Tidying up international nucleotide sequence databases

Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi

Men’s Condom Use in Higher-Risk Sex: Trends and Determinants in Five Sub-Saharan Countries

This paper examines men’s condom use at last higher-risk sex (i.e., nonmarital, noncohabiting partner) in five sub-Saharan countries: Burkina Faso, Cameroon, Kenya, Tanzania, and Zambia. The two most recent Demographic and Health Surveys (DHS) in each country are analyzed to show trends in various indicators. Condom use is an important way to prevent the transmission of HIV, the virus that causes AIDS. Encouragingly, use of condoms has increased substantially in Burkina Faso, Cameroon,and Tanzania, with smaller increases in Kenya and Zambia. At the same time, levels of higher-risk sex have declined in four of the five countries, although use of a condom at last higher-risk sex remains below 50 percent in Kenya and Zambia. Multivariate analysis shows that higher education is a consistently strong, positive predictor of condom use at last higher-risk sex, whereas higher wealth status is not significant in most surveys. Knowledge that use of condoms can reduce the risk of HIV transmission is a consistently strong, positive predictor of condom use, but urban-rural residence and region are significant only in some surveys. Comparing the two most recent DHS surveys in each of the five countries, there are no clear patterns of change in the predictive strength of explanatory variables. However, there is evidence of widening gaps in condom use by level of education in Cameroon and by urban-rural residence in Kenya. One important policy finding that emerged from this study is that low wealth status is not a barrier to condom use in most countries, but lack of education is.\u

RELEVANSI STRUKTUR KEPEMILIKAN TENTANG PROFITABILITAS DAN NILAI PERUSAHAAN (Studi pada Industri Manufaktur yang Terdaftar di Bursa Efek Indonesia Periode 2010-2017)

ABSTRAKPenelitian ini bertujuan untuk menguji pengaruh secara parsial dan simultan antara struktur kepemilikan terhadap kinerja perusahaan dan nilai perusahaan pada perusahaan manufaktur di Indonesia.Populasi dalam penelitian ini adalah Industri Manufaktur di Indonesia 2010 hingga periode 2017. Sampel dalam penelitian ini adalah Industri Manufaktur sesuai dengan kriteria yang ditentukan. Analisis regresi dilakukan berdasarkan hasil analisis pool data.Penelitian ini menyimpulkan beberapa hal sebagai berikut:. (1) Variabel Insider Ownership (INSD) berpengaruh negatif signifikan terhadap Profitabilitas (ROE), (2). Institusional  Ownership (INST) berpengaruh positif tidak signifikan terhadap Profitabilitas (ROE) (3). Foreign Ownership (FORG) berpengaruh positif tidak signifikan terhadap Profitabilitas (ROE) (4) Public Ownership (PUBL) berpengaruh positif signifikan terhadap Profitabilitas (ROE) (5). INSD, INST, FORG, dan PUBL secara simultan berpengaruh positif signifikan terhadap Profitabilitas (ROE) dan mampu menjelaskan variabel Profitabilitas sebesar 0.795130, atau 79,51 persen, (6) Variabel Insider Ownership (INSD) berpengaruh positif tidak signifikan terhadap Nilai Perusahaan (PBV), 7). Institusional  Ownership (INST) berpengaruh positif tidak signifikan terhadap nilai perusahaan (PBV) (8). Foreign Ownership (FORG) berpengaruh positif signifikan terhadap nilai perusahaan (PBV)  (9) Public Ownership (PUBL) berpengaruh positif signifikan terhadap nilai perusahaan (PBV) (10). INSD, INST, FORG, dan PUBL secara simultan berpengaruh positif signifikan terhadap Nilai Perusahaan Manufaktur di Indonesia periode 2010-2017, dan mampu menjelaskan variabel Nilai Perusahaan  sebesar 0.645845, atau 64,58 persen. Kata Kunci: Struktur Kepemilikan, Profitabilitas, Nilai Perusahaa

PPNID : a reference database and molecular identification pipeline for plant-parasitic nematodes

