High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

The 1000 Genomes Project (1kGP) is the largest fully open resource of whole-genome sequencing (WGS) data consented for public distribution without access or use restrictions. The final, phase 3 release of the 1kGP included 2,504 unrelated samples from 26 populations and was based primarily on low-coverage WGS. Here, we present a high-coverage 3,202-sample WGS 1kGP resource, which now includes 602 complete trios, sequenced to a depth of 30X using Illumina. We performed single-nucleotide variant (SNV) and short insertion and deletion (INDEL) discovery and generated a comprehensive set of structural variants (SVs) by integrating multiple analytic methods through a machine learning model. We show gains in sensitivity and precision of variant calls compared to phase 3, especially among rare SNVs as well as INDELs and SVs spanning frequency spectrum. We also generated an improved reference imputation panel, making variants discovered here accessible for association studies

More than a method? Organisational ethnography as a way of imagining the social

© 2016 Informa UK Limited, trading as Taylor & Francis Group. The authors–two anthropologists and an organisational theorist, all organisational ethnographers–discuss their understanding and practices of organisational ethnography (OE) as a way of imagining and reflect on how similar this understanding may be for young organisational researchers and students in particular. The discussion leads to the conclusion that OE may be regarded as a methodology but that it has a much greater potential when it is reclaiming its roots: to become a mode of doing social science on the meso-level. The discussion is based on an analysis of both historical material and the contemporary learning experiences of teaching OE as more than a method to our students

Prawno-organizacyjne problemy realizacji "Programu usuwania azbestu i wyrobów zawierających azbest na terytorium Polski"

After the introduction dealing with the occurrence, application and harmfulness of asbestos, the paper presents basic legal regulations concerning the use and disposal of asbestos-containing products. The main assumptions of "Programme for the disposal of asbestos and asbestos-containing products in Poland" were discussed. The assessment of the programme implementation was presented on the basis of inspection report prepared by the Ministry of Economy and NIK (Supreme Chamber of Control).W pracy, po krótkim wprowadzeniu dotyczącym występowania, zastosowania oraz szkodliwości azbestu, przedstawiono podstawowe regulacje prawne w zakresie użytkowania i usuwania wyrobów zawierających azbest. Omówiono główne założenia "Programu usuwania azbestu i wyrobów zawierających azbest stosowanych na terytonum Polski". Ocenę realizacji Programu przedstawiono na podstawie raportów kontrolnych Ministerstwa Gospodarki oraz NIK

