Recovering and harmonizing research cruises information

The IEO has maintained since late 60s, a local database with basic information on oceanographic campaigns, formerly known as ROSCOF reports, which were established in the framework of IODE initiatives, as a low-level inventory for future access to data. Technological advances in recent decades and different coordination activities between NODCs have favored the implementation of these reports in standardized digital formats (Cruise Summary Reports, CSR) that allow their integration in international repositories as SeaDataNet or POGO. However, this inventory and cataloging activity has suffered ups and downs over 40 years of activity, changes in storage criteria and periods of less activity. In the search for a unique criterion that can last over time and that unifies this information as much as possible with the data generated in these campaigns, an exhaustive review of the existing information has been carried out

Evaluation of Natural Language Processing for the Identification of Crohn Disease-Related Variables in Spanish Electronic Health Records:A Validation Study for the PREMONITION-CD Project

Background: The exploration of clinically relevant information in the free text of electronic health records (EHRs) holds the potential to positively impact clinical practice as well as knowledge regarding Crohn disease (CD), an inflammatory bowel disease that may affect any segment of the gastrointestinal tract. The EHRead technology, a clinical natural language processing (cNLP) system, was designed to detect and extract clinical information from narratives in the clinical notes contained in EHRs. Objective: The aim of this study is to validate the performance of the EHRead technology in identifying information of patients with CD. Methods: We used the EHRead technology to explore and extract CD-related clinical information from EHRs. To validate this tool, we compared the output of the EHRead technology with a manually curated gold standard to assess the quality of our cNLP system in detecting records containing any reference to CD and its related variables. Results: The validation metrics for the main variable (CD) were a precision of 0.88, a recall of 0.98, and an F1 score of 0.93. Regarding the secondary variables, we obtained a precision of 0.91, a recall of 0.71, and an F1 score of 0.80 for CD flare, while for the variable vedolizumab (treatment), a precision, recall, and F1 score of 0.86, 0.94, and 0.90 were obtained, respectively. Conclusions: This evaluation demonstrates the ability of the EHRead technology to identify patients with CD and their related variables from the free text of EHRs. To the best of our knowledge, this study is the first to use a cNLP system for the identification of CD in EHRs written in Spanish. © 2022 JMIR Medical Informatics. All rights reserved

Recovering and harmonizing research cruises information

The IEO has maintained since late 60s, a local database with basic information on oceanographic campaigns, formerly known as ROSCOF reports, which were established in the framework of IODE initiatives, as a low-level inventory for future access to data. Technological advances in recent decades and different coordination activities between NODCs have favored the implementation of these reports in standardized digital formats (Cruise Summary Reports, CSR) that allow their integration in international repositories as SeaDataNet or POGO. However, this inventory and cataloging activity has suffered ups and downs over 40 years of activity, changes in storage criteria and periods of less activity. In the search for a unique criterion that can last over time and that unifies this information as much as possible with the data generated in these campaigns, an exhaustive review of the existing information has been carried out. The result has been the retrieval of information from short-term campaigns carried out on smaller vessels with great coastal activity, as well as updating information regarding old campaigns performed on the first half of the 20th century onboard of decommissioned vessels. All this is completed with the systematic campaigns carried out by INTECMAR in the Galician rias, research vessels operated by the national Fisheries Administration, and information on research surveys carried out by foreign ships in national waters, forming a catalog of more than 4000 entries. This approach is also followed by the UTM-CSIC, on its own-managed vessels and campaigns carried out since 1991. The common approach allows a unified response to the governmental needs for the planning of future campaigns, and in successive improvements in data recovering, archiving and accessing at NODC/CEDO

