gSeaGen: The KM3NeT GENIE-based code for neutrino telescopes

Program summary Program Title: gSeaGen CPC Library link to program files: http://dx.doi.org/10.17632/ymgxvy2br4.1 Licensing provisions: GPLv3 Programming language: C++ External routines/libraries: GENIE [1] and its external dependencies. Linkable to MUSIC [2] and PROPOSAL [3]. Nature of problem: Development of a code to generate detectable events in neutrino telescopes, using modern and maintained neutrino interaction simulation libraries which include the state-of-the-art physics models. The default application is the simulation of neutrino interactions within KM3NeT [4]. Solution method: Neutrino interactions are simulated using GENIE, a modern framework for Monte Carlo event generators. The GENIE framework, used by nearly all modern neutrino experiments, is considered as a reference code within the neutrino community. Additional comments including restrictions and unusual features: The code was tested with GENIE version 2.12.10 and it is linkable with release series 3. Presently valid up to 5 TeV. This limitation is not intrinsic to the code but due to the present GENIE valid energy range. References: [1] C. Andreopoulos at al., Nucl. Instrum. Meth. A614 (2010) 87. [2] P. Antonioli et al., Astropart. Phys. 7 (1997) 357. [3] J. H. Koehne et al., Comput. Phys. Commun. 184 (2013) 2070. [4] S. Adrián-Martínez et al., J. Phys. G: Nucl. Part. Phys. 43 (2016) 084001.The gSeaGen code is a GENIE-based application developed to efficiently generate high statistics samples of events, induced by neutrino interactions, detectable in a neutrino telescope. The gSeaGen code is able to generate events induced by all neutrino flavours, considering topological differences between tracktype and shower-like events. Neutrino interactions are simulated taking into account the density and the composition of the media surrounding the detector. The main features of gSeaGen are presented together with some examples of its application within the KM3NeT project.French National Research Agency (ANR) ANR-15-CE31-0020Centre National de la Recherche Scientifique (CNRS)European Union (EU)Institut Universitaire de France (IUF), FranceIdEx program, FranceUnivEarthS Labex program at Sorbonne Paris Cite ANR-10-LABX-0023 ANR-11-IDEX-000502Paris Ile-de-France Region, FranceShota Rustaveli National Science Foundation of Georgia (SRNSFG), Georgia FR-18-1268German Research Foundation (DFG)Greek Ministry of Development-GSRTIstituto Nazionale di Fisica Nucleare (INFN)Ministry of Education, Universities and Research (MIUR)PRIN 2017 program Italy NAT-NET 2017W4HA7SMinistry of Higher Education, Scientific Research and Professional Training, MoroccoNetherlands Organization for Scientific Research (NWO) Netherlands GovernmentNational Science Centre, Poland 2015/18/E/ST2/00758National Authority for Scientific Research (ANCS), RomaniaMinisterio de Ciencia, Innovacion, Investigacion y Universidades (MCIU): Programa Estatal de Generacion de Conocimiento, Spain (MCIU/FEDER) PGC2018-096663-B-C41 PGC2018-096663-A-C42 PGC2018-096663-BC43 PGC2018-096663-B-C44Severo Ochoa Centre of Excellence and MultiDark Consolider (MCIU), Junta de Andalucia, Spain SOMM17/6104/UGRGeneralitat Valenciana: Grisolia, Spain GRISOLIA/2018/119GenT, Spain CIDEGENT/2018/034La Caixa Foundation LCF/BQ/IN17/11620019EU: MSC program, Spain 71367

The global burden of cancer attributable to risk factors, 2010–19: a systematic analysis for the Global Burden of Disease Study 2019

