A consensus platform for antibody characterization.

PurposeTo determine the Community-Based Participatory Research (CBPR) training interests and needs of researchers interested in CBPR to inform efforts to build infrastructure for conducting community-engaged research.MethodA 20-item survey was completed by 127 academic health researchers at Harvard Medical School, Harvard School of Public Health, and Harvard affiliated hospitals.ResultsSlightly more than half of the participants reported current or prior experience with CBPR (58%). Across all levels of academic involvement, approximately half of the participants with CBPR experience reported lacking skills in research methods and dissemination, with even fewer reporting skills in training of community partners. Regardless of prior CBPR experience, about half of the respondents reported having training needs in funding, partnership development, evaluation, and dissemination of CBPR projects. Among those with CBPR experience, more than one third of the participants wanted a mentor in CBPR; however only 19% were willing to act as a mentor.ConclusionsDespite having experience with CBPR, many respondents did not have the comprehensive package of CBPR skills, reporting a need for training in a variety of CBPR skill sets. Further, the apparent mismatch between the need for mentors and availability in this sample suggests an important area for development.

Editorial: Quality Research. Outstanding Publications.

The field of computer entertainment technology has aroused great interest recently amongst researchers and developers in both academic and industrial / business fields as it is duly recognized as showing high promise of bringing on exciting new forms of human computer interaction. Now deemed deserving of both serious academic research, as well as major industry and business uptake, techniques used in computer entertainment are also seen to translate into advances in research work ranging from industrial training, collaborative work, novel interfaces, novel multimedia, network computing and ubiquitous computing.The purpose of this conference is to bring together academic and industry researchers, artists and designers and computer entertainment developers and practitioners, to address and advance the research and development issues related to computer entertainment.ACM, the world's leading computer science society will be publishing all accepted papers, and the conference is fully sponsored by the prestigious ACM SiGCHI. The best papers of the conference will be published in the ACM Computers in Enterteinment journal, and the Journal of Virtual Reality and Broadcasting.The following, non exclusive, topics are called for:• Art and Media• Augmented/Mixed Reality• Avatars and Virtual Action• Computer Entertainment and Sports• Evolutionary Platforms/Hardware• Entertainment Psychology• Entertainment Philosophy• Entertainment Robots• Graphics Techniques• Haptics• Interfaces• Military Training/Simulation Applications of Games• Mobile Entertainment• Narratives• Networking• New Genres• New Standards• Novel Hardware Devices• Physics/AI• Social Computing• Sound and Music

ABSTRACTThe institutional contexts of research increasingly require researchers to anticipate their productivity and the uncertainties inherent in their research. This applies to both academic researchers and to researchers in start-up companies. This creates a specific kind of uncertainty, anticipatory uncertainty, that we define as the state of being uncertain as to whether research processes will be productive in a specific time frame and along situated definitions of good performance. In the life sciences, this anticipatory uncertainty is experienced and managed differently, depending on how research is organized and the cultural resources available in specific institutional contexts. In biotechnology companies, there is a readiness to embrace dynamic changes in both research strategies and the organization of work in response to new developments in the progress of the overall research agenda. In academia, the ability of research groups to react with similar flexibility seems significantly constrained by the individual attribution of research work and credit, and the correspondingly high level of individual anticipatory uncertainty. This raises questions about how far the current organization of academic research allows epistemic uncertainty to be embraced and corresponding risks to be taken, rather than safe questions to be pursued.

Diagnostic Tests for Antiribosomal P Protein Antibodies: A Comparative Evaluation of Immunoblotting and ELISA Assays

Postdocs should be considered to be at the last stage before becoming fully independent researchers, working on a research topic of interest with the purpose of carving out their future career trajectory, under the mentorship of an independent investigator. However, the academic landscape in the U.S. is changing fast, and with increased hyper-competition for funding, and most postdocs being funded from research project grants and thus fulfilling the aims of another investigator, true intellectual independence may be difficult to attain. Gaining a better understanding of the scientific enterprise is important to ensure its sustainability, and that junior researchers can adapt to the shifting baseline of research funding. The non-profit organization Future of Research (FoR) wants to champion, engage and empower early career scientists with evidence-based resources to improve the scientific research endeavor. FoR organized workshops in Chicago, USA (University of Chicago, PDA; University of Illinois Chicago) and Okinawa, Japan (Okinawa Institute of Technology) on the topic of transitioning from academic dependence to independence. Breakout sessions identified barriers to independence and suggested possible solutions to overcome them. Responses from multiple workshops were collected and are summarized here. In the present scientific research scenario, it is advisable to remain associated with one’s advisor in order to achieve future growth and attain success in academia by securing an independent faculty position. The definition of an independent researcher in academia also needs to be revisited. With changes in the biomedical research workforce, this independence also needs to accommodate non-tenure-track researchers, and those working in large research teams. Thus, along with changing the definition of the research independence itself, there must also be inclusion of the multiple roles played by postdocs in research, and the development of independent thinking, including freedom to define the problem of interest and develop the best approaches to address problems. Objectives: Help junior researchers identify barriers faced in conducting independent research and career independence. Propose solutions at multiple levels: research groups, principal investigators, institutions and funding agencies.

