A Model for Collaborative Curation, The IEDB and ChEBI Curation of Non-peptidic Epitopes

The Immune Epitope Database (IEDB) recently expanded and enhanced its non-peptidic epitope related data utilizing a collaboration with Chemical Entities of Biological Interest (ChEBI), resulting in the first resource that brings together published immunological data with the expertise of the ChEBI database. This procedure took advantage of the distinct expertise of the IEDB and ChEBI databases to improve content and enhance interoperability of both databases. This project has resulted in the comprehensive inventory and curation of immune epitope data related to non-peptidic structures and serves as a model for successful collaborative curation between established resources.     

Research project: Charleston Bioengineered Kidney Project

The goal of Charleston Bioengineered Kidney Project is to engineer a functional living human kidney suitable for surgical implantation using principles of directed tissue self-assembly and tissue fusion. This is a multidisciplinary project which incorporates multiple innovative bioengineering technologies and expertise from a broad spectrum of disciplines. The conceptual framework, engineering principles, design, potential cell source as well as the first preliminary data demonstrating the feasibility of the proposed Charleston Bioengineered Kidney Project are outlined. The potential challenges are described. Finally, the experts' opinion about the proposed project is also presented.     

On brain activity mapping: insights and lessons from Brain Decoding Project to map memory patterns in the hippocampus

The BRAIN project recently announced by the president Obama is the reflection of unrelenting human quest for cracking the brain code, the patterns of neuronal activity that define who we are and what we are. While the Brain Activity Mapping proposal has rightly emphasized on the need to develop new technologies for measuring every spike from every neuron, it might be helpful to consider both the theoretical and experimental aspects that would accelerate our search for the organizing principles of the brain code. Here we share several insights and lessons from the similar proposal, namely, Brain Decoding Project that we initiated since 2007. We provide a specific example in our initial mapping of real-time memory traces from one part of the memory circuit, namely, the CA1 region of the mouse hippocampus. We show how innovative behavioral tasks and appropriate mathematical analyses of large datasets can play equally, if not more, important roles in uncovering the specific-to-general feature-coding cell assembly mechanism by which episodic memory, semantic knowledge, and imagination are generated and organized. Our own experiences suggest that the bottleneck of the Brain Project is not only at merely developing additional new technologies, but also the lack of efficient avenues to disseminate cutting edge platforms and decoding expertise to neuroscience community. Therefore, we propose that in order to harness unique insights and extensive knowledge from various investigators working in diverse neuroscience subfields, ranging from perception and emotion to memory and social behaviors, the BRAIN project should create a set of International and National Brain Decoding Centers at which cutting-edge recording technologies and expertise on analyzing large datasets analyses can be made readily available to the entire community of neuroscientists who can apply and schedule to perform cutting-edge research.     

Breeding sovereignty: the production of race,nature, and capital in Venezuela

This article explores the efforts of the Venezuelan government to improve food security and rural livelihoods with an experimental cattle-breeding project. It investigates the activities of a state enterprise in the western plains and how the selective-breeding practices of veterinary experts intersect with the logic of capital and biopolitics. Contributing to debates on the interaction between society and environment, the analysis suggests that ‘endogenous development’, or the reduction of poverty through internal markets, draws on systems of knowledge that treat the biology of animals as a field of intervention for the resolution of social contradictions. To reduce reliance on petroleum rent and food imports, Venezuelan experts have sought to create a new breed of cattle suited to the nation's diverse ecologies. But the knowledge systems which guide this project are embedded with a host of cultural and economic assumptions that subvert the successful application of this biotechnology. Ultimately, this article seeks to increase knowledge of the techno-politics of resource states at the start of the twenty-first century and the ways in which cultures of expertise impact food sovereignty.     

