Event-based contact angle measurements inside porous media using time-resolved micro-computed tomography

Hypothesis: Capillary-dominated multiphase flow in porous materials is strongly affected by the pore walls' wettability. Recent micro-computed tomography (mCT) studies found unexpectedly wide contact angle distributions measured on static fluid distributions inside the pores. We hypothesize that analysis on time-resolved mCT data of fluid invasion events may be more directly relevant to the fluid dynamics. Experiment: We approximated receding contact angles locally in time and space on time-resolved mCT datasets of drainage in a glass bead pack and a limestone. Whenever a meniscus suddenly entered one or more pores, geometric and thermodynamically consistent contact angles in the surrounding pores were measured in the time step just prior to the displacement event. We introduced a new force-based contact angle, defined to recover the measured capillary pressure in the invaded pore throat prior to interface movement. Findings: Unlike the classical method, the new geometric and force-based contact angles followed plausible, narrower distributions and were mutually consistent. We were unable to obtain credible results with the thermodynamically consistent method, likely because of sensitivity to common imaging artifacts and neglecting dissipation. Time-resolved mCT analysis can yield a more appropriate wettability characterization for pore scale models, despite the need to further reduce image analysis uncertainties. (C) 2020 The Authors. Published by Elsevier Inc

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated data from a defined "true tree" using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree. Results: We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree topology, whereas genes involved in recombination events gave inaccurate branch lengths. We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other. Conclusions: We recommend three approaches, depending on requirements for accuracy and computational time. Quicker approaches that do not perform full maximum likelihood optimisation may be useful for many analyses requiring a phylogeny, as generating a high quality input alignment is likely to be the major limiting factor of accurate tree topology. We have publicly released our simulated data and code to enable further comparisons

A Comprehensive Overview of Computational Nuclei Segmentation Methods in Digital Pathology

In the cancer diagnosis pipeline, digital pathology plays an instrumental role in the identification, staging, and grading of malignant areas on biopsy tissue specimens. High resolution histology images are subject to high variance in appearance, sourcing either from the acquisition devices or the H\&E staining process. Nuclei segmentation is an important task, as it detects the nuclei cells over background tissue and gives rise to the topology, size, and count of nuclei which are determinant factors for cancer detection. Yet, it is a fairly time consuming task for pathologists, with reportedly high subjectivity. Computer Aided Diagnosis (CAD) tools empowered by modern Artificial Intelligence (AI) models enable the automation of nuclei segmentation. This can reduce the subjectivity in analysis and reading time. This paper provides an extensive review, beginning from earlier works use traditional image processing techniques and reaching up to modern approaches following the Deep Learning (DL) paradigm. Our review also focuses on the weak supervision aspect of the problem, motivated by the fact that annotated data is scarce. At the end, the advantages of different models and types of supervision are thoroughly discussed. Furthermore, we try to extrapolate and envision how future research lines will potentially be, so as to minimize the need for labeled data while maintaining high performance. Future methods should emphasize efficient and explainable models with a transparent underlying process so that physicians can trust their output.Comment: 47 pages, 27 figures, 9 table

Impact of Security Factors in Software Project Risk Assessment Using Neural Networks

"Software risk” is the measurement of the probability of an unwanted output that could affect the software product’s development process. It always includes the chance of being uncertain and a potential for loss. This paper extends the concepts of Constructive Cost Model (COCOMO) model into fuzzy Expert COCOMO by introducing security factors as additional parameters for the assessment of risk of a software project. This approach is validated with the NASA60 project data and proved that Genetic Algorithm provided efficient risk values with different levels of security parameters. However, in the earlier methods, there was a limitation in effectively dealing with linguistic forms of imprecise and uncertain inputs. This resulted in increase in the cost of designing the mechanisms for security purposes, that formed a major part in the overall cost in the development process of the software product. The risk value of a software project could well be reduced by taking security factors into consideration. The neural network techniques used for validating the risk values are Kohonen neural network, Radial Basis neural (RBF) network, Learning Vector Quantization, Genetic Algorithm(GA). A comparison study has been provided for all the neural network models implemented in order to examine their performances

Internet-based solutions to support distributed manufacturing

With the globalisation and constant changes in the marketplace, enterprises are adapting themselves to face new challenges. Therefore, strategic corporate alliances to share knowledge, expertise and resources represent an advantage in an increasing competitive world. This has led the integration of companies, customers, suppliers and partners using networked environments. This thesis presents three novel solutions in the tooling area, developed for Seco tools Ltd, UK. These approaches implement a proposed distributed computing architecture using Internet technologies to assist geographically dispersed tooling engineers in process planning tasks. The systems are summarised as follows. TTS is a Web-based system to support engineers and technical staff in the task of providing technical advice to clients. Seco sales engineers access the system from remote machining sites and submit/retrieve/update the required tooling data located in databases at the company headquarters. The communication platform used for this system provides an effective mechanism to share information nationwide. This system implements efficient methods, such as data relaxation techniques, confidence score and importance levels of attributes, to help the user in finding the closest solutions when specific requirements are not fully matched In the database. Cluster-F has been developed to assist engineers and clients in the assessment of cutting parameters for the tooling process. In this approach the Internet acts as a vehicle to transport the data between users and the database. Cluster-F is a KD approach that makes use of clustering and fuzzy set techniques. The novel proposal In this system is the implementation of fuzzy set concepts to obtain the proximity matrix that will lead the classification of the data. Then hierarchical clustering methods are applied on these data to link the closest objects. A general KD methodology applying rough set concepts Is proposed In this research. This covers aspects of data redundancy, Identification of relevant attributes, detection of data inconsistency, and generation of knowledge rules. R-sets, the third proposed solution, has been developed using this KD methodology. This system evaluates the variables of the tooling database to analyse known and unknown relationships in the data generated after the execution of technical trials. The aim is to discover cause-effect patterns from selected attributes contained In the database. A fourth system was also developed. It is called DBManager and was conceived to administrate the systems users accounts, sales engineers’ accounts and tool trial monitoring process of the data. This supports the implementation of the proposed distributed architecture and the maintenance of the users' accounts for the access restrictions to the system running under this architecture

