Children independent learning development checklist 3-5 (Child 3-5): Validity and reliability study for the turkish form

The aim of this study is to investigate the psychometric properties of the Turkish Aadaptation of Children’s Independent Learning Development Checklist (CHILD 3-5), developed by (Whitebread et al., 2009) and colleagues for assessing young children’s self-regulated learning. Towards this aim, data were gathered from two different samples. In the first phase (N=252) item statistics and factor structure of the 22-item scale were explored and due to pyschometric problems, 6 items removed from further analysis. Psychometric properties of the new 16-item scale were tested in the second phase (N=197). Test-retest reliability of the scale was calculated as .961 and internal consistency for the scale was .968. For validity, difference between the upper 27% and lower 27% of the total group were calculated and significant difference was found between the two groups. Results showed that the Turkish form of CHILD 3-5 scale is a reliable and valid tool to be used for assessing young children’s self-regulated learning

Predicting the Fission Yeast Protein Interaction Network

A systems-level understanding of biological processes and information flow requires the mapping of cellular component interactions, among which protein–protein interactions are particularly important. Fission yeast (Schizosaccharomyces pombe) is a valuable model organism for which no systematic protein-interaction data are available. We exploited gene and protein properties, global genome regulation datasets, and conservation of interactions between budding and fission yeast to predict fission yeast protein interactions in silico. We have extensively tested our method in three ways: first, by predicting with 70–80% accuracy a selected high-confidence test set; second, by recapitulating interactions between members of the well-characterized SAGA co-activator complex; and third, by verifying predicted interactions of the Cbf11 transcription factor using mass spectrometry of TAP-purified protein complexes. Given the importance of the pathway in cell physiology and human disease, we explore the predicted sub-networks centered on the Tor1/2 kinases. Moreover, we predict the histidine kinases Mak1/2/3 to be vital hubs in the fission yeast stress response network, and we suggest interactors of argonaute 1, the principal component of the siRNA-mediated gene silencing pathway, lost in budding yeast but preserved in S. pombe. Of the new high-quality interactions that were discovered after we started this work, 73% were found in our predictions. Even though any predicted interactome is imperfect, the protein network presented here can provide a valuable basis to explore biological processes and to guide wet-lab experiments in fission yeast and beyond. Our predicted protein interactions are freely available through PInt, an online resource on our website (www.bahlerlab.info/PInt)

Antifungal screening and in silico mechanistic studies of an in-house azole library

Systemic Candida infections pose a serious public health problem with high morbidity and mortality. C. albicans is the major pathogen identified in candidiasis, however non-albicans Candida spp. with antifungal resistance are now more prevalent. Azoles are first-choice antifungal drugs for candidiasis, however they are ineffective for certain infections caused by the resistant strains. Azoles block ergosterol synthesis by inhibiting fungal CYP51, which leads to disruption of fungal membrane permeability. In this study, we screened for antifungal activity of an in-house azole library of 65 compounds to identify hit matter followed by a molecular modelling study for their CYP51 inhibition mechanism. Antifungal susceptibility tests against standard Candida spp. including C. albicans revealed derivatives 12 and 13 as highly active. Furthermore, they showed potent antibiofilm activity as well as neglectable cytotoxicity in a mouse fibroblast assay. According to molecular docking studies 12 and 13 have the necessary binding characteristics for effective inhibition of CYP51. Finally, molecular dynamics (MD) simulations of the C. albicans CYP51 (CACYP51) homology model's catalytic site complexed with 13 was stable demonstrating excellent binding. This article is protected by copyright. All rights reserved

The Intercultural Skills Graduates and Businesses in Europe Need Today

It was the aim of the two surveys with European graduates and employers respectively to investigate the importance of intercultural competencies and skills for student employability and business success for European enterprise, now and in the future. The two surveys gave important insights into key factors that support the development of intercultural skills and competencies for graduates and employers across four countries and five different European regions, as well as five distinct universities. Our analysis shows clearly that one of the most important factors is the key role of experience with, and exposure to, people from different cultural backgrounds. Both students and employers scored much higher on important intercultural competencies such as cultural empathy, cognitive flexibility, open-mindedness, and tolerance for ambiguity, if they had frequent interactions with people from other cultures. This was also true for speaking at least one or more foreign languages at an intermediate or advanced level. Foreign language competence is an important intercultural skill not only for communication but also an important way in which cultural empathy and cognitive flexibility are learned and trained. In line with these results, both students and employers who had more exposure to different cultures also felt there was more need to pay attention to intercultural issues and support the development of intercultural skills than those with less experience of different cultures. Furthermore, our results from both the student and the employer surveys seem to reflect differences between more urban/metropolitan centres and more rural areas with smaller towns. London and Bursa are the two largest cities and the most metropolitan areas in our sample with a more multicultural population, whereas Worcester and Leuven are both smaller cities and the regions with the least ethnic diversity. Halmstad falls somewhere in between with a similar size and ethnic composition of the city and region as Worcester and Leuven, but the university itself has a very multicultural and mature student body that is very similar to LSBU in central London. While we cannot directly influence these regional differences in urbanisation and multiculturalism it is certainly important to be aware of them

