cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
title: Structural and biochemical characterisation of human SWI/SNF-related chromatin remodelling complexes
titleType: Other
Creators: name: Toman, Matt
Publisher: name: University of Dundee
Year: 2022

description: The genomes of eukaryotes exist as chromatin. The organisation of chromatin provides a means of regulating access to the underlying genetic information. One way in which eukaryotes regulate chromatin is through the action of chromatin remodelling motor proteins. Human forms of the SWI/SNF remodelling complex are a series of chromatin remodelling ATPases comprised of some 15 partially overlapping subunits. These complexes function at enhancers and other regulatory elements. They have been observed to be mutated at high rates in a range of human cancers. Characterisation of the structure and biochemical activities of these complexes is limited. We aimed to address this by developing a system for the expression of human SWI/SNF complex subunits in insect cells as recombinant proteins. A complex of the core proteins was successfully expressed and purified. This complex was found to have robust biochemical activity, and enabled the investigation of the effects on remodelling resulting from small molecule inhibitors targeting SWI/SNF domains, and the effects of introduced subunit mutations. Complexes bearing a tumour-associated mutation in the SMARCA4 ATPase were purified and their enzymatic activity on nucleosomes was characterised. The presence of mutant complexes was found to reduce the activity of wild-type complexes, consistent with their dominant negative phenotype in vivo. A sub-complex of human PBAF was purified by the incorporation of PBAF-specific subunits PBRM1 and BRD7 into the core complex. The biochemical activity of both complexes on nucleosomes was tested. Both complexes were then investigated for their remodelling activity on nucleosomes bearing acetylated H3 histones, which are known to stimulate binding to and remodelling of nucleosomes by yeast SWI/SNF complexes. The PBRM1 sub-complex was found to remodel acetylated nucleosomes at a reduced rate compared to the core complex. Structural analysis by cryo-EM was undertaken for both of the complexes, however only low resolution structures were obtained.
title: Identifying Legal Frameworks Impacting Institutional Investors’ Participation in Infrastructure Projects
titleType: Other
Creators: name: Taha, Mohamed
Publisher: name: University of Dundee
Year: 2022

description: The rapid changes in the financial intermediation landscape have significantly impacted the sources of funding available for infrastructure projects. While commercial banks used to dominate the funding sources for project finance, their ability to provide the long-term financing needed for infrastructure projects has been restricted due to the new capital and liquidity requirements introduced by Basel III. This was counterbalanced by an increasing appetite for institutional investors to provide such financing.

The increasing participation from institutional investors in financing infrastructure projects with a proportionate decrease in the share of commercial banks to finance these projects are not unfolding at a consistent rate worldwide. While institutional investors have been significantly increasing their relative participation in financing infrastructure projects in advanced economies, their participation in financing such projects in emerging markets has been modest, both in absolute terms and relative to the overall private infrastructure investment in these jurisdictions. Funding sources remained concentrated with commercial banks in the emerging markets but have become more diversified in advanced economies.

The thesis assesses the impact of the legal frameworks applicable to institutional financing of infrastructure projects on the appetite of institutional investors to invest in these projects, and aims to identify the legal frameworks that can directly attract or deter such institutional investment in infrastructure projects. The analysis is conducted from supply, demand, and financing instruments perspectives. The supply-side analysis comprises the legal requirements impacting investment decisions by the key types of institutional investors from the lens of the regulations applicable to such investors. The demand-side analysis comprises the legal frameworks relating to an investment in the infrastructure asset classes in the country where the infrastructure asset is located. The financial instruments analysis comprises the tools through which institutional investors can channel their funds to infrastructure projects.
Energy-efficient city logistics. Polish - Swedish - Chinese discussion panel (E-LaaS project)
Creators: name: Szczepański, Emilian
name: Lewczuk, Konrad
name: Jacyna, Marianna
Publisher: name: Zenodo
Year: 2023

description: Report from the discussion panel at a scientific conference as part of the E-LaaS (Energy optimal urban logistics As A Service) project.

The panel discussion held as part of the 12th International Scientific and Technical Conference Logistic Systems - Theory and Practice (September 3 – 5, 2023, Warsaw – Józefów) on "Energy-efficient City Logistics" was an event in the context of urban logistics research, especially in cargo transportation.

