Automatic Reassembly Method of 3D Thin-wall Fragments Based on Derivative Dynamic Time Warping

In order to address the automatic virtual reassembling of 3D thin-wall fragments, this paper proposes a 3D fragment reassembly method based on derivative dynamic time warping. Firstly, a calculation method of discrete curvature and torsion is designed to solve the difficulty of calculating curvature and torsion of discrete data points and eliminate effectively the noise interferences in the calculation process. Then, it takes curvature and torsion as the feature descriptors of the curve, searches the candidate matching line segments by the derivative dynamic time warping (DDTW) method with the feature descriptors, and records the positions of the starting and ending points of each candidate matching segment. After that, it designs a voting mechanism with the geometric invariant as the constraint information to select further the optimal matching line segments. Finally, it adopts the least squares method to estimate the rotation and transformation matrices and uses the iterative closest point (ICP) method to complete the reassembly of fragments. The experimental results show that the reassembly error is less than 1mm and that the reassembly effect is good. The method can solve the 3D curve matching in case there are partial feature defects, and can achieve the virtual restoration of the broken thin-wall fragment model quickly and effectively

A Survey of Geometric Analysis in Cultural Heritage

We present a review of recent techniques for performing geometric analysis in cultural heritage (CH) applications. The survey is aimed at researchers in the areas of computer graphics, computer vision and CH computing, as well as to scholars and practitioners in the CH field. The problems considered include shape perception enhancement, restoration and preservation support, monitoring over time, object interpretation and collection analysis. All of these problems typically rely on an understanding of the structure of the shapes in question at both a local and global level. In this survey, we discuss the different problem forms and review the main solution methods, aided by classification criteria based on the geometric scale at which the analysis is performed and the cardinality of the relationships among object parts exploited during the analysis. We finalize the report by discussing open problems and future perspectives

De novo formation of centrosomes in vertebrate cells arrested during S phase

The centrosome usually replicates in a semiconservative fashion, i.e., new centrioles form in association with preexisting “maternal” centrioles. De novo formation of centrioles has been reported for a few highly specialized cell types but it has not been seen in vertebrate somatic cells. We find that when centrosomes are completely destroyed by laser microsurgery in CHO cells arrested in S phase by hydroxyurea, new centrosomes form by de novo assembly. Formation of new centrosomes occurs in two steps: ∼5–8 h after ablation, clouds of pericentriolar material (PCM) containing γ-tubulin and pericentrin appear in the cell. By 24 h, centrioles have formed inside of already well-developed PCM clouds. This de novo pathway leads to the formation of a random number of centrioles (2–14 per cell). Although clouds of PCM consistently form even when microtubules are completely disassembled by nocodazole, the centrioles are not assembled under these conditions

A Framework for the Semantics-aware Modelling of Objects

The evolution of 3D visual content calls for innovative methods for modelling shapes based on their intended usage, function and role in a complex scenario. Even if different attempts have been done in this direction, shape modelling still mainly focuses on geometry. However, 3D models have a structure, given by the arrangement of salient parts, and shape and structure are deeply related to semantics and functionality. Changing geometry without semantic clues may invalidate such functionalities or the meaning of objects or their parts. We approach the problem by considering semantics as the formalised knowledge related to a category of objects; the geometry can vary provided that the semantics is preserved. We represent the semantics and the variable geometry of a class of shapes through the parametric template: an annotated 3D model whose geometry can be deformed provided that some semantic constraints remain satisfied. In this work, we design and develop a framework for the semantics-aware modelling of shapes, offering the user a single application environment where the whole workflow of defining the parametric template and applying semantics-aware deformations can take place. In particular, the system provides tools for the selection and annotation of geometry based on a formalised contextual knowledge; shape analysis methods to derive new knowledge implicitly encoded in the geometry, and possibly enrich the given semantics; a set of constraints that the user can apply to salient parts and a deformation operation that takes into account the semantic constraints and provides an optimal solution. The framework is modular so that new tools can be continuously added. While producing some innovative results in specific areas, the goal of this work is the development of a comprehensive framework combining state of the art techniques and new algorithms, thus enabling the user to conceptualise her/his knowledge and model geometric shapes. The original contributions regard the formalisation of the concept of annotation, with attached properties, and of the relations between significant parts of objects; a new technique for guaranteeing the persistence of annotations after significant changes in shape's resolution; the exploitation of shape descriptors for the extraction of quantitative information and the assessment of shape variability within a class; and the extension of the popular cage-based deformation techniques to include constraints on the allowed displacement of vertices. In this thesis, we report the design and development of the framework as well as results in two application scenarios, namely product design and archaeological reconstruction

