SAMP, the Simple Application Messaging Protocol: Letting applications talk to each other

SAMP, the Simple Application Messaging Protocol, is a hub-based communication standard for the exchange of data and control between participating client applications. It has been developed within the context of the Virtual Observatory with the aim of enabling specialised data analysis tools to cooperate as a loosely integrated suite, and is now in use by many and varied desktop and web-based applications dealing with astronomical data. This paper reviews the requirements and design principles that led to SAMP's specification, provides a high-level description of the protocol, and discusses some of its common and possible future usage patterns, with particular attention to those factors that have aided its success in practice.Comment: 12 pages, 3 figures. Accepted for Virtual Observatory special issue of Astronomy and Computin

IVOA Recommendation: SAMP - Simple Application Messaging Protocol Version 1.3

SAMP is a messaging protocol that enables astronomy software tools to interoperate and communicate. IVOA members have recognised that building a monolithic tool that attempts to fulfil all the requirements of all users is impractical, and it is a better use of our limited resources to enable individual tools to work together better. One element of this is defining common file formats for the exchange of data between different applications. Another important component is a messaging system that enables the applications to share data and take advantage of each other's functionality. SAMP builds on the success of a prior messaging protocol, PLASTIC, which has been in use since 2006 in over a dozen astronomy applications and has proven popular with users and developers. It is also intended to form a framework for more general messaging requirements

Recommendations for regulating the environmental risk of shedding for gene therapy and oncolytic viruses in Canada

Canadian academic and industry stakeholders are concerned about the inclusion of virus-like particles or sub-viral particles in the definition of New Substances Notification Regulations for Organisms (NSNR(O)) which impacts clinical cell and gene therapy and commercialization. The requirement of an independent 120 days Environment and Climate Change Canada (ECCC) review preceding a Health Canada review on quality and environmental concerns places an additional burden on Sponsors submitting clinical trial applications (CTA) and/or New Drug Submissions (NDS). A workshop initiated by CellCAN and BIOTECanada with participants from Environment and Climate Change Canada, Health Canada, the Public Health Agency of Canada and Innovation, Science and Economic Development (Ottawa, March 19, 2018) with invited stakeholders discussed approaches to streamline the environmental review process. The following main recommendations were the focus of the workshop: A regulatory policy to clarify Canadian Environmental Protection Act (CEPA)\u27s definition of living organism. This is currently defined as a substance that is an animate product of biotechnology. A regulatory policy could potentially exempt human cells touched by biotechnology for use in human medicinal products from this definition to clarify any unintended overreach of CEPA, particularly as it applies to non-genetically modified cell therapies.A guidance document to better interpret NSNR(O) Schedule 1 requirements by CTA/NDS sponsors to satisfy the environmental review process.An amendment at the level of regulations, to the NSNR (O) to create a deferment to postpone environmental assessment of micro-organisms used in the manufacturing during investigational clinical trials (pre-market stage). The regulations would apply at the time of market authorization evaluation and review, when sufficient clinical data on vector shedding has been collected, as part of the investigational clinical trials.Amendment to Schedule 4 of the CEPA to include the Food and Drugs Act and Regulations (Food and Drugs Act /FDR) as an exclusion to the application of CEPA. This would remove the current dual regulation of cell and gene therapies by both CEPA and Food and Drugs Act /FDR. These recommendations and other options were discussed at the workshop. These recommendations if adopted will significantly streamline the current regulatory burden and harmonize environmental assessment requirements with other jurisdictions

Hierarchical progressive surveys. Multi-resolution HEALPix data structures for astronomical images, catalogues, and 3-dimensional data cubes

Scientific exploitation of the ever increasing volumes of astronomical data requires efficient and practical methods for data access, visualisation, and analysis. Hierarchical sky tessellation techniques enable a multi-resolution approach to organising data on angular scales from the full sky down to the individual image pixels. Aims. We aim to show that the Hierarchical progressive survey (HiPS) scheme for describing astronomical images, source catalogues, and three-dimensional data cubes is a practical solution to managing large volumes of heterogeneous data and that it enables a new level of scientific interoperability across large collections of data of these different data types. Methods. HiPS uses the HEALPix tessellation of the sphere to define a hierarchical tile and pixel structure to describe and organise astronomical data. HiPS is designed to conserve the scientific properties of the data alongside both visualisation considerations and emphasis on the ease of implementation. We describe the development of HiPS to manage a large number of diverse image surveys, as well as the extension of hierarchical image systems to cube and catalogue data. We demonstrate the interoperability of HiPS and Multi-Order Coverage (MOC) maps and highlight the HiPS mechanism to provide links to the original data. Results. Hierarchical progressive surveys have been generated by various data centres and groups for ~200 data collections including many wide area sky surveys, and archives of pointed observations. These can be accessed and visualised in Aladin, Aladin Lite, and other applications. HiPS provides a basis for further innovations in the use of hierarchical data structures to facilitate the description and statistical analysis of large astronomical data sets.Comment: 21 pages, 6 figures. Accepted for publication in Astronomy & Astrophysic

Normative Percent Differences between Inter-day and Inter-Limb Upper Extremity Volume in Healthy Adult Females

Lymphedema is a frequent complication of breast cancer treatments and can become a chronic condition. Diagnosing lymphedema early is essential to reverse the condition and prevent future complications. Segmental circumferential measurements are the most efficient, reliable, and clinically relevant method to measure UE volume. Diagnosing pre-clinical lymphedema requires an understanding of normal inter-day and inter-limb volume differences among healthy women.https://ecommons.udayton.edu/dpt_symposium/1016/thumbnail.jp

