ArkMAP: integrating genomic maps across species and data sources

BACKGROUND: The visualisation of genetic and genomic maps aligned within and between species and across data sources can be used to inform studies of genome evolution, assist genome assembly projects and aid gene discovery and identification. Whilst annotation, integration and exploration of assembled genome sequences is well supported, there are fewer tools available which can display genetic maps for less well-characterized species, and integrate these maps with annotated reference genomes to support cross species comparisons. RESULTS: We have developed a desktop application to draw and align genetic and genomic maps, retrieved from remote data sources or loaded as local files. Maps can be retrieved from our public map database ArkDB or from any Ensembl data source (i.e. Ensembl and Ensembl Genomes). By using the JEnsembl API, maps can be drawn for any release version of any of the thousands of species present in Ensembl data sources, allowing not only inter-specific comparisons, but also comparisons between different versions/revisions of assembled genomes. Maps can be aligned by relating identical or synonymous markers across maps, or through the gene homology/orthology relationship data stored in the Ensembl Compara databases, allowing ready visualization of regions of conserved synteny between species. The map drawing canvas is highly configurable, supports interactive exploration of maps, markers and relationships and allows export of publication quality graphics. CONCLUSIONS: ArkMAP allows users to draw and interactively explore gene and variation maps for any version of any annotated genome curated in the Ensembl data sources, and to integrate local mapping data. The maps and inter-map relationships drawn are highly configurable and ArkMAP may be used to produce publication quality graphics. ArkMAP is freely available as an auto-updating Java ‘Web Start’ application, or as a standalone archived application

Into the Labyrinth: Tales of Organizational Nomadism

Labyrinths and mazes have constituted significant spaces for tales of transformation, from prehistoric designs through the myth of the Minotaur and the pilgrimage design in Chartres cathedral to contemporary novels and pictorial representations. Labyrinths and labyrinthine designs can also commonly be found in present-day organizations. This text, based on an ethnographic study as well as on an analysis of academic discourse, explores their significance as symbol and as physical structure. Drawing upon the notion of transitional space, it presents labyrinths as an indelible part of human experience, an archetype, and a sensemaking tool for understanding and explaining organizational complexity. The unavoidable presence of labyrinthine structures is presented as a counterpoise to the reductionist tendency towards simplification, streamlining and staying on-message, allowing or demanding space for reflection, doubt and uncertainty

Nature

The ability to associate temporally segregated information and assign positive or negative valence to environmental cues is paramount for survival. Studies have shown that different basolateral amygdala (BLA) projections are potentiated following reward or punishment learning1–7. However, we do not yet understand how valence specific information is routed to the BLA neurons with the appropriate downstream projections. Nor do we understand how to reconcile the subsecond timescales of synaptic plasticity8–11 with the longer timescales separating the predictive cues from their outcomes. Here, we demonstrate that neurotensin (NT) neurons in the paraventricular nucleus of the thalamus (PVT) projecting to the BLA (PVT-BLA:NT) mediate valence assignment by exerting concentration-dependent modulation in BLA during associative learning. We found that optogenetic activation of the PVT-BLA:NT projection promotes reward learning, while PVT-BLA projection-specific Nt gene knockout augments punishment learning. Using genetically encoded calcium and NT sensors, we further revealed that both calcium dynamics within the PVT-BLA:NT projection and NT concentrations in the BLA are enhanced after reward learning and reduced after punishment learning. Finally, we showed that CRISPR-mediated knockout of the Nt gene in the PVT-BLA pathway blunts BLA neural dynamics and attenuates the preference to active behavioral strategies to reward and punishment predictive cues. Taken together, we have identified NT as a neuropeptide that signals valence in the BLA, and showed that NT is a critical neuromodulator that orchestrates positive and negative valence assignment in amygdala neurons by extending valence-specific plasticity to behaviorally-relevant timescales

Differences in access to Emergency Paediatric Intensive Care and care during Transport (DEPICT): study protocol for a mixed methods study

Introduction Following centralisation of UK paediatric intensive care, specialist retrieval teams were established who travel to general hospitals to stabilise and transport sick children to regional paediatric intensive care units (PICUs). There is national variation among these PICU retrieval teams (PICRTs) in terms of how quickly they reach the patient’s bedside and in the care provided during transport. The impact of these variations on clinical outcomes and the experience of stakeholders (patients, families and healthcare staff) is however unknown. The primary objective of this study is to address this evidence gap. Methods and analysis This mixed-methods project involves the following: (1) retrospective analysis of linked data from routine clinical audits (2014–2016) to assess the impact of service variations on 30-day mortality and other secondary clinical outcomes; (2) a prospective questionnaire study conducted at 24 PICUs and 9 associated PICRTs in England and Wales over a 12-month period in 2018 to collect experience data from parents of transported children as well as qualitative analysis of in-depth interviews with a purposive sample of patients, parents and staff to assess the impact of service variations on patient/family experience; (3) health economic evaluation analysing transport service costs (and other associated costs) against lives saved and longer term measurements of quality of life at 12 months in transported children and (4) mathematical modelling evaluating the costs and potential impact of different service configurations. A final work stream involves a series of stakeholder workshops to synthesise study findings and generate recommendations. Ethics and dissemination The study has been reviewed and approved by the Health Research Authority, ref: 2 18 569. Study results will be actively disseminated through peer-reviewed journals, conference presentations, social media, print and broadcast media, the internet and stakeholder workshops

Propylphosphonic anhydride-catalyzed tandem approach for biginelli reaction starting from alcohols

An efficient and highly convergent route to dihydropyrimidinones (DHPMs) has been developed by one-pot threecomponent oxidative cyclocondensation of a variety of alcohols, β-ketoesters/β-oxodithioester and urea in the presence of T3Pμ/ DMSO. This new approach consistently has the advantage of tandem and good yields (6588%). © 2014 The Chemical Society of Japan

Convenient synthesis of novel N-(5-allyl-7,7-difluoro)-4,5,6,7-tetrahydro- 2H-indazol-3-yl)-carboxymides

5-Allyl-7,7-difluoro-2-(2,4-difluorophenyl)-6-(4-methoxyphenyl)-4,5,6, 7-tetrahydro-2H-pyrazolo4,3-cpyridine-3-amine represents a fluorinated heterocyclic scaffold, potentially attractive. It was synthesized via Michael addition, Mannich reaction of the difluorinated ethyl bromoacetate with a benzotriazole derivative, followed by a Dieckmann condensation. Starting from simple materials, this efficient route which gives access to novel functionalized N-(5-allyl-7,7-dihalo)-4,5,6,7-tetrahydro-2H-indazol-3-yl)- carboxymides, was explored and adapted for parallel synthesis, resulting in a compound library

One-pot tandem approach for the synthesis of benzimidazoles and benzothiazoles from alcohols

Propylphosphonic anhydride ((R) T3P) has been demonstrated to be an efficient and mild reagent for the one-pot synthesis of benzimidazoles and benzothiazoles from variety of alcohols. Mild conditions, short reaction time, broad functional group tolerance, low epimerization, easy and quick isolation of the products, excellent chemo selectivity, and excellent yields are main advantages of this procedure. Thus, the present method is utilizing alcohols instead of aldehydes. (C) 2011 Elsevier Ltd. All rights reserved