Statistical analysis of short template switch mutations in human genomes

Many complex rearrangements arise in human genomes through template switch mutations, which occur during DNA replication when there is a transient polymerase switch to an alternate template nearby in three-dimensional space. These variants are routinely captured at kilobase-to-megabase scales in studies of genetic variation by using methods for structural variant calling. However, the genomic and evolutionary consequences of replication-based rearrangements remain poorly characterised at smaller scales, where they are usually interpreted as complex clusters of independent substitutions, insertions and deletions. In this thesis, I describe statistical methods for the detection and interpretation of short template switch mutations within DNA sequence data. I then use my methods to explore small-scale template switch mutagenesis within human genome evolution, population variation, and cancer. I show that small-scale, replication- based rearrangements are a ubiquitous feature of the germline and somatic mutational landscape of human genomes.European Molecular Biology Laboratory National Institute for Health Researc

The reproducibility of incomplete skulls using freeform modeling plus software

As early as 1883, forensic artists and forensic anthropologists have utilized forensic facial reconstruction in the attempt to identify skulls from decomposed remains. Common knowledge dictates that in order to complete identification from the skull with facial reconstruction, the splanchnocranium (also known as the viscerocranium or facial portion of the skull) needs to still be intact. However, there has been very little research conducted (Colledge 1996; Ismail 2008; Wilkinson and Neave 2001) to determine the minimal amount of intact skull that can be present for a reconstruction to still be possible and accurate. Accordingly, in the present study, the researcher attempted to prove that a skull with significant damage to the splanchnocranium could be repaired and facially reconstructed to bear a likeness to the original skull and face. Utilizing FreeForm Modeling Plus Software, version 11.0 (Geomagic Solutions - Andover, MA), in conjunction with the Phantom Desktop Haptic Device (Geomagic Solutions - Andover, MA), five CT scans of males between 19 and 40 years old and of varying ethnicities (four Caucasian and one Asian) were digitally altered to present significant skull damage to the splanchnocranium. The hard tissue digital images were repaired using the same software mentioned above and template skulls (i.e., superfluous CT scanned skulls of similar age, sex, and ancestry). The soft tissue digital images were facially reconstructed also utilizing the same software mentioned above and by following basic tissue depth charts/placement rules and guidelines for feature reconstruction. The reconstructed images were compared to their original CT scans in a side-by-side comparison. Assessors were given a rating scale rubric to fill out that asked them specific questions pertaining to both certain facial features and overall similarity between the original and reconstructed images. Two of the reconstructions each ranked an overall 29% "close resemblance" to their original counterparts, one was ranked an overall 71% "no resemblance" to its original counterpart, and the other three fell somewhere in the middle ("slight" or "approximate") in the rating scale. The results reflected a number of issues related to this project (i.e., the researcher's lack of artistic skill) and to facial reconstruction in general (i.e., tissue depth measurement charts) and showed that while it is not impossible to reconstruct skulls that had been damaged in some capacity, the accuracy of the resulting facial reconstruction is questionable. Future studies would benefit from using an artist to reconstruct the images rather than someone with little to no experience in the field, a larger sample size consisting of one ancestry to avoid the cross-race effect, a comparison of the original skull to the repaired one utilizing Geomagic Qualify (Geomagic Solutions - Andover, MA) to glean an overall view of the project's accuracy, and utilization of a photo lineup as the method of comparison in addition to a side-by-side comparison to give a more realistic feel to the comparison process

Whole genome assembly and gap closure of the toxic bloom-forming cyanobacterium Anabaena sp. strain 90

Anabaena is a common member of the phytoplankton in lakes, reservoirs and ponds throughout the world. This is a filamentous, nitrogen-fixing cyanobacterial genus and is frequently present in the lakes of Finland. Anabaena sp. strain 90 was isolated from Lake Vesijärvi and produces microcystins, anabaenopeptilides and anabaenopeptins. A whole genome shotgun sequencing project was undertaken to obtain the complete genome of this organism in order to better understand the physiology and environmental impact of toxic cyanobacteria. This work describes the genome assembly and finishing, the genome structure, and the results of intensive computational analysis of the Anabaena sp. strain 90 genome. Altogether 119,316 sequence reads were generated from 3 genomic libraries with 2, 6 and 40 kb inserts from high throughput Sanger sequencing. The software package Phred/Phrap/Consed was used for whole genome assembly and finishing. A combinatorial PCR method was used to establish relationships between remaining contigs after thorough scaffolding and gap-filling. The final assembly results show that there is a single 4.3 Mb circular chromosome and 4 circular plasmids with sizes of 820, 80, 56 and 20 kb respectively. Together, these 4 plasmids comprise nearly one-fifth of the total genome. Genomic variations in the form of 79 single nucleotide polymorphisms and 3 sequence indels were identified from the assembly results. Sequence analysis revealed that 7.5 percent of the Anabaena sp. strain 90 genome consists of repetitive DNA elements. The genome sequence of Anabaena sp. strain 90 provides a more solid basis for further studies of bioactive compound production, photosynthesis, nitrogen fixation and akinete formation in cyanobacteria

