Upgrades to StellaBase facilitate medical and genetic studies on the starlet sea anemone, Nematostella vectensis

© 2007 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in Nucleic Acids Research 36 (2008): D607-D611, doi:10.1093/nar/gkm941.The starlet sea anemone, Nematostella vectensis, is a basal metazoan organism that has recently emerged as an important model system in developmental biology and evolutionary genomics. StellaBase, the Nematostella Genomics Database (http://stellabase.org), was developed in 2005 as a resource to support the Nematostella research community. Recently, it has become apparent that Nematostella may be a particularly useful system for studying (i) microevolutionary variation in natural populations, and (ii) the functional evolution of human disease genes. We have developed two new databases that will foster such studies: StellaBase Disease (http://stellabase.org/disease) is a relational database that houses 155 904 invertebrate homologous isoforms of human disease genes from four leading genomic model systems (fly, worm, yeast and Nematostella), including 14 874 predicted genes from the sea anemone itself. StellaBase SNP (http://stellabase.org/SNP) is a relational database that describes the location and underlying type of mutation for 20 063 single nucleotide polymorphisms.This work was supported by NSF grant FP-91656101-0 to J.C.S. and J.R.F. and EPA Grant F5E11155 to A.R.M. and J.R.F. and by a Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution, with funding provided by The Beacon Institute for Rivers and Estuaries, and the J. Seward Johnson Fund to A.M.R

Upgrades to StellaBase facilitate medical and genetic studies on the starlet sea anemone, Nematostella vectensis

© 2007 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in Nucleic Acids Research 36 (2008): D607-D611, doi:10.1093/nar/gkm941.The starlet sea anemone, Nematostella vectensis, is a basal metazoan organism that has recently emerged as an important model system in developmental biology and evolutionary genomics. StellaBase, the Nematostella Genomics Database (http://stellabase.org), was developed in 2005 as a resource to support the Nematostella research community. Recently, it has become apparent that Nematostella may be a particularly useful system for studying (i) microevolutionary variation in natural populations, and (ii) the functional evolution of human disease genes. We have developed two new databases that will foster such studies: StellaBase Disease (http://stellabase.org/disease) is a relational database that houses 155 904 invertebrate homologous isoforms of human disease genes from four leading genomic model systems (fly, worm, yeast and Nematostella), including 14 874 predicted genes from the sea anemone itself. StellaBase SNP (http://stellabase.org/SNP) is a relational database that describes the location and underlying type of mutation for 20 063 single nucleotide polymorphisms.This work was supported by NSF grant FP-91656101-0 to J.C.S. and J.R.F. and EPA Grant F5E11155 to A.R.M. and J.R.F. and by a Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution, with funding provided by The Beacon Institute for Rivers and Estuaries, and the J. Seward Johnson Fund to A.M.R

S100A6 preferentially labels type C nevus cells and nevic corpuscles: additional support for Schwannian differentiation of intradermal nevi

Melanocytic nevi typically show a morphologic sequence of maturation from epithelioid “type A” cells to fusiform, Schwann cell-like “type C” cells with dermal descent. Nevi may also produce Wagner-Meissner-like structures (nevic corpuscles). Previous studies have shown that this maturation of intradermal nevi recapitulates intermediate stages in Schwann cell development. In intradermal nevi, we have evaluated the pattern of S100A6 protein, a form of S100 found in Schwann cells. Methods: Formalin-fixed, paraffin-embedded archival tissues were evaluated by immunohistochemistry using antibodies specific for S100A6 and S100B in 38 intradermal nevi (IDN). Ten neurofibromas (NF), 3 Schwannomas (SCH), 2 palisaded and encapsulated neuromas (PEN), and 2 granular cell tumors (GCT) were included as positive controls since these lesions have large numbers of Schwann cells. Results: Melanocytic nevi demonstrated preferential anti-S100A6 staining of “type C” cells (36/38; 28 strong, 8 weak) and nevic corpuscles (25/38; 19 strong, 6 weak) compared to “type A” cells (17/38; 17 weak) and “type B” cells (17/38; 4 strong, 13 weak). All NF, SCH, and PEN stained strongly with anti-S100A6. Both GCT were negative with anti-S100A6 but positive with anti-S100B. Conclusions: The pattern of S100A6 expression in intradermal nevi further supports the hypothesis that maturation in these lesions recapitulates features of Schwann cell differentiation. The lack of S100A6 expression by both GCT suggests that these lesions have lost this feature of Schwann cells, which may play a role in their peculiar phenotypic appearance.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75660/1/j.1600-0560.2001.028008393.x.pd

