Compliance-Adjusted Estimates of Aspirin Effects Among Older Persons in the ASPREE Randomized Trial.

The Aspirin in Reducing Events in the Elderly (ASPREE) Trial recruited 19,114 participants across Australia and the United States during 2010-2014. Participants were randomized to receive either 100 mg of aspirin daily or matching placebo, with disability-free survival as the primary outcome. During a median 4.7 years of follow-up, 37% of participants in the aspirin group permanently ceased taking their study medication and 10% commenced open-label aspirin use. In the placebo group, 35% and 11% ceased using study medication and commenced open-label aspirin use, respectively. In order to estimate compliance-adjusted effects of aspirin, we applied rank-preserving structural failure time models. The results for disability-free survival and most secondary endpoints were similar in intention-to-treat and compliance-adjusted analyses. For major hemorrhage, cancer mortality, and all-cause mortality, compliance-adjusted effects of aspirin indicated greater risks than were seen in intention-to-treat analyses. These findings were robust in a range of sensitivity analyses. In accordance with the original trial analyses, compliance-adjusted results showed an absence of benefit with aspirin for primary prevention in older people, along with an elevated risk of clinically significant bleeding.

UniProt and Mass Spectrometry-Based Proteomics-A 2-Way Working Relationship.

The human proteome comprises of all of the proteins produced by the sequences translated from the human genome with additional modifications in both sequence and function caused by nonsynonymous variants and posttranslational modifications including cleavage of the initial transcript into smaller peptides and polypeptides. The UniProtKB database (www.uniprot.org) is the world's leading high-quality, comprehensive and freely accessible resource of protein sequence and functional information and presents a summary of experimentally verified, or computationally predicted, functional information added by our expert biocuration team for each protein in the proteome. Researchers in the field of mass spectrometry-based proteomics both consume and add to the body of data available in UniProtKB, and this review highlights the information we provide to this community and the knowledge we in turn obtain from groups via deposition of large-scale datasets in public domain databases.

The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions.

The current coronavirus disease of 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus (SARS-CoV)-2, has spurred a wave of research of nearly unprecedented scale. Among the different strategies that are being used to understand the disease and develop effective treatments, the study of physical molecular interactions can provide fine-grained resolution of the mechanisms behind the virus biology and the human organism response. We present a curated dataset of physical molecular interactions focused on proteins from SARS-CoV-2, SARS-CoV-1 and other members of the Coronaviridae family that has been manually extracted by International Molecular Exchange (IMEx) Consortium curators. Currently, the dataset comprises over 4400 binarized interactions extracted from 151 publications. The dataset can be accessed in the standard formats recommended by the Proteomics Standards Initiative (HUPO-PSI) at the IntAct database website (https://www.ebi.ac.uk/intact) and will be continuously updated as research on COVID-19 progresses.

The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions.

The current Coronavirus Disease 2019 (COVID-19) pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has spurred a wave of research of nearly unprecedented scale. Among the different strategies that are being used to understand the disease and develop effective treatments, the study of physical molecular interactions enables studying fine-grained resolution of the mechanisms behind the virus biology and the human organism response. Here we present a curated dataset of physical molecular interactions, manually extracted by IMEx Consortium curators focused on proteins from SARS-CoV-2, SARS-CoV-1 and other members of the Coronaviridae family. Currently, the dataset comprises over 2,200 binarized interactions extracted from 86 publications. The dataset can be accessed in the standard formats recommended by the Proteomics Standards Initiative (HUPO-PSI) at the IntAct database website ( www.ebi.ac.uk/intact ), and will be continuously updated as research on COVID-19 progresses.

Publisher Correction: Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.

In the original HTML version of this Article, the order of authors within the author list was incorrect. The IMEx Consortium contributing authors were incorrectly listed as the last author and should have been listed as the first author. This error has been corrected in the HTML version of the Article; the PDF version was correct at the time of publication.

CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination.