Web-based strategies in the manufacturing industry

The explosive growth of Internet-based architectures is allowing an efficient access to information resources over geographically dispersed areas. This fact is exerting a major influence on current manufacturing practices. Business activities involving customers, partners, employees and suppliers are being rapidly and efficiently integrated through networked information management environments. Therefore, efforts are required to take advantage of distributed infrastructures that can satisfy information integration and collaborative work strategies in corporate environments. In this research, Internet-based distributed solutions focused on the manufacturing industry are proposed. Three different systems have been developed for the tooling sector, specifically for the company Seco Tools UK Ltd (industrial collaborator). They are summarised as follows. SELTOOL is a Web-based open tool selection system involving the analysis of technical criteria to establish appropriate selection of inserts, toolholders and cutting data for turning, threading and grooving operations. It has been oriented to world-wide Seco customers. SELTOOL provides an interactive and crossed-way of searching for tooling parameters, rather than conventional representation schemes provided by catalogues. Mechanisms were developed to filter, convert and migrate data from different formats to the database (SQL-based) used by SELTOOL.TTS (Tool Trials System) is a Web-based system developed by the author and two other researchers to support Seco sales engineers and technical staff, who would perform tooling trials in geographically dispersed machining centres and benefit from sharing data and results generated by these tests. Through TTS tooling engineers (authorised users) can submit and retrieve highly specific technical tooling data for both milling and turning operations. Moreover, it is possible for tooling engineers to avoid the execution of new tool trials knowing the results of trials carried out in physically distant places, when another engineer had previously executed these trials. The system incorporates encrypted security features suitable for restricted use on the World Wide Web. An urgent need exists for tools to make sense of raw data, extracting useful knowledge from increasingly large collections of data now being constructed and made available from networked information environments. This explosive growth in the availability of information is overwhelming the capabilities of traditional information management systems, to provide efficient ways of detecting anomalies and significant patterns in large sets of data. Inexorably, the tooling industry is generating valuable experimental data. It is a potential and unexplored sector regarding the application of knowledge capturing systems. Hence, to address this issue, a knowledge discovery system called DISKOVER was developed. DISKOVER is an integrated Java-application consisting of five data mining modules, able to be operated through the Internet. Kluster and Q-Fast are two of these modules, entirely developed by the author. Fuzzy-K has been developed by the author in collaboration with another research student in the group at Durham. The final two modules (R-Set and MQG) have been developed by another member of the Durham group. To develop Kluster, a complete clustering methodology was proposed. Kluster is a clustering application able to combine the analysis of quantitative as well as categorical data (conceptual clustering) to establish data classification processes. This module incorporates two original contributions. Specifically, consistent indicators to measure the quality of the final classification and application of optimisation methods to the final groups obtained. Kluster provides the possibility, to users, of introducing case-studies to generate cutting parameters for particular Input requirements. Fuzzy-K is an application having the advantages of hierarchical clustering, while applying fuzzy membership functions to support the generation of similarity measures. The implementation of fuzzy membership functions helped to optimise the grouping of categorical data containing missing or imprecise values. As the tooling database is accessed through the Internet, which is a relatively slow access platform, it was decided to rely on faster Information retrieval mechanisms. Q-fast is an SQL-based exploratory data analysis (EDA) application, Implemented for this purpose

XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis

BACKGROUND: Research using the model system Xenopus laevis has provided critical insights into the mechanisms of early vertebrate development and cell biology. Large scale sequencing efforts have provided an increasingly important resource for researchers. To provide full advantage of the available sequence, we have analyzed 350,468 Xenopus laevis Expressed Sequence Tags (ESTs) both to identify full length protein encoding sequences and to develop a unique database system to support comparative approaches between X. laevis and other model systems. DESCRIPTION: Using a suffix array based clustering approach, we have identified 25,971 clusters and 40,877 singleton sequences. Generation of a consensus sequence for each cluster resulted in 31,353 tentative contig and 4,801 singleton sequences. Using both BLASTX and FASTY comparison to five model organisms and the NR protein database, more than 15,000 sequences are predicted to encode full length proteins and these have been matched to publicly available IMAGE clones when available. Each sequence has been compared to the KOG database and ~67% of the sequences have been assigned a putative functional category. Based on sequence homology to mouse and human, putative GO annotations have been determined. CONCLUSION: The results of the analysis have been stored in a publicly available database XenDB . A unique capability of the database is the ability to batch upload cross species queries to identify potential Xenopus homologues and their associated full length clones. Examples are provided including mapping of microarray results and application of 'in silico' analysis. The ability to quickly translate the results of various species into 'Xenopus-centric' information should greatly enhance comparative embryological approaches. Supplementary material can be found at