112 research outputs found
The loss of personal privacy and its consequences for social research
No full textThis article chronicles more than 30 years of public opinion, politics, and law and policy on privacy and confidentiality that have had far-reaching consequences for access by the social research community to administrative and statistical records produced by government. A hostile political environment, public controversy over the decennial census long form, media coverage, and public fears about the vast accumulations of personal information by the private sector were catalysts for a recent proposal by the U.S. Bureau of the Census that would have significantly altered the contents of the 2000 census Public Use Microdata Sample (PUMS). These events show clearly that science does not operate independently from the political sphere but may be transformed by a political world where powerful interests lead government agencies to assume responsibility for privacy protection that can result in reducing access to statistical data
Social scientists at work on the electronic network
No full textThe purpose of this article is to contribute to our stock of knowledge about who uses networks, how they are used, and what contribution the networks make to advancing the scientific enterprise. Between 1985 and 1990, the Survey of Income and Program Participation (SIPP) ACCESS data facility at the University of Wisconsin-Madison provided social scientists in the United States and elsewhere with access through the electronic networks to complex and dynamic statistical data; the 1984 SIPP is a longitudinal panel survey designed to examine economic well-being in the United States. This article describes the conceptual framework and design of SIPP ACCESS; examines how network users communicated with the SIPP ACCESS profect staff about the SIPP data; and evaluates one outcome derived from the communications, the improvement of the quality of the SIPP data. The direct and indirect benefits to social scientists of electronic networks are discussed. The author concludes with a series of policy recommendations that link the assessment of our inadequate knowledge base for evaluating how electronic networks advance the scientific enterprise and the SIPP ACCESS research network experience to the policy initiatives of the High Performance Computing Act of 1991 (P.L. 102-194) and the related extensive recommendations embodied in Grand Challenges 1993 High Performance Computing and Communications (The FY 1993 U.S. Research and Development Program)
The difference is in the details : predicting the LC-IM-MS behaviour of metabolites and peptides
No full textIntensity and retention time prediction improves the rescoring of protein‐nucleic acid cross‐links
No full textAbstract
In protein‐RNA cross‐linking mass spectrometry, UV or chemical cross‐linking introduces stable bonds between amino acids and nucleic acids in protein‐RNA complexes that are then analyzed and detected in mass spectra. This analytical tool delivers valuable information about RNA‐protein interactions and RNA docking sites in proteins, both in vitro and in vivo. The identification of cross‐linked peptides with oligonucleotides of different length leads to a combinatorial increase in search space. We demonstrate that the peptide retention time prediction tasks can be transferred to the task of cross‐linked peptide retention time prediction using a simple amino acid composition encoding, yielding improved identification rates when the prediction error is included in rescoring. For the more challenging task of including fragment intensity prediction of cross‐linked peptides in the rescoring, we obtain, on average, a similar improvement. Further improvement in the encoding and fine‐tuning of retention time and intensity prediction models might lead to further gains, and merit further research.Deutsche Forschungsgemeinschaft https://doi.org/10.13039/50110000165
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No full textSearches perfomed with Sage (Sage: An Open-Source Tool for Fast Proteomics Searching and Quantification at Scale | Journal of Proteome Research (acs.org)) on benchmarking data (A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics | Scientific Data (nature.com))</p
Seeking explanation in theory: Reflections on the social practices of organizations that distribute public use microdata files for research purposes
No full textPublic concern about personal privacy has recently focused on issues of Internet data security and personal information as big business. The scientific discourse about information privacy focuses on the cross-pressures of maintaining confidentiality and ensuring access in the context of the production of statistical data for public policy and social research and the associated technical solutions for releasing statistical data. This article reports some of the key findings from a small-scale survey of organizational practices to limit disclosure of confidential information prior to publishing public use microdata files, and illustrates how the rules for preserving confidentiality were applied in practice. Explanation for the apparent deficits and wide variations in the extent of knowledge about statistical disclosure limitation (SDL) methods is located in theories of organizational life and communities of practice. The article concludes with suggestions for improving communication between communities of practice to enhance the knowledge base of those responsible for producing public use microdata files