MOTIVATION: Combining multiple layers of information underlying biological complexity into a structured framework represent a challenge in systems biology. A key task is the formalization of such information in models describing how biological entities interact to mediate the response to external and internal signals. Several databases with signalling information, focus on capturing, organizing and displaying signalling interactions by representing them as binary, causal relationships between biological entities. The curation efforts that build these individual databases demand a concerted effort to ensure interoperability among resources. RESULTS: Aware of the enormous benefits of standardization efforts in the molecular interaction research field, representatives of the signalling network community agreed to extend the PSI-MI controlled vocabulary to include additional terms representing aspects of causal interactions. Here, we present a common standard for the representation and dissemination of signalling information: the PSI Causal Interaction tabular format (CausalTAB) which is an extension of the existing PSI-MI tab-delimited format, now designated PSI-MITAB 2.8. We define the new term 'causal interaction', and related child terms, which are children of the PSI-MI 'molecular interaction' term. The new vocabulary terms in this extended PSI-MI format will enable systems biologists to model large-scale signalling networks more precisely and with higher coverage than before. AVAILABILITY AND IMPLEMENTATION: PSI-MITAB 2.8 format and the new reference implementation of PSICQUIC are available online (https://psicquic.github.io/ and https://psicquic.github.io/MITAB28Format.html). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.

The current wealth of genomic variation data identified at nucleotide level presents the challenge of understanding by which mechanisms amino acid variation affects cellular processes. These effects may manifest as distinct phenotypic differences between individuals or result in the development of disease. Physical interactions between molecules are the linking steps underlying most, if not all, cellular processes. Understanding the effects that sequence variation has on a molecule's interactions is a key step towards connecting mechanistic characterization of nonsynonymous variation to phenotype. We present an open access resource created over 14 years by IMEx database curators, featuring 28,000 annotations describing the effect of small sequence changes on physical protein interactions. We describe how this resource was built, the formats in which the data is provided and offer a descriptive analysis of the data set. The data set is publicly available through the IntAct website and is enhanced with every monthly release.

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.

BACKGROUND: Systems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order to effectively achieve this goal, it is critical that researchers have high quality interaction datasets available to them, in a standard data format, and also a suite of tools with which to analyse such data and form experimentally testable hypotheses from them. The PSI-MI XML standard interchange format was initially published in 2004, and expanded in 2007 to enable the download and interchange of molecular interaction data. PSI-XML2.5 was designed to describe experimental data and to date has fulfilled this basic requirement. However, new use cases have arisen that the format cannot properly accommodate. These include data abstracted from more than one publication such as allosteric/cooperative interactions and protein complexes, dynamic interactions and the need to link kinetic and affinity data to specific mutational changes. RESULTS: The Molecular Interaction workgroup of the HUPO-PSI has extended the existing, well-used XML interchange format for molecular interaction data to meet new use cases and enable the capture of new data types, following extensive community consultation. PSI-MI XML3.0 expands the capabilities of the format beyond simple experimental data, with a concomitant update of the tool suite which serves this format. The format has been implemented by key data producers such as the International Molecular Exchange (IMEx) Consortium of protein interaction databases and the Complex Portal. CONCLUSIONS: PSI-MI XML3.0 has been developed by the data producers, data users, tool developers and database providers who constitute the PSI-MI workgroup. This group now actively supports PSI-MI XML2.5 as the main interchange format for experimental data, PSI-MI XML3.0 which additionally handles more complex data types, and the simpler, tab-delimited MITAB2.5, 2.6 and 2.7 for rapid parsing and download.

JAMI: a Java library for molecular interactions and data interoperability.

BACKGROUND: A number of different molecular interactions data download formats now exist, designed to allow access to these valuable data by diverse user groups. These formats include the PSI-XML and MITAB standard interchange formats developed by Molecular Interaction workgroup of the HUPO-PSI in addition to other, use-specific downloads produced by other resources. The onus is currently on the user to ensure that a piece of software is capable of read/writing all necessary versions of each format. This problem may increase, as data providers strive to meet ever more sophisticated user demands and data types. RESULTS: A collaboration between EMBL-EBI and the University of Cambridge has produced JAMI, a single library to unify standard molecular interaction data formats such as PSI-MI XML and PSI-MITAB. The JAMI free, open-source library enables the development of molecular interaction computational tools and pipelines without the need to produce different versions of software to read different versions of the data formats. CONCLUSION: Software and tools developed on top of the JAMI framework are able to integrate and support both PSI-MI XML and PSI-MITAB. The use of JAMI avoids the requirement to chain conversions between formats in order to reach a desired output format and prevents code and unit test duplication as the code becomes more modular. JAMI's model interfaces are abstracted from the underlying format, hiding the complexity and requirements of each data format from developers using JAMI as a library.