Shikimate pathway in apicomplexan parasites

No abstract available

Low-Background gamma counting at the Kimballton Underground Research Facility

The next generation of low-background physics experiments will require the use of materials with unprecedented radio-purity. A gamma-counting facility at the Kimballton Underground Research Facility (KURF) has been commissioned to perform initial screening of materials for radioactivity primarily from nuclides in the 238U and 232Th decay chains, 40K and cosmic-ray induced isotopes. The facility consists of two commercial low-background high purity germanium (HPGe) detectors. A continuum background reduction better than a factor of 10 was achieved by going underground. This paper describes the facility, detector systems, analysis techniques and selected assay results.Comment: 7 pages, 7 figures. Submitted to NIM

Non-invasive measurement of hepatic venous oxygen saturation (ShvO₂) with quantitative susceptibility mapping in normal mouse liver and livers bearing colorectal metastases

PURPOSE: The purpose of this prospective study was to investigate the potential of QSM to noninvasively measure hepatic venous oxygen saturation (ShvO2). Materials & Methods: All animal studies were performed in accordance with the UK Home Office Animals Science Procedures Act (1986) and UK National Cancer Research Institute (NCRI) guidelines. QSM data was acquired from a cohort of mice (n=10) under both normoxic (medical air, 21% O2/balance N), and hyperoxic conditions (100% O2). Susceptibility measurements were taken from large branches of the portal and hepatic vein under each condition and were used to calculate venous oxygen saturation in each vessel. Blood was extracted from the IVC of three mice under norm- and hyperoxic conditions, and oxygen saturation was measured using a blood gas analyser to act as a gold standard. QSM data was also acquired from a cohort of mice bearing colorectal liver metastases (CRLM). SvO2 was calculated from susceptibility measurements made in the portal and hepatic veins, and compared to the healthy animals. RESULTS: SvO2 calculated from QSM measurements showed a significant increase of 14.93% in the portal vein (p < 0.05), and an increase of 21.39% in the hepatic vein (p < 0.01). Calculated results showed excellent agreement with those from the blood gas analyser (26.14% increase). ShvO2 was significantly lower in the disease cohort (30.18 ± 11.6%), than the healthy animals (52.67 ± 17.8%) (p < 0.05), but differences in the portal vein were not significant. CONCLUSION: QSM is a feasible tool for non-invasively measuring hepatic venous oxygen saturation and can detect differences in oxygen consumption in livers bearing colorectal metastases

The Role of Northeast Ohio Central Cities in the Regional Economy, 2000-2007

This report examines the four central cities in Northeast Ohio – Akron, Canton, Cleveland, and Youngstown — in the context of their metropolitan areas. A central city is the largest or most important city of a metropolitan area. A metropolitan area combines a large city with adjacent urbanized areas and peripheral areas that are closely bound to the center with strong ties to commuting, commerce, and a common labor market

The Role of Northeast Ohio Central Cities in the Regional Economy, 2000-2007

This report examines the four central cities in Northeast Ohio – Akron, Canton, Cleveland, and Youngstown — in the context of their metropolitan areas. A central city is the largest or most important city of a metropolitan area. A metropolitan area combines a large city with adjacent urbanized areas and peripheral areas that are closely bound to the center with strong ties to commuting, commerce, and a common labor market

