EzArray: A web-based highly automated Affymetrix expression array data management and analysis system

<p>Abstract</p> <p>Background</p> <p>Though microarray experiments are very popular in life science research, managing and analyzing microarray data are still challenging tasks for many biologists. Most microarray programs require users to have sophisticated knowledge of mathematics, statistics and computer skills for usage. With accumulating microarray data deposited in public databases, easy-to-use programs to re-analyze previously published microarray data are in high demand.</p> <p>Results</p> <p>EzArray is a web-based Affymetrix expression array data management and analysis system for researchers who need to organize microarray data efficiently and get data analyzed instantly. EzArray organizes microarray data into projects that can be analyzed online with predefined or custom procedures. EzArray performs data preprocessing and detection of differentially expressed genes with statistical methods. All analysis procedures are optimized and highly automated so that even novice users with limited pre-knowledge of microarray data analysis can complete initial analysis quickly. Since all input files, analysis parameters, and executed scripts can be downloaded, EzArray provides maximum reproducibility for each analysis. In addition, EzArray integrates with Gene Expression Omnibus (GEO) and allows instantaneous re-analysis of published array data.</p> <p>Conclusion</p> <p>EzArray is a novel Affymetrix expression array data analysis and sharing system. EzArray provides easy-to-use tools for re-analyzing published microarray data and will help both novice and experienced users perform initial analysis of their microarray data from the location of data storage. We believe EzArray will be a useful system for facilities with microarray services and laboratories with multiple members involved in microarray data analysis. EzArray is freely available from <url>http://www.ezarray.com/</url>.</p

Towards sustainability: An assessment of an urbanisation bubble in China using a hierarchical - stochastic multicriteria acceptability analysis - Choquet integral method

Urbanisation bubbles have become an increasingly serious problem. Attention has been paid to the speed of urbanisation; however, the issue of quality has been neglected, particularly in the case of China. Therefore, the aim of this research is to evaluate China’s urbanisation bubbles by employing a hierarchical - stochastic multicriteria acceptability analysis (SMAA) - Choquet integral method. In order to highlight regional disparities, we measure the urbanisation bubbles at a provincial level. Our study aggregates the urbanisation bubble indices using the Choquet integral preference model, and considers the interactions between various indicators. Furthermore, robust ordinal regression and SMAA are applied to resolve the robustness issues associated with the entire set of weights assigned to the urbanisation bubble composite indicator. In addition, by employing a multiple criteria hierarchy process, the study aggregates urbanisation bubble indices not only at the comprehensive level, but also at the intermediate levels of the hierarchy. Our findings suggest that the ranking of urbanisation bubbles is positively related to the level of regional development. This study contributes to the evaluation of regional urbanisation and sustainable development

Plant Natural Products: Promising Resources for Cancer Chemoprevention

Cancer is a major factor threatening human health and life safety, and there is a lack of safe and effective therapeutic drugs. Intervention and prevention in premalignant process are effective ways to reverse carcinogenesis and prevent cancer from occurring. Plant natural products are rich in sources and are a promising source for cancer chemoprevention. This article reviews the chemopreventive effects of natural products, especially focused on polyphenols, flavonoids, monoterpene and triterpenoids, sulfur compounds, and cellulose. Meanwhile, the main mechanisms include induction of apoptosis, antiproliferation and inhibition of metastasis are briefly summarized. In conclusion, this article provides evidence for natural products remaining a prominent source of cancer chemoprevention

Transcriptome Profiling of Petal Abscission Zone and Functional Analysis of an Aux/IAA Family Gene RhIAA16 Involved in Petal Shedding in Rose.

Roses are one of the most important cut flowers among ornamental plants. Rose flower longevity is largely dependent on the timing of petal shedding occurrence. To understand the molecular mechanism underlying petal abscission in rose, we performed transcriptome profiling of the petal abscission zone during petal shedding using Illumina technology. We identified a total of 2592 differentially transcribed genes (DTGs) during rose petal shedding. Gene ontology term enrichment and pathway analysis revealed that major biochemical pathways the DTGs were involved in included ethylene biosynthesis, starch degradation, superpathway of cytosolic glycolysis, pyruvate dehydrogenase and TCA cycle, photorespiration and the lactose degradation III pathway. This suggests that alterations in carbon metabolism are an important part of rose petal abscission. Among these DTGs, approximately 150 genes putatively encoding transcription factors were identified in rose abscission zone. These included zinc finger, WRKY, ERF, and Aux/IAA gene families, suggesting that petal abscission involves complex transcriptional reprogramming. Approximately 108 DTGs were related to hormone pathways, of which auxin and ethylene related DTGs were the largest groups including 52 and 41 genes, respectively. These also included 12 DTGs related to gibberellin and 6 DTGs in jasmonic acid pathway. Surprisingly, no DTGs involved in the biosynthesis/signaling of abscisic acid, cytokinin, brassinosteroid, and salicylic acid pathways were detected. Moreover, among DTGs related to auxin, we identified an Aux/IAA gene RhIAA16 that was up-regulated in response to petal shedding. Down-regulation of RhIAA16 by virus-induced gene silencing in rose promoted petal abscission, suggesting that RhIAA16 plays an important role in rose petal abscission

