Smart Environmental Data Infrastructures: Bridging the Gap between Earth Sciences and Citizens

The monitoring and forecasting of environmental conditions is a task to which much effort and resources are devoted by the scientific community and relevant authorities. Representative examples arise in meteorology, oceanography, and environmental engineering. As a consequence, high volumes of data are generated, which include data generated by earth observation systems and different kinds of models. Specific data models, formats, vocabularies and data access infrastructures have been developed and are currently being used by the scientific community. Due to this, discovering, accessing and analyzing environmental datasets requires very specific skills, which is an important barrier for their reuse in many other application domains. This paper reviews earth science data representation and access standards and technologies, and identifies the main challenges to overcome in order to enable their integration in semantic open data infrastructures. This would allow non-scientific information technology practitioners to devise new end-user solutions for citizen problems in new application domainsThis research was co-funded by (i) the TRAFAIR project (2017-EU-IA-0167), co-financed by the Connecting Europe Facility of the European Union, (ii) the RADAR-ON-RAIA project (0461_RADAR_ON_RAIA_1_E) co-financed by the European Regional Development Fund (ERDF) through the Iterreg V-A Spain-Portugal program (POCTEP) 2014-2020, and (iii) the Consellería de Educación, Universidade e Formación Profesional of the regional government of Galicia (Spain), through the support for research groups with growth potential (ED431B 2018/28)S

Infrared Thermography for Estimating Supraclavicular Skin Temperature and BAT Activity in Humans: A Systematic Review

Objective: Brown adipose tissue (BAT) is a thermogenic tissue with potential as a therapeutic target in the treatment of obesity and related metabolic disorders. The most used technique for quantifying human BAT activity is the measurement of 18F-fluorodeoxyglucose uptake via a positron emission tomography/computed tomography scan following exposure to cold. However, several studies have indicated the measurement of the supraclavicular skin temperature (SST) by infrared thermography (IRT) to be a less invasive alternative. This work reviews the state of the art of this latter method as a means of determining BAT activity in humans. Methods: The data sources for this review were PubMed, Web of Science, and EBSCOhost (SPORTdiscus), and eligible studies were those conducted in humans. Results: In most studies in which participants were first cooled, an increase in IRT-measured SST was noted. However, only 5 of 24 such studies also involved a nuclear technique that confirmed increased activity in BAT, and only 2 took into account the thickness of the fat layer when measuring SST by IRT. Conclusions: More work is needed to understand the involvement of tissues other than BAT in determining IRTmeasured SST; at present, IRT cannot determine whether any increase in SST is due to increased BAT activity.This study was supported by the Spanish Ministry of Economy and Competitiveness (MINECO) via the Fondo de Investigación Sanitaria del Instituto de Salud Carlos III (PI13/01393), Retos de la Sociedad (DEP2016-79512-R) and European Regional Development Funds (ERDF), the Fundación Iberoamericana de Nutrición (FINUT), the Redes Temáticas de Investigación Cooperativa RETIC (Red SAMID RD16/0022), the AstraZeneca HealthCare Foundation, the University of Granada Plan Propio de Investigación 2016 Excellence actions: Unit of Excellence on Exercise and Health (UCEES), and Plan Propio de Investigación 2018 and the Junta de Andalucía, Consejería de Conocimiento, Investigación y Universidades (ERDF: SOMM17/6107/UGR). DSI is an Investigator of the Miguel Servet Fund from Carlos III National Institute of Health, Spain (CP15/00106). DJP is supported by grants from the Spanish Ministry of Science and Innovation-MINECO (RYC-2014-16938), MINECO/European Fund for Regional Development (FEDER) (DEP2016-76123-R), the Government of Andalusia, the Integrated Territorial Initiative 2014-2020 for the Province of Cádiz (PI-0002-2017), the European Union's ERASMUS+SPORT program (Grant Agreement 603121-EPP-1-2018-1-ES-SPO-SCP), and the EXERNET Research Network on Exercise and Health in Special Populations (DEP2005-00046/ACTI)

Increasing breast milk betaine modulates Akkermansia abundance in mammalian neonates and improves long-term metabolic health