Optimization of drilling costs on shale gas deposits – concept outline

Polska w ostatniej dekadzie stała się jednym z najbardziej aktywnych rynków poszukiwania niekonwencjonalnych złóż węglowodorów. Obecnie na terenie kraju obowiązuje 20 koncesji na poszukiwanie i/lub rozpoznawanie złóż, w tym gazu z łupków. Powierzchnia objęta koncesjami poszukiwawczymi to 7,5% powierzchni kraju. W cyklu życia projektu zagospodarowania i eksploatacji gazu z zasobów łupkowych można wyróżnić cztery główne etapy: wybór i przygotowanie miejsca wykonania odwiertów, etap wiercenia i szczelinowania hydraulicznego, eksploatacja (produkcja) i marketing oraz „wygaszenie” eksploatacji i rekultywacja terenu. W artykule przedstawiono koncepcję analizy kosztów projektu inwestycyjnego związanego z poszukiwaniem i zagospodarowaniem złoża/obszaru gazu z łupków. Poddano analizie dwa pierwsze etapy dotyczące prac przygotowawczych, realizowanych na wybranym placu oraz prac wiertniczych i szczelinowania hydraulicznego. Ze względów ekonomicznych jedynym racjonalnym sposobem udostępnienia złóż gazu łupkowego jest stosowanie otworów poziomych, wykonywanych pojedynczo lub grupowo. Ilość padów wiertniczych, pokrywających obszar koncesji jest podstawowym determinantem kosztów zagospodarowania złoża. W artykule przedstawiono wyniki analizy kosztów różnego rodzaju sposobu rozwiercania złoża o powierzchni 25 000 000 m2 . Oszacowań kosztów dokonano dla dwóch wariantów: grupowego wiercenia dla trzech rodzajów padów wiertniczych − z trzema, pięcioma i siedmioma otworami oraz dla otworów wykonywanych pojedynczo. Wyniki analizy pokazują, że wraz ze wzrostem liczby odwiertów w padzie maleją sumaryczne koszty rozwiercania złoża o założonej powierzchni. Dla padów z trzema odwiertami są mniejsze w stosunku do wariantu drugiego o ponad 7%, przy pięciu są mniejsze o 11%, a przy siedmiu odwiertach realizowanych z jednego placu budowy są mniejsze w stosunku do wariantu drugiego o 11,5%. Autorzy poprzez zastosowaną metodykę wskazują kierunek oraz sposoby dalszych badań i analiz, które umożliwią optymalizację prac wiertniczych na złożach gazu z łupków.In the last decade, Poland has become one of the most active markets for unconventional hydrocarbon deposits exploration. At present, there are twenty concessions for the exploration and/or discovery of reserves, including shale gas. The area covered by exploration concessions constitutes ca. 7.5% of the country’s area. Four main stages can be distinguished In the shale gas development and exploitation project: the selection and preparation of the place of development of the wells, hydraulic drilling and fracturing, exploitation (production) and marketing, exploitation suppression and land reclamation. In the paper, the concept of cost analysis of an investment project related to the exploration and development of a shale gas field/area was presented. The first two stages related to the preparatory work, carried out on the selected site, as well as drilling and hydraulic fracturing were analyzed. For economic reasons, the only rational way to make shale gas reserves available is to use horizontal drilling, either singly or in groups. The number of drilling pads covering the concession area is a fundamental determinant of the development cost of the deposit. In the paper, the results of the cost analysis of various types of reaming method with an area of 25,000,000 m2 were presented. Cost estimates were prepared for two variants: group drilling for three types of drilling pads: with three, five and seven wells and for single wells. The results show that, as the number of horizontal wells increases, the total cost of the development of the deposit is reduced. For tree-wells pad, these costs are 7% lower than in the second variant, for five-well pads they are 11% lower, and for seven-well pads they are 11.5% smaller than in the second variant. Authors, using applied methodology, indicate the direction of further research that will enable the optimization of shale gas drilling operations

Comparison of the Stress Relaxation of Biodegradable Surgical Threads Made of Mg and Zn Alloys and Some Commercial Synthetic Materials

The mechanical properties of the commercial synthetic surgical threads (i.e., monofilament MonosynR and polyfilament PolysorbTM) and threads made of pure zinc and selected magnesium alloys were compared. Tensile and relaxation tests of fine fibers/wires without and with a surgical knot were performed on a Zwick 250 tensile machine and on the specially constructed tensile machine dedicated for ultra-thin samples. An about 50% decrease in the maximum tensile load was registered for both synthetic and Mg-based threads due to the presence of a surgical knot while only an about 10% decrease was documented for the zinc threads

De Novo Mutation in an Enhancer of EBF3 in simplex autism

AbstractPrevious research in autism and other neurodevelopmental disorders (NDDs) has indicated an important contribution of de novo protein-coding variants within specific genes. The role of de novo noncoding variation has been observable as a general increase in genetic burden but has yet to be resolved to individual functional elements. In this study, we assessed whole-genome sequencing data in 2,671 families with autism, with a specific focus on de novo variation in enhancers with previously characterized in vivo activity. We identified three independent de novo mutations limited to individuals with autism in the enhancer hs737. These mutations result in similar phenotypic characteristics, affect enhancer activity in vitro, and preferentially occur in AAT motifs in the enhancer with predicted disruptions of transcription factor binding. We also find that hs737 is enriched for copy number variation in individuals with NDDs, is dosage sensitive in the human population, is brain-specific, and targets the NDD gene EBF3 that is genome-wide significant for protein coding de novo variants, demonstrating the importance of understanding all forms of variation in the genome.One Sentence SummaryWhole-genome sequencing in thousands of families reveals variants relevant to simplex autism in a brain enhancer of the well-established neurodevelopmental disorder gene EBF3