Reports Of Conferences, Institutes, And Seminars

This quarter\u27s column offers coverage of multiple sessions from the 2016 Electronic Resources & Libraries (ER&L) Conference, held April 3–6, 2016, in Austin, Texas. Topics in serials acquisitions dominate the column, including reports on altmetrics, cost per use, demand-driven acquisitions, and scholarly communications and the use of subscriptions agents; ERMS, access, and knowledgebases are also featured

Does the tail wag the dog? : stock index futures

Includes bibliographic footnotes

Domain duplication, divergence, and loss events in vertebrate Msx paralogs reveal phylogenomically informed disease markers

<p>Abstract</p> <p>Background</p> <p>Msx originated early in animal evolution and is implicated in human genetic disorders. To reconstruct the functional evolution of Msx and inform the study of human mutations, we analyzed the phylogeny and synteny of 46 metazoan Msx proteins and tracked the duplication, diversification and loss of conserved motifs.</p> <p>Results</p> <p>Vertebrate Msx sequences sort into distinct Msx1, Msx2 and Msx3 clades. The sister-group relationship between <it>MSX1 </it>and <it>MSX2 </it>reflects their derivation from the 4p/5q chromosomal paralogon, a derivative of the original "MetaHox" cluster. We demonstrate physical linkage between Msx and other MetaHox genes (<it>Hmx</it>, <it>NK1</it>, <it>Emx</it>) in a cnidarian. Seven conserved domains, including two Groucho repression domains (N- and C-terminal), were present in the ancestral Msx. In cnidarians, the Groucho domains are highly similar. In vertebrate Msx1, the N-terminal Groucho domain is conserved, while the C-terminal domain diverged substantially, implying a novel function. In vertebrate Msx2 and Msx3, the C-terminal domain was lost. MSX1 mutations associated with ectodermal dysplasia or orofacial clefting disorders map to conserved domains in a non-random fashion.</p> <p>Conclusion</p> <p>Msx originated from a MetaHox ancestor that also gave rise to Tlx, Demox, NK, and possibly EHGbox, Hox and ParaHox genes. Duplication, divergence or loss of domains played a central role in the functional evolution of Msx. Duplicated domains allow pleiotropically expressed proteins to evolve new functions without disrupting existing interaction networks. Human missense sequence variants reside within evolutionarily conserved domains, likely disrupting protein function. This phylogenomic evaluation of candidate disease markers will inform clinical and functional studies.</p

A survey of fertiliser use in 2000 for grassland and arable crops.

End of Project ReportThe national farm survey data for 2000 was used as the basis for a fertilizer use survey. The farms which took part in the survey were randomly selected to represent the major farm systems and sizes using information from the CSO Census of Agriculture. Farms were classified into 6 main farm systems namely: dairying, dairying with other enterprises, cattle rearing, cattle with other systems, mainly sheep and tillage systems. These systems refer to the dominant enterprise in each group

A conserved cluster of three PRD-class homeobox genes (homeobrain, rx and orthopedia) in the Cnidaria and Protostomia