Accelerated postnatal growth is a potentially modifiable risk factor for future obesity. To study how specific breast milk components contribute to early growth and obesity risk, we quantified one-carbon metabolism-related metabolites in human breast milk and found an inverse association between milk betaine content and infant growth. This association was replicated in an independent and geographically distinct cohort. To determine the potential role of milk betaine in modulating offspring obesity risk, we performed maternal betaine supplementation experiments in mice. Higher betaine intake during lactation increased milk betaine content in dams and led to lower adiposity and improved glucose homeostasis throughout adulthood in mouse offspring. These effects were accompanied by a transient increase in Akkermansia spp. abundance in the gut during early life and a long-lasting increase in intestinal goblet cell number. The link between breast milk betaine and Akkermansia abundance in the gut was also observed in humans, as infants exposed to higher milk betaine content during breastfeeding showed higher fecal Akkermansia muciniphila abundance. Furthermore, administration of A. muciniphila to mouse pups during the lactation period partially replicated the effects of maternal breast milk betaine, including increased intestinal goblet cell number, lower adiposity, and improved glucose homeostasis during adulthood. These data demonstrate a link between breast milk betaine content and long-term metabolic health of offspring.info:eu-repo/semantics/acceptedVersio

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Hybrid Sequencing Approach Applied to Human Fecal Metagenomic Clone Libraries Revealed Clones with Potential Biotechnological Applications

<div><p>Natural environments represent an incredible source of microbial genetic diversity. Discovery of novel biomolecules involves biotechnological methods that often require the design and implementation of biochemical assays to screen clone libraries. However, when an assay is applied to thousands of clones, one may eventually end up with very few positive clones which, in most of the cases, have to be “domesticated” for downstream characterization and application, and this makes screening both laborious and expensive. The negative clones, which are not considered by the selected assay, may also have biotechnological potential; however, unfortunately they would remain unexplored. Knowledge of the clone sequences provides important clues about potential biotechnological application of the clones in the library; however, the sequencing of clones one-by-one would be very time-consuming and expensive. In this study, we characterized the first metagenomic clone library from the feces of a healthy human volunteer, using a method based on 454 pyrosequencing coupled with a clone-by-clone Sanger end-sequencing. Instead of whole individual clone sequencing, we sequenced 358 clones in a pool. The medium-large insert (7–15 kb) cloning strategy allowed us to assemble these clones correctly, and to assign the clone ends to maintain the link between the position of a living clone in the library and the annotated contig from the 454 assembly. Finally, we found several open reading frames (ORFs) with previously described potential medical application. The proposed approach allows planning <em>ad-hoc</em> biochemical assays for the clones of interest, and the appropriate sub-cloning strategy for gene expression in suitable vectors/hosts.</p> </div

Nerve Growth Factor Levels in Term Human Infants: Relationship to Prenatal Growth and Early Postnatal Feeding

Background. Nerve growth factor (NGF) plays a key role in neuroprotection and developmental maturity. We assessed longitudinally the circulating concentrations of NGF in term healthy human newborns and infants as well as their association with prenatal growth and early postnatal feeding patterns. Methods. Circulating NGF and anthropometric measures (weight, length, body mass index, and ponderal index) were assessed longitudinally—at birth and at age 4 months—in 86 term infants born appropriate (AGA), small (SGA), or large for gestational age (LGA). Results. Cord blood NGF levels in SGA newborns were higher than those in AGA newborns (1.41 ± 0.2 pg/mL vs. 0.66 ± 0.1 pg/mL; p=0.02) and not different from those in LGA neonates (0.79 ± 0.2 pg/mL). At age 4 months, SGA-breastfed infants showed the highest NGF concentrations (p=0.02 and p=0.01 vs. AGA and SGA-formula-fed infants, respectively), while LGA infants depicted a marginal increase. NGF levels in cord blood correlated negatively with the ponderal index at birth (r=−0.36; p=0.0008). Conclusions. Circulating NGF is related to both prenatal growth and early postnatal nutrition. The maintenance of increased NGF concentrations in SGA-breastfed infants at age 4 months might be a potential mechanism to counterbalance potential risks for developing cognitive and psychomotor disadvantages

InterProScan annotation overview.

<p>Total number of matches and total number of unique protein names assigned by different annotation tools provided by InterProScan. This table summarizes <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047654#pone.0047654.s003" target="_blank">Table S1</a>, which contains the whole list of protein matches in our assembly. The number of matches is higher than the number of unique protein names because one type of protein could be found in several contigs or one ORF could contain several matches to the same protein.</p

KEGG categories distribution.

<p>Distribution of KEGG categories identified among ORFs.</p