Motivation: The phylum Nematoda comprises the most cosmopolitan and abundant metazoans on Earth and plant-parasitic nematodes represent one of the most significant nematode groups, causing severe losses in agriculture. Practically, the demands for accurate nematode identification are high for ecological, agricultural, taxonomic and phylogenetic researches. Despite their importance, the morphological diagnosis is often a difficult task due to phenotypic plasticity and the absence of clear diagnostic characters while molecular identification is very difficult due to the problematic database and complex genetic background. Results: The present study attempts to make up for currently available databases by creating a manually-curated database including all up-to-date authentic barcoding sequences. To facilitate the laborious process associated with the interpretation and identification of a given query sequence, we developed an automatic software pipeline for rapid species identification. The incorporated alignment function facilitates the examination of mutation distribution and therefore also reveals nucleotide autapomorphies, which are important in species delimitation. The implementation of genetic distance, plot and maximum likelihood phylogeny analysis provides more powerful optimality criteria than similarity searching and facilitates species delimitation using evolutionary or phylogeny species concepts. The pipeline streamlines several functions to facilitate more precise data analyses, and the subsequent interpretation is easy and straightforward

PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences

DNA sequences accumulating in the International Nucleotide Sequence Databases (INSD) form a rich source of information for taxonomic and ecological meta-analyses. However, these databases include many erroneous entries, and the data itself is poorly annotated with metadata, making it difficult to target and extract entries of interest with any degree of precision. Here we describe the web-based workbench PlutoF, which is designed to bridge the gap between the needs of contemporary research in biology and the existing software resources and databases. Built on a relational database, PlutoF allows remote-access rapid submission, retrieval, and analysis of study, specimen, and sequence data in INSD as well as for private datasets though web-based thin clients. In contrast to INSD, PlutoF supports internationally standardized terminology to allow very specific annotation and linking of interacting specimens and species. The sequence analysis module is optimized for identification and analysis of environmental ITS sequences of fungi, but it can be modified to operate on any genetic marker and group of organisms. The workbench is available at http://plutof.ut.ee

Growth and Poverty in Burkina Faso: A Reassessment of the Paradox

Previous poverty assessments for Burkina Faso were due to the neglect of some important methodological issues misleading and led to the so-called 'Burkinabè Growth-Poverty-Paradox', i.e. relatively sustained macro-economic growth, but almost constant poverty. We estimate that poverty significantly decreased between 1994 and 2003 at least on the national level, i.e. growth was in contrast to what previous poverty estimates suggested 'pro-poor'. However, we also demonstrate that between 1994 and 1998 poverty indeed increased despite a good macro-economic performance. This was due to a severe drought and a resulting profound deterioration of the purchasing power of the poor; an issue which was also overseen by previous studies.Poverty; Pro-poor growth; Differential inflation; Sub-Saharan Africa; Burkina Faso

Universal Banking and the Performance of German Firms

Universal banking is an alternative mechanism to a stock market for risk-sharing, for providing information for guiding investment, and for contesting corporate governance. In Germany, where the stock market has historically been small, banks hold equity stakes in firms and have proxy voting rights over other agents' shares. In addition, banks lend to firms and have representatives on corporate boards. If a banking relationship is a substitute for the stock market, then interaction with a bank should improve the performance of firms. But, if banks have private information about firms that they lend to and have monopolistic control over access to external capital markets, then bank interests may conflict with those of other equityholders, especially those whose shares are voted by the banks in proxy. We empirically investigate the influence of banks on the performance of German firms taking account of banks' equity holdings, the extent of banks' proxy voting rights, and the ownership structure of the firms' equity. We test for conflicts-of-interest in bank behavior and ask whether the relationship between banks and firms has changed between the 1970s and 1980s.

Household welfare and poverty dynamics in Burkina Faso : empirical evidence from household surveys

The authors investigate the dynamics of poverty and income inequality in a cross-section of socio-economic groups and geographical regions over the five-year growth period following the 1994 devaluation of the CFA franc in Burkina Faso. Results show rapidly increasing urban poverty accompanied by rising income inequality, declining poverty -growth elasticities, and significant changes in the poverty map. In rural areas, the incidence of poverty remained the same and income inequality did not increase. In contrast, the distribution of welfare across socio-economic groups was more stable. The rank ordering of socioeconomic groups on the welfare scale did not change during the post-devaluation growth period. Poverty remains largely a rural phenomenon, whose inelastic nature may justify a shift toward growth-oriented policies that at least maintain the rural poor's share of income to reduce poverty in the medium term. Among factors that feed into income inequality: disparities in wages and in educational attainment and unequal access to productive assets (especially human capital).Economic Theory&Research,Environmental Economics&Policies,Services&Transfers to Poor,Economic Conditions and Volatility,Public Health Promotion,Achieving Shared Growth,Poverty Assessment,Environmental Economics&Policies,Rural Poverty Reduction,Safety Nets and Transfers