binding properties of xenavidin.ConclusionThe novel data reported here provide information about the biochemically and structurally important determinants of biotin binding. This information may facilitate the discovery of novel tools for biotechnology.
Quantitative data management in quality improvement collaboratives
Authors: van den Berg Mireille , Frenken Rianne , Bal Roland 
Published: September 2009

Abstract

Background
Collaborative approaches in quality improvement have been promoted since the introduction of the Breakthrough method. The effectiveness of this method is inconclusive and further independent evaluation of the method has been called for. For any evaluation to succeed, data collection on interventions performed within the collaborative and outcomes of those interventions is crucial. Getting enough data from Quality Improvement Collaboratives (QICs) for evaluation purposes, however, has proved to be difficult. This paper provides a retrospective analysis on the process of data management in a Dutch Quality Improvement Collaborative. From this analysis general failure and success factors are identified.

Discussion
This paper discusses complications and dilemma's observed in the set-up of data management for QICs. An overview is presented of signals that were picked up by the data management team. These signals were used to improve the strategies for data management during the program and have, as far as possible, been translated into practical solutions that have been successfully implemented.
The recommendations coming from this study are:
From our experience it is clear that quality improvement programs deviate from experimental research in many ways. It is not only impossible, but also undesirable to control processes and standardize data streams. QIC's need to be clear of data protocols that do not allow for change. It is therefore minimally important that when quantitative results are gathered, these results are accompanied by qualitative results that can be used to correctly interpret them.
Monitoring and data acquisition interfere with routine. This makes a database collecting data in a QIC an intervention in itself. It is very important to be aware of this in reporting the results. Using existing databases when possible can overcome some of these problems but is often not possible given the change objective of QICs.
Introducing a standardized spreadsheet to the teams is a very practical and helpful tool in collecting standardized data within a QIC. It is vital that the spreadsheets are handed out before baseline measurements start.