205 research outputs found
Letter from a Brazilian Supporter to Geraldine Ferraro
Letter from a Brazilian supporter to Geraldine Ferraro.https://ir.lawnet.fordham.edu/vice_presidential_campaign_correspondence_1984_international/1257/thumbnail.jp
Determination of the Change in Electrical Conductivity of Single, Bimetallic and Trimetallic Cylindrical Billets with Plastic Deformation Induced by Upsetting Process
In this study, measurement of the effect of singular, bimetallic and multimetallic materials exposed to cold plastic deformation on electrical conductivity properties was investigated. The main subject of this research is plastic deformation occurring in the upsetting process and changing the conductivity properties of the parts. In the experiments, steel, aluminium, copper, brass, bimetallic and multimetallic materials designed with different combinations of these materials were used as test materials. Experimental upsetting tests were performed as a height reduction ratio 10%, 20% and 30%. The electrical conductivity measurement results of the deformed samples were obtained with a conductivity measuring device. The results obtained from the experiments are presented in graphs with electrical conductivity axis that change due to deformation. As a result of the experiments and measurements, it was concluded that the electrical conductivity of the deformed materials generally decreased slightly due to the plastic deformation of the deformed materials, and the bimetallic and multimetallic materials were similar to the properties of the majority material
Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data
The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%â5% of sequence generated as part of primate genome sequencing projects consists of this material, which is fragmented or not assembled as part of published genome sequences due to its highly repetitive nature. Here, we develop computational methods to rapidly recover and categorize alpha-satellite sequences from previously uncharacterized whole-genome shotgun sequence data. We present an algorithm to computationally predict potential higher-order array structure based on paired-end sequence data and then experimentally validate its organization and distribution by experimental analyses. Using whole-genome shotgun data from the human, chimpanzee, and macaque genomes, we examine the phylogenetic relationship of these sequences and provide further support for a model for their evolution and mutation over the last 25 million years. Our results confirm fundamental differences in the dispersal and evolution of centromeric satellites in the Old World monkey and ape lineages of evolution
Autonomous car parking system with various trajectories
In this study, an algorithm presents a solution to 4-wheel-car parking. This algorithm is suitable for parallel parking between two objects or two cars. Firstly the system verifies whether enough space. After finding a valid parking space, system makes the suitable movements for a perfect parking. This parking operation is tested in a simulation environment using MatLab-Simulink
Manipulating multiple sequence alignments via MaM and WebMaM
MaM is a software tool that processes and manipulates multiple alignments of genomic sequence. MaM computes the exact location of common repeat elements, exons and unique regions within aligned genomics sequences using a variety of user identified programs, databases and/or tables. The program can extract subalignments, corresponding to these various regions of DNA to be analyzed independently or in conjunction with other elements of genomic DNA. Graphical displays further allow an assessment of sequence variation throughout these different regions of the aligned sequence, providing separate displays for their repeat, non-repeat and coding portions of genomic DNA. The program should facilitate the phylogenetic analysis and processing of different portions of genomic sequence as part of large-scale sequencing efforts. MaM source code is freely available for non-commercial use at ; and the web interface WebMaM is hosted at
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery
Recent years have witnessed an increase in research activity for the detection of structural variants (SVs) and their association to human disease. The advent of next-generation sequencing technologies make it possible to extend the scope of structural variation studies to a point previously unimaginable as exemplified by the 1000 Genomes Project. Although various computational methods have been described for the detection of SVs, no such algorithm is yet fully capable of discovering transposon insertions, a very important class of SVs to the study of human evolution and disease. In this article, we provide a complete and novel formulation to discover both loci and classes of transposons inserted into genomes sequenced with high-throughput sequencing technologies. In addition, we also present âconflict resolutionâ improvements to our earlier combinatorial SV detection algorithm (VariationHunter) by taking the diploid nature of the human genome into consideration. We test our algorithms with simulated data from the Venter genome (HuRef) and are able to discover >85% of transposon insertion events with precision of >90%. We also demonstrate that our conflict resolution algorithm (denoted as VariationHunter-CR) outperforms current state of the art (such as original VariationHunter, BreakDancer and MoDIL) algorithms when tested on the genome of the Yoruba African individual (NA18507)
Non-alignment comparison of human and high primate genomes
Compositional spectra (CS) analysis based on k-mer scoring of DNA sequences
was employed in this study for dot-plot comparison of human and primate
genomes. The detection of extended conserved synteny regions was based on
continuous fuzzy similarity rather than on chains of discrete anchors (genes or
highly conserved noncoding elements). In addition to the high correspondence
found in the comparisons of whole-genome sequences, a good similarity was also
