Characterising strengths, weakness, opportunities and threats in producing naked oat as a novel crop for northern growing conditions

Selostus: Paljasjyväinen kaura uutena viljelykasvina Suomen kasvuoloissa

Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption

Coffee, a major dietary source of caffeine, is among the most widely consumed beverages in the world and has received considerable attention regarding health risks and benefits. We conducted a genome-wide (GW) meta-analysis of predominately regular-type coffee consumption (cups per day) among up to 91 462 coffee consumers of European ancestry with top single-nucleotide polymorphisms (SNPs) followed-up in ~30 062 and 7964 coffee consumers of European and African-American ancestry, respectively. Studies from both stages were combined in a trans-ethnic meta-analysis. Confirmed loci were examined for putative functional and biological relevance. Eight loci, including six novel loci, met GW significance (log10Bayes factor (BF)>5.64) with per-allele effect sizes of 0.03-0.14 cups per day. Six are located in or near genes potentially involved in pharmacokinetics (ABCG2, AHR, POR and CYP1A2) and pharmacodynamics (BDNF and SLC6A4) of caffeine. Two map to GCKR and MLXIPL genes related to metabolic traits but lacking known roles in coffee consumption. Enhancer and promoter histone marks populate the regions of many confirmed loci and several potential regulatory SNPs are highly correlated with the lead SNP of each. SNP alleles near GCKR, MLXIPL, BDNF and CYP1A2 that were associated with higher coffee consumption have previously been associated with smoking initiation, higher adiposity and fasting insulin and glucose but lower blood pressure and favorable lipid, inflammatory and liver enzyme profiles (P<5 × 10-8).Our genetic findings among European and African-American adults reinforce the role of caffeine in mediating habitual coffee consumption and may point to molecular mechanisms underlying inter-individual variability in pharmacological and health effects of coffee.

The Classification of Vitreous Seeds in Retinoblastoma and Response to Intravitreal Melphalan.

PURPOSE: To evaluate the clinical characteristics of the 3 classifications of vitreous seeds in retinoblastoma-dust (class 1), spheres (class 2), and clouds (class 3)-and their responses to intravitreal melphalan. DESIGN: Retrospective, bi-institutional cohort study. PARTICIPANTS: A total of 87 patient eyes received 475 intravitreal injections of melphalan (median dose, 30 μg) given weekly, a median of 5 times (range, 1-12 times). METHODS: At presentation, the vitreous seeds were classified into 3 groups: dust, spheres, and clouds. Indirect ophthalmoscopy, fundus photography, ultrasonography, and ultrasonic biomicroscopy were used to evaluate clinical response to weekly intravitreal melphalan injections and time to regression of vitreous seeds. Kaplan-Meier estimates of time to regression and ocular survival, patient survival, and event-free survival (EFS) were calculated and then compared using the Mantel-Cox test of curve. MAIN OUTCOME MEASURES: Time to regression of vitreous seeds, patient survival, ocular survival, and EFS. RESULTS: The difference in time to regression was significantly different for the 3 seed classes (P < 0.0001): the median time to regression was 0.6, 1.7, and 7.7 months for dust, spheres, and clouds, respectively. Eyes with dust received significantly fewer injections and a lower median and cumulative dose of melphalan, whereas eyes with clouds received significantly more injections and a higher median and cumulative dose of melphalan. Overall, the 2-year Kaplan-Meier estimates for ocular survival, patient survival, and EFS (related to target seeds) were 90.4% (95% confidence interval [CI], 79.7-95.6), 100%, and 98.5% (95% CI, 90-99.7), respectively. CONCLUSIONS: The regression and response of vitreous seeds to intravitreal melphalan are different for each seed classification. The vitreous seed classification can be predictive of time to regression, number, median dose, and cumulative dose of intravitreal melphalan injections required.