<p>Abstract</p> <p>Background</p> <p>Homeobox genes are a superclass of transcription factors with diverse developmental regulatory functions, which are found in plants, fungi and animals. In animals, several Antennapedia (ANTP)-class homeobox genes reside in extremely ancient gene clusters (for example, the Hox, ParaHox, and NKL clusters) and the evolution of these clusters has been implicated in the morphological diversification of animal bodyplans. By contrast, similarly ancient gene clusters have not been reported among the other classes of homeobox genes (that is, the LIM, POU, PRD and SIX classes).</p> <p>Results</p> <p>Using a combination of <it>in silico </it>queries and phylogenetic analyses, we found that a cluster of three PRD-class homeobox genes (<it>Homeobrain (hbn)</it>, <it>Rax (rx) </it>and <it>Orthopedia (otp)</it>) is present in cnidarians, insects and mollusks (a partial cluster comprising hbn and rx is present in the placozoan <it>Trichoplax adhaerens</it>). We failed to identify this 'HRO' cluster in deuterostomes; in fact, the <it>Homeobrain </it>gene appears to be missing from the chordate genomes we examined, although it is present in hemichordates and echinoderms. To illuminate the ancestral organization and function of this ancient cluster, we mapped the constituent genes against the assembled genome of a model cnidarian, the sea anemone <it>Nematostella vectensis</it>, and characterized their spatiotemporal expression using <it>in situ </it>hybridization. In <it>N. vectensis</it>, these genes reside in a span of 33 kb with the same gene order as previously reported in insects. Comparisons of genomic sequences and expressed sequence tags revealed the presence of alternative transcripts of Nv-otp and two highly unusual protein-coding polymorphisms in the terminal helix of the Nv-rx homeodomain. A population genetic survey revealed the Rx polymorphisms to be widespread in natural populations. During larval development, all three genes are expressed in the ectoderm, in non-overlapping territories along the oral-aboral axis, with distinct temporal expression.</p> <p>Conclusion</p> <p>We report the first evidence for a PRD-class homeobox cluster that appears to have been conserved since the time of the cnidarian-bilaterian ancestor, and possibly even earlier, given the presence of a partial cluster in the placozoan <it>Trichoplax</it>. Very similar clusters comprising these three genes exist in <it>Nematostella </it>and diverse protostomes. Interestingly, in chordates, one member of the ancestral cluster (<it>homeobrain</it>) has apparently been lost, and there is no linkage between <it>rx </it>and <it>orthopedia </it>in any of the vertebrates. In <it>Nematostella</it>, the spatial expression of these three genes along the body column is not colinear with their physical order in the cluster but the temporal expression is, therefore, using the terminology that has been applied to the Hox cluster genes, the HRO cluster would appear to exhibit temporal but not spatial colinearity. It remains to be seen whether the mechanisms responsible for the evolutionary conservation of the HRO cluster are the same mechanisms responsible for cohesion of the Hox cluster and other ANTP-class homeobox clusters that have been widely conserved throughout animal evolution.</p

Multifluorescence High‐Resolution Episcopic Microscopy for 3D Imaging of Adult Murine Organs

3D microscopy of large biological samples (>0.5 cm^{3})is transforming biological research. Many existing techniques require trade-offs between image resolution, sample size, and method complexity. A simple robust instrument with the potential to conduct large-volume 3D imaging currently exists in the form of the optical high-resolution episcopic microscopy (HREM). However, the development of the instrument to date is limited to single-fluorescent wavelength imaging with nonspecific eosin staining. Herein, developments to realize the potential of the HREM to become multifluorescent high-resolution episcopic microscopy (MF-HREM) are presented. MF-HREM is a serial-sectioning and block-facing wide-field fluorescence imaging technique, which does not require tissue clearing or optical sectioning. Multiple developments are detailed in sample preparation and image postprocessing to enable multiple specific stains in large samples and show how these enable segmentation and quantification of the data. The application of MF-HREM is demonstrated in a variety of biological contexts: 3D imaging of whole tumor vascular networks and tumor cell invasion in xenograft tumors up to 7.5 mm^{3} at resolutions of 2.75 μm, quantification of glomeruli volume in the adult mouse kidney, and quantification of vascular networks and white-matter track orientation in adult mouse brain

Delivering Behaviour Change Interventions: Development of a Mode of Delivery Ontology [version 1; peer review: 1 approved, 1 approved with reservations]

Background: Investigating and improving the effects of behaviour change interventions requires detailed and consistent specification of all aspects of interventions. An important feature of interventions is the way in which these are delivered, i.e. their mode of delivery. This paper describes an ontology for specifying the mode of delivery of interventions, which forms part of the Behaviour Change Intervention Ontology, currently being developed in the Wellcome Trust funded Human Behaviour-Change Project. / Methods: The Mode of Delivery Ontology was developed in an iterative process of annotating behaviour change interventions evaluation reports, and consulting with expert stakeholders. It consisted of seven steps: 1) annotation of 110 intervention reports to develop a preliminary classification of modes of delivery; 2) open review from international experts (n=25); 3) second round of annotations with 55 reports to test inter-rater reliability and identify limitations; 4) second round of expert review feedback (n=16); 5) final round of testing of the refined ontology by two annotators familiar and two annotators unfamiliar with the ontology; 6) specification of ontological relationships between entities; and 7) transformation into a machine-readable format using the Web Ontology Language (OWL) language and publishing online. / Results: The resulting ontology is a four-level hierarchical structure comprising 65 unique modes of delivery, organised by 15 upper-level classes: Informational, Environmental change, Somatic, Somatic alteration, Individual-based/ Pair-based /Group-based, Uni-directional/Interactional, Synchronous/ Asynchronous, Push/ Pull, Gamification, Arts feature. Relationships between entities consist of is_a. Inter-rater reliability of the Mode of Delivery Ontology for annotating intervention evaluation reports was a=0.80 (very good) for those familiar with the ontology and a= 0.58 (acceptable) for those unfamiliar with it. / Conclusion: The ontology can be used for both annotating and writing behaviour change intervention evaluation reports in a consistent and coherent manner, thereby improving evidence comparison, synthesis, replication, and implementation of effective interventions

