The Horizontal Component of Photospheric Plasma Flows During the Emergence of Active Regions on the Sun

The dynamics of horizontal plasma flows during the first hours of the emergence of active region magnetic flux in the solar photosphere have been analyzed using SOHO/MDI data. Four active regions emerging near the solar limb have been considered. It has been found that extended regions of Doppler velocities with different signs are formed in the first hours of the magnetic flux emergence in the horizontal velocity field. The flows observed are directly connected with the emerging magnetic flux; they form at the beginning of the emergence of active regions and are present for a few hours. The Doppler velocities of flows observed increase gradually and reach their peak values 4-12 hours after the start of the magnetic flux emergence. The peak values of the mean (inside the +/-500 m/s isolines) and maximum Doppler velocities are 800-970 m/s and 1410-1700 m/s, respectively. The Doppler velocities observed substantially exceed the separation velocities of the photospheric magnetic flux outer boundaries. The asymmetry was detected between velocity structures of leading and following polarities. Doppler velocity structures located in a region of leading magnetic polarity are more powerful and exist longer than those in regions of following polarity. The Doppler velocity asymmetry between the velocity structures of opposite sign reaches its peak values soon after the emergence begins and then gradually drops within 7-12 hours. The peak values of asymmetry for the mean and maximal Doppler velocities reach 240-460 m/s and 710-940 m/s, respectively. An interpretation of the observable flow of photospheric plasma is given.Comment: 20 pages, 10 figures, 3 tables. The results of article were presented at the ESPM-13 (12-16 September 2011, Rhodes, Greece, Abstract Book p. 102, P.4.12, http://astro.academyofathens.gr/espm13/documents/ESPM13_abstract_programme_book.pdf

Modeling the Subsurface Structure of Sunspots

While sunspots are easily observed at the solar surface, determining their subsurface structure is not trivial. There are two main hypotheses for the subsurface structure of sunspots: the monolithic model and the cluster model. Local helioseismology is the only means by which we can investigate subphotospheric structure. However, as current linear inversion techniques do not yet allow helioseismology to probe the internal structure with sufficient confidence to distinguish between the monolith and cluster models, the development of physically realistic sunspot models are a priority for helioseismologists. This is because they are not only important indicators of the variety of physical effects that may influence helioseismic inferences in active regions, but they also enable detailed assessments of the validity of helioseismic interpretations through numerical forward modeling. In this paper, we provide a critical review of the existing sunspot models and an overview of numerical methods employed to model wave propagation through model sunspots. We then carry out an helioseismic analysis of the sunspot in Active Region 9787 and address the serious inconsistencies uncovered by \citeauthor{gizonetal2009}~(\citeyear{gizonetal2009,gizonetal2009a}). We find that this sunspot is most probably associated with a shallow, positive wave-speed perturbation (unlike the traditional two-layer model) and that travel-time measurements are consistent with a horizontal outflow in the surrounding moat.Comment: 73 pages, 19 figures, accepted by Solar Physic

Joint Analysis of Multiple Metagenomic Samples

The availability of metagenomic sequencing data, generated by sequencing DNA pooled from multiple microbes living jointly, has increased sharply in the last few years with developments in sequencing technology. Characterizing the contents of metagenomic samples is a challenging task, which has been extensively attempted by both supervised and unsupervised techniques, each with its own limitations. Common to practically all the methods is the processing of single samples only; when multiple samples are sequenced, each is analyzed separately and the results are combined. In this paper we propose to perform a combined analysis of a set of samples in order to obtain a better characterization of each of the samples, and provide two applications of this principle. First, we use an unsupervised probabilistic mixture model to infer hidden components shared across metagenomic samples. We incorporate the model in a novel framework for studying association of microbial sequence elements with phenotypes, analogous to the genome-wide association studies performed on human genomes: We demonstrate that stratification may result in false discoveries of such associations, and that the components inferred by the model can be used to correct for this stratification. Second, we propose a novel read clustering (also termed “binning”) algorithm which operates on multiple samples simultaneously, leveraging on the assumption that the different samples contain the same microbial species, possibly in different proportions. We show that integrating information across multiple samples yields more precise binning on each of the samples. Moreover, for both applications we demonstrate that given a fixed depth of coverage, the average per-sample performance generally increases with the number of sequenced samples as long as the per-sample coverage is high enough

Insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3) overexpression in pancreatic ductal adenocarcinoma correlates with poor survival

<p>Abstract</p> <p>Background</p> <p>Pancreatic ductal adenocarcinoma is a lethal disease with a 5-year survival rate of 4% and typically presents in an advanced stage. In this setting, prognostic markers identifying the more agrressive tumors could aid in managment decisions. Insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3, also known as IMP3 or KOC) is an oncofetal RNA-binding protein that regulates targets such as insulin-like growth factor-2 (IGF-2) and ACTB (beta-actin).</p> <p>Methods</p> <p>We evaluated the expression of IGF2BP3 by immunohistochemistry using a tissue microarray of 127 pancreatic ductal adenocarcinomas with tumor grade 1, 2 and 3 according to WHO criteria, and the prognostic value of IGF2BP3 expression.</p> <p>Results</p> <p>IGF2BP3 was found to be selectively overexpressed in pancreatic ductal adenocarcinoma tissues but not in benign pancreatic tissues. Nine (38%) patient samples of tumor grade 1 (n = 24) and 27 (44%) of tumor grade 2 (n = 61) showed expression of IGF2BP3. The highest rate of expression was seen in poorly differentiated specimen (grade 3, n = 42) with 26 (62%) positive samples. Overall survival was found to be significantly shorter in patients with IGF2BP3 expressing tumors (P = 0.024; RR 2.3, 95% CI 1.2-4.8).</p> <p>Conclusions</p> <p>Our data suggest that IGF2BP3 overexpression identifies a subset of pancreatic ductal adenocarcinomas with an extremely poor outcome and supports the rationale for developing therapies to target the IGF pathway in this cancer.</p

Two Isoforms of the mRNA Binding Protein IGF2BP2 Are Generated by Alternative Translational Initiation

IGF2BP2 is a member of a family of mRNA binding proteins that, collectively, have been shown to bind to several different mRNAs in mammalian cells, including one of the mRNAs encoding insulin-like growth factor-2. Polymorphisms in the Igf2bp2 gene are associated with risk of developing type 2 diabetes, but detailed functional characterisation of IGF2BP2 protein is lacking. By immunoblotting with C-terminally reactive antibodies we identified a novel IGF2BP2 isoform with a molecular weight of 58 kDa in both human and rodents, that is expressed at somewhat lower levels than the full-length 65 kDa protein. We demonstrated by mutagenesis that this isoform is generated by alternative translation initiation at the internal Met69. It lacks a conserved N-terminal RNA Recognition Motif (RRM) and would be predicted to differ functionally from the canonical full length isoform. We further investigated IGF2BP2 mRNA transcripts by amplification of cDNA using 5′-RACE. We identified multiple transcription start sites of the human, mouse and rat Igf2bp2 genes in a highly conserved region only 50–90 nts upstream of the major translation start site, ruling out the existence of N-terminally extended isoforms. We conclude that structural heterogeneity of IGF2BP2 protein should be taken into account when considering cellular function

A prospective cohort study of dietary patterns of non-western migrants in the Netherlands in relation to risk factors for cardiovascular diseases: HELIUS-Dietary Patterns

<p>Abstract</p> <p>Background</p> <p>In Western countries the prevalence of cardiovascular disease (CVD) is often higher in non-Western migrants as compared to the host population. Diet is an important modifiable determinant of CVD. Increasingly, dietary patterns rather than single nutrients are the focus of research in an attempt to account for the complexity of nutrient interactions in foods. Research on dietary patterns in non-Western migrants is limited and may be hampered by a lack of validated instruments that can be used to assess the habitual diet of non-western migrants in large scale epidemiological studies. The ultimate aims of this study are to (1) understand whether differences in dietary patterns explain differences in CVD risk between ethnic groups, by developing and validating ethnic-specific Food Frequency Questionnaires (FFQs), and (2) to investigate the determinants of these dietary patterns. This paper outlines the design and methods used in the HELIUS-Dietary Patterns study and describes a systematic approach to overcome difficulties in the assessment and analysis of dietary intake data in ethnically diverse populations.</p> <p>Methods/Design</p> <p>The HELIUS-Dietary Patterns study is embedded in the HELIUS study, a Dutch multi-ethnic cohort study. After developing ethnic-specific FFQs, we will gather data on the habitual intake of 5000 participants (18-70 years old) of ethnic Dutch, Surinamese of African and of South Asian origin, Turkish or Moroccan origin. Dietary patterns will be derived using factor analysis, but we will also evaluate diet quality using hypothesis-driven approaches. The relation between dietary patterns and CVD risk factors will be analysed using multiple linear regression analysis. Potential underlying determinants of dietary patterns like migration history, acculturation, socio-economic factors and lifestyle, will be considered.</p> <p>Discussion</p> <p>This study will allow us to investigate the contribution of the dietary patterns on CVD risk factors in a multi-ethnic population. Inclusion of five ethnic groups residing in one setting makes this study highly innovative as confounding by local environment characteristics is limited. Heterogeneity in the study population will provide variance in dietary patterns which is a great advantage when studying the link between diet and disease.</p