From Mexico to Michigan and back: An international collaboration investigating primate behavior,ecology, and evolution from multiple perspectives

Evolutionary research benefits form the integration of laboratory and field components to determine factors and processes that affect the evolutionary trajectories of species. Our shared interest in understanding hybridization with genetic admixture as a process that may impact social, behavioral, and ecological features of primates, brought us together in a collaborative project aimed at addressing how vocal variation in two species of howler monkeys in Mexico affects and is affected by hybridization. To achieve this goal, we joined our academic expertise in studying primate genetics, ecology, and behavior under different natural and experimental conditions. We took advantage of decades of experience studying and handing wild howler monkeys for translocation projects to safely sample and study wild populations for this project. Here, we describe the history of our collaboration highlighting how our different perspectives, academic realities, and individual strengths built the foundation for our successful collaboration. We also share our perspectives on how this collaboration opened up new academic venues, broadened our individual perspectives on the integration of different research approaches to address a complex topic, and allowed us to recognize the strength of international collaboration.     

Recipe for success: A network perspective of partnership in nature conservation

Successful conservation initiatives require collaboration between stakeholders across a range of organisational foci and expertise. In Romania, the EU LIFE Nature programme is the most important financing instrument for nature conservation, and projects commonly involve partnerships between public authorities, NGOs, enterprises, and research institutions. To understand strengths and gaps in conservation partnerships for LIFE Nature projects implemented in Romania, we applied a Social Network Analysis approach to 85 partner organisations across 35 projects. We complemented this approach with a questionnaire directed to project managers to identify the criteria for selecting partners, and the role of partners in the project. The network included mostly public authorities (50%), yet the Romanian Ornithological Society (NGO) and the University of Bucharest were the most influent organisations in the network. Public authorities, park authorities, and enterprises were often selected as partners because of their financial contributions and local connections. In contrast, research institutions and NGOs were selected as partners because of their technical expertise and policy influence at the national level. Furthermore, research institutions, parks authorities and NGOs were involved in proposal writing, preparatory and management activities, while public authorities had no predefined roles in LIFE projects. The analysis also showed that the Romanian conservation system is polycentric, with influence shared between research organisations, NGOs, and public authorities. Interviews with project managers revealed that Romania submits relatively fewer projects compared to Western EU countries because public agencies have low technical and logistic capacity. We recommend a national level strategy for increasing project submission rates and quality of proposals that addresses the need for strengthening ties between core organisations and public authorities, especially at the local level. These findings are likely to be applicable to other EU member states that are currently struggling to get funding for conservation projects, ultimately moving the EU closer to achieving the European Union Biodiversity Strategy 2020 targets.     

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

The SWISS-PROT protein knowledgebase (http://www.expasy.org/sprot/ and http://www.ebi.ac.uk/swissprot/) connects amino acid sequences with the current knowledge in the Life Sciences. Each protein entry provides an interdisciplinary overview of relevant information by bringing together experimental results, computed features and sometimes even contradictory conclusions. Detailed expertise that goes beyond the scope of SWISS-PROT is made available via direct links to specialised databases. SWISS-PROT provides annotated entries for all species, but concentrates on the annotation of entries from human (the HPI project) and other model organisms to ensure the presence of high quality annotation for representative members of all protein families. Part of the annotation can be transferred to other family members, as is already done for microbes by the High-quality Automated and Manual Annotation of microbial Proteomes (HAMAP) project. Protein families and groups of proteins are regularly reviewed to keep up with current scientific findings. Complementarily, TrEMBL strives to comprise all protein sequences that are not yet represented in SWISS-PROT, by incorporating a perpetually increasing level of mostly automated annotation. Researchers are welcome to contribute their knowledge to the scientific community by submitting relevant findings to SWISS-PROT at swiss-prot@expasy.org.     

The Scottish Structural Proteomics Facility: targets, methods and outputs

The Scottish Structural Proteomics Facility was funded to develop a laboratory scale approach to high throughput structure determination. The effort was successful in that over 40 structures were determined. These structures and the methods harnessed to obtain them are reported here. This report reflects on the value of automation but also on the continued requirement for a high degree of scientific and technical expertise. The efficiency of the process poses challenges to the current paradigm of structural analysis and publication. In the 5 year period we published ten peer-reviewed papers reporting structural data arising from the pipeline. Nevertheless, the number of structures solved exceeded our ability to analyse and publish each new finding. By reporting the experimental details and depositing the structures we hope to maximize the impact of the project by allowing others to follow up the relevant biology.     

