Risks and benefits of oral modified-release compared with oral immediate-release opioid use after surgery: a systematic review and meta-analysis

Prescription of modified-release opioids for acute postoperative pain is widespread despite evidence to show their use may be associated with an increased risk of adverse effects. This systematic review and meta-analysis aimed to examine the available evidence on the safety and efficacy of modified-release, compared with immediate-release, oral opioids for postoperative pain in adults. We searched five electronic databases from 1 January 2003 to 1 January 2023. Published randomised clinical trials and observational studies on adults who underwent surgery which compared those who received oral modified-release opioids postoperatively with those receiving oral immediate-release opioids were included. Two reviewers independently extracted data on the primary outcomes of safety (incidence of adverse events) and efficacy (pain intensity, analgesic and opioid use, and physical function) and secondary outcomes (length of hospital stay, hospital readmission, psychological function, costs, and quality of life) up to 12 months postoperatively. Of the eight articles included, five were randomised clinical trials and three were observational studies. The overall quality of evidence was low. Modified-release opioid use was associated with a higher incidence of adverse events (n = 645, odds ratio (95%CI) 2.76 (1.52-5.04)) and worse pain (n = 550, standardised mean difference (95%CI) 0.2 (0.04-0.37)) compared with immediate-release opioid use following surgery. Our narrative synthesis concluded that modified-release opioids showed no superiority over immediate-release opioids for analgesic consumption, length of hospital stay, hospital readmissions or physical function after surgery. One study showed that modified-release opioid use is associated with higher rates of persistent postoperative opioid use compared with immediate-release opioid use. None of the included studies reported on psychological function, costs or quality of life.

From ArrayExpress to BioStudies

ArrayExpress (https://www.ebi.ac.uk/arrayexpress) is an archive of functional genomics data at EMBL-EBI, established in 2002, initially as an archive for publication-related microarray data and was later extended to accept sequencing-based data. Over the last decade an increasing share of biological experiments involve multiple technologies assaying different biological modalities, such as epigenetics, and RNA and protein expression, and thus the BioStudies database (https://www.ebi.ac.uk/biostudies) was established to deal with such multimodal data. Its central concept is a study, which typically is associated with a publication. BioStudies stores metadata describing the study, provides links to the relevant databases, such as European Nucleotide Archive (ENA), as well as hosts the types of data for which specialized databases do not exist. With BioStudies now fully functional, we are able to further harmonize the archival data infrastructure at EMBL-EBI, and ArrayExpress is being migrated to BioStudies. In future, all functional genomics data will be archived at BioStudies. The process will be seamless for the users, who will continue to submit data using the online tool Annotare and will be able to query and download data largely in the same manner as before. Nevertheless, some technical aspects, particularly programmatic access, will change. This update guides the users through these changes.

ArrayExpress update - from bulk to single-cell expression data

ArrayExpress (https://www.ebi.ac.uk/arrayexpress) is an archive of functional genomics data from a variety of technologies assaying functional modalities of a genome, such as gene expression or promoter occupancy. The number of experiments based on sequencing technologies, in particular RNA-seq experiments, has been increasing over the last few years and submissions of sequencing data have overtaken microarray experiments in the last 12 months. Additionally, there is a significant increase in experiments investigating single cells, rather than bulk samples, known as single-cell RNA-seq. To accommodate these trends, we have substantially changed our submission tool Annotare which, along with raw and processed data, collects all metadata necessary to interpret these experiments. Selected datasets are re-processed and loaded into our sister resource, the value-added Expression Atlas (and its component Single Cell Expression Atlas), which not only enables users to interpret the data easily but also serves as a test for data quality. With an increasing number of studies that combine different assay modalities (multi-omics experiments), a new more general archival resource the BioStudies Database has been developed, which will eventually supersede ArrayExpress. Data submissions will continue unchanged; all existing ArrayExpress data will be incorporated into BioStudies and the existing accession numbers and application programming interfaces will be maintained.

