Conservation Team Research Articles

Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database.

Cardiovascular diseases are complex diseases caused by a combination of genetic and environmental factors. To facilitate progress in complex disease research, the Rat Genome Database (RGD) provides the community with a disease portal where genome objects and biological data related to cardiovascular diseases are systematically organized. The purpose of this study is to present biocuration at RGD, including disease, genetic, and pathway data. The RGD curation team uses controlled vocabularies/ontologies to organize data curated from the published literature or imported from disease and pathway databases. These organized annotations are associated with genes, strains, and quantitative trait loci (QTLs), thus linking functional annotations to genome objects. Screen shots from the web pages are used to demonstrate the organization of annotations at RGD. The human cardiovascular disease genes identified by annotations were grouped according to data sources and their annotation profiles were compared by in-house tools and other enrichment tools available to the public. The analysis results show that the imported cardiovascular disease genes from ClinVar and OMIM are functionally different from the RGD manually curated genes in terms of pathway and Gene Ontology annotations. The inclusion of disease genes from other databases enriches the collection of disease genes not only in quantity but also in quality.

Caught Between Mediation and Local Dependence: Understanding the Role of Non-government Organisations in Co-management of Coastal Resources in Eastern Indonesia

ABSTRACTResolving contestations over resource management rights around coastal villages remains a focal challenge for co-management initiatives in remote coastal zones. Contemporary socio-political settings increasingly see local people having to negotiate between local long-standing (horizontal) relationships and new emerging (vertical) relationships which involve collaborations with outside actors who try to assume neutral mediating positions. Using two conflicts, this article examines the rise and fall of a participatory coastal resource management program in eastern Indonesia involving a fishing community engaged in a co-management arrangement with a conservation non-government organisation (NGO). An actor-oriented approach is applied to analyse how these conflicts shape, drive and direct collaborations across the community–NGO interface. We discuss how these impact the implementation of the conservation ethics and sustainable natural resource management practices, and show how particular mediating capacities of an NGO may overcome, and even build forth on, conflict in some contexts but fall short in others. We argue that local resource user groups and conservation teams operate according to strong local relationships that are entrenched in cultural–historical hierarchies of power. We moreover note that these local relationships significantly influence the extent of neutrality of external groups in their mediating, coordinating and technical advisory roles. The effectiveness of co-management partnerships hinges on the ability to balance actors’ mediating capacity with their local dependence for operation.

To Touch and Be Touched

In my article, I will present as a case study the collection exhibition shown at the Museum of Contemporary Art Kiasma in 2016.[1] The starting point for the exhibition was the metaphor of touch. As a concept, touch is ambivalent: it is more intimate than sight, which has been the traditional metaphor for knowledge in Western thinking. Yet touching is also about grasping or understanding, as in it we are taking hold of something. Our curatorial team, Eija Aarnio, Arja Miller, and myself, was interested in touch early on, because with it the distance to the observed is lost: when touching something we, too, are being touched. To be clear, we did not want to create an exhibition where spectators are actually able to touch. Instead, we were looking at the collections of the museum and searching for artworks that would “touch” us—works that were able get under our skin. While forming the conceptual core of the exhibition, our curatorial team recognized a tension in the way in which “touchy issues,” affects and emotions, are perceived in our society. On the one hand, we were interested in emotions and affects raised by the artworks. We wanted to focus on the immersive dimension of the art that seems to escape verbalization, a dimension that makes use of the multisensory experience and addresses the viewer in a direct manner. On the other hand, we also became aware of how society in general has been taken over by an emotional surge. If previously feelings and emotions were not meant to be shown in public, today they have become commonplace. What was emotional and affective seems no longer to be private, but shared and public.[2] In fact, strong emotions seem to be a prerequisite for success, be it a matter of reality television or politics. This is also connected to the search for extreme emotions and experiences, an aspect we felt needed to be included in the exhibition—not the least because in museums’ competition for audiences, the experience-laden works are often seen as an answer.

Black Mountain and Beyond – Research Practices between Universities and Museums

In 2013, everything began with a few general questions. How can universities and museums benefit from each other? How can they complement one another? Where are their thresholds, and where are common grounds? What is their educational agenda? And finally, can they unite theoretical and curatorial endeavors into, well, what exactly? How could they actually bring theory and practice together? In other words, how could students, scholars, curators, and artists cooperate within one project? As a small team based at the Institute for Theater Studies at Freie Universität Berlin—namely Verena Kittel, Annette Jael Lehmann, and Anna-Lena Werner—we wanted to find answers for these questions, and started an in-depth conversation with a part of the curatorial team of Hamburger Bahnhof – Museum für Gegenwart – Berlin, about opportunities to collaborate. The university is in need of practice, of social experiences with people, and of the expertise of preserving and exhibiting. In turn, the museum is in need of research, of alternatives to public programs, and of creating a fundamental analysis of art historical events, aesthetic questions, and philosophical contributions. On both sides there was not only a desire for supplementation, but also a frustration about the growing economization and instrumentalization of educational institutions. What we were looking for might sound idealistic, but we later figured that this attribute was exactly key to our aim: developing a collaborative practice-based research.

The importance of multidisciplinary work within archaeological conservation projects: assembly of the Staffordshire Hoard die-impressed sheets

AbstractThe Anglo-Saxon Staffordshire Hoard contains, alongside the well-publicised gold and silver objects, a large collection of over 1000 fragments of die-impressed silver sheet or foil. The majority of these fragments probably decorated one high-status helmet, but were removed from it before burial. These fragments constitute a significant element of the collection, and their conservation, analysis and reassembly forms a major strand of the wider Staffordshire Hoard research project. This paper provides a background to the die-impressed sheets as a class of object within the hoard, and examines the multidisciplinary approach taken by the archaeological conservation team to this challenging but interesting body of material. It explores how this approach has contributed significantly to the results that are being delivered, particularly by the recognition of the dies used to create the impressed sheets, and from this, the development of their overall interpretation.

Interview with Bryony Dixon, British Film Institute National Archive, January 13, 2015

FIGURE 1. Bryony Dixon, curator of silent film, British Film Institute (BFI) National Archive. > victoria duckett:Thank you, Bryony, for agreeing to talk with me today. I thought we would begin with an explanation of what you do professionally. What do you do, what is your post, and what is your job? > bryony dixon:I'm one of the curators at the BFI National Archive, which is the United Kingdom's national collection of film. I'm one of a team of curators. There are curators that specialize in all different subjects and categories of the archive. We have, broadly speaking, fiction, nonfiction, and television. Then there are two “odd” curators: one deals with artists, film, video, and I deal with silent film, because it is a sort of category in and of itself, and there are slightly different issues, perhaps, with dealing with silent film in terms of how you might treat it. It also accounts for a good, solid block of cinema's history, film's history. > vd:Has there always been silent film curation? You're a curator, you're a programmer; do you restore? > bd:Yes, we do all that. Each of the curators does all aspects of the job, which used to be—in former days, before about 2005 [when the curatorial unit was formed]—done in a different way. It used to be a kind of linear method, so you'd have somebody acquiring the films, you'd have somebody doing technical work on the films, you'd have people doing things like cataloguing, and then you'd have someone at the end doing things like access, programming, taking it out and about in the world, doing educational work, and that kind of thing. What the reorganization into a curatorial model did was to give people specialist subjects. So now, if I am doing silent …

Alternative methodology for traditional interventions: A colonial painting and its lining with the nap bond method

Abstract Lining treatments used in the conservation-restoration field can be classified according to the adhesive used. Traditional methods include those based on glue-starch and wax-resin whilst those using synthetic adhesives are considered alternative methods. Rise of new materials and mechanical equipment like the low-pressure table expanded possibilities of intervention. However, alternative methods require previous exhaustive testing of procedures, tools and supplies. This paper describes research carried out by an interdisciplinary team of conservators, historians and chemists from the IIPC-TAREA that elucidated fundamental aspects of a painting of San Luis Gonzaga from the South American colonial period, deteriorated but with an important documentary value. In the case here presented a minimal intervention restoration criterion was applied and the nap bond method used proved to be the most suitable alternative lining for this particular situation.

Reportage: Small exhibits, major steps: four post-Soviet Jewish museums

The small-scale Jewish museums in Chișinău (Moldova), Odessa (Ukraine), Lviv (Ukraine), and Minsk (Belarus) narrate the history of once flourishing Jewish communities, and document their disappearance. Their permanent collections, which consist of the private belongings that emigrating Jewish families gave them in the early 1990s, are the basis for their exhibitions. These museums opened in the early 2000s under the auspices of local Jewish cultural and charitable organizations. They are not state museums and lack a solid financial foundation and stable professional curatorial team. Much depends on the personal vision of their directors. Despite both limited exhibition space and locations not frequented by tourists, these museums are important agents of memory and identity for local Jewish and non-Jewish audiences, as well as for international visitors.

Documentation and dissemination of the sculptural elements of Canada's Parliamentary Buildings: Methodology development and evolution, a case study

Abstract. Parliament Hill consists of four historic gothic revival buildings, which form part of the Parliament Buildings National Historic Site of Canada in the National Capital of Ottawa. There are more than 2000 masonry sculptural elements throughout the four buildings. Three of the buildings are in the middle of multi-year rehabilitation projects. Extensive Heritage Documentation is being undertaken to support various activities and conservation teams throughout the interior and exterior of the buildings while also serving as a key posterity records. One of the significant heritage documentation projects is the 3D digitization of the 2000+ heritage character defining sculptural elements. The Heritage Conservation Directorate (HCD) of Public Works and Government Services Canada (PWGSC) was tasked by the Parliamentary Precinct Branch (PPB) of PWGSC to document these character defining elements. The sculptures vary in size from as small as 100mm in width to up to 2 meters in size. This project is in its third year and much has been learned and researched about the most appropriate and efficient means by which to document these elements. Although a methodology was in place to document the sculptures at the inception of the project, it has gone through several iterations in order to improve the gathered data, and in turn increase the efficiency, quality and speed of data acquisition. This paper will describe the evolution of the methodology, as well as the rationale for the alterations in technique. With over 600 of the approximate 2000 (heritage character defining) sculptural elements captured to date, the project is entering a critical phase where an efficient and effective method for sharing and disseminating the information to a wide audience is being explored and evaluated. The end result is intended to allow the client (PPB) and the general public a way to look at and interactively manipulate the viewpoint of each digital model. This will provide a unique opportunity for a wide audience to evaluate and appreciate these elaborate works of art. This database of information can also be of use for academic study and research. To date the data captured by HCD has been utilized by conservation professionals and by the Carleton Immersive Media Studio (CIMS) of Carleton University. HCD has partnered with CIMS to explore a wide variety of potential uses for the data including the creation of 2D-drawings, stone carving profile templates, 3D printed scale models, CNC carved maquettes, robotic stone carving, and digitally-designed replacement elements. CIMS and HCD have tested the limits of digital technologies to assist stone carvers in restoring carved elements while also learning from the sculptors and masons to better understand their approach when conserving or restoring a sculptural element. Examples of how the conservation team, specifically the stone carvers have been working with the data and technology will also be presented.

The Application of 3D Laser Scanning in the Survey and Measuring of Guyue Bridge of Song Dynasty in Yiwu City

Abstract. It is believed that folding-arch is the transitional form from beam to curved arch. Guyue Bridge, built in JiaDing 6year (A.D 1213) of Southern Song Dynasty, located in Yiwu City, Zhejiang Province in China, is one of typical objective examples for this transition. It possesses high historical, scientific, artistic, cultural and social values. Facing severe environmental problems and deteriorated heritage situation, our conservation team selected 3D laser scanning as basic recording method, then acquired the precise threedimensional model. Measured the fundamental dimension and components’ sizes, we analysed its stable state. Moreover, combined with historic documents, we reasonably speculated and calculated the original sizes and important scales at the building time. These findings have significant research values as well as evidential meanings for future conservation.

Finding small molecules for the 'next Ebola'.

The current Ebola virus epidemic may provide some suggestions of how we can better prepare for the next pathogen outbreak. We propose several cost effective steps that could be taken that would impact the discovery and use of small molecule therapeutics including: 1. text mine the literature, 2. patent assignees and/or inventors should openly declare their relevant filings, 3. reagents and assays could be commoditized, 4. using manual curation to enhance database links, 5. engage database and curation teams, 6. consider open science approaches, 7. adapt the "box" model for shareable reference compounds, and 8. involve the physician's perspective.

Application of comparative biology in GO functional annotation: the mouse model.

The Gene Ontology (GO) is an important component of modern biological knowledge representation with great utility for computational analysis of genomic and genetic data. The Gene Ontology Consortium (GOC) consists of a large team of contributors including curation teams from most model organism database groups as well as curation teams focused on representation of data relevant to specific human diseases. Key to the generation of consistent and comprehensive annotations is the development and use of shared standards and measures of curation quality. The GOC engages all contributors to work to a defined standard of curation that is presented here in the context of annotation of genes in the laboratory mouse. Comprehensive understanding of the origin, epistemology, and coverage of GO annotations is essential for most effective use of GO resources. Here the application of comparative approaches to capturing functional data in the mouse system is described.

Finding small molecules for the ‘next Ebola’

The current Ebola virus epidemic may provide some suggestions of how we can better prepare for the next pathogen outbreak. We propose several cost effective steps that could be taken that would impact the discovery and use of small molecule therapeutics including: 1. text mine the literature, 2. patent assignees and/or inventors should openly declare their relevant filings, 3. reagents and assays could be commoditized, 4. using manual curation to enhance database links, 5. engage database and curation teams, 6. consider open science approaches, 7. adapt the “box” model for shareable reference compounds, and 8. involve the physician’s perspective.

Evaluation of Non-Reference Quality Assessment Algorithms to Curate Born-Digital Video Collections

As the production, the variety, and the consumption of born-digital video grows, so does the demand for acquiring, curating and preserving large-scale digital video collections. A multidisciplinary team of curators, computer scientists and video engineers we explore the use of Non-Reference Image and Video Quality Algorithms (I/VQA), specifically of BRISQUE in this paper, to automatically derive ranges of video quality. An important characteristic of these algorithms is that they are modeled to human perception. We run the algorithms in a High Performance Computing (HPC) environment to obtain results for many videos at the same time, accelerating time to results and precision in computing per-frame and per-video quality assessment scores. Results, which were evaluated quantitatively and qualitatively, suggest that BRISQUE identifies the distortions in which it was trained, and performs well in videos that have natural scenes and do not have drastic scene changes. While we found that this particular model is not apt for evaluating collections with varied content, the results suggest that research into other I/VQA models is promising, and that their implementation at large scale can narrow the problem of curating very digital video collections and lead to preservation and access decisions based on informed priorities.

Most highly expressed protein-coding genes have a single dominant isoform.

Although eukaryotic cells express a wide range of alternatively spliced transcripts, it is not clear whether genes tend to express a range of transcripts simultaneously across cells, or produce dominant isoforms in a manner that is either tissue-specific or regardless of tissue. To date, large-scale investigations into the pattern of transcript expression across distinct tissues have produced contradictory results. Here, we attempt to determine whether genes express a dominant splice variant at the protein level. We interrogate peptides from eight large-scale human proteomics experiments and databases and find that there is a single dominant protein isoform, irrespective of tissue or cell type, for the vast majority of the protein-coding genes in these experiments, in partial agreement with the conclusions from the most recent large-scale RNAseq study. Remarkably, the dominant isoforms from the experimental proteomics analyses coincided overwhelmingly with the reference isoforms selected by two completely orthogonal sources, the consensus coding sequence variants, which are agreed upon by separate manual genome curation teams, and the principal isoforms from the APPRIS database, predicted automatically from the conservation of protein sequence, structure, and function.

Finding small molecules for the 'next Ebola'.

The current Ebola virus epidemic may provide some suggestions of how we can better prepare for the next pathogen outbreak. We propose several cost effective steps that could be taken that would impact the discovery and use of small molecule therapeutics including: 1. text mine the literature, 2. patent assignees and/or inventors should openly declare their relevant filings, 3. reagents and assays could be commoditized, 4. using manual curation to enhance database links, 5. engage database and curation teams, 6. consider open science approaches, 7. adapt the "box" model for shareable reference compounds, and 8. involve the physician's perspective.

The Fine Art of Being Indigenous

In 1973 I was part of the curatorial team that organized a major exhibition on the art of contemporary Haudenosaunee (Six Nations, or Iroquois) for the Everson Museum of Art in Syracuse, New York. ...

Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy.

The diverse phenotypes of living organisms have been described for centuries, and though they may be digitized, they are not readily available in a computable form. Using over 100 morphological studies, the Phenoscape project has demonstrated that by annotating characters with community ontology terms, links between novel species anatomy and the genes that may underlie them can be made. But given the enormity of the legacy literature, how can this largely unexploited wealth of descriptive data be rendered amenable to large-scale computation? To identify the bottlenecks, we quantified the time involved in the major aspects of phenotype curation as we annotated characters from the vertebrate phylogenetic systematics literature. This involves attaching fully computable logical expressions consisting of ontology terms to the descriptions in character-by-taxon matrices. The workflow consists of: (i) data preparation, (ii) phenotype annotation, (iii) ontology development and (iv) curation team discussions and software development feedback. Our results showed that the completion of this work required two person-years by a team of two post-docs, a lead data curator, and students. Manual data preparation required close to 13% of the effort. This part in particular could be reduced substantially with better community data practices, such as depositing fully populated matrices in public repositories. Phenotype annotation required ∼40% of the effort. We are working to make this more efficient with Natural Language Processing tools. Ontology development (40%), however, remains a highly manual task requiring domain (anatomical) expertise and use of specialized software. The large overhead required for data preparation and ontology development contributed to a low annotation rate of approximately two characters per hour, compared with 14 characters per hour when activity was restricted to character annotation. Unlocking the potential of the vast stores of morphological descriptions requires better tools for efficiently processing natural language, and better community practices towards a born-digital morphology.Database URL: http://kb.phenoscape.org

UC Cooperative Extension helps Californians use water wisely

UC Cooperative Extension helps Californians use water wisely

Carcass Traits and Growth Curve Parameters in Santa Inês Sheep

The aim of this study was to evaluate carcass traits and growth curves in Santa Inês sheep. We used weight data collected from 51 developing sheep from birth to 336 days of age, from March 2012 to May 2013. The sheep belonged to the Core Conservation Team of the Federal University of Piauí and were located at two properties, one in Bom Jesus - PI and one in Cristino Castro - PI. The model used to represent the growth curve was the Gompertz model, in which the model parameters were estimated by using a Gauss-Newton algorithm modified by the NLIN procedure in SAS. The rib eye area (REA) and subcutaneous backfat thickness (SBT) of lambs were evaluated by ultrasound. These results were used to study the growth curve and the relationship between the estimated model growth curve parameters and the evaluated carcass traits. The estimated correlation between A and K was negative. The correlations between the carcass traits (REA and SBT) and the growth curve parameters (A and K) show that animals with a high adult weight and a high rate of precocity do not always yield good carcasses. Birth weight is a good indicator of animals that can achieve better weights in adulthood. The management effect influenced the growth pattern of Santa Inês sheep, indicating a need to adapt management decisions. These adaptations would mainly relate to fodder storage during periods of food scarcity, which indirectly relates to climate effects, so there would be no influence on animal growth.