BACKGROUND: Understanding the magnitude of cancer burden attributable to potentially modifiable risk factors is crucial for development of effective prevention and mitigation strategies. We analysed results from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019 to inform cancer control planning efforts globally. METHODS: The GBD 2019 comparative risk assessment framework was used to estimate cancer burden attributable to behavioural, environmental and occupational, and metabolic risk factors. A total of 82 risk–outcome pairs were included on the basis of the World Cancer Research Fund criteria. Estimated cancer deaths and disability-adjusted life-years (DALYs) in 2019 and change in these measures between 2010 and 2019 are presented. FINDINGS: Globally, in 2019, the risk factors included in this analysis accounted for 4·45 million (95% uncertainty interval 4·01–4·94) deaths and 105 million (95·0–116) DALYs for both sexes combined, representing 44·4% (41·3–48·4) of all cancer deaths and 42·0% (39·1–45·6) of all DALYs. There were 2·88 million (2·60–3·18) risk-attributable cancer deaths in males (50·6% [47·8–54·1] of all male cancer deaths) and 1·58 million (1·36–1·84) risk-attributable cancer deaths in females (36·3% [32·5–41·3] of all female cancer deaths). The leading risk factors at the most detailed level globally for risk-attributable cancer deaths and DALYs in 2019 for both sexes combined were smoking, followed by alcohol use and high BMI. Risk-attributable cancer burden varied by world region and Socio-demographic Index (SDI), with smoking, unsafe sex, and alcohol use being the three leading risk factors for risk-attributable cancer DALYs in low SDI locations in 2019, whereas DALYs in high SDI locations mirrored the top three global risk factor rankings. From 2010 to 2019, global risk-attributable cancer deaths increased by 20·4% (12·6–28·4) and DALYs by 16·8% (8·8–25·0), with the greatest percentage increase in metabolic risks (34·7% [27·9–42·8] and 33·3% [25·8–42·0]). INTERPRETATION: The leading risk factors contributing to global cancer burden in 2019 were behavioural, whereas metabolic risk factors saw the largest increases between 2010 and 2019. Reducing exposure to these modifiable risk factors would decrease cancer mortality and DALY rates worldwide, and policies should be tailored appropriately to local cancer risk factor burden

A novel crumbs homolog 1 mutation in a family with retinitis pigmentosa, nanophthalmos, and optic disc drusen

Contains fulltext : 111029.pdf (publisher's version ) (Open Access)PURPOSE: The purpose of this study is to identify the genetic defect in a Turkish family with autosomal recessive retinitis pigmentosa, nanophthalmos, and optic disc drusen. METHODS: Ophthalmological examinations consisted of measuring the best-corrected visual acuity and the refractive error, electroretinography, optical coherence tomography, B-mode ultrasonography, and fundus photography. The involvement of the membrane frizzled-related protein (MFRP) gene in this family was studied with direct DNA sequencing of the coding exons of MFRP and with linkage analysis with microsatellite markers. After MFRP was excluded, genome-wide homozygosity mapping was performed with 250 K single nucleotide polymorphism (SNP) microarrays. Mutation analysis of the crumbs homolog 1 (CRB1) gene was performed with direct sequencing. RESULTS: Ophthalmological evaluation of both affected individuals in the family revealed a decreased axial length (18-19 mm), retinal dystrophy, macular edema, and hyperopia of >+8.0 diopters. Sequencing of MFRP did not reveal any pathogenic changes, and microsatellite marker analysis showed that the chromosomal region did not segregate within the disease in this family. Genome-wide homozygosity mapping using single nucleotide polymorphism microarrays revealed a 28-Mb homozygous region encompassing the CRB1 gene, and direct sequencing disclosed a novel homozygous missense mutation (p.Gly833Asp) in CRB1. CONCLUSIONS: Previous studies associated mutations in the MFRP gene with the syndrome nanophthalmos-retinitis pigmentosa-foveoschisis-optic disc drusen. In this study, we demonstrated that a similar disease complex can be caused by mutations in the CRB1 gene

High-resolution homozygosity mapping is a powerful tool to detect novel mutations causative of autosomal recessive RP in the Dutch population