HelexKids:a word frequency database for Greek and Cypriot primary school children

In this article, we introduce HelexKids, an online written-word database for Greek-speaking children in primary education (Grades 1 to 6). The database is organized on a grade-by-grade basis, and on a cumulative basis by combining Grade 1 with Grades 2 to 6. It provides values for Zipf, frequency per million, dispersion, estimated word frequency per million, standard word frequency, contextual diversity, orthographic Levenshtein distance, and lemma frequency. These values are derived from 116 textbooks used in primary education in Greece and Cyprus, producing a total of 68,692 different word types. HelexKids was developed to assist researchers in studying language development, educators in selecting age-appropriate items for teaching, as well as writers and authors of educational books for Greek/Cypriot children. The database is open access and can be searched online at www.helexkids.org

Seaweed consumption in the Netherlands

De indruk bestaat dat steeds meer mensen in Nederland zeewierproducten eten. Sushi is de bekendste vorm, maar zeewier zit in verschillende producten. Er was nog weinig bekend over om hoeveel mensen het gaat. Het RIVM heeft dat nu voor het eerst onderzocht. Daaruit blijkt dat ongeveer een kwart van de Nederlandse bevolking regelmatig producten met zeewier eet. De meeste zeewier wordt gegeten in de vorm van chips/kroepoek of wraps met zeewier, noedels op basis van zeewier, zeespaghetti en zeewiersalade. Zeewier wordt door alle lagen van de bevolking gegeten. Hoogopgeleiden, mensen die meer dan modaal verdienen, bewoners van steden en jongvolwassenen eten dit in verhouding vaker. Mensen die dit soort producten eten, krijgen per dag 0,05 gram zeewier per kilogram lichaamsgewicht binnen. Omgerekend naar gedroogd zeewier is dit 0,5 gram per dag (beide hoeveelheden zijn medianen). Het verschilt sterk per persoon hoeveel en hoe vaak ze zeewier eten. Het RIVM heeft dit onderzoek in opdracht van de NVWA gedaan. De NVWA gaat de resultaten gebruiken om de voedselveiligheid van producten met zeewier te beoordelen. Aan dit onderzoek hebben 2710 mensen tussen de 1 en 80 jaar meegedaan. Hen (of de verzorgers van jonge kinderen) is gevraagd hoe vaak zij zeewier eten en in welke vorm. 632 mensen gaven aan zeewier te hebben gegeten in de vier weken voorafgaand aan de enquête.It seems that more and more people in the Netherlands are eating seaweed products. Sushi is the best known form, but seaweed is contained in various products. Little was known about how many people are involved. The RIVM has now investigated this for the first time. This shows that about a quarter of the Dutch population regularly eats products with seaweed. Most seaweed is eaten in the form of chips/ prawn crackers or wraps with seaweed, seaweed-based noodles, sea spaghetti, and seaweed salad. Seaweed is eaten by all parts of the population. However, highly educated people, people who earn more than a modal income, residents of cities, and young adults eat it more often than others. People who eat these types of products consume 0.05 grams of seaweed per kilogram of body weight per day. Converted to dried seaweed, this is 0.5 grams per day (both quantities are medians). It varies greatly per person how much and how often they eat seaweed. The RIVM carried out this research on behalf of the NVWA. The NVWA will use the results to assess the food safety of products with seaweed. This study involved 2710 people between the age of 1 and 80. They (or the caregivers of young children) were asked how often they eat seaweed and in what form. Of those, 632 said they had done so in the four weeks before the survey