1,951 research outputs found
cnvOffSeq: detecting intergenic copy number variation using off-target exome sequencing data.
No full textMotivation: Exome sequencing technologies have transformed the field of Mendelian genetics and allowed for efficient detection of genomic variants in protein-coding regions. The target enrichment process that is intrinsic to exome sequencing is inherently imperfect, generating large amounts of unintended off-target sequence. Off-target data are characterized by very low and highly heterogeneous coverage and are usually discarded by exome analysis pipelines. We posit that off-target read depth is a rich, but overlooked, source of information that could be mined to detect intergenic copy number variation (CNV). We propose cnvOffseq, a novel normalization framework for off-target read depth that is based on local adaptive singular value decomposition (SVD). This method is designed to address the heterogeneity of the underlying data and allows for accurate and precise CNV detection and genotyping in off-target regions.Results: cnvOffSeq was benchmarked on whole-exome sequencing samples from the 1000 Genomes Project. In a set of 104 gold standard intergenic deletions, our method achieved a sensitivity of 57.5% and a specificity of 99.2%, while maintaining a low FDR of 5%. For gold standard deletions longer than 5 kb, cnvOffSeq achieves a sensitivity of 90.4% without increasing the FDR. cnvOffSeq outperforms both whole-genome and whole-exome CNV detection methods considerably and is shown to offer a substantial improvement over naïve local SVD
Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions
No full textBackground: The power of haplotype-based methods for association studies, identification of regions under selection, and ancestral inference, is well-established for diploid organisms. For polyploids, however, the difficulty of determining phase has limited such approaches. Polyploidy is common in plants and is also observed in animals. Partial polyploidy is sometimes observed in humans (e. g. trisomy 21; Down's syndrome), and it arises more frequently in some human tissues. Local changes in ploidy, known as copy number variations (CNV), arise throughout the genome. Here we present a method, implemented in the software polyHap, for the inference of haplotype phase and missing observations from polyploid genotypes. PolyHap allows each individual to have a different ploidy, but ploidy cannot vary over the genomic region analysed. It employs a hidden Markov model (HMM) and a sampling algorithm to infer haplotypes jointly in multiple individuals and to obtain a measure of uncertainty in its inferences.Results: In the simulation study, we combine real haplotype data to create artificial diploid, triploid, and tetraploid genotypes, and use these to demonstrate that polyHap performs well, in terms of both switch error rate in recovering phase and imputation error rate for missing genotypes. To our knowledge, there is no comparable software for phasing a large, densely genotyped region of chromosome from triploids and tetraploids, while for diploids we found polyHap to be more accurate than fastPhase. We also compare the results of polyHap to SATlotyper on an experimentally haplotyped tetraploid dataset of 12 SNPs, and show that polyHap is more accurate.Conclusion: With the availability of large SNP data in polyploids and CNV regions, we believe that polyHap, our proposed method for inferring haplotypic phase from genotype data, will be useful in enabling researchers analysing such data to exploit the power of haplotype-based analyses
A novel method to allow noninvasive, longitudinal imaging of the murine immune system in vivo
No full textIn vivo imaging has revolutionized understanding of the spatiotemporal complexity that subserves the generation of successful effector and regulatory immune responses. Until now, invasive surgery has been required for microscopic access to lymph nodes (LNs), making repeated imaging of the same animal impractical and potentially affecting lymphocyte behavior. To allow longitudinal in vivo imaging, we conceived the novel approach of transplanting LNs into
the mouse ear pinna. Transplanted LNs maintain the structural and cellular organization of conventional secondary lymphoid organs. They participate in lymphocyte
recirculation and exhibit the capacity to receive and respond to local antigenic challenge. The same LN could be repeatedly imaged through time without the requirement for surgical exposure, and the dynamic behavior of the cells within the transplanted LN could be characterized. Crucially, the use of blood vessels as fiducial markers also allowed precise re-registration of the same regions for
longitudinal imaging. Thus, we provide the first demonstration of a method for repeated, noninvasive, in vivo imaging of lymphocyte behavior
»LJ« Artist book
No full textThe thesis paper deals with the artist book, an art form that has become a part of the university curriculum since the beginning of my university studies. It is most closely connected with the fields of sketch and photography. Both personl sketch and the field of photography have been of particular interest to me during my university years and I prepared an exhibition on the subject, presented by Faculty of Education Gallery. This thesis covers the historical and theoretical background of the artist book and maps the creation of my own artist book, an artistic superaddition titled LJ.
Some of the pioneers of the artist book are also mentioned, including Ed Ruscha, the author of the Twenty Six Gasoline Stations. He was one of the first artist to draw attention to the various artistic possibilities of this art form intertwining different graphic components including sketch, photography, font, paper characteristic, and other visual effects. Franc zagoričnik is presented as a native artist interested in the art form. He was a member of the OHO group, which reached the same conclusions as Ruscha in the 1970s.
The thesis places the artist book within the field of education, since this particular pedagogical approach has been shown to give the pupil freedom of choice and thus enrich his sensibilty to artistic expression. Pratical reasearch was conducted at a high school in Koper, while theoretical research heavily relied on the MGLC library, which is the only Slovene library to carry contemporary literature on this particular art form
Correction to: Photoacoustic Measurements of the Thermal and Elastic Properties of n-Type Silicon Using Neural Networks (Silicon, (2020), 12, 6, (1289-1300), 10.1007/s12633-019-00213-6)
No full textThe original version of the article unfortunately contained an error. © 2020, Springer Nature B.V.