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study.

The evidence that two molecules interact in a living cell is often inferred from multiple different experiments. Experimental data is captured in multiple repositories, but there is no simple way to assess the evidence of an interaction occurring in a cellular environment. Merging and scoring of data are commonly required operations after querying for the details of specific molecular interactions, to remove redundancy and assess the strength of accompanying experimental evidence. We have developed both a merging algorithm and a scoring system for molecular interactions based on the proteomics standard initiative-molecular interaction standards. In this manuscript, we introduce these two algorithms and provide community access to the tool suite, describe examples of how these tools are useful to selectively present molecular interaction data and demonstrate a case where the algorithms were successfully used to identify a systematic error in an existing dataset.

The IntAct molecular interaction database in 2010.

IntAct is an open-source, open data molecular interaction database and toolkit. Data is abstracted from the literature or from direct data depositions by expert curators following a deep annotation model providing a high level of detail. As of September 2009, IntAct contains over 200.000 curated binary interaction evidences. In response to the growing data volume and user requests, IntAct now provides a two-tiered view of the interaction data. The search interface allows the user to iteratively develop complex queries, exploiting the detailed annotation with hierarchical controlled vocabularies. Results are provided at any stage in a simplified, tabular view. Specialized views then allows 'zooming in' on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available at http://www.ebi.ac.uk/intact.

IntAct--open source resource for molecular interaction data.

IntAct is an open source database and software suite for modeling, storing and analyzing molecular interaction data. The data available in the database originates entirely from published literature and is manually annotated by expert biologists to a high level of detail, including experimental methods, conditions and interacting domains. The database features over 126,000 binary interactions extracted from over 2100 scientific publications and makes extensive use of controlled vocabularies. The web site provides tools allowing users to search, visualize and download data from the repository. IntAct supports and encourages local installations as well as direct data submission and curation collaborations. IntAct source code and data are freely available from http://www.ebi.ac.uk/intact.

A rapid response toxicity test based on the feeding rate of the tropical cladoceran Moinodaphnia macleayi.

Recent research has reported that the feeding rate of the cladoceran Daphnia magna (measured over 24 h) is a sensitive indicator of toxicity. Using a methodology similar to that used for D. magna, a feeding test for the Australian tropical cladoceran Moinodaphnia macleayi was developed and the sensitivity of the test was compared with the currently used reproduction test. The results of the study revealed that the feeding rate of M. macleayi was a more sensitive indicator of toxicity than reproduction for cadmium; a mean concentration of 1.4 microg/L caused significant inhibition of feeding (P < or = 0.05), while reproduction was significantly reduced at 3.1 microg/L (P < or = 0.05). No feeding inhibition was detected when M. macleayi were exposed to copper, despite significant mortality. The difference in feeding and reproductive responses of M. macleayi to cadmium and copper suggest differing modes of action for the two metals. The feeding test was validated on two samples of mine release water containing various metals. Results demonstrated that a cladoceran feeding test, performed over a 20-h period, was comparable in sensitivity to a reproduction test performed over a 5- to 6-day period.

Synthesis, spectroscopic, and structural studies on transition metal complexes involving homoleptic tripodal selenoether and telluroether coordination.