 

Energy optimal urban Logistics As A Service - Project funding informationProject implemented as part of the call ERA-NET Cofund Urban Accessibility and Connectivity (ENUAC China Call) organized by JPI Urban Europe and the National Natural Science Foundation of China (NSFC). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 875022. E-Laas project is carried out in an international consortium. Project coordinator in Europe: Chalmers University of Technology (Sweden), project coordinator in China: Shanghai University (China), consortium members: Tsinghua University (China), Warsaw University of Technology (Poland), cooperation partners: Stockholms stad, Trafikkontoret (Sweden), ParkUnload (Spain), Metropolis GZM (Poland), Shanghai Urban-Rural Construction and Transportation Department (China), Volvo Group Trucks Technology and Operations (Sweden).

The Chinese part of the project is funded by National Natural Science Foundation of China.

The Swedish part of the project is funded by Swedish Energy Agency.

The Polish part of the project is funded by the National Science Centre, Poland (project no. 2022/04/Y/ST8/00134). The value of the co-financing is PLN 878,107.00. Project duration 27/04/2023 - 26/04/2026 (36 months).
Additional file 1 of An overview of methods to address distinct research questions on environmental mixtures: an application to persistent organic pollutants and leukocyte telomere length
Creators: name: Gibson, Elizabeth A.
name: Yanelli Nunez
name: Abuawad, Ahlam
name: Zota, Ami R.
name: Renzetti, Stefano
name: Devick, Katrina L.
name: Gennings, Chris
name: Goldsmith, Jeff
name: Coull, Brent A.
name: Marianthi-Anna Kioumourtzoglou
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: FOS: Biological sciences

description: Supplemental description of methods and additional tables and figures. Table S1 Useful resources for included methods. Table S2 Overview of method characteristics. Table S3 POP characteristics. Table S4 Demographic Characteristics. Figure S1 Hierarchical clustering dendrogram. Figure S2 PCA loadings. Figure S3 EFA loadings. Figure S4 BKMR Interactions (Plot 1). Figure S5 BKMR Interactions (Plot 2). (PDF 1233 kb)
title: Impact of ethanol on regulated cell death Crithidia Fasciculata
Creators: name: McCraw, Morgan
Publisher: name: Georgia State University
Year: 2022

description:
Given the early divergence of trypanosomatids in evolution and absence of genes central to classical cell death pathways, induction, and mechanisms of regulated cell death in these species will shed light on origin of these processes. The early divergence of eukaryotic cells can be observed with the Trypanosomatids taxa (Green, 2015)


Crithidia fasciculata is a trypanosomatid, mosquito parasite. We explored sensitivity of Crithidia to ethanol (?20%) on cell death and externalization of phosphatidylserine (PS) using propidium iodide (PI) and annexin V-FITC (AV). While 20% ethanol killed cells necrotically (PI+ /AV+), 9% ethanol resulted elicited nonlethal, PS externalization in a subset (2%) of the population (PI- /AV+). To elucidate the mechanism of this cell death-like phenotype, alcohol dehydrogenases (ADH) and aldehyde dehydrogenases (ALDH) were inhibited. I hypothesized inhibition of (ALDH) with disulfiram will increase proportion of stressed, alive cells (PI-/AV+) because of (ALDH) is used to process acetaldehyde with the enzyme (ALDH) that produces acetate that is used in many metabolic processes. While disulfiram yielded an increase in this subset of cells, effects of inhibition were ethanol independent. In contrast, the (ADH) inhibitor 4- methyl pyrazole caused necrosis. The different patterns of cellular death can be observed by the different staining. These results suggest cell death pathways are sensitive to fermentation products produced by trypanosomatids and that early evolution of classical, cell death pathways could have been driven by responses to sublethal stress.
Monopoles on 3 dimensional AC manifolds
Creators: name: Oliveira, Goncalo
Publisher: name: arXiv
Year: 2014
Subjects: subject: Differential Geometry (math.DG)
subject: Mathematical Physics (math-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: 53C07, 53C05, 53C80