Contains fulltext : 96984.pdf (publisher's version ) (Closed access)PURPOSE: To determine the genetic defects underlying autosomal recessive retinitis pigmentosa (arRP) in the Dutch population and in a subset of patients originating from other countries. The hypothesis was that, because there has been little migration over the past centuries in certain areas of The Netherlands, a significant fraction of Dutch arRP patients carry their genetic defect in the homozygous state. METHODS: High-resolution genome-wide SNP genotyping on SNP arrays and subsequent homozygosity mapping were performed in a large cohort of 186 mainly nonconsanguineous arRP families living in The Netherlands. Candidate genes residing in homozygous regions were sequenced. RESULTS: In ~94% of the affected individuals, large homozygous sequences were identified in their genome. In 42 probands, at least one of these homozygous regions contained one of the 26 known arRP genes. Sequence analysis of the corresponding genes in each of these patients revealed 21 mutations and two possible pathogenic changes, 14 of which were novel. All mutations were identified in only a single family, illustrating the genetic diversity within the Dutch population. CONCLUSIONS: This report demonstrates that homozygosity mapping is a powerful tool for identifying the genetic defect underlying genetically heterogeneous recessive disorders like RP, even in populations with little consanguinity

BBS1 Mutations in a Wide Spectrum of Phenotypes Ranging From Nonsyndromic Retinitis Pigmentosa to Bardet-Biedl Syndrome

Item does not contain fulltex

Nanobeacon: A time calibration device for the KM3NeT neutrino telescope

International audienceThe KM3NeT Collaboration is currently constructing a multi-site high-energy neutrino telescope in the Mediterranean Sea consisting of matrices of pressure-resistant glass spheres, each holding a set of 31 small-area photomultipliers. The main goals of the telescope are the observation of neutrino sources in the Universe and the measurement of the neutrino oscillation parameters with atmospheric neutrinos. A relative time synchronisation between photomultipliers of the nanosecond order needed to guarantee the required angular resolution of the detector. Due to the large detector volumes to be instrumented by KM3NeT, a cost reduction of the different systems is a priority. To this end, the inexpensive Nanobeacon has been designed and developed by the KM3NeT Collaboration to be used for detector time-calibration studies. At present, more than 600 Nanobeacons have been already produced. The characterisation of the optical pulse and the wavelength emission profile of the devices is critical for the time calibration. The optical pulse rise time has been quantified as less than 3 ns, while the Full Width Half Maximum is less than 6 ns. The wavelength drift, due to a variation of the supply voltage, has also been qualified as lower than 10 nm for the full range of the Nanobeacon. In this paper, more details about the main features of the Nanobeacon design, production and operation, together with the main properties of the light pulse generated are described

Deep-sea deployment of the KM3NeT neutrino telescope detection units by self-unrolling

KM3NeT is a research infrastructure being installed in the deep Mediterranean Sea. It will house a neutrino telescope comprising hundreds of networked moorings — detection units or strings — equipped with optical instrumentation to detect the Cherenkov radiation generated by charged particles from neutrino-induced collisions in its vicinity. In comparison to moorings typically used for oceanography, several key features of the KM3NeT string are different: the instrumentation is contained in transparent and thus unprotected glass spheres; two thin Dyneema® ropes are used as strength members; and a thin delicate backbone tube with fibre-optics and copper wires for data and power transmission, respectively, runs along the full length of the mooring. Also, compared to other neutrino telescopes such as ANTARES in the Mediterranean Sea and GVD in Lake Baikal, the KM3NeT strings are more slender to minimise the amount of material used for support of the optical sensors. Moreover, the rate of deploying a large number of strings in a period of a few years is unprecedented. For all these reasons, for the installation of the KM3NeT strings, a custom-made, fast deployment method was designed. Despite the length of several hundreds of metres, the slim design of the string allows it to be compacted into a small, re-usable spherical launching vehicle instead of deploying the mooring weight down from a surface vessel. After being lowered to the seafloor, the string unfurls to its full length with the buoyant launching vehicle rolling along the two ropes. The design of the vehicle, the loading with a string, and its underwater self-unrolling are detailed in this paper. © 2020 The Author(s). Published by IOP Publishing Ltd on behalf of Sissa Medialab. Original content from this work may be used under the terms of the Creative Commons Attribution 4.0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI