MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses.

The development of high-throughput technologies revealed the existence of non-canonical short open reading frames (sORFs) on most eukaryotic ribonucleic acids. They are ubiquitous genetic elements conserved across species and suspected to be involved in numerous cellular processes. MetamORF (https://metamorf.hb.univ-amu.fr/) aims to provide a repository of unique sORFs identified in the human and mouse genomes with both experimental and computational approaches. By gathering publicly available sORF data, normalizing them and summarizing redundant information, we were able to identify a total of 1 162 675 unique sORFs. Despite the usual characterization of ORFs as short, upstream or downstream, there is currently no clear consensus regarding the definition of these categories. Thus, the data have been reprocessed using a normalized nomenclature. MetamORF enables new analyses at locus, gene, transcript and ORF levels, which should offer the possibility to address new questions regarding sORF functions in the future. The repository is available through an user-friendly web interface, allowing easy browsing, visualization, filtering over multiple criteria and export possibilities. sORFs can be searched starting from a gene, a transcript and an ORF ID, looking in a genome area or browsing the whole repository for a species. The database content has also been made available through track hubs at UCSC Genome Browser. Finally, we demonstrated an enrichment of genes harboring upstream ORFs among genes expressed in response to reticular stress. Database URL  https://metamorf.hb.univ-amu.fr/.

Neutrophil-to-Lymphocyte Ratios and Infections after Traumatic Brain Injury: Associations with Hospital Resource Utilization and Long-Term Outcome.

Traumatic brain injury (TBI) induces immune dysfunction that can be captured clinically by an increase in the neutrophil-to-lymphocyte ratio (NLR). However, few studies have characterized the temporal dynamics of NLR post-TBI and its relationship with hospital-acquired infections (HAI), resource utilization, or outcome. We assessed NLR and HAI over the first 21 days post-injury in adults with moderate-to-severe TBI (n = 196) using group-based trajectory (TRAJ), changepoint, and mixed-effects multivariable regression analysis to characterize temporal dynamics. We identified two groups with unique NLR profiles: a high (n = 67) versus a low (n = 129) TRAJ group. High NLR TRAJ had higher rates (76.12% vs. 55.04%, p = 0.004) and earlier time to infection (p = 0.003). In changepoint-derived day 0-5 and 6-20 epochs, low lymphocyte TRAJ, early in recovery, resulted in more frequent HAIs (p = 0.042), subsequently increasing later NLR levels (p ≤ 0.0001). Both high NLR TRAJ and HAIs increased hospital length of stay (LOS) and days on ventilation (p ≤ 0.05 all), while only high NLR TRAJ significantly increased odds of unfavorable six-month outcome as measured by the Glasgow Outcome Scale (GOS) (p = 0.046) in multivariable regression. These findings provide insight into the temporal dynamics and interrelatedness of immune factors which collectively impact susceptibility to infection and greater hospital resource utilization, as well as influence recovery.

Separation of peptides with polyionic nanosponges for MALDI-MS analysis.

A polymer brush consisting of 70% poly(N-isopropylacrylamide) (PNIPAAM) and 30% polymethacrylic acid (PMAA) was synthesized from gold substrates with a "grafting from" AIBN-type free-radical initiator. Fractionation of two peptides, bradykinin and buccalin, was accomplished in less than 120 s by placing a 30 pM (pH approximately 6.2) droplet onto the polymer brush substrate. The eluant containing the anionic buccalin is pipetted away for MALDI analysis while the cationic bradykinin adsorbed to the swollen anionic brush and was subsequently released by adding a droplet of formic acid to the substrate. This caused the brush to collapse and release the bradykinin, much like squeezing a sponge; these nanosponge substrates exhibited very high loading capacity (>2.0 mg/mL) compared to plasma-polymer-modified MALDI substrates. Ellipsometric measurements showed that complementary peptides adsorb rapidly while those of the same charge do not, and MALDI-MS analysis of the two fractions showed separation of both peptides. The adsorption of bradykinin was monitored over time, and 85% of the peptide had been adsorbed to the nanosponge in 1 min from a 0.5 mg/mL aqueous solution.