Tandemly repeated DNA families in the mouse genome

<p>Abstract</p> <p>Background</p> <p>Functional and morphological studies of tandem DNA repeats, that combine high portion of most genomes, are mostly limited due to the incomplete characterization of these genome elements. We report here a genome wide analysis of the large tandem repeats (TR) found in the mouse genome assemblies.</p> <p>Results</p> <p>Using a bioinformatics approach, we identified large TR with array size more than 3 kb in two mouse whole genome shotgun (WGS) assemblies. Large TR were classified based on sequence similarity, chromosome position, monomer length, array variability, and GC content; we identified four superfamilies, eight families, and 62 subfamilies - including 60 not previously described. 1) The superfamily of centromeric minor satellite is only found in the unassembled part of the reference genome. 2) The pericentromeric major satellite is the most abundant superfamily and reveals high order repeat structure. 3) Transposable elements related superfamily contains two families. 4) The superfamily of heterogeneous tandem repeats includes four families. One family is found only in the WGS, while two families represent tandem repeats with either single or multi locus location. Despite multi locus location, TRPC-21A-MM is placed into a separated family due to its abundance, strictly pericentromeric location, and resemblance to big human satellites.</p> <p>To confirm our data, we next performed <it>in situ </it>hybridization with three repeats from distinct families. TRPC-21A-MM probe hybridized to chromosomes 3 and 17, multi locus TR-22A-MM probe hybridized to ten chromosomes, and single locus TR-54B-MM probe hybridized with the long loops that emerge from chromosome ends. In addition to <it>in silico </it>predicted several extra-chromosomes were positive for TR by <it>in situ </it>analysis, potentially indicating inaccurate genome assembly of the heterochromatic genome regions.</p> <p>Conclusions</p> <p>Chromosome-specific TR had been predicted for mouse but no reliable cytogenetic probes were available before. We report new analysis that identified <it>in silico </it>and confirmed <it>in situ </it>3/17 chromosome-specific probe TRPC-21-MM. Thus, the new classification had proven to be useful tool for continuation of genome study, while annotated TR can be the valuable source of cytogenetic probes for chromosome recognition.</p

Advanced material against human (Including Covid‐19) and plant viruses: nanoparticles as a feasible strategy

The SARS‐CoV‐2 virus outbreak revealed that these nano‐pathogens have the ability to rapidly change lives. Undoubtedly, SARS‐CoV‐2 as well as other viruses can cause important global impacts, affecting public health, as well as, socioeconomic development. But viruses are not only a public health concern, they are also a problem in agriculture. The current treatments are often ineffective, are prone to develop resistance, or cause considerable adverse side effects. The use of nanotechnology has played an important role to combat viral diseases. In this review three main aspects are in focus: first, the potential use of nanoparticles as carriers for drug delivery. Second, its use for treatments of some human viral diseases, and third, its application as antivirals in plants. With these three themes, the aim is to give to readers an overview of the progress in this promising area of biotechnology during the 2017–2020 period, and to provide a glance at how tangible is the effectiveness of nanotechnology against viruses. Future prospects are also discussed. It is hoped that this review can be a contribution to general knowledge for both specialized and non‐specialized readers, allowing a better knowledge of this interesting topic.REDES‐ANID. Grant Number: 180003 Universidad de La Frontera. Grant Number: DI20‐1003 FAPESP. Grant Numbers: 2018/08194‐2, 2018/02832‐7 CNPq. Grant Numbers: 404815/2018‐9, 313117/2019‐5 CONICYT/FAPESP. Grant Number: 2018/08194‐2 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior. Grant Numbers: 001, ANID/FONDAP/15130015 FCT. Grant Number: PTDC/CTM‐TEX/28295/2017 FEDER POCI Portugal 2020 program COMPETE. Grant Number: UID/CTM/00264/2019 FCT/MCTE

A Kinetic Study of Acrylamide/ Acrylic Acid Copolymerization

Homo- and co-polymers of acrylamide (AAm) and acrylic acid (or acrylate salt) (AA) or methacrylic acid (MAA)) are important classes of water-soluble polymers due to their numerous applications in fields such as super absorbents, additives in cosmetics, membrane technology, waste-water treatment and oil field operations. These polymers are generally made by free radical polymerization. For copolymerization reactions it is extremely important to know the details of reaction kinetics in order to ascertain the kinetic effects of different reaction parameters, which ultimately dictate final copolymer composition, microstructure and properties. The reactivity ratios for copolymerization of AAm and AA have been shown to be dependent on pH and they also change with reaction solvent. The present experimental investigation has been performed to study the kinetics of copolymerization of these monomers in aqueous and alcoholic media by considering factors such as type of initiator and solvent, and pH, in order to determine how they affect the reactivity ratios of these monomers. Reactivity ratios were determined by non-linear least squares (NLLS) and the error-in-variables-model (EVM) techniques and full conversion range kinetic investigations were carried out to confirm these values

