SARS-CoV2 hospital surveillance and control system with contact tracing for patients and health care workers at a large reference hospital in Spain during the first wave: An observational descriptive study

Background and Aims During the first peak of the COVID-19 pandemic, the Preventive Medicine Department and the Occupational Health Department at Hospital Clinic de Barcelona (HCB), a large Spanish referral hospital, developed an innovative comprehensive SARS-CoV2 Surveillance and Control System (CoSy-19) in order to preserve patients' and health care workers' (HCWs) safety. We aim to describe the CoSy-19 and to assess the impact in the number of contacts that new cases generated along this time. Methods Observational descriptive study of the findings of the activity of contact tracing of all cases received at the HCB during the first peak of COVID-19 in Spain (February 25th-May 3rd, 2020). Results A team of 204 professionals and volunteers performed 384 in-hospital contact-tracing studies which generated contacts, detecting 298 transmission chains which suggested preventive measures, generated around 22¿000 follow-ups and more than 30¿000¿days of work leave. The number of contacts that new cases generated decreased during the study period. Conclusion Coordination between Preventive Medicine and Occupational Health departments and agile information systems were necessary to preserve non-COVID activity and workers safety.Peer ReviewedPostprint (published version

The influence of semantic and phonological factors on syntactic decisions: An event-related brain potential study

During language production and comprehension, information about a word's syntactic properties is sometimes needed. While the decision about the grammatical gender of a word requires access to syntactic knowledge, it has also been hypothesized that semantic (i.e., biological gender) or phonological information (i.e., sound regularities) may influence this decision. Event-related potentials (ERPs) were measured while native speakers of German processed written words that were or were not semantically and/or phonologically marked for gender. Behavioral and ERP results showed that participants were faster in making a gender decision when words were semantically and/or phonologically gender marked than when this was not the case, although the phonological effects were less clear. In conclusion, our data provide evidence that even though participants performed a grammatical gender decision, this task can be influenced by semantic and phonological factors

Molecular genetic analyses in familial and sporadic congenital primary erythrocytosis

Dominant mutations in the erythropoietin receptor (EPOR) gene account for only about 15% of cases of primary congenital erythrocytosis. To search for molecular alterations in patients with this disorder. Sixteen patients with Ep

Automated download and clean-up of family-specific databases for kmer-based virus identification.

SUMMARY: Here, we present an automated pipeline for Download Of NCBI Entries (DONE) and continuous updating of a local sequence database based on user-specified queries. The database can be created with either protein or nucleotide sequences containing all entries or complete genomes only. The pipeline can automatically clean the database by removing entries with matches to a database of user-specified sequence contaminants. The default contamination entries include sequences from the UniVec database of plasmids, marker genes and sequencing adapters from NCBI, an E.coli genome, rRNA sequences, vectors and satellite sequences. Furthermore, duplicates are removed and the database is automatically screened for sequences from green fluorescent protein, luciferase and antibiotic resistance genes that might be present in some GenBank viral entries, and could lead to false positives in virus identification. For utilizing the database, we present a useful opportunity for dealing with possible human contamination. We show the applicability of DONE by downloading a virus database comprising 37 virus families. We observed an average increase of 16 776 new entries downloaded per month for the 37 families. In addition, we demonstrate the utility of a custom database compared to a standard reference database for classifying both simulated and real sequence data. AVAILABILITYAND IMPLEMENTATION: The DONE pipeline for downloading and cleaning is deposited in a publicly available repository (https://bitbucket.org/genomicepidemiology/done/src/master/). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Impact of adjunct cytogenetic abnormalities for prognostic stratification in patients with myelodysplastic syndrome and deletion 5q.

This cooperative study assessed prognostic factors for overall survival (OS) and risk of transformation to acute myeloid leukemia (AML) in 541 patients with de novo myelodysplastic syndrome (MDS) and deletion 5q. Additional chromosomal abnormalities were strongly related to different patients' characteristics. In multivariate analysis, the most important predictors of both OS and AML transformation risk were number of chromosomal abnormalities (P<0.001 for both outcomes), platelet count (P<0.001 and P=0.001, respectively) and proportion of bone marrow blasts (P<0.001 and P=0.016, respectively). The number of chromosomal abnormalities defined three risk categories for AML transformation (del(5q), del(5q)+1 and del(5q)+ ≥ 2 abnormalities) and two for OS (one group: del(5q) and del(5q)+1; and del(5q)+ ≥ 2 abnormalities, as the other one); with a median survival time of 58.0 and 6.8 months, respectively. Platelet count (P=0.001) and age (P=0.034) predicted OS in patients with '5q-syndrome'. This study demonstrates the importance of additional chromosomal abnormalities in MDS patients with deletion 5q, challenges the current '5q-syndrome' definition and constitutes a useful reference series to properly analyze the results of clinical trials in these patients