The BioStudies database-one stop shop for all data supporting a life sciences study

BioStudies (www.ebi.ac.uk/biostudies) is a new public database that organizes data from biological studies. Typically, but not exclusively, a study is associated with a publication. BioStudies offers a simple way to describe the study structure, and provides flexible data deposition tools and data access interfaces. The actual data can be stored either in BioStudies or remotely, or both. BioStudies imports supplementary data from Europe PMC, and is a resource for authors and publishers for packaging data during the manuscript preparation process. It also can support data management needs of collaborative projects. The growth in multiomics experiments and other multi-faceted approaches to life sciences research mean that studies result in a diversity of data outputs in multiple locations. BioStudies presents a solution to ensuring that all these data and the associated publication(s) can be found coherently in the longer term.

Two-Day Hydrophobic Grid Membrane Filter Method for Yeast and Mold Enumeration in Foods Using YM-11 Agar: Collaborative Study

Twenty laboratories participated in a collaborative study to validate a 2-day hydrophobic grid membrane filter method using YM-11 agar for enumeration of yeast and mold in foods. Six naturally contaminated food products were included in the study: garlic powder, raw ground beef, walnuts, flour/meal, orange juice, and yogurt. The test method produced significantly higher results than the 5-day pour plate reference method for orange juice and significantly lower, though numerically similar, results for walnuts and yogurt. Differences between the test and reference methods were not significant for garlic powder, raw ground beef, or flour/meal. Repeatability and reproducibility were similar for both the test and reference methods in all cases. The hydrophobic grid membrane filter method for enumeration of yeast and mold in foods has been adopted by AOAC INTERNATIONAL.

Methyl transferases induced during chemical adaptation of M. luteus

Three peaks of methyltransferase activity specific for MNNG alkylated DNA have been identified from extracts of chemically adapted M. luteus. They are designated as TI to TIII in order to their elution from a Sephadex G-75 column. The first one of these peaks has been purified to homogeneity. TI, is an inducible, unusually salt resistant, heat labile protein which corrects O6-methylguanine in alkylated DNA by the transfer of the O6-alkyl group to a cysteine amino acid in the TI protein. There is a stoichiometric relationship between the loss of O6-methylguanine from the DNA and the production of S-methylcysteine. Partially purified TII & TIII proteins show specificity for O4-alkylthymine and methyl phosphotriesters respectively. The mode of repair by the isolated methyltransferases is similar yet there is no competition for substrate specificity. The apparent molecular weights of TI, TII & TIII proteins are 31Kd, 22Kd, and 13Kd respectively.

DNA glycosylase enzymes induced during chemical adaptation of M. luteus

Five peaks of DNA glycosylase activity showing a preference for MNNG alkylated DNA have been identified from extracts of adapted M. luteus. They are numerically designated as GI to GV in order of their decreasing molecular weights. The first two of these peaks have been highly purified. GI, is a constitutive heat labile protein, 35% stimulated by the presence of 50 mM NaCl, acts exclusively on 3 MeA residues in alkylated DNA, 60-70% inhibited by the presence of 2 mM free 3MeA and has been designated as 3MeA DNA glycosylase enzyme. GII, which is an inducible protein, is heat stable, 28% inhibited by the presence of 50 mM NaCl, removes 3MeA, 3MeG, 7MeA & 7MeG with different efficiency, and has been designated as 3,7 methylpurine DNA glycosylase enzyme. The rate of release of 3 methylpurines is 30 times that of 7MeG. There is no activity of either enzyme on O2-MeC, O2-MeT, O4-MeT or O6-MeG. The apparent molecular weights of GI and GII proteins are 28 Kd and 22 Kd respectively.

Chemical adaptation of M. luteus induces repair functions for O-alkylated DNA pyrimidines

A partially purified extract prepared from adapted M. luteus cells contains repair functions for oxygen methylated pyrimidine residues present in alkylated DNA. The removal of O2-MeT is mediated by a DNA glycosylase enzyme whereas disappearance of O4-MeT is effected by a methyltransferase in a manner similar to the in situ repair of O6-MeG. O4-MeT methyltransferase enzyme is unusually heat resistant. Synthesis of these repair proteins, which are distinctly different from the previously known inducible 3-MeA DNA glycosylase and O6-MeG methyltransferase activities, forms a part of the adaptive response.