Ship- and island-based soundings from the 2016 El Niño Rapid Response (ENRR) field campaign

As the 2015/2016 El Niño was gathering strength in late 2015, scientists at the Earth System Research Laboratory's Physical Sciences Division proposed and led the implementation of the National Oceanic and Atmospheric Administration's (NOAA's) El Niño Rapid Response (ENRR) Field Campaign. ENRR observations included wind and thermodynamic profiles of the atmosphere over the near-equatorial eastern central Pacific Ocean, many of which were collected from two field sites and transmitted in near-real time for inclusion in global forecasting models. From 26 January to 28 March 2016, twice-daily rawinsonde observations were made from Kiritimati (pronounced Christmas) Island (2.0° N, 157.4° E; call sign CXENRR). From 16 February to 16 March 2016, three to eight radiosondes were launched each day from NOAA Ship Ronald H. Brown (allocated call sign WTEC) as it travelled southeast from Hawaii to service Tropical Atmosphere Ocean (TAO) buoys along longitudes 140 and 125° W and then north to San Diego, California. Both the rapid and remote nature of these deployments created particular difficulties in collecting and disseminating the soundings; these are described together with the methods used to reprocess the data after the field campaign finished. The reprocessed and lightly quality-controlled data have been put into an easy-to-read text format, qualifying them to be termed Level 2 soundings. They are archived and freely available for public access at NOAA's National Centers for Environmental Information (NCEI) in the form of two separate data sets: one consisting of 125 soundings from Kiritimati (https://doi.org/10.7289/V55Q4T5K), the other of 193 soundings from NOAA Ship Ronald H. Brown (https://doi.org/10.7289/V5X63K15). Of the Kiritimati soundings, 94 % reached the tropopause and 88 % reached 40 hPa, while 89 % of the ship's soundings reached the tropopause and 87 % reached 40 hPa. The soundings captured the repeated advance and retreat of the Intertropical Convergence Zone (ITCZ) at Kiritimati, a variety of marine tropospheric environments encountered by the ship, and lower-stratospheric features of the 2015–2016 QBO (quasi-biennial oscillation), all providing a rich view of the local atmosphere's response to the eastern central Pacific's extremely warm waters during the 2015/16 El Niño

Detection of long repeat expansions from PCR-free whole-genome sequence data

Identifying large expansions of short tandem repeats (STRs) such as those that cause amyotrophic lateral sclerosis (ALS) and fragile X syndrome is challenging for short-read whole-genome sequencing (WGS) data. A solution to this problem is an important step towards integrating WGS into precision medicine. We have developed a software tool called ExpansionHunter that, using PCR-free WGS short-read data, can genotype repeats at the locus of interest, even if the expanded repeat is larger than the read length. We applied our algorithm to WGS data from 3,001 ALS patients who have been tested for the presence of the C9orf72 repeat expansion with repeat-primed PCR (RP-PCR). Compared against this truth data, ExpansionHunter correctly classified all (212/212, 95% CI [0.98, 1.00]) of the expanded samples as either expansions (208) or potential expansions (4). Additionally, 99.9% (2,786/2,789, 95% CI [0.997, 1.00]) of the wild type samples were correctly classified as wild type by this method with the remaining three samples identified as possible expansions. We further applied our algorithm to a set of 152 samples where every sample had one of eight different pathogenic repeat expansions including those associated with fragile X syndrome, Friedreich's ataxia and Huntington's disease and correctly flagged all but one of the known repeat expansions. Thus, ExpansionHunter can be used to accurately detect known pathogenic repeat expansions and provides researchers with a tool that can be used to identify new pathogenic repeat expansions. The software is licensed under GPL v3.0 and the source code is freely available on GitHub