法医学司法鉴定中吸毒与艾滋病群体隐私权与知情权的伦理学问题探讨

在法医学司法鉴定过程中,当事人所具有的隐私权与司法鉴定工作所需要的知情权之间必然存在着一定的矛盾与冲突。如何在尊重当事人隐私权的基础上充分获取司法鉴定工作所需的知情权,是司法鉴定机构在司法鉴定工作中所面临的重要任务。本文对法医学司法鉴定中吸毒与艾滋病群体隐私权与知情权的医学伦理学相关问题进行分析探讨。     

Der Census of Marine Life zieht Bilanz. Globale “Volkszählung” unter Wasser

Global Underwater Census – a large‐scale project is taking stock The Census of Marine Life, an international large‐scale project to assess the diversity of life in the ocean, will end this fall after a decade of discovery with a grand finale in London. Many so‐called field projects were established to study life from tropical beaches, seamounts, hydrothermal vents, to polar seas and abyssal plains in order to get a better estimate of marine species diversity and gain insight into processes that influence the diversity of life in the oceans. Some of the field projects are presented, including the project CeDAMar under the leadership of the Senckenberg Institute. The study area of CeDAMar is abyssal plains, which comprise about half of the Earth's surface yet are very little known. Mankind's growing demand on minerals and other resources has awoken the industry's interest in a part of the ocean that so far has been relatively pristine. CeDAMar scientists have helped with their expertise to establish guidelines for the protection of the seafloor in international waters, thus demonstrating how concrete the influence of deep‐sea exploration on human society can become.     

Medicen Paris Région: A world-class 'competitiveness cluster' in the Paris region incorporating a neuroscience 'subcluster'

The French public-private partnerships known as "competitive clusters" [p?les de compétitivité (PdC)] are intended to be novel and ambitious engines of regional growth, employment and biomedical innovation. Partly funded by government and local councils, they aim to capitalize on regional expertise by bringing together basic scientists, clinicians, innovative entrepreneurs and local decision-makers around specific themes that have become too costly and complex for any of these actors to tackle alone. Clusters provide the critical mass required both to underpin innovation potential and to authenticate regional claims to international competitiveness. Medicen is a biomedicine and therapeutics cluster comprising 120 partners from four broad "colleges" in the greater Paris region: major industry, small and medium-sized businesses, teaching hospitals/State research bodies, and local councils. Chief among its cooperative R&D projects is the neuroscience subcluster, in which "TransAl" the neurodegenerative disease project, counts Sanofi-Aventis, Servier and the French Atomic Energy Commission [Commissariat à l'Energie Atomique (CEA)] as key partners. One main aim is to develop an experimental model in rhesus monkeys in which a putative cause of Alzheimer's disease, intracerebral accumulation of b-amyloid peptide, is generated by impairing the peptide's clearance. The other aim, in which the nuclear medicine expertise of the CEA will be crucial, is to identify, characterize and validate markers for magnetic resonance and positron emission tomography imaging, and to source biomarkers from cerebrospinal fluid proteomics. A human biological resource centre (DNA and tissue banks) project dedicated to neurological and psychiatric disease should be up and running in 2007. Only through fundamental restructuring of resources on such a large cooperative scale are solutions likely to be found to the major problems of modern medicine, bringing healthcare and regional socioeconomic benefits in its wake.     

Sub-specialization or Super-specialization in Surgery?

A special centre for prosthetic hip replacement set up 10 years ago has been successful in its primary objectives, producing high quality work at low cost and stimulating research. The project has not yet been successful in achieving a permanent staffing structure, but this is the effect of certain British ideologies in surgical training, with the result that craftsmanship and technology cannot be reconciled with pure intellectual attainment.The success of the project suggests the importance of isolating elective surgery from emergency surgery in the interests of cost-effectiveness. Problems of isolation from teaching hospitals are not insurmountable, but isolation to some degree is essential to achieve the minimum size necessary for efficiency and to ensure unbroken professional team-work among all levels of staff. While maximum efficiency in this field can be achieved only in special centres, too many primary operations will be required every year to insist that total hip replacement should be done only in special centres. A special feature of this field is the need for a permanent staffing structure to hand on technical expertise as an unbroken tradition.     

