Toward an interactive article: integrating journals and biological databases.

BACKGROUND: Journal articles and databases are two major modes of communication in the biological sciences, and thus integrating these critical resources is of urgent importance to increase the pace of discovery. Projects focused on bridging the gap between journals and databases have been on the rise over the last five years and have resulted in the development of automated tools that can recognize entities within a document and link those entities to a relevant database. Unfortunately, automated tools cannot resolve ambiguities that arise from one term being used to signify entities that are quite distinct from one another. Instead, resolving these ambiguities requires some manual oversight. Finding the right balance between the speed and portability of automation and the accuracy and flexibility of manual effort is a crucial goal to making text markup a successful venture. RESULTS: We have established a journal article mark-up pipeline that links GENETICS journal articles and the model organism database (MOD) WormBase. This pipeline uses a lexicon built with entities from the database as a first step. The entity markup pipeline results in links from over nine classes of objects including genes, proteins, alleles, phenotypes and anatomical terms. New entities and ambiguities are discovered and resolved by a database curator through a manual quality control (QC) step, along with help from authors via a web form that is provided to them by the journal. New entities discovered through this pipeline are immediately sent to an appropriate curator at the database. Ambiguous entities that do not automatically resolve to one link are resolved by hand ensuring an accurate link. This pipeline has been extended to other databases, namely Saccharomyces Genome Database (SGD) and FlyBase, and has been implemented in marking up a paper with links to multiple databases. CONCLUSIONS: Our semi-automated pipeline hyperlinks articles published in GENETICS to model organism databases such as WormBase. Our pipeline results in interactive articles that are data rich with high accuracy. The use of a manual quality control step sets this pipeline apart from other hyperlinking tools and results in benefits to authors, journals, readers and databases.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

A NEW SECTION IN THE GOLDFIELD GENUS LASTHENIA (COMPOSITAE: HELIANTHEAE SENSU LATO)

Volume: 48Start Page: 38End Page: 3

TAXONOMIC CHANGES AND A NEW SPECIES IN LASTHENIA SECT. AMPHIACHAENIA (COMPOSITAE: HELIANTHEAE SENSU LATO)

Volume: 48Start Page: 205End Page: 21

Two new genera, Hoffmannanthus and Jeffreycia, mostly from East Africa (Erlangeinae, Vernonieae, Asteraceae)

Two genera of Vernonieae subtribe Erlangeinae with Type A pollen, 5-ribbed achenes, and blunt-tipped sweeping hairs on the styles are described as new, Hoffmannanthus with one species and with Vernonia brachycalyx O. Hoffm. as type, and Jeffreycia with five known species, with Vernonia zanzibarensis Less. as type. Vernonia abbotiana O. Hoffm. is neotypified and is an older name for V. brachycalyx

Figure 6 from: Robinson H, Keeley S, Skvarla J, Chan R (2014) Two new genera, Hoffmannanthus and Jeffreycia, mostly from East Africa (Erlangeinae, Vernonieae, Asteraceae). PhytoKeys 39: 49-64. https://doi.org/10.3897/phytokeys.39.7624

Two genera of Vernonieae subtribe Erlangeinae with Type A pollen, 5-ribbed achenes, and blunt-tipped sweeping hairs on the styles are described as new, Hoffmannanthus with one species and with Vernonia brachycalyx O. Hoffm. as type, and Jeffreycia with five known species, with Vernonia zanzibarensis Less. as type. Vernonia abbotiana O. Hoffm. is neotypified and is an older name for V. brachycalyx

A comparison of conventional and miniprimer PCR to elucidate bacteria diversity in Malaysia Ulu Slim hot spring using 16S rDNA clone library