In its nine chapters, this book provides an overview of the state-of-the-art and best practice in several sub-fields of evaluation of text and speech systems and components. The evaluation aspects covered include speech and speaker recognition, speech synthesis, animated talking agents, part-of-speech tagging, parsing, and natural language software like machine translation, information retrieval, question answering, spoken dialogue systems, data resources, and annotation schemes. With its broad coverage and original contributions this book is unique in the field of evaluation of speech and language technology. This book is of particular relevance to advanced undergraduate students, PhD students, academic and industrial researchers, and practitioners.

Combining data from multiple sources is a means of enabling unified and comprehensive description of objects in high-dimensional space and helping unlock the potential value of such data. In recent years, more and more studies have focused on this field of research. However, challenges posed by separately stored data and comprehension barriers about different systems hinder the integration of data from different sources. To overcome these problems, this paper proposes a Transparent Data as a Service framework, a novel approach combining Transparent Computing and Representational State Transfer (REST) Web Services based on Linked Data. This framework is capable of integrating data from different sources and offering data services in a transparent way. That is, consumers use data services without the need to know details of where or how the data are stored. Our framework is transparent on three levels: transparent data resource integration, transparent data fusion and transparent data service provision. The Data Model Pool and Data Resource Pool are able to evolve as new data models and datasets are generated in the provision of data services. Finally, we demonstrate the feasibility of the framework by implementing a prototype system.

The promyelocytic leukemia (PML) protein is a major component to govern the PML nuclear body (NB) assembly and function. Although it is well defined that PML NB is a site recruiting sumoylated proteins, the mechanism by which PML protein regulates the process remains unclear. Here we show that PML3, a specific PML isoform, interacts with and recruits TIP60 to PML NBs. Our biochemical characterization demonstrates that PML3 physically interacts with TIP60 via its N-terminal 364 amino acids. Importantly, this portion of TIP60 is sufficient to target to the PML NBs, suggesting that PML3-TIP60 interaction is sufficient for targeting TIP60 to the NBs. The PML3-TIP60 interaction is specific, since the region of TIP60 binding is not conserved in other PML isoforms. The physical interaction between PML3 and TIP60 protects TIP60 from Mdm2-mediated degradation, suggesting that PML3 competes with MDM2 for binding to TIP60. Fluorescence recovery after photobleaching analysis indicates that the PML3-TIP60 interaction modulates the nuclear body distribution and mobility of TIP60. Conversely, the distribution and mobility of TIP60 are perturbed in PML3-deficient cells, accompanied by aberrations in DNA damage-repairing response. Thus, PML3 orchestrates the distribution, dynamics, and function of TIP60. Our findings suggest a novel regulatory mechanism by which the PML3 and TIP60 tumor suppressors cooperate to ensure genomic stability.

BackgroundCompelling evidence has demonstrated that a large proportion of investment in biomedical research is wasted; this waste is avoidable. Academic institutions have, thus far, shown limited response to recommendations for increasing value and reducing waste. We formulated an academic response by (i) achieving consensus across a wide range of stakeholder groups on a comprehensive framework for quality of patient-oriented clinical research and (ii) highlighting first successful examples of its operationalization to facilitate waste-reducing strategies at academic institutions.Methods and findingsBased on a systematic review of quality definitions, concepts, and criteria in the medical literature (systematic MEDLINE search up to February 15, 2015, with independent and in duplicate article selection) and on stakeholder websites from 13 countries (Australia, Austria, Canada, France, Germany, Italy, Japan, Norway, Spain, Sweden, Switzerland, United Kingdom, and United States), we systematically developed a comprehensive framework for the quality of clinical research. We identified websites through personal contacts with experts in clinical research or public health who also suggested, for each country, websites of the following 7 stakeholder groups: patient organizations; academic research infrastructures; governmental bodies; regulatory agencies; ethics committees; the pharmaceutical industry; and funding agencies. In addition, we searched websites of inter- or supranational bodies involved in clinical research until no further insights emerged. After consolidation of the identified definitions, concepts, and criteria of quality in a basic framework structure, we conducted 4 rounds of an adapted online Delphi process among the same 7 stakeholder groups from 16 countries. The Delphi process ultimately achieved consensus on structure and content. The framework addresses 5 study stages (concept, planning and feasibility, conduct, analysis and interpretation, and reporting and knowledge translation) and includes the following dimensions: (i) protection of patient safety and rights, (ii) relevance/patient centeredness and involvement, (iii) minimization of bias (internal validity), (iv) precision, (v) transparency/access to data, and (vi) generalizability (external validity) of study results. These dimensions interact with 2 promoters—infrastructure and sustainability through education—that include a set of factors that may enhance all listed quality dimensions. Each quality dimension contains specific questions and explanatory items that guide quality assessment at each research stage from conceptualization of the research question through reporting and knowledge translation of study results. In the last survey round, Delphi participants from 9 countries (Austria, Australia, Canada, Germany, Italy, the Netherlands, Switzerland, UK, and US) agreed on the structure, content, and wording of the research stages, quality dimensions, specific questions, and descriptive examples of the final framework. In Switzerland, INQUIRE has resulted in a roadmap that guides initiatives to increase value within the Swiss Clinical Trial Organization network and through affiliated researchers.ConclusionsWe present a framework based on a consensus of different stakeholder groups guiding the practical assessment of clinical research quality at all stages of a research project. Operationalization of this common structure will support the increase of value by guiding academic institutions and researchers in developing quality enhancement initiatives, from posing the right research question to the transparent publication of results.