The reaction of [MCl2(NCMe)2] (M = Pd or Pt) with 2 molar equiv of MeC(CH2ER)3 (E = Se, R = Me; E = Te, R = Me or Ph) and 2 molar equiv of TlPF6 affords the bis ligand complexes [M(MeC(CH2ER)3)2][PF6]2. The crystal structure of [Pt(MeC(CH2SeMe)3)2][PF6]2 (C16H36F12P2PtSe6, a = 12.272(10) A, b = 18.563(9) A, c = 15.285(7) A, beta = 113.18(3) degrees, monoclinic, P2(1)/n, Z = 4) confirms distorted square planar Se4 coordination at Pt(II), derived from two bidentate tripod selenoethers with the remaining arm not coordinated and directed away from the metal center. Solution NMR studies indicate that these species are fluxional and that the telluroether complexes are rather unstable in solution. The octahedral bis tripod complexes [Ru(MeC(CH2SMe)3)2][CF3-SO3]2 and [Ru(MeC(CH2TePh)3)2][CF3SO3]2 are obtained from [Ru(dmf)6][CF3SO3]3 and tripod ligand in EtOH solution. The thioether complex (C18H36F6O6RuS8, a = 8.658(3) A, b = 11.533(3) A, c = 8.659(2) A, alpha = 108.33(2) degrees, beta = 91.53(3) degrees, gamma = 106.01(2) degrees, triclinic, P1, Z = 1) is isostructural with its selenoether analogue, involving two facially coordinated trithioether ligands in the syn configuration. NMR spectroscopy confirms that this configuration is retained in solution for all of the bis tripod Ru(II) complexes. These low-spin d6 complexes show unusually high ligand field splittings. The hexaselenoether Rh(III) complex [Rh(MeC(CH2SeMe)3)2][PF6]3 was obtained by treatment of [Rh(H2O)6]3+ with 2 molar equiv of MeC(CH2SeMe)3 in aqueous MeOH in the presence of excess PF6- anion, while the iridium(III) analogue [Ir(MeC(CH2SeMe)3)2][PF6]3 was obtained via the reaction of the Ir(I) precursor [IrCl(C8H14)2]2 with the selenoether tripod in MeOH/aqueous HBF4. NMR studies reveal different invertomers in solution for both the Rh and Ir species. The Cu(I) complexes [Cu(MeC(CH2ER)3)2]PF6 were obtained from [Cu(NCMe)4]PF6 and tripod ligand in CH2Cl2 solution. The corresponding Ag(I) species [Ag(MeC(CH2TeR)3)2]CF3SO3 (R = Me or Ph) were obtained from Ag[CF3SO3] and tripod telluroether. In contrast, a similar reaction with 2 molar equiv of MeC(CH2SeMe)3 afforded only the 1:1 complex [Ag(MeC(CH2SeMe)3)]CF3SO3. The structure of this species (C9H18AgF3O3SSe3, a = 8.120(3) A, b = 15.374(3) A, c = 14.071(2) A, beta = 93.86(2) degrees, monoclinic, P2(1)/n, Z = 4) reveals a distorted trigonal planar geometry at Ag(I) derived from one bidentate selenoether and one monodentate selenoether. These units are then linked to adjacent Ag(I) ions to give a one-dimensional linear chain cation.

Poison ivy/oak dermatitis. Use of polyamine salts of a linoleic acid dimer for topical prophylaxis.

Closed patch tests were used to evaluate the ability of 156 different preparations (based on 22 different chemicals) to prevent poison ivy dermatitis. Several polyamine salts of a linoleic acid dimer were identified that were totally able to prevent the usual dermatitis in approximately 70% of subjects. The effectiveness of the preparations improved when the antigen and the protectant were washed off within eight to 12 hours, instead of remaining on the skin for 48 hours. When washed off, and depending on the protectant, concentration, and vehicle used, several of the preparations were totally able to prevent a dermatitis in a range of 56% to 100% of subjects tested. Further work with these compounds may greatly benefit the many people currently plagued by their allergy to poison ivy and poison oak.

Corrosion measurements by potential-step chronoamperometry.

A solid-state computer-controlled system has been developed for the measurement of corrosion currents under potentiostatic anodic conditions. The system applies a potential step and measures the resulting current for a variable number of cycles. Data are stored and manipulated by the computer. Tests show that corrosion behaviour of metals in various environments can be evaluated.