Designing Service-Oriented Chatbot Systems Using a Construction Grammar-Driven Natural Language Generation System

Service oriented chatbot systems are used to inform users in a conversational manner about a particular service or product on a website. Our research shows that current systems are time consuming to build and not very accurate or satisfying to users. We find that natural language understanding and natural language generation methods are central to creating an e�fficient and useful system. In this thesis we investigate current and past methods in this research area and place particular emphasis on Construction Grammar and its computational implementation. Our research shows that users have strong emotive reactions to how these systems behave, so we also investigate the human computer interaction component. We present three systems (KIA, John and KIA2), and carry out extensive user tests on all of them, as well as comparative tests. KIA is built using existing methods, John is built with the user in mind and KIA2 is built using the construction grammar method. We found that the construction grammar approach performs well in service oriented chatbots systems, and that users preferred it over other systems

Advancing the analysis of bisulfite sequencing data in its application to ecological plant epigenetics

The aim of this thesis is to bridge the gap between the state-of-the-art bioinformatic tools and resources, currently at the forefront of epigenetic analysis, and their emerging applications to non-model species in the context of plant ecology. New, high-resolution research tools are presented; first in a specific sense, by providing new genomic resources for a selected non-model plant species, and also in a broader sense, by developing new software pipelines to streamline the analysis of bisulfite sequencing data, in a manner which is applicable to a wide range of non-model plant species. The selected species is the annual field pennycress, Thlaspi arvense, which belongs in the same lineage of the Brassicaceae as the closely-related model species, Arabidopsis thaliana, and yet does not benefit from such extensive genomic resources. It is one of three key species in a Europe-wide initiative to understand how epigenetic mechanisms contribute to natural variation, stress responses and long-term adaptation of plants. To this end, this thesis provides a high-quality, chromosome-level assembly for T. arvense, alongside a rich complement of feature annotations of particular relevance to the study of epigenetics. The genome assembly encompasses a hybrid approach, involving both PacBio continuous long reads and circular consensus sequences, alongside Hi-C sequencing, PCR-free Illumina sequencing and genetic maps. The result is a significant improvement in contiguity over the existing draft state from earlier studies. Much of the basis for building an understanding of epigenetic mechanisms in non-model species centres around the study of DNA methylation, and in particular the analysis of bisulfite sequencing data to bring methylation patterns into nucleotide-level resolution. In order to maintain a broad level of comparison between T. arvense and the other selected species under the same initiative, a suite of software pipelines which include mapping, the quantification of methylation values, differential methylation between groups, and epigenome-wide association studies, have also been developed. Furthermore, presented herein is a novel algorithm which can facilitate accurate variant calling from bisulfite sequencing data using conventional approaches, such as FreeBayes or Genome Analysis ToolKit (GATK), which until now was feasible only with specifically-adapted software. This enables researchers to obtain high-quality genetic variants, often essential for contextualising the results of epigenetic experiments, without the need for additional sequencing libraries alongside. Each of these aspects are thoroughly