Biomechanical effects of different staging and attachment designs in maxillary molar distalization with clear aligner: a finite element study

Abstract Background In the present study, the effects of distalizations of one and two molars with different step distances and attachment designs have been analyzed. Methods A 3D finite element analysis model has been developed in order to determine the tendency of tooth displacement and stress distribution with clear aligner treatment. Results Under the condition of single-molar distalization, when the step distance was set to 0.25 mm, the total displacement was 0.086 mm for central incisors, 0.080 mm for lateral incisors, 0.084 mm for canines, 0.102 mm for the first premolar and 0.076 mm for the second premolar. The von Mises stress of roots and the principal stress of the periodontal ligament was slightly lower than in the control group when the step distance was set to 0.130 mm. Under the condition of two-molar distalization, when the step distance was set to 0.130 mm, the total displacements for central incisors, lateral incisors and canines as well as both the first and second maxillary molars were basically the same as with a distance of 0.250 mm for one-molar distalization. In addition, when the step distance was 0.130 mm with two-molar distalization, the rotation center of the first and second molar was closer to the apex of the root indicating that the smaller step distance led to more bodily movement during the two-molar distalization. However, displacement tendencies of the first molar and the second molar were basically the same whether horizontal or vertical rectangular attachments were added. Conclusions A step distance of moving two molars to 0.130 mm can achieve the same reaction force on the anterior teeth as moving one molar 0.250 mm without effects on horizontal or vertical rectangular attachments. Clinical relevance Our results provide a theoretical basis and guidance for simultaneously moving two molars backward in clinical practice using a clear aligner

Broad-leaved Forest’s Impact on Spontaneous Activities of Mice and their Mental State

Empirical studies on the effects of urban forests on the health of humans and other animals are needed to rationalize the construction of urban forests for healthcare. The effects of urban forests (coniferous, broad-leaved, and mixed coniferous and broad-leaved) were studied relative to the physical and mental health of mice and the major environmental factors influencing them. Compared with the control group, the total movement distance of the mice that stayed in the coniferous forest, mixed coniferous and broad-leaved forest, and broad-leaved forest increased 9.7% to 18.1%, the central grid movement distance increased 7.2% to 23.9%, central grid dwell time increased 10.7% to 16.3%, and the number of entries increased 5.2% to 18.6%, indicating that the mental state and the exploration and cognitive abilities of mice were significantly improved in the three urban forests. The broad-leaved forest had greater positive effects than the other two forest types. This can be attributed to a decrease in temperature and the increases in humidity and concentrations of oxygen and negative ions in the air in the broad-leaved forest. The research results provide a theoretical basis for building urban forests that are beneficial to the health of urban residents

Transcriptome profiling of petal abscission zone and functional analysis of an Aux/IAA family gene RhIAA16 involved in petal shedding in rose

Roses are one of the most important cut flowers among ornamental plants. Rose flower longevity is largely dependent on the timing of petal shedding occurrence. To understand the molecular mechanism underlying petal abscission in rose, we performed transcriptome profiling of the petal abscission zone during petal shedding using Illumina technology. We identified a total of 2592 differentially transcribed genes (DTGs) during rose petal shedding. Gene ontology term enrichment and pathway analysis revealed that major biochemical pathways the DTGs were involved in included ethylene biosynthesis, starch degradation, superpathway of cytosolic glycolysis, pyruvate dehydrogenase and TCA cycle, photorespiration and the lactose degradation III pathway. This suggests that alterations in carbon metabolism are an important part of rose petal abscission. Among these DTGs, approximately 150 genes putatively encoding transcription factors were identified in rose abscission zone. These included zinc finger, WRKY, ERF, and Aux/IAA gene families, suggesting that petal abscission involves complex transcriptional reprogramming. Approximately 108 DTGs were related to hormone pathways, of which auxin and ethylene related DTGs were the largest groups including 52 and 41 genes, respectively. These also included 12 DTGs related to gibberellin and 6 DTGs in jasmonic acid pathway. Surprisingly, no DTGs involved in the biosynthesis/signaling of abscisic acid, cytokinin, brassinosteroid, and salicylic acid pathways were detected. Moreover, among DTGs related to auxin, we identified an Aux/IAA gene RhIAA16 that was up-regulated in response to petal shedding. Down-regulation of RhIAA16 by virus-induced gene silencing in rose promoted petal abscission, suggesting that RhIAA16 plays an important role in rose petal abscission