Microarray Analysis of Late Response to Boron Toxicity in Barley (Hordeum vulgare L.) Leaves

DNA microarrays, being high-density and high-throughput, allow quantitative analyses of thousands of genes and their expression patterns in parallel. In this study, Barley1 GereChip was used to investigate transcriptome changes associated with boron (B) toxicity in a sensitive barley cultivar (Hordeum vulgare L. cv. Hamidye). Eight-day-old aseptically grown seedlings were subjected to 5 or 10 mM boric acid (B(OH)(3)) treatments for 5 days and expression profiles were determined with DNA microarrays using total RNA from leaf tissues. Among the 22,840 transcripts - each represented with a probe set on the GeneChip - 19,424 probe sets showed intensity values greater than 20(th) percentile in at least one of the hybridizations. Compared to control (10 mu M B(OH)(3)), 5 mM B(OH)(3) treatment resulted in differential expression of 168 genes at least by twofold. Moreover, 10 mM B(OH)(3) treatment resulted in at least twofold induction or reduction in expression of 312 transcripts. Among these genes, 37 and 61 exhibited significantly (P <0.05) altered levels of expression under 5 and 10 mM B(OH)(3) treatments, respectively. Differentially expressed genes were characterized using expression-based clustering and HarvEST:Barley. Investigations of expression profiles revealed that B toxicity results in global changes in the barley transcriptome and networks of signaling or molecular responses. A noticeable feature of response to 8 was that it is highly interconnected with responses to various environmental stresses. Additionally, induction of jasmonic acid related genes was found to be an important late response to B toxicity. Determination of responsive genes will shed light on successive studies aiming to elucidate molecular mechanism of B toxicity or tolerance. To the best of our knowledge, this is the first report on global expression analysis of barley seedlings under B toxicity

Search Result Diversification in Short Text Streams

We consider the problem of search result diversification for streams of short texts. Diversifying search results in short text streams is more challenging than in the case of long documents, as it is difficult to capture the latent topics of short documents. To capture the changes of topics and the probabilities of documents for a given query at a specific time in a short text stream, we propose a dynamic Dirichlet multinomial mixture topic model, called D2M3, as well as a Gibbs sampling algorithm for the inference. We also propose a streaming diversification algorithm, SDA, that integrates the information captured by D2M3 with our proposed modified version of the PM-2 (Proportionality-based diversification Method -- second version) diversification algorithm. We conduct experiments on a Twitter dataset and find that SDA statistically significantly outperforms state-of-the-art non-streaming retrieval methods, plain streaming retrieval methods, as well as streaming diversification methods that use other dynamic topic models

Issue framing and institutional constraints in EU agenda-setting: an analysis of European Union sports policy

The article uses agenda-setting to analyse the process which saw sport included in the new EU programme, Erasmus+, despite cuts in the EU’s budget. In doing so, the article addresses gaps in two bodies on literature. On the one hand, it contributes to developing the study of EU agenda-setting. On the other hand, the article analyses recent developments in EU sport policy, a body of literature that has not paid attention yet to decisions taken after the entering into force of the Treaty of Lisbon (2009). The article applies conceptually guided process-tracing through written documents and 25 semi-structured interviews with representatives from the European Commission, European Parliament and the Council of Ministers. The analysis shows how the Commission overcame blockades by framing sport initiatives as part of the wider agenda on economic growth through education, training and participation in grassroots sport, thus obtaining a funding stream for a new policy area in a time of austerity measures. The research illustrates that agenda-setting is a useful conceptual framework to explaining not just radical but also incremental policy changes on the EU agenda

Inferring Dynamic User Interests in Streams of Short Texts for User Clustering

User clustering has been studied from different angles. In order to identify shared interests, behavior-based methods consider similar browsing or search patterns of users, whereas content-based methods use information from the contents of the documents visited by the users. So far, content-based user clustering has mostly focused on static sets of relatively long documents. Given the dynamic nature of social media, there is a need to dynamically cluster users in the context of streams of short texts. User clustering in this setting is more challenging than in the case of long documents, as it is difficult to capture the users’ dynamic topic distributions in sparse data settings. To address this problem, we propose a dynamic user clustering topic model (UCT). UCT adaptively tracks changes of each user’s time-varying topic distributions based both on the short texts the user posts during a given time period and on previously estimated distributions. To infer changes, we propose a Gibbs sampling algorithm where a set of word pairs from each user is constructed for sampling. UCT can be used in two ways: (1) as a short-term dependency model that infers a user’s current topic distribution based on the user’s topic distributions during the previous time period only, and (2) as a long-term dependency model that infers a user’s current topic distributions based on the user’s topic distributions during multiple time periods in the past. The clustering results are explainable and human-understandable, in contrast to many other clustering algorithms. For evaluation purposes, we work with a dataset consisting of users and tweets from each user. Experimental results demonstrate the effectiveness of our proposed short-term and long-term dependency user clustering models compared to state-of-the-art baselines