Art and human embryonic stem cells: From the bench to the high street

ESTOOLS, a project funded by the European Commission (FP6), gathers expertise on human embryonic stem cells in 10 countries of the European Research Area. The ESTOOLS outreach program uses Art extensively as the only universal cross-cultural and cross-religion means of communication. The Smile of a Stem Cell photo exhibition, a major component of this program, aims to fill a missing link between public dissemination of science and science-illiterate citizens. Scientists are also engaged to stand at a distance from their work and observe it with an outsider’s perspective, which enhances their competency to communicate science. The photo exhibition, by its situation upstream of scientific education, makes itself open to interest and enthusiasm among a public with no prerequired scientific knowledge or abilities.     

Expertise in expert systems: knowledge acquisition for biological expert systems

In this paper it is argued that an expert system requires morethan factual knowledge before it can display expertise in agiven domain. The additional knowledge consists of the heuristicsor ‘rules of thumb’ used by an expert to manipulateand interpret the factual knowledge. The knowledge acquisitionphase of an expert system project involves determining the factualknowledge (which may be obtained from published sources) andthe heuristics used by an expert to manipulate that knowledge-theseheuristics can only be obtained from an expert. In reviewingexisting biological expert systems it is apparent that manycontain only the factual knowledge relating to the domain, andlack the heuristics that enable such systems to show expertise.This paper reviews a number of knowledge acquisition techniqueswhich could be used for acquiring heuristic knowledge and discusseswhen their use is appropriate. The knowledge acquisition techniquesdiscussed are those suitable for the development of small-scaleexpert systems as these are most likely to be of interest tobiologists. The techniques include the use of questionnaires,interview techniques and protocol analysis; particular emphasisis placed on a mod cation to the ‘twenty questions’interview technique which was developed specifically to elicittaxonomic knowledge relating to water mite identification.     

Are All Types of Expertise Created Equal? Car Experts Use Different Spatial Frequency Scales for Subordinate Categorization of Cars and Faces

A much-debated question in object recognition is whether expertise for faces and expertise for non-face objects utilize common perceptual information. We investigated this issue by assessing the diagnostic information required for different types of expertise. Specifically, we asked whether face categorization and expert car categorization at the subordinate level relies on the same spatial frequency (SF) scales. Fifteen car experts and fifteen novices performed a category verification task with spatially filtered images of faces, cars, and airplanes. Images were categorized based on their basic (e.g. “car”) and subordinate level (e.g. “Japanese car”) identity. The effect of expertise was not evident when objects were categorized at the basic level. However, when the car experts categorized faces and cars at the subordinate level, the two types of expertise required different kinds of SF information. Subordinate categorization of faces relied on low SFs more than on high SFs, whereas subordinate expert car categorization relied on high SFs more than on low SFs. These findings suggest that expertise in the recognition of objects and faces do not utilize the same type of information. Rather, different types of expertise require different types of diagnostic visual information.     

Striking a balance: socioeconomic development and conservation in grassland through community-based zoning

The goal of preserving nature is often in conflict with economic development and the aspirations of the rural poor. Nowhere is this more striking than in native grasslands, which have been extensively converted until a mere fraction of their original extent remains. This is not surprising; grasslands flourish in places coveted by humans, primed for agriculture, plantations, and settlements that nearly always trump conservation efforts. The Umgano grassland conservation and poverty reduction project in KwaZulu-Natal Province, South Africa uses community-based spatial planning to balance the conversion of its lower-conservation value grasslands to a timber plantation, while conserving higher-value grasslands for heritage purposes and managed livestock grazing. Ten years after project launch, we measured the ecological and socioeconomic impacts of the project using Normalized Differential Vegetation Index remote sensing data and over 500 household interviews, as compared with similar non-conserved areas. Zoned management of the Umgano area had resulted in between 9% and 17% greater average peak production in the grassland areas compared to control sites. There was also a 21% gain in incomes for the roughly one hundred people employed by the forestry efforts, when compared to others in their village. Community-based spatial zoning is an overlooked tool for balancing conservation and development but may require, as we found in Umgano, certain critical factors including strong local leadership, an accountable financial management mechanism to distribute income, outside technical expertise for the zoning design, and community support.     

Prevención de las caídas basada en la evidencia en Europa

ProFaNE (Prevention of Falls Network Europe) is a thematic network funded by the European Commission. This network brings together scientists, clinicians and other health professionals from across Europe to focus on four main topics (taxonomy and co-ordination of trials, clinical assessment and management of falls, assessment of balance function, and psychological aspects of falls). There are 24 members across Europe as well as Network Associates who contribute expertise at workshops and meetings. ProFa- NE, a 4-year project which started in January 2003, aims to improve and standardise healthcare processes by introducing and promoting good practice throughout Europe. ProFaNE has its own website (http://www.profane.eu.org) and undertakes workshops to bring together experts and observers involved in specific topics to exchange knowledge, expertise and resources on interventions to reduce falls. The present article discusses ProFaNE's achievements to date and the work in progress to achieve good clinical practice and research into the prevention of falls across Europe.     

Redrawing the boundary of medical expertise: medically assisted reproduction and the debate on Italian bioconstitutionalism

In 2004, the Italian Parliament passed a controversial law on medically assisted reproduction (Law 40/2004). The Law obliged clinicians to create a maximum of three embryos during one in vitro fertilization (IVF) cycle and transfer them simultaneously into the patient’s uterus. With this “three embryo” standard, the Parliament sought to secure the realization of rights of IVF embryos. Drawing on the concepts of boundary-work [Gieryn, T. F. 1983. “Boundary-Work and the Demarcation of Science from Non-Science: Strains and Interests in Professional Ideologies of Scientists.” American Sociological Review 48 (6): 781–795] and bioconstitutionalism [Jasanoff, S., ed. 2011. Reframing Rights: Bioconstitutionalism in the Genetic Age. Cambridge, MA: MIT Press.], this article explores the role that the constitutional obligations of the Italian State towards its citizens, including IVF embryos as its new “citizen subjects,” played in how it envisaged and demarcated the professional boundaries of medical expertise. It argues that the latter depended upon how it balanced its commitments to protect the rights of IVF embryos and those of adult citizens. As such, the demarcation of the jurisdictional boundaries of medical expertise, and the definition of constitutional rights, formed two sides of the same governing project.     

Clinical expertise and the limits of explicit knowledge

This article questions the view that medical decision-making can be reduced to a series of explicit rules, adherence to which will necessarily improve outcomes. Instead, it attempts to rehabilitate the concepts of clinical expertise and clinical experience, arguing that medicine, like other areas of expertise, depends on forms of implicit knowledge that can only be acquired through years of experience. Recent research on "fast and frugal" heuristics in medical decision-making suggest that statistical techniques are not necessarily superior to clinician judgment. Since clinical decisions are made on individual patients within the constraint of limited information, they must rest on clinical expertise and not clinical rules.     

Darwin’s “Mr. Arthrobalanus”: Sexual Differentiation,Evolutionary Destiny and the Expert Eye of the Beholder

Darwin’s Cirripedia project was an exacting exercise in systematics, as well as an encrypted study of evolution in action. Darwin had a long-standing interest and expertise in marine invertebrates and their sexual arrangements. The surprising and revealing sexual differentiation he would uncover amongst barnacles represented an important step in his understanding of the origins of sexual reproduction. But it would prove difficult to reconcile these findings with his later theorizing. Moreover, the road to discovery was hardly straightforward. Darwin was both helped and hindered by the tacit expectations generated by his transformist theorizing, and had to overcome culturally-embedded assumptions about gender and reproductive roles. Significant observational backtracking was required to correct several oversights and misapprehensions, none more so than those relating to the chronically misunderstood “Mr. Arthrobalanus.” With careful attention to chronology, this paper highlights some curious and overlooked aspects of Darwin’s epic project.