Representation of behaviour change interventions and their evaluation: Development of the Upper Level of the Behaviour Change Intervention Ontology [version 2; peer review: 1 approved, 1 approved with reservations]

Background: Behaviour change interventions (BCI), their contexts and evaluation methods are heterogeneous, making it difficult to synthesise evidence and make recommendations for real-world policy and practice. Ontologies provide a means for addressing this. They represent knowledge formally as entities and relationships using a common language able to cross disciplinary boundaries and topic domains. This paper reports the development of the upper level of the Behaviour Change Intervention Ontology (BCIO), which provides a systematic way to characterise BCIs, their contexts and their evaluations. Methods: Development took place in four steps. (1) Entities and relationships were identified by behavioural and social science experts, based on their knowledge of evidence and theory, and their practical experience of behaviour change interventions and evaluations. (2) The outputs of the first step were critically examined by a wider group of experts, including the study ontology expert and those experienced in annotating relevant literature using the initial ontology entities. The outputs of the second step were tested by (3) feedback from three external international experts in ontologies and (4) application of the prototype upper-level BCIO to annotating published reports; this informed the final development of the upper-level BCIO. Results: The final upper-level BCIO specifies 42 entities, including the BCI scenario, elaborated across 21 entities and 7 relationship types, and the BCI evaluation study comprising 10 entities and 9 relationship types. BCI scenario entities include the behaviour change intervention (content and delivery), outcome behaviour, mechanism of action, and its context, which includes population and setting. These entities have corresponding entities relating to the planning and reporting of interventions and their evaluations. Conclusions: The upper level of the BCIO provides a comprehensive and systematic framework for representing BCIs, their contexts and their evaluations. Keyword

A multitude of fears coupled with excitement – children’s nursing students feelings prior to their first practice placement

Introduction: The first practice placement is of upmost importance for nursing students, causing considerable anxiety (Brien, 2012) and is part-way attributed to an increased risk of attrition during and after this experience (Melling, 2011). Providing students with adequate preparation for and support during placement is central to their learning and development, thus ensuring that they are fit for professional practice and registration at qualification (NMC, 2010). Aims: Taken from a study examining preparation for and support during the first practice placement as children’s nursing students, from the perspective of both students and professionals, this paper highlights the anxieties experienced by students and the strategies which helped prepare and support them during their introduction to nursing practice. Methods: Data were collected by a specifically designed self-administered questionnaire from 21 children’s nursing students prior to their first placement. A focus group was held with 5 students following the placement and used the Nominal Group technique to build consensus around what helped prepare them for practice and made suggestions for future preparation. Results: The questionnaire suggested that most students, although looking forward to their first clinical experience, were anxious to appear interested and helpful. Fitting in and getting on with their mentor(s) was also of concern. They were also fearful of making mistakes and keen to demonstrate their professionalism, despite being novices. The focus group highlighted that, of the activities provided by the university educators, meeting a senior student was the most helpful, followed by making pre-placement visits, telephone calls, peer support and the placement website. During the placement the relationship with their mentor(s) and other staff were highly valued. Discussion/Implications/Conclusions: Whilst the students had worries prior to placement, the preparation provided by both the hosting trust and the academic institution helped buffer the anxiety experienced, alongside a welcoming mentor. If the mentor was not particularly friendly the student attached themselves to someone who they perceived to be more helpful, in some cases that person being a third year student. Peer support and sharing of knowledge was therefore crucial and involving a senior student in a preparation for practice session is a clear recommendation. References: Brien, S (2012) Beyond Competence – Literature Review Final Report. Southampton University: HEA. Melling, S. (2011) Transition: an exploration of student nurse experience in their first practice placement. Unpublished D.Ed. thesis. University of Nottingham. Nursing and Midwifery Council (2010) Standards for Pre-Registration Nursing Education. London: NMC