The Intercultural Skills Graduates and Businesses in Europe Need Today

This ERASMUS+ funded project, “Developing the cross-cultural skills of graduates in response to the needs of European enterprise”, is developed in response to recent research highlighting the importance of intercultural competencies for graduates wanting to work in Europe, the employers’ needs, and the intercultural competencies and skills higher education institutions provide. This project aims to develop the intercultural competencies of graduates in the EU by enhancing the quality and relevance of their knowledge and skills to enable them to be active professionals in the European working environment. Five Higher Education Institutions have participated in this study: University of Worcester (Project lead, UK), London South Bank University (UK), UC Leuven-Limburg (Belgium), Halmstad University (Sweden), and Bursa Uludağ University (Turkey). The diversity of these partners, their respective regional and national contexts, and their experience in working together with regional businesses are central to achieve the project aims. As the first output of the project, this report presents results based on two types of analysis methods and data collected from four European countries (UK, Sweden, Belgium, and Turkey). Firstly, two surveys and the quantitative analysis of data collected from 585 student surveys responses and 403 employer survey responses and secondly, on an analysis of qualitative data collected through 50 interviews with employees in European organizations and 50 interviews with students studying in European universities

Focused Screening Identifies Different Sensitivities of Human TET Oxygenases to the Oncometabolite 2-Hydroxyglutarate

Ten-eleven translocation enzymes (TETs) are Fe(II)/2-oxoglutarate (2OG) oxygenases that catalyze the sequential oxidation of 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine in eukaryotic DNA. Despite their roles in epigenetic regulation, there is a lack of reported TET inhibitors. The extent to which 2OG oxygenase inhibitors, including clinically used inhibitors and oncometabolites, modulate DNA modifications via TETs has been unclear. Here, we report studies on human TET1–3 inhibition by a set of 2OG oxygenase-focused inhibitors, employing both enzyme-based and cellular assays. Most inhibitors manifested similar potencies for TET1–3 and caused increases in cellular 5hmC levels. (R)-2-Hydroxyglutarate, an oncometabolite elevated in isocitrate dehydrogenase mutant cancer cells, showed different degrees of inhibition, with TET1 being less potently inhibited than TET3 and TET2, potentially reflecting the proposed role of TET2 mutations in tumorigenesis. The results highlight the tractability of TETs as drug targets and provide starting points for selective inhibitor design

GOPred: GO Molecular Function Prediction by Combined Classifiers

Functional protein annotation is an important matter for in vivo and in silico biology. Several computational methods have been proposed that make use of a wide range of features such as motifs, domains, homology, structure and physicochemical properties. There is no single method that performs best in all functional classification problems because information obtained using any of these features depends on the function to be assigned to the protein. In this study, we portray a novel approach that combines different methods to better represent protein function. First, we formulated the function annotation problem as a classification problem defined on 300 different Gene Ontology (GO) terms from molecular function aspect. We presented a method to form positive and negative training examples while taking into account the directed acyclic graph (DAG) structure and evidence codes of GO. We applied three different methods and their combinations. Results show that combining different methods improves prediction accuracy in most cases. The proposed method, GOPred, is available as an online computational annotation tool (http://kinaz.fen.bilkent.edu.tr/gopred)

Determining the origin of synchronous multifocal bladder cancer by exome sequencing

BACKGROUND: Synchronous multifocal tumours are commonly observed in urothelial carcinomas of the bladder. The origin of these physically independent tumours has been proposed to occur by either intraluminal migration (clonal) or spontaneous transformation of multiple cells by carcinogens (field effect). It is unclear which model is correct, with several studies supporting both hypotheses. A potential cause of this uncertainty may be the small number of genetic mutations previously used to quantify the relationship between these tumours. METHODS: To better understand the genetic lineage of these tumours we conducted exome sequencing of synchronous multifocal pTa urothelial bladder cancers at a high depth, using multiple samples from three patients. RESULTS: Phylogenetic analysis of high confidence single nucleotide variants (SNV) demonstrated that the sequenced multifocal bladder cancers arose from a clonal origin in all three patients (bootstrap value 100 %). Interestingly, in two patients the most common type of tumour-associated SNVs were cytosine mutations of TpC* dinucleotides (Fisher’s exact test p < 10(−41)), likely caused by APOBEC-mediated deamination. Incorporating these results into our clonal model, we found that TpC* type mutations occurred 2-5× more often among SNVs on the ancestral branches than in the more recent private branches (p < 10(−4)) suggesting that TpC* mutations largely occurred early in the development of the tumour. CONCLUSIONS: These results demonstrate that synchronous multifocal bladder cancers frequently arise from a clonal origin. Our data also suggests that APOBEC-mediated mutations occur early in the development of the tumour and may be a driver of tumourigenesis in non-muscle invasive urothelial bladder cancer. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12885-015-1859-8) contains supplementary material, which is available to authorized users