Immunoglobulin, glucocorticoid, or combination therapy for multisystem inflammatory syndrome in children: a propensity-weighted cohort study

Background: Multisystem inflammatory syndrome in children (MIS-C), a hyperinflammatory condition associated with SARS-CoV-2 infection, has emerged as a serious illness in children worldwide. Immunoglobulin or glucocorticoids, or both, are currently recommended treatments. Methods: The Best Available Treatment Study evaluated immunomodulatory treatments for MIS-C in an international observational cohort. Analysis of the first 614 patients was previously reported. In this propensity-weighted cohort study, clinical and outcome data from children with suspected or proven MIS-C were collected onto a web-based Research Electronic Data Capture database. After excluding neonates and incomplete or duplicate records, inverse probability weighting was used to compare primary treatments with intravenous immunoglobulin, intravenous immunoglobulin plus glucocorticoids, or glucocorticoids alone, using intravenous immunoglobulin as the reference treatment. Primary outcomes were a composite of inotropic or ventilator support from the second day after treatment initiation, or death, and time to improvement on an ordinal clinical severity scale. Secondary outcomes included treatment escalation, clinical deterioration, fever, and coronary artery aneurysm occurrence and resolution. This study is registered with the ISRCTN registry, ISRCTN69546370. Findings: We enrolled 2101 children (aged 0 months to 19 years) with clinically diagnosed MIS-C from 39 countries between June 14, 2020, and April 25, 2022, and, following exclusions, 2009 patients were included for analysis (median age 8·0 years [IQR 4·2–11·4], 1191 [59·3%] male and 818 [40·7%] female, and 825 [41·1%] White). 680 (33·8%) patients received primary treatment with intravenous immunoglobulin, 698 (34·7%) with intravenous immunoglobulin plus glucocorticoids, 487 (24·2%) with glucocorticoids alone; 59 (2·9%) patients received other combinations, including biologicals, and 85 (4·2%) patients received no immunomodulators. There were no significant differences between treatments for primary outcomes for the 1586 patients with complete baseline and outcome data that were considered for primary analysis. Adjusted odds ratios for ventilation, inotropic support, or death were 1·09 (95% CI 0·75–1·58; corrected p value=1·00) for intravenous immunoglobulin plus glucocorticoids and 0·93 (0·58–1·47; corrected p value=1·00) for glucocorticoids alone, versus intravenous immunoglobulin alone. Adjusted average hazard ratios for time to improvement were 1·04 (95% CI 0·91–1·20; corrected p value=1·00) for intravenous immunoglobulin plus glucocorticoids, and 0·84 (0·70–1·00; corrected p value=0·22) for glucocorticoids alone, versus intravenous immunoglobulin alone. Treatment escalation was less frequent for intravenous immunoglobulin plus glucocorticoids (OR 0·15 [95% CI 0·11–0·20]; p<0·0001) and glucocorticoids alone (0·68 [0·50–0·93]; p=0·014) versus intravenous immunoglobulin alone. Persistent fever (from day 2 onward) was less common with intravenous immunoglobulin plus glucocorticoids compared with either intravenous immunoglobulin alone (OR 0·50 [95% CI 0·38–0·67]; p<0·0001) or glucocorticoids alone (0·63 [0·45–0·88]; p=0·0058). Coronary artery aneurysm occurrence and resolution did not differ significantly between treatment groups. Interpretation: Recovery rates, including occurrence and resolution of coronary artery aneurysms, were similar for primary treatment with intravenous immunoglobulin when compared to glucocorticoids or intravenous immunoglobulin plus glucocorticoids. Initial treatment with glucocorticoids appears to be a safe alternative to immunoglobulin or combined therapy, and might be advantageous in view of the cost and limited availability of intravenous immunoglobulin in many countries. Funding: Imperial College London, the European Union's Horizon 2020, Wellcome Trust, the Medical Research Foundation, UK National Institute for Health and Care Research, and National Institutes of Health