The diversity of the bacterial community in Ulu Slim hot spring was examined using a 16S ribosomal DNA culture-independent approach. A total of 144 different 16S rDNA sequences were cloned and analyzed. The majority of sequences were found to be within the Betaproteobacteria and Gammaproteobacteria while the remaining sequences belonged to the Bacteroidetes, Acidobacteria, Cloroflexi, Nitrospira and candidate divisions. Some of the bacteria 16S sequences could be novel and indigenous to this hot spring as their sequences are low in similarity when compared with known sequences. The 16S ribosomal DNA clone library was assembled using conventional PCR amplification with degenerate 27F and 1492R primers specific for bacterial rDNA. A new miniprimer PCR assay was also used to construct a library. When compared, we conclude that the latter approach which using mutagenized Dynamo-II polymerase utilizing 10-mer primers was a better approach than the conventional PCR as the environmental humid acid inhibition effect was less. Ideally, to best understand the overall prokaryote diversity in the hot spring, it is better to use a combined conventional and miniprimer PCR approach

Believers of fortune telling: Who are they?

The purpose of this study is to characterize the believers of fortune telling. Believers was describe in terms of four areas, namely: (1) The demographic and psychological profile, (2) fortune telling method the believers predominantly subscribe to, )3) objectives of the believers for consulting and lastly, (4) the extent to which they abide to the advices given to them. A survey was employed to 90 participants (42 males, 48 females) with ages raging from 20-65 years old. The results show that males and females cater to fortune telling and yet most of the participants have internal locus of control. The method mostly preferred is palmistry. Reason for consulting is to help them understand things and give them control over their lives. Main issue early adults consult is about love life, for middel adults, they are concern with business and family matters. Both groups do not have full compliance to the advices given to them

A comparison of conventional and miniprimer PCR to elucidate bacteria diversity in Malaysia Ulu Slim hot spring using 16S rDNA clone library

Abstrac

A phylogeny of the Gochnatieae: Understanding a critically placed tribe in the Compositae

Subfamily Gochnatioideae is the sister group of ~96% of the species in Compositae (Asteraceae). It is of particular interest not only because of its position in the phylogeny, but also because, in recent molecular studies, the node it occupies is not strongly supported making difficult any inferences on the direction of character evolution in the family. The recognition of tribe Gochnatieae was one of the results of a comprehensive molecular analysis of the family that showed the traditional cir-cumscription of the Mutisieae to be non-monophyletic. The four genera of Gochnatieae (Cnicothamnus, Cyclolepis, Gochnatia, Richterago) were defined by the presence of apiculate anther appendages and dorsally smooth style branches. Gochnatia, which contained about 70 species, was the largest and most complex genus and in the last decade some of its sections have been moved (or returned) to the rank of genus. This study includes a large selection of potential outgroups and over 60% of all species in the tribe, including all the genera and all but one of the sections of Gochnatia, to examine evolutionary relationships among the taxa. Both cpDNA and nrDNA were used in a phylogenetic analysis using parsimony, likelihood, and Bayesian approaches. The results suggest a non-monophyletic Gochnatia that is here resolved by the recognition of segregate genera. Morphologi-cal characters support these new genera and allow the adoption of a new classification for the Gochnatieae. A biogeographic analysis shows a possible southern South American/Andean origin followed by movement in three directions: into the Central Andes, into central and northern Brazil, and into Mexico and the Caribbean. The dating analysis gives an age of the split of the core Gochnatieae from the Wunderlichieae-Cyclolepis clade, and hence the age of the tribe, of 36–45 Ma and an age of 23–25 Ma for the first split within the core Gochnatieae (Andean vs. Brazil-Mexico-Caribbean). Cnicothamnus remains in Gochnatieae but Cyclolepis is designated incertae sedis.Fil: Funk, Vicki. Smithsonian Institution. Washington; Estados UnidosFil: Sancho, Gisela. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo; ArgentinaFil: Roque, Nadia. Universidade Federal da Bahia; BrasilFil: Kelloff, Carol L.. Smithsonian Institution. Washington; Estados UnidosFil: Ventosa Rodriguez, Iralys. Instituto de Ecología y Sistemática. La Habana; CubaFil: Díaz Granados, Mauricio. Smithsonian Institution. Washington; Estados UnidosFil: Bonifacino, J. Mauricio. Universidad de la República; UruguayFil: Chan, Raymund. Smithsonian Institution. Washington; Estados Unido