AnnoTALE : bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences

Transcription activator-like effectors (TALEs) are virulence factors, produced by the bacterial plant-pathogen Xanthomonas, that function as gene activators inside plant cells. Although the contribution of individual TALEs to infectivity has been shown, the specific roles of most TALEs, and the overall TALE diversity in Xanthomonas spp. is not known. TALEs possess a highly repetitive DNA-binding domain, which is notoriously difficult to sequence. Here, we describe an improved method for characterizing TALE genes by the use of PacBio sequencing. We present 'AnnoTALE', a suite of applications for the analysis and annotation of TALE genes from Xanthomonas genomes, and for grouping similar TALEs into classes. Based on these classes, we propose a unified nomenclature for Xanthomonas TALEs that reveals similarities pointing to related functionalities. This new classification enables us to compare related TALEs and to identify base substitutions responsible for the evolution of TALE specificities

Liberating Visions: Religion and the Challenge of Change in Maine,1820 to the Present

Liberating Visions: Religion and the Challenge of Change in Maine, 1820 to the Present. Each of the Sampson Center’s three scholars has crafted an original essay related to one of the Sampson Center collections—African-American, Judaic, and Lesbian, Gay, Bisexual, and Transgender—thereby reflecting on how religious institutions have fostered minority identity and have framed social and cultural transformation. Table of Contents: Religion and Transformation (Joseph S. Wood, Provost and Vice President for Academic Affairs) Jean Byers Sampson Center for Diversity in Maine Programming (Susie Bock, Director, Sampson Center for Diversity in Maine and Head, USM Special Collections) The African American Collection “There’s a Blessing in Pressing:” Change in Maine’s African American Churches (Maureen Elgersman Lee, Associate Professor of History and Faculty Scholar for USM’s African American Collection) The Judaica Collection “Orthodox and Yet thoroughly Liberal:” Jews and Judaism in Maine Between Tradition and Change (Abraham J. Peck, Director, Academic Council for Post-Holocaust Christian, Jewish, and Islamic Studies and Scholar-in-residence for USM’s Judaica Collection) The Lesbian, Gay, Bisexual, and Transgender Collection Coming Out, Going In: Spirituality and Religion in Maine’s LGBT Communities (Howard M. Solomon, Adjunct Professor of History and Scholar-in-Residence for USM’s LGBT Collection)https://digitalcommons.usm.maine.edu/event_catalog/1001/thumbnail.jp

Reviewing the Carbonation Resistance of Concrete

The paper reviews the studies on one of the important durability properties of concrete i.e. Carbonation. One of the main causes of deterioration of concrete is carbonation, which occurs when carbon dioxide (CO2) penetrates the concrete’s porous system to create an environment with lower pH around the reinforcement in which corrosion can proceed. Carbonation is a major cause of degradation of concrete structures leading to expensive maintenance and conservation operations. Herein, the importance, process and effect of various parameters such as water/cement ratio, water/binder ratio, curing conditions, concrete cover, super plasticizers, type of aggregates, grade of concrete, porosity, contaminants, compaction, gas permeability, supplementary cementitious materials (SCMs)/ admixtures on the carbonation of concrete has been reviewed. Various methods for estimating the carbonation depth are also reported briefl

Increased fibrosis in a mouse model of anti-laminin 332 mucous membrane pemphigoid remains unaltered by inhibition of aldehyde dehydrogenase

Mucous membrane pemphigoid (MMP) is an autoimmune blistering disease characterized by autoantibodies against the basal membrane zone of skin and surface-close epithelia and predominant mucosal lesions. The oral cavity and conjunctivae are most frequently affected, albeit clinical manifestations can also occur on the skin. MMP-associated lesions outside the oral cavity typically lead to scarring. Mechanisms underlying scarring are largely unknown in MMP and effective treatment options are limited. Herein, we assessed the collagen architecture in tissue samples of an antibody-transfer mouse model of anti-laminin-332 MMP. In MMP mice, increased collagen fibril density was observed in skin and conjunctival lesions compared to mice injected with normal rabbit IgG. The extracellular matrix of MMP skin samples also showed altered post-translational collagen cross-linking with increased levels of both lysine- and hydroxylysine-derived collagen crosslinks supporting the fibrotic phenotype in experimental MMP compared to control animals. In addition, we evaluated a potential anti-fibrotic therapy in experimental anti-laminin-332 MMP using disulfiram, an inhibitor of the aldehyde dehydrogenase (ALDH), which has been implicated in immune-mediated mucosal scarring. In addition, disulfiram also acts as a copper chelator that was shown to block lysyl oxidase activity, an enzyme involved in formation of collagen crosslinks. Topical use of disulfiram (300 μM in 2 [w/v] methocel) did not improve ocular lesions in experimental MMP over the 12-day treatment period in disulfiram-treated mice compared to vehicle-treated mice (n=8/group). Furthermore, C57BL6/J mice (n=8/group) were treated prophylactically with 200 mg/kg p.o. disulfiram or the solvent once daily over a period of 12 days. Systemic treatment did not show any reduction in the severity of oral and ocular lesions in MMP mice, albeit some improvement in skin lesions was observed in disulfiram- vs. vehicle-treated mice (p=0.052). No reduction in fibrosis was seen, as assessed by immunohistochemistry. Whilst blocking of ALDH failed to significantly ameliorate disease activity, our data provide new insight into fibrotic processes highlighting changes in the collagenous matrix and cross-linking patterns in IgG-mediated MMP