Updated MS²PIP web server supports cutting-edge proteomics applications
No full textInterest in the use of machine learning for peptide fragmentation spectrum prediction has been strongly on the rise over the past years, especially for applications in challenging proteomics identification workflows such as immunopeptidomics and the full-proteome identification of data independent acquisition spectra. Since its inception, the MS²PIP peptide spectrum predictor has been widely used for various downstream applications, mostly thanks to its accuracy, ease-of-use, and broad applicability. We here present a thoroughly updated version of the MS²PIP web server, which includes new and more performant prediction models for both tryptic- and non-tryptic peptides, for immunopeptides, and for CID-fragmented TMT-labeled peptides. Additionally, we have also added new functionality to greatly facilitate the generation of proteome-wide predicted spectral libraries, requiring only a FASTA protein file as input. These libraries also include retention time predictions from DeepLC. Moreover, we now provide pre-built and ready-to-download spectral libraries for various model organisms in multiple DIA-compatible spectral library formats. Besides upgrading the back-end models, the user experience on the MS²PIP web server is thus also greatly enhanced, extending its applicability to new domains, including immunopeptidomics and MS3-based TMT quantification experiments. MS²PIP is freely available at https://iomics.ugent.be/ms2pip/.Arthur Declercq, Lennart Martens and Ralf Gabriels acknowledge funding from the Research Foundation Flanders (FWO) [12B7123N, G010023N, G028821N, 1SE3722]; Robbin Bouwmeester acknowledges funding from the Vlaams Agentschap Innoveren en Ondernemen [HBC.2020.2205]; Sven Degroeve and Lennart Martens acknowledge funding from the European Union's Horizon 2020 Programme (H2020-INFRAIA-2018-1) [823839]; Lennart Martens acknowledges funding from the Ghent University Concerted Research Action [BOF21/GOA/033]. Eduard Sabidó and Cristina Chiva acknowledge support from the Spanish Ministry of Science, Innovation and Universities (PID2020-115092GB-I00), “Centro de Excelencia Severo Ochoa 2013-2017”, SEV-2012-0208, and “Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya” (2017SGR595). The CRG/UPF Proteomics Unit is part of the Spanish Infrastructure for Omics Technologies (ICTS OmicsTech). This work has been supported by EPIC-XS, project number 823839, funded by the Horizon 2020 programme of the European Union. Funding for open access charge: the Research Foundation Flanders (FWO) [G028821N]
Communication Activism: Vol. 1, Communication for Social Change
No full textRobbin Crabtree is a contributing author, Chapter 6.
Book description: The need for communication scholars to engage in direct vigorous action in support of needed social change has never been more apparent and important, for there is no shortage of social issues and problems that demand attention. In short, communication scholars need to engage in communication activism. The two volumes showcase how scholars have engaged in communication activism to assist individuals, groups, organizations, and communities to secure social reform. Volume 1 presents research studies that promote public dialogue, debate, and discussion and that demonstrate how communication consulting can be used to accomplish needed social change. Together the two texts demonstrate the significant effects that communication scholars, working from many different theoretical and methodological traditions within the discipline, can have on promoting social change, especially for those who are most marginalized, when they engage in communication activism. – Publisher Descriptionhttps://digitalcommons.fairfield.edu/communications-books/1002/thumbnail.jp
The Cohomological Meaning of Maslov's Lagrangian Path Intersection Index
No full textWe study the relation between the complete Maslov index defined by Leray and the author, and the Lagrangian path intersection index defined by Robbin and Salamon, and used by McDuff and Salamon in their study of symplectic topology.</p
Generalized calibration across liquid chromatography setups for generic prediction of small-molecule retention times
No full textAccurate prediction of liquid chromatographic retention times from small-molecule structures is useful for reducing experimental measurements and for improved identification in targeted and untargeted MS. However, different experimental setups (e.g., differences in columns, gradients, solvents, or stationary phase) have given rise to a multitude of prediction models that only predict accurate retention times for a specific experimental setup. In practice this typically results in the fitting of a new predictive model for each specific type of setup, which is not only inefficient but also requires substantial prior data to be accumulated on each such setup. Here we introduce the concept of generalized calibration, which is capable of the straightforward mapping of retention time models between different experimental setups. This concept builds on the database-controlled calibration approach implemented in PredRet and fits calibration curves on predicted retention times instead of only on observed retention times. We show that this approach results in substantially higher accuracy of elution-peak prediction than is achieved by setup-specific models
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