description: We construct monopoles in any asymptotically conical (AC) $3$-manifold $X$ with $b^2(X)=0$. For sufficiently large mass, our construction covers an open set in the moduli space of monopoles. We also give a more general construction of Dirac monopoles in any AC manifold, which may be useful for generalizing our result to the case when $b^2(X) \neq 0$.
description: Definition of moduli changed in order to directly use the results in one of the key references. Exposition improved
Does Dirichlet Prior Smoothing Solve the Shannon Entropy Estimation Problem?
Creators: name: Han, Yanjun
name: Jiao, Jiantao
name: Weissman, Tsachy
Publisher: name: arXiv
Year: 2015
Subjects: subject: Information Theory (cs.IT)
subject: FOS: Computer and information sciences

description: The Dirichlet prior is widely used in estimating discrete distributions and functionals of discrete distributions. In terms of Shannon entropy estimation, one approach is to plug-in the Dirichlet prior smoothed distribution into the entropy functional, while the other one is to calculate the Bayes estimator for entropy under the Dirichlet prior for squared error, which is the conditional expectation. We show that in general they do \emph{not} improve over the maximum likelihood estimator, which plugs-in the empirical distribution into the entropy functional. No matter how we tune the parameters in the Dirichlet prior, this approach cannot achieve the minimax rates in entropy estimation, as recently characterized by Jiao, Venkat, Han, and Weissman, and Wu and Yang. The performance of the minimax rate-optimal estimator with $n$ samples is essentially \emph{at least} as good as that of the Dirichlet smoothed entropy estimators with $n\ln n$ samples. We harness the theory of approximation using positive linear operators for analyzing the bias of plug-in estimators for general functionals under arbitrary statistical models, thereby further consolidating the interplay between these two fields, which was thoroughly developed and exploited by Jiao, Venkat, Han, and Weissman. We establish new results in approximation theory, and apply them to analyze the bias of the Dirichlet prior smoothed plug-in entropy estimator. This interplay between bias analysis and approximation theory is of relevance and consequence far beyond the specific problem setting in this paper.
description: 27 pages, 1 figure, published on IEEE Transactions on Information Theory, merged with https://arxiv.org/abs/1406.6959
Boosted Simon-Wolff Spectral Criterion and Resonant Delocalization
Creators: name: Aizenman, Michael
name: Warzel, Simone
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mathematical Physics (math-ph)
subject: Probability (math.PR)
subject: Spectral Theory (math.SP)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: Discussed here are criteria for the existence of continuous components in the spectra of operators with random potential. First, the essential condition for the Simon-Wolff criterion is shown to be measurable at infinity. By implication, for the iid case and more generally potentials with the K-property the criterion is boosted by a zero-one law. The boosted criterion, combined with tunneling estimates, is then applied for sufficiency conditions for the presence of continuous spectrum for random Schrödinger operators. The general proof strategy which this yields is modeled on the resonant delocalization arguments by which continuous spectrum in the presence of disorder was previously established for random operators on tree graphs. In another application of the Simon-Wolff rank-one analysis we prove the almost sure simplicity of the pure point spectrum for operators with random potentials of conditionally continuous distribution.
description: In version 2 the presentation was somewhat streamlined, and a related new (/improved) result was added (Appendix B)
title: Assessing the impact of administering the 'Challenges of Living with Cystic Fibrosis' questionnaire on the self-efficacy of caregivers of children with cystic fibrosis
Creators: name: Patel, Tulsi Prafull
Publisher: name: University of Liverpool Repository
Year: 2012