Genotypic classification of patients with Wolfram syndrome: insights into the natural history of the disease and correlation with phenotype

Purpose: Wolfram syndrome is a degenerative, recessive rare disease with an onset in childhood. It is caused by mutations in WFS1 or CISD2 genes. More than 200 different variations in WFS1 have been described in patients with Wolfram syndrome, which complicates the establishment of clear genotype-phenotype correlation. The purpose of this study was to elucidate the role of WFS1 mutations and update the natural history of the disease. Methods: This study analyzed clinical and genetic data of 412 patients with Wolfram syndrome published in the last 15 years. Results: (i) 15% of published patients do not fulfill the current ­inclusion criterion; (ii) genotypic prevalence differences may exist among countries; (iii) diabetes mellitus and optic atrophy might not be the first two clinical features in some patients; (iv) mutations are nonuniformly distributed in WFS1; (v) age at onset of diabetes mellitus, hearing defects, and diabetes insipidus may depend on the patient"s genotypic class; and (vi) disease progression rate might depend on genotypic class. Conclusion: New genotype-phenotype correlations were established, disease progression rate for the general population and for the genotypic classes has been calculated, and new diagnostic criteria have been proposed. The conclusions raised could be important for patient management and counseling as well as for the development of treatments for Wolfram syndrome.

Classification-Based compression of Multispectral Images

The purpose of this thesis is to present a new approach to the lossy compression of multispectral images. Proposed algorithm is based on combination of quantization and clustering. Clustering was investigated for compression of the spatial dimension and the vector quantization was applied for spectral dimension compression. Presenting algo¬rithms proposes to compress multispectral images in two stages. During the first stage we define the classes' etalons, another words to each uniform areas are located inside the image the number of class is given. And if there are the pixels are not yet assigned to some of the clusters then it doing during the second; pass and assign to the closest eta¬lons. Finally a compressed image is represented with a flat index image pointing to a codebook with etalons. The decompression stage is instant too. The proposed method described in this paper has been tested on different satellite multispectral images from different resources. The numerical results and illustrative examples of the method are represented too.

The effects of inter-crop cultivation Between rows of citrus crop on spreading of Guignardia citricarpa Ascospores and in the citrus black spot occurrence

This study highlighted the effect of planting coast-cross grass and forage peanut cv. Amarilis between rows of Natal oranges on spreading of Guignardia citricarpa ascospores and consequent citrus black spot control. Treatments evaluated were: 1- conventional cultivation, free of fungicides; 2- conventional cultivation, using protective fungicides; 3- inter-crop cultivation of coast-cross grass between rows of citrus crops and; 4- inter-cropping cultivation of forage peanut between the rows of citrus crops. Quest Volumetric Spore SystemTM traps were set in order to determine the number of ascospores released. A total of 33 inspections were conducted weekly, from the end of August until early September the following year. A diagrammatic scale was used to determine the severity of the disease as well as the percentage of fruits having a commercial standard. The coast-cross grass was more effective in reducing the number of ascospores produced, whose average statistics were lower than in the conventional treatments, free-fungicides. The inter-crop and conventional cultivation method coupled with fungicide treatment was more effective in reducing the severity of citrus black spot symptoms, and differs statistically from the fungicide-free control method. These methods also resulted in a higher percentage of fruits of a commercial standard, ranging from the 89% through the 91% percentile, and the cultivation, free of fungicides, fell within the 73%.

A survey of transposable element classification systems--a call for a fundamental update to meet the challenge of their diversity and complexity.

The increase of publicly available sequencing data has allowed for rapid progress in our understanding of genome composition. As new information becomes available we should constantly be updating and reanalyzing existing and newly acquired data. In this report we focus on transposable elements (TEs) which make up a significant portion of nearly all sequenced genomes. Our ability to accurately identify and classify these sequences is critical to understanding their impact on host genomes. At the same time, as we demonstrate in this report, problems with existing classification schemes have led to significant misunderstandings of the evolution of both TE sequences and their host genomes. In a pioneering publication Finnegan (1989) proposed classifying all TE sequences into two classes based on transposition mechanisms and structural features: the retrotransposons (class I) and the DNA transposons (class II). We have retraced how ideas regarding TE classification and annotation in both prokaryotic and eukaryotic scientific communities have changed over time. This has led us to observe that: (1) a number of TEs have convergent structural features and/or transposition mechanisms that have led to misleading conclusions regarding their classification, (2) the evolution of TEs is similar to that of viruses by having several unrelated origins, (3) there might be at least 8 classes and 12 orders of TEs including 10 novel orders. In an effort to address these classification issues we propose: (1) the outline of a universal TE classification, (2) a set of methods and classification rules that could be used by all scientific communities involved in the study of TEs, and (3) a 5-year schedule for the establishment of an International Committee for Taxonomy of Transposable Elements (ICTTE).