Funding agencies, journal editors, and hiring and promotion committees expend large amounts of time and resources deciding how to allocate precious funds, what science to publish, and which scientists deserve a job or promotion because of their scientific contributions.Now imagine an automated information system that can make this process much more efficient.Every academic researcher in the world is ranked based on a productivity index.Let us call it the Metric for Evaluation of Scientific Scholarship (MESS).This system works with an algorithm that tabulates the number of grants awarded to a researcher, the award amount for each grant, the number of publications authored, and the number of times those publications were downloaded and cited.In addition, the MESS would include a variable reflecting the prestige of the journals in which a researcher's work was published.The MESS would be adopted to rank all researchers in the world, providing the basis for hiring, funding, and promotion decisions.And no need for a Nobel Prize selection committee, either!We have the MESS.The MESS algorithm would be undisclosed proprietary information, but the MESS rankings would be available to anyone willing to pay a fee for access to this means of ranking researchers.Such a frightening system might have a few minor flaws, like favoring senior investigators and researchers in fields with more funding and more publications and replacing the quest for deeper understanding with a quest for a higher MESS.As absurd as this imaginary system might seem, sadly, the research community often relies on a system that is almost as absurd as this

Huntingtin encodes a 3144 amino acid protein, with a polyglutamine repeat tract at the N-terminus. Expansion of this repeat tract above a pathogenic threshold of 36 repeats is the causative mutation of Huntington's disease, a neurodegenerative disorder characterized by loss of striatal neurons. Here we have characterized twenty Huntingtin commercial antibodies for western blot, immunoprecipitation, and immunofluorescence using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. These studies are part of a larger, collaborative initiative seeking to address antibody reproducibility issues by characterizing commercially available antibodies for human proteins and publishing the results openly as a resource for the scientific community. While use of antibodies and protocols vary between laboratories, we encourage readers to use this report as a guide to select the most appropriate antibodies for their specific needs.

Rab1 is a highly conserved small GTPase that exists in humans as two isoforms: Rab1A and Rab1B, sharing 92% sequence identity. These proteins regulate vesicle trafficking between the endoplasmic reticulum (ER) and Golgi and within the Golgi stacks. Rab1A and Rab1B may be oncogenes, as they are frequently dysregulated in various human cancers. Moreover, they contribute to the progression of Parkinson’s disease. The availability of high-quality antibodies specific for Rab1A or Rab1B is essential to understand the distinct functions of these Rab1 proteins in both health and diseaseand to enhance the reproducibility of research involving these proteins. In this study, we characterized seven antibodies targeting Rab1A and five antibodies targeting Rab1B for Western Blot, immunoprecipitation, and immunofluorescence using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. These studies are part of a much larger, collaborative initiative seeking to address the antibody reproducibility issue by characterizing commercially available antibodies for human proteins and publishing the results openly as a valuable resource for the scientific community. While uses of antibodies and protocols vary between laboratories, we encourage readers to use this report as a guide to select the most appropriate antibodies for their specific needs.

Sphingosine 1-phosphate receptor 1 (S1PR1) is a G-coupled protein receptor that induces crucial biological processes when bound by sphingosine 1-phosphate. Here, we have characterized nine S1PR1 commercial antibodies for western blot, immunoprecipitation, and immunofluorescence using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. These studies are part of a larger, collaborative initiative seeking to address antibody reproducibility issues by characterizing commercially available antibodies for human proteins and publishing the results openly as a resource for the scientific community. While use of antibodies and protocols vary between laboratories, we encourage readers to use this report as a guide to select the most appropriate antibodies for their specific needs.

Valosin-containing protein (VCP) is a highly conserved and essential ATPase involved in many cellular processes like neuronal function, protein degradation, organelle maintenance, and stress response regulation. Understanding the specific mechanisms by which VCP plays in health and disease can provide novel insides in therapeutic targets, a process that would be facilitated by the availability of high-quality antibodies. Here we have characterized sixteen VCP commercial antibodies for western blot, immunoprecipitation, and immunofluorescence using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. These studies are part of a larger, collaborative initiative seeking to address antibody reproducibility issues by characterizing commercially available antibodies for human proteins and publishing the results openly as a resource for the scientific community. While the use of antibodies and protocols vary between laboratories, we encourage readers to use this report as a guide to select the most appropriate antibodies for their specific needs.