Genomic sequencing capacity, data retention, and personal access to raw data in Europe

Whole genome/exome sequencing (WGS/WES) has become widely adopted in research and, more recently, in clinical settings. Many hope that the information obtained from the interpretation of these data will have medical benefits for patients and—in some cases—also their biological relatives. Because of the manifold possibilities to reuse genomic data, enabling sequenced individuals to access their own raw (uninterpreted) genomic data is a highly debated issue. This paper reports some of the first empirical findings on personal genome access policies and practices. We interviewed 39 respondents, working at 33 institutions in 21 countries across Europe. These sequencing institutions generate massive amounts of WGS/WES data and represent varying organisational structures and operational models. Taken together, in total, these institutions have sequenced ∼317,259 genomes and exomes to date. Most of the sequencing institutions reported that they are able to store raw genomic data in compliance with various national regulations, although there was a lack of standardisation of storage formats. Interviewees from 12 of the 33 institutions included in our study reported that they had received requests for personal access to raw genomic data from sequenced individuals. In the absence of policies on how to process such requests, these were decided on an ad hoc basis; in the end, at least 28 requests were granted, while there were no reports of requests being rejected. Given the rights, interests, and liabilities at stake, it is essential that sequencing institutions adopt clear policies and processes for raw genomic data retention and personal access

Corrosion Behavior of Composite Coatings Obtained by Electrolytic Codeposition of Copper with Al2O3 Nanoparticles

Composite coatings of copper incorporating Al2O3 nanoparticles electrodeposited on carbon steel were obtained and characterized. By using electrochemical methods such as open circuit potential (ocp) measurements, polarization curves and electrochemical impedance spectroscopy, the corrosion behavior of the Al2O3-copper nanocomposite coatings was examined. The corrosion parameters determined from the polarization curves recorded in Na2SO4 solution (pH 3) indicate that the corrosion process on copper-Al2O3 composite surface is slower than on pure copper. The impedance spectra recorded at the ocp showed in all cases an increase of the polarization resistance in time, which may be explained by the development of corrosion products on the electrode surface. Using a (2RC) equivalent electrical circuit, the process parameters were estimated by non-linear regression calculations with a Simplex method. The Al2O3 particles embedded in the electroplated copper, increase the polarization resistance and decrease the corrosion rates as compared with electrodeposited pure copper. The electrochemical results were corroborated with those obtained by SEM and EDX investigations

Towards retrieving dispersion profiles using quantum-mimic Optical Coherence Tomography and Machine Learnin

Artefacts in quantum-mimic Optical Coherence Tomography are considered detrimental because they scramble the images even for the simplest objects. They are a side effect of autocorrelation which is used in the quantum entanglement mimicking algorithm behind this method. Interestingly, the autocorrelation imprints certain characteristics onto an artefact - it makes its shape and characteristics depend on the amount of dispersion exhibited by the layer that artefact corresponds to. This unique relationship between the artefact and the layer's dispersion can be used to determine Group Velocity Dispersion (GVD) values of object layers and, based on them, build a dispersion-contrasted depth profile. The retrieval of GVD profiles is achieved via Machine Learning. During training, a neural network learns the relationship between GVD and the artefacts' shape and characteristics, and consequently, it is able to provide a good qualitative representation of object's dispersion profile for never-seen-before data: computer-generated single dispersive layers and experimental pieces of glass.Comment: 11 pages, 5 figure

Investigating human mitochondrial genomes in single cells

Mitochondria host multiple copies of their own small circular genome that has been extensively studied to trace the evolution of the modern eukaryotic cell and discover important mutations linked to inherited diseases. Whole genome and exome sequencing have enabled the study of mtDNA in a large number of samples and experimental conditions at single nucleotide resolution, allowing the deciphering of the relationship between inherited mutations and phenotypes and the identification of acquired mtDNA mutations in classical mitochondrial diseases as well as in chronic disorders, ageing and cancer. By applying an ad hoc computational pipeline based on our MToolBox software, we reconstructed mtDNA genomes in single cells using whole genome and exome sequencing data obtained by different amplification methodologies (eWGA, DOP-PCR, MALBAC, MDA) as well as data from single cell Assay for Transposase Accessible Chromatin with high-throughput sequencing (scATAC-seq) in which mtDNA sequences are expected as a byproduct of the technology. We show that assembled mtDNAs, with the exception of those reconstructed by MALBAC and DOP-PCR methods, are quite uniform and suitable for genomic investigations, enabling the study of various biological processes related to cellular heterogeneity such as tumor evolution, neural somatic mosaicism and embryonic development

ТРОЛЛОП И СЛАВЯНСКИЙ МИР: ЗНАКОМСТВО НА РАССТОЯНИИ

The article deals with the “otherness” in A.Trollope’s “Nina Balakka”. The representations of European culture of 19th century Prague is under analysis. Trollope mixes the British and European culture to arrange a “distance game” between the reader and the characters. Discovering Prague with its cultural, historical and linguistic peculiarities reader allows himself to feel the collision of the novel more acutely and to sympathize with the characters more.Статья посвящена анализу романа Э.Троллопа «Нина Балатка» как произведения, в котором автор пытается воспроизвести иной, славянский, мир, рисуя драму любви чешки и еврея. При этом Троллоп не ставит задачу подробного воспроизведения «другой» культуры. Обращаясь к культурным приметам жизни Праги XIX в., Троллоп, прибегая к средствам психологического анализа, акцентирует общечеловеческое содержание национального и расового антагонизма, по его мнению, пронизывающего социальную жизнь знаменитого славянского города. Постоянно «работая» с главным адресатом – читателем-англичанином, писатель подчеркивает, насколько далеко вперед ушел Лондон и Британия в решении подобных проблем

Inclusion of a dithiadiazolyl radical in a seemingly non-porous solid

Inclusion of the dithiadiazolyl radical PhCNSSN• into the dynamically porous metallocycle [Cu2(L1)2Cl4], where L1 is the bidentate ligand 1,3-bis(imidazol-1-ylmethyl)-2,4,6- trimethylbenzene, has been achieved by gas phase diffusion. Single crystal X-ray diffraction, powder X-ray diffraction, UV-visible spectroscopy, EPR and SQUID magnetometry studies confirm inclusion of the radical into this seemingly non-porous material, and illustrate the presence of antiferromagnetic coupling between the paramagnetic host and guest species. The radical guest is readily released by heating or by the addition of solvent (CH2Cl2)