The author name ‘Кatarina Lj. Djordjevic’ was inadvertently
captured twice. The correct author group is shown above.Link to the corrected article: [https://vinar.vin.bg.ac.rs/handle/123456789/8759
Episodic encoding is more than the sum of its parts: An fMRI investigation of multifeatural contextual encoding
No full textEpisodic memories are characterized by their contextual richness, yet little is known about how the various features comprising an episode are brought together in memory. Here we employed fMRI and a multidimensional source memory procedure to investigate processes supporting the mnemonic binding of item and contextual information. Volunteers were scanned while encoding items for which the contextual features (color and location) varied independently, allowing activity elicited at the time of study to be segregated according to whether both, one, or neither feature was successfully retrieved on a later memory test. Activity uniquely associated with successful encoding of both features was identified in the intra-parietal sulcus, a region strongly implicated in the support of attentionally mediated perceptual binding. The findings suggest that the encoding of disparate features of an episode into a common memory representation requires that the features be conjoined in a common perceptual representation when the episode is initially experienced
On the vapor-liquid equilibrium of attractive chain fluids with variable degree of molecular flexibility
No full textWe study the isotropic (vapor and liquid) phase behavior of attractive chain fluids. Special emphasis is placed on the role of molecular flexibility, which is studied by means of a rod-coil model. Two new equations of state (EoSs) are developed for square-well- (SW) and Lennard-Jones (LJ) chain fluids. The EoSs are developed by applying the perturbation theory of Barker and Henderson (BH) to a reference fluid of hard chain molecules. The novelty of the approach is based on (1) the use of a recently developed hard-chain reference EoS that explicitly incorporates the effects of molecular flexibility, (2) the use of recent molecular simulation data for the radial distribution function of hard-chain fluids, and (3) a newly developed effective segment size, which effectively accounts for the soft repulsion between segments of LJ chains. It is shown that the effective segment size needs to be temperature-, density-, and chain-length dependent. To obtain a simplified analytical EoS, the perturbation terms are fitted by polynomials in density (SW and LJ), chain length (SW and LJ), and temperature (only for LJ). It is shown that the equations of state result in an accurate description of molecular simulation data for vapor-liquid equilibria (VLE) and isotherms of fully flexible SW- and LJ chain fluids and their mixtures. To evaluate the performance of the equations of state in describing the effects of molecular flexibility on VLE, we present new Monte Carlo simulation results for the VLE of rigid linear- and partially flexible SW- and LJ chain fluids. For SW chains, the developed EoS is in a good agreement with simulation results. For increased rigidity of the chains, both theory and simulations predict an increase of the VL density difference and a slight increase of the VL critical temperature. For LJ chains, the EoS proves incapable of reproducing part of these trends.Process and EnergyMechanical, Maritime and Materials Engineerin
PLANNER: a multi-scale deep language model for the origins of replication site prediction
No full textOrigins of replication sites (ORIs) are crucial genomic regions where DNA replication initiation takes place, playing pivotal roles in fundamental biological processes like cell division, gene expression regulation, and DNA integrity. Accurate identification of ORIs is essential for comprehending cell replication, gene expression, and mutation-related diseases. However, experimental approaches for ORI identification are often expensive and time-consuming, leading to the growing popularity of computational methods. In this study, we present PLANNER (DeeP LeArNiNg prEdictor for ORI), a novel approach for species-specific and cell-specific prediction of eukaryotic ORIs. PLANNER uses the multi-scale ktuple sequences as input and employs the DNABERT pre-training model with transfer learning and ensemble learning strategies to train accurate predictive models. Extensive empirical test results demonstrate that PLANNER achieved superior predictive performance compared to state-of-the-art approaches, including iOri-Euk, Stack-ORI, and ORI-Deep, within specific cell types and across different cell types. Furthermore, by incorporating an interpretable analysis mechanism, we provide insights into the learned patterns, facilitating the mapping from discovering important sequential determinants to comprehensively analysing their biological functions. To facilitate the widespread utilisation of PLANNER, we developed an online webserver and local stand-alone software, available at http://planner.unimelb-biotools.cloud.edu.au/ and https://github.com/CongWang3/PLANNER, respectivelyNo Full Tex
The reality of media freedom in Swaziland under the new constitutional dispensation
No full textThe study concludes that there is still lack of media freedom in Swaziland under the new constitutional dispensation. Its significant finding is that the lack of media freedom is a consequence of constitutional, legal and extra-legal constraints
Statistical Associating Fluid Theory (SAFT) Equation of State
No full textThe SAFT equation of state, which is based on Wertheim’s theory (1984a,b, 1986a-c) was developed by Chapman et al in 1990. The SAFT model has been derived for a reference fluid that is defined as a mixture of Lennard-Jones (LJ) spheres. The equation of state takes into account the following interactions between the spheres: • Repulsive and attractive forces. • The formation of clusters due to molecular association; and • The formation of chains by covalent bonding. The SAFT equation of state is expressed in terms of the molar residual Helmholtz energy of the reference fluid, which is a sum of the following three Helmholtz energy terms: • The hard sphere term and the dispersion term (corresponding respectively to them change in Helmholtz energy due to the repulsive and attractive forces between the LJ segments). • The association term (represents the change in Helmholtz energy due to associative bonding between the LJ segments); and • The chain term (represents the change in Helmholtz energy due to covalent bonding between the LJ segments to form chains)...Applied Science
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