Assembling defenses against therapy-resistant leukemic stem cells: Bcl6 joins the ranks

The resistance of leukemic stem cells in response to targeted therapies such as tyrosine kinase inhibitors (TKIs) relies on the cooperative activity of multiple signaling pathways and molecules, including TGF&#946;, AKT, and FOXO transcription factors (TFs). B cell lymphoma 6 (BCL6) is a transcriptional repressor whose translocation or mutation is associated with diffuse large BCL. New data now show that BCL6 is critical for the maintenance of leukemias driven by the BCR-ABL translocation (Philadelphia chromosome), suggesting that BCL6 is a novel, targetable member of the complex signaling pathways critical for leukemic stem cell survival

Salimicrobium salexigens sp. nov., a moderately halophilic bacterium from salted hides

Two Gram-positive, moderately halophilic bacteria, designated strains 29CMIT and 53CMI, were isolated from salted hides. Both strains were non-motile, strictly aerobic cocci, growing in the presence of 3-25 % (w/v) NaCl (optimal growth at 7.5-12.5 % [w/v] NaCl), between pH 5.0 and 10.0 (optimal growth at pH 7.5) and at temperatures between 15 and 40 ºC (optimal growth at 37 ºC). Phylogenetic analysis based on 16S rRNA gene sequence comparison showed that both strains showed a similarity of 98.7 % and were closely related to species of the genus Salimicrobium, within the phylum Firmicutes. Strains 29CMIT and 53CMI exhibited 16S rRNA gene sequence similarity values of 97.9 % to 97.6 % with Salimicrobium album DSM 20748T, Salimicrobium halophilum DSM 4771T, Salimicrobium flavidum ISL-25T and Salimicrobium luteum BY-5T. The DNA G+C content was 50.7 mol% and 51.5 mol% for strains 29CMIT and 53CMI, respectively. The DNA-DNA hybridization between both strains was 98 %, whereas the values between strain 29CMIT and the species Salimicrobium album CCM 3517T, Salimicrobium luteum BY-5T, Salimicrobium flavidum ISL-25T and Salimicrobium halophilum CCM 4074T were 45 %, 28 %,

Could Intelligent Speed Adaptation make overtaking unsafe?

This driving simulator study investigated how mandatory and voluntary ISA might affect a driver's overtaking decisions on rural roads, by presenting drivers with a variety of overtaking scenarios designed to evaluate both the frequency and safety of the manoeuvres. In half the overtaking scenarios, ISA was active and in the remainder ISA was switched off. A rural road was modelled with a number of 2 + 1 road sections, thus allowing drivers a protected overtaking opportunity. The results indicate that drivers became less inclined to initiate an overtaking manoeuvre when the mandatory ISA was active and this was particularly so when the overtaking opportunity was short. In addition to this, when ISA was activated drivers were more likely to have to abandon an overtaking, presumably due to running out of road. They also spent more time in the critical hatched area - a potentially unsafe behaviour. The quality of the overtaking manoeuvre was also affected when mandatory ISA was active, with drivers pulling out and cutting back in more sharply. In contrast, when driving with a voluntary ISA, overtaking behaviour remained mostly unchanged: drivers disengaged the function in approximately 70% of overtaking scenarios. The results of this study suggest that mandatory ISA could affect the safety of overtaking manoeuvres unless coupled with an adaptation period or other driver support functions that support safe overtaking

Study of the music preferences of preschool children : an examination of the effects of the learning environment on the extension of listening parameters

BACKGROUND: There is no consensus regarding resection of the primary tumour with few or absent symptoms in patients with synchronous unresectable metastatic colorectal cancer (CRC). A potential benefit of resection of the primary tumour is to prevent complications of the primary tumour in later stages of the disease. We here propose a randomized trial in order to demonstrate that resection of the primary tumour improves overall survival. METHODS/DESIGN: The CAIRO4 study is a multicentre, randomized, phase III study of the Dutch Colorectal Cancer Group (DCCG). Patients with synchronous unresectable metastases of CRC and few or absent symptoms of the primary tumour are randomized 1:1 between systemic therapy only, and resection of the primary tumour followed by systemic therapy. Systemic therapy will consist of fluoropyrimidine-based chemotherapy in combination with bevacizumab. The primary objective of this study is to determine the clinical benefit in terms of overall survival of initial resection of the primary tumour. Secondary endpoints include progression free survival, surgical morbidity, quality of life and the number of patients requiring resection of the primary tumour in the control arm. DISCUSSION: The CAIRO4 study is a multicentre, randomized, phase III study that will assess the benefit of resection of the primary tumour in patients with synchronous metastatic CRC. TRIAL REGISTRATION: The CAIRO4 study is registered at clinicaltrials.gov (NCT01606098)