benchmarked, integrated to a robust workflow management system, and adhere to the principles of FAIR (Findability, Accessibility, Interoperability and Reusability). Finally, further consideration is given to the unique difficulties presented by population-scale data, and a number of concepts and ideas are explored in order to improve the feasibility of such analyses. In summary, this thesis introduces new high-resolution tools to facilitate the analysis of epigenetic mechanisms, specifically relating to DNA methylation, in non-model plant data. In addition, thorough benchmarking standards are applied, showcasing the range of technical considerations which are of principal importance when developing new pipelines and tools for the analysis of bisulfite sequencing data. The complete “Epidiverse Toolkit” is available at https://github.com/EpiDiverse and will continue to be updated and improved in the future.:ABSTRACT ACKNOWLEDGEMENTS 1 INTRODUCTION 1.1 ABOUT THIS WORK 1.2 BIOLOGICAL BACKGROUND 1.2.1 Epigenetics in plant ecology 1.2.2 DNA methylation 1.2.3 Maintenance of 5mC patterns in plants 1.2.4 Distribution of 5mC patterns in plants 1.3 TECHNICAL BACKGROUND 1.3.1 DNA sequencing 1.3.2 The case for a high-quality genome assembly 1.3.3 Sequence alignment for NGS 1.3.4 Variant calling approaches 2 BUILDING A SUITABLE REFERENCE GENOME 2.1 INTRODUCTION 2.2 MATERIALS AND METHODS 2.2.1 Seeds for the reference genome development 2.2.2 Sample collection, library preparation, and DNA sequencing 2.2.3 Contig assembly and initial scaffolding 2.2.4 Re-scaffolding 2.2.5 Comparative genomics 2.3 RESULTS 2.3.1 An improved reference genome sequence 2.3.2 Comparative genomics 2.4 DISCUSSION 3 FEATURE ANNOTATION FOR EPIGENOMICS 3.1 INTRODUCTION 3.2 MATERIALS AND METHODS 3.2.1 Tissue preparation for RNA sequencing 3.2.2 RNA extraction and sequencing 3.2.3 Transcriptome assembly 3.2.4 Genome annotation 3.2.5 Transposable element annotations 3.2.6 Small RNA annotations 3.2.7 Expression atlas 3.2.8 DNA methylation 3.3 RESULTS 3.3.1 Transcriptome assembly 3.3.2 Protein-coding genes 3.3.3 Non-coding loci 3.3.4 Transposable elements 3.3.5 Small RNA 3.3.6 Pseudogenes 3.3.7 Gene expression atlas 3.3.8 DNA Methylation 3.4 DISCUSSION 4 BISULFITE SEQUENCING METHODS 4.1 INTRODUCTION 4.2 PRINCIPLES OF BISULFITE SEQUENCING 4.3 EXPERIMENTAL DESIGN 4.4 LIBRARY PREPARATION 4.4.1 Whole Genome Bisulfite Sequencing (WGBS) 4.4.2 Reduced Representation Bisulfite Sequencing (RRBS) 4.4.3 Target capture bisulfite sequencing 4.5 BIOINFORMATIC ANALYSIS OF BISULFITE DATA 4.5.1 Quality Control 4.5.2 Read Alignment 4.5.3 Methylation Calling 4.6 ALTERNATIVE METHODS 5 FROM READ ALIGNMENT TO DNA METHYLATION ANALYSIS 5.1 INTRODUCTION 5.2 MATERIALS AND METHODS 5.2.1 Reference species 5.2.2 Natural accessions 5.2.3 Read simulation 5.2.4 Read alignment 5.2.5 Mapping rates 5.2.6 Precision-recall 5.2.7 Coverage deviation 5.2.8 DNA methylation analysis 5.3 RESULTS 5.4 DISCUSSION 5.5 A PIPELINE FOR WGBS ANALYSIS 6 THERE AND BACK AGAIN: INFERRING GENOMIC INFORMATION 6.1 INTRODUCTION 6.1.1 Implementing a new approach 6.2 MATERIALS AND METHODS 6.2.1 Validation datasets 6.2.2 Read processing and alignment 6.2.3 Variant calling 6.2.4 Benchmarking 6.3 RESULTS 6.4 DISCUSSION 6.5 A PIPELINE FOR SNP VARIANT ANALYSIS 7 POPULATION-LEVEL EPIGENOMICS 7.1 INTRODUCTION 7.2 CHALLENGES IN POPULATION-LEVEL EPIGENOMICS 7.3 DIFFERENTIAL METHYLATION 7.3.1 A pipeline for case/control DMRs 7.3.2 A pipeline for population-level DMRs 7.4 EPIGENOME-WIDE ASSOCIATION STUDIES (EWAS) 7.4.1 A pipeline for EWAS analysis 7.5 GENOTYPING-BY-SEQUENCING (EPIGBS) 7.5.1 Extending the epiGBS pipeline 7.6 POPULATION-LEVEL HAPLOTYPES 7.6.1 Extending the EpiDiverse/SNP pipeline 8 CONCLUSION APPENDICES A. SUPPLEMENT: BUILDING A SUITABLE REFERENCE GENOME B. SUPPLEMENT: FEATURE ANNOTATION FOR EPIGENOMICS C. SUPPLEMENT: FROM READ ALIGNMENT TO DNA METHYLATION ANALYSIS D. SUPPLEMENT: INFERRING GENOMIC INFORMATION BIBLIOGRAPH