description: INTRODUCTION Cystic Fibrosis is a multi-organ, genetic disorder with the most pronounced effects observed in the lungs, pancreas and the gastrointestinal system. From a young age, patients suffer from chronic pulmonary infections, poor digestion and malabsorption of nutrients from the gut. As a result, patients have to perform numerous therapeutic tasks regularly to remain healthy. These treatments come at the expense of a considerable treatment burden and burden of care to the patient and family involved. METHODS The ‘Challenges of Living with Cystic Fibrosis Questionnaire’ (CLCF-Q) has been developed to measure the burden felt by caregivers of children with CF. The aim of this study was to investigate the effect of administering the CLCF-Q to caregivers during their child’s annual review on the carer’s self-efficacy. Self-efficacy was measured by the ‘Cystic Fibrosis Self-Efficacy Questionnaire’ (CFSE-Q). Participants were randomised into the intervention or control groups. Those in the intervention group completed the CLCF-Q during the annual review process and received feedback at a later date. All participants completed the CFSE-Q at baseline and endpoint to measure their self-efficacy. RESULTS Thirty seven participants (17 Intervention, 20 Control) completed the whole study. The CLCF-Q identified some of the burdens faced by caregivers of children with CF. Total self-efficacy scores ranged from 36-53 in the intervention group and 37-51 in the control group at baseline. End-point scores ranged from 38-54 for the intervention group and 31-53 for the control group. Statistical analysis revealed that the self-efficacy of the intervention group remained stable over time and that of the control group decreased significantly by the end of the study. Self-efficacy scores decreased for six items and increased for six items in the intervention group. Only two items had higher scores in the control group and 10 items had lower scores at the end of the study. DISCUSSION The CLCF-Q may be used as a tool to measure burden in caregivers of children with CF. It helps health care providers recognise the burdens faced by these families. The feedback process aims to involve the caregiver and encourage them in areas of treatment which they find challenging. The combination of these two processes as an intervention may be used to maintain a high level of self-efficacy in caregivers of children with CF. The CFSE-Q was able to detect changes in self-efficacy and may be used in future self-efficacy trials in caregivers of patients with CF.
title: Evaluating Electricity Deployment through Regulatory Systems and the Worldwide Governance Indicators in Post-conflict countries: A Comparison of Rwanda and Burundi
titleType: Other
Creators: name: Ruragaragaza, Desire
Publisher: name: University of Dundee
Year: 2022

description: The independent regulatory model has been instrumental and applied in different developed and developing countries in the electricity sector. Reforms initiated through this regulatory model have been evaluated in different peaceful countries using an evaluation questionnaire to ascertain whether the reforms help or hinder the sector outcomes. In addition, the rule of law worldwide governance indicator has been considered as the most important indicator to measure the level of commitment and capacity to carry out the required reforms. The more a country improves its rule of law, the more it is committed and capable of implementing the independent regulatory model and the electricity sector thereof.

Countries emerging from war face numerous challenges that affect the very key pillars of the independent regulatory model, the investment attractiveness, and the electricity sector outcomes. However, little is known about the independent regulatory model’s effect in post-conflict developing countries in need of electricity investment.

This thesis, in addition to the rule of law and the existing evaluation questionnaire, uses for the first time the political stability and absence of violence/terrorism Worldwide Governance Indicator to analyse the two indicators’ implications with respect to the electricity regulation in post conflict countries. In addition, it looks at the regulatory implications on electricity in a post-conflict environment and shines light on effective electricity indicators in post-conflict environment. In a comparative study approach, this thesis focuses on Burundi and Rwanda, two countries that share the same characteristics, use the independent regulatory model but took different paths to improving the rule of law and the political stability and absence of violence indicators. It shows that instability and an unpredictable political environment affect the rule of law, institutional governance, institutional substance and the meta-principles, and standards required to build a strong independent regulatory model capable of producing good regulatory outcomes.

Key words: Burundi, Rwanda, rule of law, political stability and absence of violence/Terrorism, policy, legislation, independent regulatory model, and electricity deployment.
title: Long-Range Target Classification in a Cluttered Environment Using Multi-Sensor Image Sequences
Creators: name: Yaman, Cenk
Publisher: name: Old Dominion University
publisherIdentifier: https://ror.org/04zjtrb98
publisherIdentifierScheme: ROR
Year: 2007

description: Accurate identification of unknown contacts is crucial in military intelligence. Automated systems which quickly and accurately determine the identity of a contact could be a benefit in backing up electronic signal identification methods such as Identification Friend and Foe (IFF) systems. Radio Detection and Ranging (RADAR) images are often undesirable in military applications since they reveal the location of the imaging system. So we explore the use of visible and infrared images of which are generally more consistent than RADAR images and for which it is easy to compensate for environmental effects. Recent advances in visible and IR imaging technology improve the ability to observe objects at very long distances, but it is still militarily desirable to stay away as far as possible from potential enemy ships that may be observed at different viewing angles.

A Principal Component Analysis (PCA) based pattern recognition technique is presented in this thesis for small boat classification from visible and IR images. Extracting features from naval ship images is a difficult task to solve since the background may contain rough-textured regions. Conventional edge and comer operators tend to fail due to high contrast in these regions. Appropriate preprocessing steps are necessary to separate the object from the background. Subsequent feature extraction techniques can be applied to the whole object region. Two efficient segmentation algorithms are used for the extraction of small boat regions from visible and IR images. A popular and convenient approach named Adaptive Progressive Thresholding (APT) technique is used for segmentation of boat region from visible images. Infrared images in general are not sharp in displaying objects compared to the visible images. In fact, the noise components present in these images are always much greater than typical visible images. Therefore, pure edge-based image segmentation will not be sufficient in this case. We applied SUSAN-APT and Graph cut image segmentation algorithms for small boat region extraction from IR images. We obtained 86% accuracy in classification rate in visible images and 77% in IR images. The classification accuracy can be improved by using more training images captured in every 15 degrees viewing angle for all classes as opposed to only 5 training images used in this work for every class. This research can also be easily applied to air and land based target classification systems.
Outcome orientation - a misconception of probability that harms medical research and practice
Creators: name: Humphrey, Parris Taylor
name: Masel, Joanna
Publisher: name: arXiv
Year: 2014
Subjects: subject: Physics Education (physics.ed-ph)
subject: FOS: Physical sciences

description: Human understanding of randomness and variation is shaped by a number of cognitive biases. Here we relate a lesser-known cognitive bias, the "outcome orientation", to medical questions and describe the harm that the outcome orientation can do to medical research and practice. People who reason according to an outcome orientation interpret probability as a subjective degree of belief that is constrained to consider events one at a time, in a way that is incompatible with Bayesian reasoning. Instead of accepting that uncertainty is inevitable, and generalizing from the frequency of similar events, the outcome orientation prefers one-off causal narratives. In medicine, the outcome orientation therefore erodes support for randomized controlled trials in favor of reductionist approaches. The rhetoric of personalized medicine resonates with, and can promote, the outcome orientation, by emphasizing how the measurable attributes of individual patients, rather than chance or unknowable factors, causally produce each particular patient's outcome.
title: Modelling root-soil interaction in variably saturated fine-grained soil
titleType: Other
Creators: name: Nur, Abdullah Ahmed
Publisher: name: University of Dundee
Year: 2022

description: Plant roots stabilise soil via mechanical reinforcement and by increasing soil matric suction through root-water uptake. However, previous research studies have focused on the mechanical reinforcement without the hydrological effect. In realistic cases, root-soil interaction modelling through hydro-mechanical mechanism is needed. It is known that an increased suction can increase soil shear strength, which will therefore affect the mechanical root reinforcement, but this coupling effect is not quantified. In addition, most of the existing models lack the fundamental features of partially saturated soil behaviour and therefore the real performance is not modelled.

This project uses numerical modelling by the Finite Element (FE) Method, employing a sophisticated hypoplastic soil model to realistically capture suction-induced change in soil behaviour in partially saturated clay. Also, the FE analysis considers fully coupled flow deformation behaviour with a definition of the soil water characteristic.

FE models of soil translating transversely past a root were developed and validated against saturated cases from the literature. Parametric studies were then performed to identify factors affecting root reinforcement, including root embedment depth, loading rate, loading direction and soil degree of saturation. Based on the simulation results, semi-empirical design charts are proposed to estimate the mechanical strength of root reinforced soil under varying hydrological conditions for different practical applications including slope stabilisation and tree wind throw.
Room Temperature Operation of a Buried Heterostructure Photonic Crystal Quantum Cascade Laser
Creators: name: Peretti, R.
name: Liverini, V.
name: Wolf, J. M.
name: Bonzon, C.
name: Süess, M. J.
name: Lourdudoss, S.
name: Metaferia, W.
name: Beck, M.
name: Faist, J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: High power single mode quantum cascade lasers with a narrow far field are important for several applications including surgery or military countermeasure. Existing technologies suffer from drawbacks such as operation temperature and scalability. In this paper we introduce a fabrication approach that potentially solves simultaneously these remaining limitations. We demonstrate and characterize deep etched, buried photonic crystal quantum cascade lasers emitting around a wavelength of 8.5 μm. The active region was dry etched before being regrown with semi-insulating Fe:InP. This fabrication strategy results in a refractive index contrast of 10% allowing good photonic mode control, and simultaneously provides good thermal extraction during operation. Single mode emission with narrow far field pattern and peak powers up to 0.88 W at 263 K were recorded from the facet of the photonic crystal laser, and lasing operation was maintained up to room temperature. The lasing modes emitted from square photonic crystal mesas with a side length of 550μm, were identified as slow Bloch photonic crystal modes by means of three-dimensional photonic simulations and measurements.
title: The role of mitochondrial dysfunction in acute pancreatitis
Creators: name: Booth, David
Publisher: name: University of Liverpool Repository
Year: 2012

description: Acute pancreatitis is a serious and often lethal inflammatory disease. Its causes are diverse and incompletely understood; however, gallstones and alcohol abuse are the principal triggers. Oxidative stress has been proposed as a determinant of acute pancreatitis (AP) severity, and has been the subject of recent clinical trials. The major AP precipitants, alcohol, alcohol metabolites and bile salts, were investigated for their potential role in the production of reactive oxygen species (ROS), and their effects upon cell fate. Application of the bile salt taurolithocholic acid sulphate (TLC-S) to isolated human and murine pancreatic acinar cells generated significant Ca2+-dependent mitochondrial ROS which were inhibited with the antioxidant N-acetyl-L-cysteine (NAC), and promoted with dimethoxy-2-methylnaphthalene (DMN), an inhibitor of the antioxidant enzyme NAD(P)H quinone oxidoreductase (NQO1). Elevations of ROS mediated by bile salts were crucial in the determination of cell fate, producing apoptosis rather than necrosis. In contrast, ethanol and its metabolites, both oxidative (acetaldehyde) and non-oxidative (fatty acid ethyl esters: FAEEs), were shown to produce no significant ROS in similar circumstances. Assessment of ethanol and its metabolites revealed that ethanol and acetaldehyde showed little effect on cell fate. Low concentrations of ethanol with fatty acid, however, induced toxic elevations of [Ca2+]C, mitochondrial dysfunction and necrosis when oxidative metabolism was compromised. This effect was reversed by inhibition of FAEE synthase, suggesting important deleterious actions of non-oxidative alcohol metabolism in the pancreas.
The Mass-Concentration Relation and the Stellar-to-Halo Mass Ratio in the CFHT Stripe 82 Survey
Creators: name: Shan, Huanyuan
name: Kneib, Jean-Paul
name: Li, Ran
name: Comparat, Johan
name: Erben, Thomas
name: Makler, Martin
name: Moraes, Bruno
name: Van Waerbeke, Ludovic
name: Taylor, James E.
name: Charbonnier, Aldée
name: Pereira, Maria E. S.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We present a new measurement of the mass-concentration relation and the stellar-to-halo mass ratio over the halo mass range $5\times 10^{12}$ to $2\times 10^{14}M_{\odot}$. To achieve this, we use weak lensing measurements from the CFHT Stripe 82 Survey (CS82), combined with the central galaxies from the redMaPPer cluster catalogue and the LOWZ/CMASS galaxy sample of the Sloan Digital Sky Survey-III Baryon Oscillation Spectroscopic Survey Tenth Data Release. The stacked lensing signals around these samples are modelled as a sum of contributions from the central galaxy, its dark matter halo, and the neighboring halos, as well as a term for possible centering errors. We measure the mass-concentration relation: $c_{200c}(M)=A(\frac{M_{200c}}{M_0})^{B}$ with $A=5.24\pm1.24, B=-0.13\pm0.10$ for $0.2
description: 10 pages, 3 figures, 3 tables
title: Ontology modularization: principles and practice
Creators: name: Doran, Paul
Publisher: name: University of Liverpool Repository
Year: 2011

description: Technological advances have provided us with the capability to build large intelligent systems capable of using knowledge, which relies on being able to represent the knowledge in a way that machines can process and interpret. This is achieved by using ontologies; that is logical theories that capture the knowledge of a domain. It is widely accepted that ontology development is a non-trivial task and can be expedited through the reuse of existing ontologies. However, it is likely that the developer would only require a part of the original ontology; obtaining this part is the purpose of ontology modularization. In this thesis a graph traversal based technique for performing ontology module extraction is presented. We present an extensive evaluation of the various ontology modularization techniques in the literature; including a proposal for an entropy inspired measure. A task-based evaluation is included, which demonstrates that traversal based ontology module extraction techniques have comparable performance to the logical based techniques. Agents, autonomous software components, use ontologies in complex systems; with each agent having its own, possibly different, ontology. In such systems agents need to communicate and successful communication relies on the agents ability to reach an agreement on the terms they will use to communicate. Ontology modularization allows the agents to agree on only those terms relevant to the purpose of the communication. Thus, this thesis presents a novel application of ontology modularization as a space reduction mechanism for the dynamic selection of ontology alignments in multi-agent systems. The evaluation of this novel application shows that ontology modularization can reduce the search space without adversely affecting the quality of the agreed ontology alignment.
Finite temperature free fermions and the Kardar-Parisi-Zhang equation at finite time
Creators: name: Dean, David S.
name: Doussal, Pierre Le
name: Majumdar, Satya N.
name: Schehr, Gregory
Publisher: name: arXiv
Year: 2014
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Quantum Gases (cond-mat.quant-gas)
subject: Mathematical Physics (math-ph)
subject: Probability (math.PR)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We consider the system of $N$ one-dimensional free fermions confined by a harmonic well $V(x) = mω^2 {x^2}/{2}$ at finite inverse temperature $β= 1/T$. The average density of fermions $ρ_N(x,T)$ at position $x$ is derived. For $N \gg 1$ and $β\sim {\cal O}(1/N)$, $ρ_N(x,T)$ is given by a scaling function interpolating between a Gaussian at high temperature, for $β\ll 1/N$, and the Wigner semi-circle law at low temperature, for $β\gg N^{-1}$. In the latter regime, we unveil a scaling limit, for $β{\hbar ω}= b N^{-1/3}$, where the fluctuations close to the edge of the support, at $x \sim \pm \sqrt{2\hbar N/(mω)}$, are described by a limiting kernel $K^{\rm ff}_b(s,s')$ that depends continuously on $b$ and is a generalization of the Airy kernel, found in the Gaussian Unitary Ensemble of random matrices. Remarkably, exactly the same kernel $K^{\rm ff}_b(s,s')$ arises in the exact solution of the Kardar-Parisi-Zhang (KPZ) equation in 1+1 dimensions at finite time $t$, with the correspondence $t= b^3$.
description: 5 pages + 6 pages of supplementary material, 3 figures, published version
title: Social capital and organisational resilience
Creators: name: Johnson, Noel
Publisher: name: University of Liverpool Repository
Year: 2011

description: Over recent years, natural and man-made crises and disasters have raised an awareness of the need for organisational resilience. Many organisations are now part of complex supply networks, and developing good business relationships can be central to supply network resilience. The aim of the research is to gain a fuller understanding of how organisations can exploit their social capital for building resilience. Although previous research has shown social capital to influence the resilience of place based communities, bringing the constructs together in an organisational or business community context has received little attention. The research has three objectives: 1) Identify ways in which organisations exploit their social capital for resilience; 2) Explore how four emergent ‘enabling conditions’ (time and continuity, interaction, interdependence, and closure and brokerage) help organisations exploit social capital for building resilience; and 3) Develop a reflective framework to help organisations consider how they can exploit their social capital for building resilience. The focus group is a community of construction contractors working in partnership for the UK Highways Agency. Working within the so called Construction Management Framework, a concept very different from traditional ‘aggressive’ frameworks, the research explores how contractors have developed good working relationships, collective behaviours including resource sharing and information exchange underpinned by the community’s espoused values, equal status, and peer pressure. Observed, is the contractor community’s willingness and ability to collaborate in order to improve performance and achieve shared goals. The research identifies many examples of the contractor community maintaining positive adjustment under challenging conditions – resilience.
title: Structure and function of chromatin remodelling ATPases and their dysfunction in human diseases
titleType: Other
Creators: name: Corsie, Abigail
Publisher: name: University of Dundee
Year: 2022