found after masking gene sequences, indicating that CS analysis manages to
reveal phylogenetic signal in the organization of noncoding part of the genome
sequences, including repetitive DNA and the genome "dark matter". Obviously,
the possibility to reveal parallel ordering depends on the signal of common
ancestor sequence organization varying locally along the corresponding segments
of the compared genomes. We explored two sources contributing to this signal:
sequence composition (GC content) and sequence organization (abundances of
k-mers in the usual A,T,G,C or purine-pyrimidine alphabets). Whole-genome
comparisons based on GC distribution along the analyzed sequences indeed gives
reasonable results, but combining it with k-mer abundances dramatically
improves the ordering quality, indicating that compositional and organizational
heterogeneity comprise complementary sources of information on evolutionary
conserved similarity of genome sequences
Robustness of Massively Parallel Sequencing Platforms
The improvements in high throughput sequencing technologies (HTS) made clinical sequencing projects such as ClinSeq and Genomics England feasible. Although there are significant improvements in accuracy and reproducibility of HTS based analyses, the usability of these types of data for diagnostic and prognostic applications necessitates a near perfect data generation. To assess the usability of a widely used HTS platform for accurate and reproducible clinical applications in terms of robustness, we generated whole genome shotgun (WGS) sequence data from the genomes of two human individuals in two different genome sequencing centers. After analyzing the data to characterize SNPs and indels using the same tools (BWA, SAMtools, and GATK), we observed significant number of discrepancies in the call sets. As expected, the most of the disagreements between the call sets were found within genomic regions containing common repeats and segmental duplications, albeit only a small fraction of the discordant variants were within the exons and other functionally relevant regions such as promoters. We conclude that although HTS platforms are sufficiently powerful for providing data for first-pass clinical tests, the variant predictions still need to be confirmed using orthogonal methods before using in clinical applications
Structural variation and fusion detection using targeted sequencing data from circulating cell free DNA
MOTIVATION:
Cancer is a complex disease that involves rapidly evolving cells, often forming multiple distinct clones. In order to effectively understand progression of a patient-specific tumor, one needs to comprehensively sample tumor DNA at multiple time points, ideally obtained through inexpensive and minimally invasive techniques. Current sequencing technologies make the 'liquid biopsy' possible, which involves sampling a patient's blood or urine and sequencing the circulating cell free DNA (cfDNA). A certain percentage of this DNA originates from the tumor, known as circulating tumor DNA (ctDNA). The ratio of ctDNA may be extremely low in the sample, and the ctDNA may originate from multiple tumors or clones. These factors present unique challenges for applying existing tools and workflows to the analysis of ctDNA, especially in the detection of structural variations which rely on sufficient read coverage to be detectable.
RESULTS:
Here we introduce SViCTâ, a structural variation (SV) detection tool designed to handle the challenges associated with cfDNA analysis. SViCTâcan detect breakpoints and sequences of various structural variations including deletions, insertions, inversions, duplications and translocations. SViCTâextracts discordant read pairs, one-end anchors and soft-clipped/split reads, assembles them into contigs, and re-maps contig intervals to a reference genome using an efficient k-mer indexing approach. The intervals are then joined using a combination of graph and greedy algorithms to identify specific structural variant signatures. We assessed the performance of SViCTâand compared it to state-of-the-art tools using simulated cfDNA datasets with properties matching those of real cfDNA samples. The positive predictive value and sensitivity of our tool was superior to all the tested tools and reasonable performance was maintained down to the lowest dilution of 0.01% tumor DNA in simulated datasets. Additionally, SViCTâwas able to detect all known SVs in two real cfDNA reference datasets (at 0.6-5% ctDNA) and predict a novel structural variant in a prostate cancer cohort
Multiparametric, Longitudinal Optical Coherence Tomography Imaging Reveals Acute Injury and Chronic Recovery in Experimental Ischemic Stroke
Progress in experimental stroke and translational medicine could be accelerated by high-resolution in vivo imaging of disease progression in the mouse cortex. Here, we introduce optical microscopic methods that monitor brain injury progression using intrinsic optical scattering properties of cortical tissue. A multi-parametric Optical Coherence Tomography (OCT) platform for longitudinal imaging of ischemic stroke in mice, through thinned-skull, reinforced cranial window surgical preparations, is described. In the acute stages, the spatiotemporal interplay between hemodynamics and cell viability, a key determinant of pathogenesis, was imaged. In acute stroke, microscopic biomarkers for eventual infarction, including capillary non-perfusion, cerebral blood flow deficiency, altered cellular scattering, and impaired autoregulation of cerebral blood flow, were quantified and correlated with histology. Additionally, longitudinal microscopy revealed remodeling and flow recovery after one week of chronic stroke. Intrinsic scattering properties serve as reporters of acute cellular and vascular injury and recovery in experimental stroke. Multi-parametric OCT represents a robust in vivo imaging platform to comprehensively investigate these properties
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