Immunoglobulin, glucocorticoid, or combination therapy for multisystem inflammatory syndrome in children: a propensity-weighted cohort study

Background Multisystem inflammatory syndrome in children (MIS-C), a hyperinflammatory condition associated with SARS-CoV-2 infection, has emerged as a serious illness in children worldwide. Immunoglobulin or glucocorticoids, or both, are currently recommended treatments. Methods The Best Available Treatment Study evaluated immunomodulatory treatments for MIS-C in an international observational cohort. Analysis of the first 614 patients was previously reported. In this propensity-weighted cohort study, clinical and outcome data from children with suspected or proven MIS-C were collected onto a web-based Research Electronic Data Capture database. After excluding neonates and incomplete or duplicate records, inverse probability weighting was used to compare primary treatments with intravenous immunoglobulin, intravenous immunoglobulin plus glucocorticoids, or glucocorticoids alone, using intravenous immunoglobulin as the reference treatment. Primary outcomes were a composite of inotropic or ventilator support from the second day after treatment initiation, or death, and time to improvement on an ordinal clinical severity scale. Secondary outcomes included treatment escalation, clinical deterioration, fever, and coronary artery aneurysm occurrence and resolution. This study is registered with the ISRCTN registry, ISRCTN69546370. Findings We enrolled 2101 children (aged 0 months to 19 years) with clinically diagnosed MIS-C from 39 countries between June 14, 2020, and April 25, 2022, and, following exclusions, 2009 patients were included for analysis (median age 8·0 years [IQR 4·2–11·4], 1191 [59·3%] male and 818 [40·7%] female, and 825 [41·1%] White). 680 (33·8%) patients received primary treatment with intravenous immunoglobulin, 698 (34·7%) with intravenous immunoglobulin plus glucocorticoids, 487 (24·2%) with glucocorticoids alone; 59 (2·9%) patients received other combinations, including biologicals, and 85 (4·2%) patients received no immunomodulators. There were no significant differences between treatments for primary outcomes for the 1586 patients with complete baseline and outcome data that were considered for primary analysis. Adjusted odds ratios for ventilation, inotropic support, or death were 1·09 (95% CI 0·75–1·58; corrected p value=1·00) for intravenous immunoglobulin plus glucocorticoids and 0·93 (0·58–1·47; corrected p value=1·00) for glucocorticoids alone, versus intravenous immunoglobulin alone. Adjusted average hazard ratios for time to improvement were 1·04 (95% CI 0·91–1·20; corrected p value=1·00) for intravenous immunoglobulin plus glucocorticoids, and 0·84 (0·70–1·00; corrected p value=0·22) for glucocorticoids alone, versus intravenous immunoglobulin alone. Treatment escalation was less frequent for intravenous immunoglobulin plus glucocorticoids (OR 0·15 [95% CI 0·11–0·20]; p<0·0001) and glucocorticoids alone (0·68 [0·50–0·93]; p=0·014) versus intravenous immunoglobulin alone. Persistent fever (from day 2 onward) was less common with intravenous immunoglobulin plus glucocorticoids compared with either intravenous immunoglobulin alone (OR 0·50 [95% CI 0·38–0·67]; p<0·0001) or glucocorticoids alone (0·63 [0·45–0·88]; p=0·0058). Coronary artery aneurysm occurrence and resolution did not differ significantly between treatment groups. Interpretation Recovery rates, including occurrence and resolution of coronary artery aneurysms, were similar for primary treatment with intravenous immunoglobulin when compared to glucocorticoids or intravenous immunoglobulin plus glucocorticoids. Initial treatment with glucocorticoids appears to be a safe alternative to immunoglobulin or combined therapy, and might be advantageous in view of the cost and limited availability of intravenous immunoglobulin in many countries. Funding Imperial College London, the European Union's Horizon 2020, Wellcome Trust, the Medical Research Foundation, UK National Institute for Health and Care Research, and National Institutes of Health