Information about bacterial subcellular localization (SCL) is important for protein function prediction and identification of suitable drug/vaccine/diagnostic targets. PSORTdb (http://db.psort.org/) ...is a web-accessible database of SCL for bacteria that contains both information determined through laboratory experimentation and computational predictions. The dataset of experimentally verified information (∼2000 proteins) was manually curated by us and represents the largest dataset of its kind. Earlier versions have been used for training SCL predictors, and its incorporation now into this new PSORTdb resource, with its associated additional annotation information and dataset version control, should aid researchers in future development of improved SCL predictors. The second component of this database contains computational analyses of proteins deduced from the most recent NCBI dataset of completely sequenced genomes. Analyses are currently calculated using PSORTb, the most precise automated SCL predictor for bacterial proteins. Both datasets can be accessed through the web using a very flexible text search engine, a data browser, or using BLAST, and the entire database or search results may be downloaded in various formats. Features such as GO ontologies and multiple accession numbers are incorporated to facilitate integration with other bioinformatics resources. PSORTdb is freely available under GNU General Public License.
The innate immune response is the first line of defence against invading pathogens and is regulated by complex signalling and transcriptional networks. Systems biology approaches promise to shed new ...light on the regulation of innate immunity through the analysis and modelling of these networks. A key initial step in this process is the contextual cataloguing of the components of this system and the molecular interactions that comprise these networks. InnateDB (http://www.innatedb.com) is a molecular interaction and pathway database developed to facilitate systems-level analyses of innate immunity.
Here, we describe the InnateDB curation project, which is manually annotating the human and mouse innate immunity interactome in rich contextual detail, and present our novel curation software system, which has been developed to ensure interactions are curated in a highly accurate and data-standards compliant manner. To date, over 13,000 interactions (protein, DNA and RNA) have been curated from the biomedical literature. Here, we present data, illustrating how InnateDB curation of the innate immunity interactome has greatly enhanced network and pathway annotation available for systems-level analysis and discuss the challenges that face such curation efforts. Significantly, we provide several lines of evidence that analysis of the innate immunity interactome has the potential to identify novel signalling, transcriptional and post-transcriptional regulators of innate immunity. Additionally, these analyses also provide insight into the cross-talk between innate immunity pathways and other biological processes, such as adaptive immunity, cancer and diabetes, and intriguingly, suggests links to other pathways, which as yet, have not been implicated in the innate immune response.
In summary, curation of the InnateDB interactome provides a wealth of information to enable systems-level analysis of innate immunity.
Analysis of microbial genomes often requires the general organization and comparison of tens to thousands of genomes both from public repositories and unpublished sources. MicrobeDB provides a ...foundation for such projects by the automation of downloading published, completed bacterial and archaeal genomes from key sources, parsing annotations of all genomes (both public and private) into a local database, and allowing interaction with the database through an easy to use programming interface. MicrobeDB creates a simple to use, easy to maintain, centralized local resource for various large-scale comparative genomic analyses and a back-end for future microbial application design.
MicrobeDB is freely available under the GNU-GPL at: http://github.com/mlangill/microbedb/
As exemplified by the lead compound 2, octahydrophenanthrene-2,7-diol analogues exhibit the profile of a pathway-selective or “dissociated” agonist of the glucocorticoid receptor (GR), retaining the ...potent activity that glucocorticoids have for transrepression (as measured by inhibition of IL-1 induced MMP-13 expression) but showing an attenuated capacity for transactivation (as measured in an MMTV luciferase reporter assay). With the guidance of a homology model of the GR ligand binding domain, structural modifications to 2 were carried out that were successful in replacing the allyl and propynyl side chains with groups likely to be more chemically stable and less likely to produce toxic metabolites. Key to success was the introduction of an additional hydroxyl group onto the tricyclic carbon framework of the series.
Abstract The purposes of this study were to determine success and survival rates for implants and teeth adjacent to implants and the incidence of endodontic implantitis (E-I) (endodontic involvement ...in adjacent teeth causing implant failure) and implant endodontitis (I-E) (implant placement causing endodontic failure). The data were from 233 single-tooth implants placed in 116 subjects by postgraduate periodontal students with recall radiographs taken ≥9 months after implant placement. Three groups were analyzed: group A, implants with no adjacent teeth ( n = 90); group B, implants with nonendodontically treated adjacent teeth ( n = 123); and group C, implants with endodontically treated adjacent teeth ( n = 20). The success and survival rates for implants were both 92.2% in group A, 98.4% and 99.2% for group B, and 85% and 95% for group C, respectively. For adjacent teeth, they were both 99.4% in group B compared with 75% and 90% in group C. However, after case review, none of the implants or adjacent teeth in group B were considered to have E-I or I-E, and one (5%) of the implants in group C had E-I and two (10%) of the adjacent teeth may have had I-E. The results of the present study agree with previous research, which suggests that endodontically treated teeth adjacent to single-tooth implants are usually successful and should be maintained.
A Focus on Ratios and Proportions Petit, Marjorie M.; Laird, Robert E.; Wyneken, Matthew F. ...
2020, 20200517, 2020-06-15, 2020-05-17
eBook
This resource offers a groundbreaking effort to make mathematics education research on ratios and proportions readily accessible and understandable to preservice and in-service teachers of grades 6 ...to 8. Using extensive annotated samples of student work and based on research gathered in the Ongoing Assessment Project (OGAP), A Focus on Ratios and Proportions teaches readers how students develop understanding and fluency involving ratio and proportion concepts.
Special features include:
A close focus on student work, including 150+ annotated pieces of student work, to help teachers improve their ability to recognize, assess and monitor their students' errors and misconceptions, as well as their developing conceptual understanding.
A focus on the OGAP Ratio and Proportions Progression, based on research conducted with hundreds of teachers and thousands of pieces of student work.
Sections on how Common Core State Standards for Math (CCSSM) are supported by math education research.
Student work samples and vignettes to illuminate the research, as well as end-of-chapter Looking Back questions and Instructional Links, which allow teachers to analyze evidence of student thinking and strategies and consider instructional responses.
An accompanying eResource, available online, offers an answer key as well as extensive explanation of the Looking Back questions.
Like A Focus on Multiplication and Division and A Focus on Fractions, this book is designed to bridge the gap between what math education researchers know and what teachers need to know in order to better understand evidence in student work and make effective instructional decisions.
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