Delivering Behaviour Change Interventions: Development of a Mode of Delivery Ontology [version 2; peer review: 2 approved]

Background: Investigating and improving the effects of behaviour change interventions requires detailed and consistent specification of all aspects of interventions. An important feature of interventions is the way in which these are delivered, i.e. their mode of delivery. This paper describes an ontology for specifying the mode of delivery of interventions, which forms part of the Behaviour Change Intervention Ontology, currently being developed in the Wellcome Trust funded Human Behaviour-Change Project. Methods: The Mode of Delivery Ontology was developed in an iterative process of annotating behaviour change interventions evaluation reports, and consulting with expert stakeholders. It consisted of seven steps: 1) annotation of 110 intervention reports to develop a preliminary classification of modes of delivery; 2) open review from international experts (n=25); 3) second round of annotations with 55 reports to test inter-rater reliability and identify limitations; 4) second round of expert review feedback (n=16); 5) final round of testing of the refined ontology by two annotators familiar and two annotators unfamiliar with the ontology; 6) specification of ontological relationships between entities; and 7) transformation into a machine-readable format using the Web Ontology Language (OWL) and publishing online. Results: The resulting ontology is a four-level hierarchical structure comprising 65 unique modes of delivery, organised by 15 upper-level classes: Informational, Environmental change, Somatic, Somatic alteration, Individual-based/ Pair-based /Group-based, Uni-directional/Interactional, Synchronous/ Asynchronous, Push/ Pull, Gamification, Arts feature. Relationships between entities consist of is_a. Inter-rater reliability of the Mode of Delivery Ontology for annotating intervention evaluation reports was a=0.80 (very good) for those familiar with the ontology and a= 0.58 (acceptable) for those unfamiliar with it. Conclusion: The ontology can be used for both annotating and writing behaviour change intervention evaluation reports in a consistent and coherent manner, thereby improving evidence comparison, synthesis, replication, and implementation of effective interventions

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 cnidarian-bilaterian ancestor possessed at least 56 homeoboxes: evidence from the starlet sea anemone, Nematostella vectensis

BACKGROUND: Homeodomain transcription factors are key components in the developmental toolkits of animals. While this gene superclass predates the evolutionary split between animals, plants, and fungi, many homeobox genes appear unique to animals. The origin of particular homeobox genes may, therefore, be associated with the evolution of particular animal traits. Here we report the first near-complete set of homeodomains from a basal (diploblastic) animal. RESULTS: Phylogenetic analyses were performed on 130 homeodomains from the sequenced genome of the sea anemone Nematostella vectensis along with 228 homeodomains from human and 97 homeodomains from Drosophila. The Nematostella homeodomains appear to be distributed among established homeodomain classes in the following fashion: 72 ANTP class; one HNF class; four LIM class; five POU class; 33 PRD class; five SINE class; and six TALE class. For four of the Nematostella homeodomains, there is disagreement between neighbor-joining and Bayesian trees regarding their class membership. A putative Nematostella CUT class gene is also identified. CONCLUSION: The homeodomain superclass underwent extensive radiations prior to the evolutionary split between Cnidaria and Bilateria. Fifty-six homeodomain families found in human and/or fruit fly are also found in Nematostella, though seventeen families shared by human and fly appear absent in Nematostella. Homeodomain loss is also apparent in the bilaterian taxa: eight homeodomain families shared by Drosophila and Nematostella appear absent from human (CG13424, EMXLX, HOMEOBRAIN, MSXLX, NK7, REPO, ROUGH, and UNC4), and six homeodomain families shared by human and Nematostella appear absent from fruit fly (ALX, DMBX, DUX, HNF, POU1, and VAX)