Water consumption and soil moisture distribution in melon crop with mulching and in a protected environment

Mulching has become an important technique for land cover, but there are some technical procedures which should be adjusted for these new modified conditions to establish optimum total water depth. It is also important to observe the soil-water relations as soil water distribution and wetted volume dimensions. The objective of the present study was to estimate melon evapotranspiration under mulching in a protected environment and to verify the water spatial distribution around the melon root system in two soil classes. Mulching provided 27 mm water saving by reducing water evaporation. In terms of volume each plant received, on average, the amount of 175.2 L of water in 84 days of cultivation without mulching, while when was used mulching the water requirement was 160.2 L per plant. The use of mulching reduced the soil moisture variability throughout the crop cycle and allowed a greater distribution of soil water that was more intense in the clay soil. The clayey soil provided on average 43 mm more water depth retention in 0.50 m soil deep relative to the sandy loam soil, and reduced 5.6 mm the crop cycle soil moisture variation compared to sandy loam soil.

Coffee polyphenols change the expression of STAT5b and ATF-2 modifying cyclin D1 levels in cancer cells

Background: Epidemiological studies suggest that coffee consumption reduces the risk of cancer, but the molecular mechanisms of its chemopreventive effects remain unknown. Objective: To identify differentially expressed genes upon incubation of HT29 colon cancer cells with instant caffeinated coffee (ICC) or caffeic acid (CA) using whole genome microarrays. Results: ICC incubation of HT29 cells caused the overexpression of 57 genes and the underexpression of 161, while CA incubation induced the overexpression of 12 genes and the underexpression of 32. Using Venn-Diagrams, we built a list of five overexpressed genes and twelve underexpressed genes in common between the two experimental conditions. This list was used to generate a biological association network in which STAT5B and ATF-2 appeared as highly interconnected nodes. STAT5B overexpression was confirmed at the mRNA and protein levels. For ATF-2, the changes in mRNA levels were confirmed for both ICC and CA, whereas the decrease in protein levels was only observed in CA-treated cells. The levels of cyclin D1, a target gene for both STAT5B and ATF-2, were dowregulated by CA in colon cancer cells and by ICC and CA in breast cancer cells. Conclusions: Coffee polyphenols are able to affect cyclin D1 expression in cancer cells through the modulation of STAT5B and ATF-2.

Text Classification and Indexing in IP Networks

Internet on elektronisen postin perusrakenne ja ollut tärkeä tiedonlähde akateemisille käyttäjille jo pitkään. Siitä on tullut merkittävä tietolähde kaupallisille yrityksille niiden pyrkiessä pitämään yhteyttä asiakkaisiinsa ja seuraamaan kilpailijoitansa. WWW:n kasvu sekä määrällisesti että sen moninaisuus on luonut kasvavan kysynnän kehittyneille tiedonhallintapalveluille. Tällaisia palveluja ovet ryhmittely ja luokittelu, tiedon löytäminen ja suodattaminen sekä lähteiden käytön personointi ja seuranta. Vaikka WWW:stä saatavan tieteellisen ja kaupallisesti arvokkaan tiedon määrä on huomattavasti kasvanut viime vuosina sen etsiminen ja löytyminen on edelleen tavanomaisen Internet hakukoneen varassa. Tietojen hakuun kohdistuvien kasvavien ja muuttuvien tarpeiden tyydyttämisestä on tullut monimutkainen tehtävä Internet hakukoneille. Luokittelu ja indeksointi ovat merkittävä osa luotettavan ja täsmällisen tiedon etsimisessä ja löytämisessä. Tämä diplomityö esittelee luokittelussa ja indeksoinnissa käytettävät yleisimmät menetelmät ja niitä käyttäviä sovelluksia ja projekteja, joissa tiedon hakuun liittyvät ongelmat on pyritty ratkaisemaan.

Gas exchanges in annonaceae species under different crop protections

This study aims to investigate the gas exchanges of different species of Annonaceae due to environmental variations provided by different types of crop protection. 'Araticum-de-terra-fria', 'araticum-mirim', 'biribá' and atemoya seedlings were cultived in three different crop protections: nursery, greenhouse and warm house. Gas exchanges were obtained in six plants, from 9:00 am to 11:00 am, with IRGA, LI-6400, at 180 Days After Transplanting. The different types of crop protection had a direct influence on gas exchanges of these species. Thus, nursery provided suitable conditions for 'araticum-de-terra-fria', 'araticum-mirim' and 'biribá', increasing their gas exchanges. To atemoya the best crop protection was the greenhouse.