Mapping and characterization of structural variation in 17,795 human genomes

A key goal of whole-genome sequencing for studies of human genetics is to interrogate all forms of variation, including single-nucleotide variants, small insertion or deletion (indel) variants and structural variants. However, tools and resources for the study of structural variants have lagged behind those for smaller variants. Here we used a scalable pipeline1 to map and characterize structural variants in 17,795 deeply sequenced human genomes. We publicly release site-frequency data to create the largest, to our knowledge, whole-genome-sequencing-based structural variant resource so far. On average, individuals carry 2.9 rare structural variants that alter coding regions; these variants affect the dosage or structure of 4.2 genes and account for 4.0–11.2% of rare high-impact coding alleles. Using a computational model, we estimate that structural variants account for 17.2% of rare alleles genome-wide, with predicted deleterious effects that are equivalent to loss-of-function coding alleles; approximately 90% of such structural variants are noncoding deletions (mean 19.1 per genome). We report 158,991 ultra-rare structural variants and show that 2% of individuals carry ultra-rare megabase-scale structural variants, nearly half of which are balanced or complex rearrangements. Finally, we infer the dosage sensitivity of genes and noncoding elements, and reveal trends that relate to element class and conservation. This work will help to guide the analysis and interpretation of structural variants in the era of whole-genome sequencing

Ship- and island-based soundings from the 2016 El Niño Rapid Response (ENRR) field campaign

Abstract. As the 2015/2016 El Niño was gathering strength in late 2015, scientists at the Earth System Research Laboratory's Physical Sciences Division proposed and led the implementation of NOAA's El Niño Rapid Response (ENRR) Field Campaign. ENRR observations included wind and thermodynamic profiles of the atmosphere over the near-equatorial east-central Pacific Ocean, many of which were collected from two field sites and transmitted in near-real time for inclusion in global forecasting models. From 26 January to 28 March 2016, twice-daily rawinsonde observations were made from Kiritimati (pronounced Christmas) Island (2.0°N, 157.4°E; call sign CXENRR). From 16 February to 16 March 2016, three to eight radiosondes were launched each day from the NOAA Ship Ronald H. Brown (allocated call sign WTEC) as it travelled southeast from Hawaii to service Tropical Atmosphere Ocean (TAO) buoys along longitudes 140°W and 125°W and then north to San Diego, California. Both the rapid and the remote nature of these deployments created particular difficulties in collecting and disseminating the soundings; these are described together with the methods used to reprocess the data after the field campaign finished. The reprocessed and lightly quality-controlled data have been put into an easy-to-read text format, qualifying them to be termed Level 2 soundings. They are archived and freely available for public access at NOAA's National Centers for Environmental Information (NCEI) in the form of two separate data sets: one consisting of 125 soundings from Kiritimati Island (doi:10.7289/V55Q4T5K), the other of 193 soundings from the NOAA Ship Ronald H. Brown (doi:10.7289/V5X63K15). Of the Kiritimati soundings, 94 % reached the tropopause and 88 % reached 40 hPa, while 89 % of the ship's soundings reached the tropopause and 87 % reached 40 hPa. The soundings captured the repeated advance and retreat of the ITCZ at Kiritimati, a variety of marine tropospheric environments encountered by the ship, and lower-stratospheric features of the 2015–2016 QBO (quasi-biennial oscillation), all providing a rich view of the local atmosphere's response to the east-central Pacific's extremely warm waters during the 2015/16 El Niño. </jats:p

Environmental sustainability of engineering works: geological and geotechnical aspects

The design and construction of engineering works such as road infrastructures, port facilities and waste disposal plants require that important environmental issues be addressed, in order to guarantee sustainability and facilitate acceptability by the population. With these objectives, much of the scientific work produced by the geological and geotechnical research group of the Università Politecnica delle Marche in the past 50 years has involved aspects such as understanding the effects of human activities on the environment in order to prevent or minimize the risks of permanent damage, exploration of solutions that optimize the use of natural resources, implementation of technologies that promote the use of improved natural materials for construction, application of design procedures that are based on high quality geological, geotechnical and geo-environmental models of the construction sites. This paper will present, via the illustration of some practical examples, the contribution that such research activities have provided on the solution of some important engineering problems in the past decades