description: Snf2 proteins are a large family of proteins present across all eukaryotes that have many roles in remodelling chromatin to regulate gene expression. Analysis of cancer tumour sequencing datasets has shown that several Snf2 proteins are included in the top 200 tumour suppressor genes, particularly SMARCA4, the Snf2 ATPase subunit of the human SWI/SNF complex. Most mutations in Snf2 proteins found in tumours are missense mutations; however, the mode of action through which these mutations may cause disease remains uncertain. Here, an analysis of sequencing data was performed to uncover particular sites which are both functionally important for enzyme activity and frequently mutated in cancer. Mutations were generated in recombinant Snf2 proteins and shown to affect the biochemical activity of proteins and alter their structure to be inactive. A point mutation was generated in SMARCA4 in mouse embryonic stem cells. This mutation did not affect cell viability but reduced chromatin accessibility in a manner similar to SMARCA4 inhibitors. Additionally, a heterozygous mutant affected chromatin accessibility similarly to a homozygous mutant, providing evidence for SMARCA4 missense mutations having dominant-negative phenotypes.
Wedge-local fields in integrable models with bound states
Creators: name: Cadamuro, Daniela
name: Tanimoto, Yoh
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mathematical Physics (math-ph)
subject: High Energy Physics - Theory (hep-th)
subject: Operator Algebras (math.OA)
subject: FOS: Physical sciences
subject: FOS: Mathematics
subject: 81T05, 81T40, 81U99

description: Recently, large families of two-dimensional quantum field theories with factorizing S-matrices have been constructed by the operator-algebraic methods, by first showing the existence of observables localized in wedge-shaped regions. However, these constructions have been limited to the class of S-matrices whose components are analytic in rapidity in the physical strip. In this work, we construct candidates for observables in wedges for scalar factorizing S-matrices with poles in the physical strip and show that they weakly commute on a certain domain. We discuss some technical issues concerning further developments, especially the self-adjointness of the candidate operators here and strong commutativity between them.
description: 40 pages, no figure. The final version is available under Open Access. CC-BY
title: The effects of maternal obesity on neonatal anthropometry and placental regulation of cytokine production
Creators: name: Mahoney, Sarah
Publisher: name: University of Liverpool Repository
Year: 2011

description: Introduction: The prevalence of obesity is rising and maternal obesity has been implicated as a perpetuating factor. Maternal obesity has been linked to the development of macrosomic neonates who are at increased risk of becoming obese themselves. Current understanding of the mechanisms instigating this are unknown, however the pro-inflammatory status associated with obesity has been suggested. Method: Anthropometric estimation of fat mass and percentage body fat was conducted on neonates of lean and obese women and their placentae analysed for morphological changes by light microscopy. Placental explants from both cohorts of women were incubated in order to determine the regulatory role of glucose, leptin, tumour-necrosis factor-α (TNF-α), and insulin on the production of interleukin-1 (IL-1β), interleukin-6 (IL-6), and TNF-α. Results: Neonates of obese mothers were found to have increased birth weight, fat mass, fat free mass, and percentage body fat in comparison to neonates of lean mothers. The rise in birth weight, fat mass, fat free mass, and percentage body fat were not shown to significantly correlate to maternal booking BMI on univariate analysis. Placentae of obese women were shown to produce more IL-6 under basal conditions and in response to TNF-α stimulation. Glucose was shown to reduce placental production of IL-1β, IL-6, and TNF-α in both cohorts, and leptin and insulin stimulation had no effect on cytokine production. There was no evidence of placental inflammation on examination by light microscopy. Conclusion: Maternal obesity is associated with neonates of increased birth weight and adiposity, and increased production of inflammatory mediators by the placenta which is not evidenced in overall placental appearance. It is hoped that by elucidating the mechanisms by which obesity may be perpetuated, via the in-utero environment for example, foundations for future research can be established which are aimed at tackling the epidemic of obesity.
Isotropy constraints on powerful sources of ultrahigh-energy cosmic rays at $10^{19}$ eV
Creators: name: Takami, Hajime
name: Murase, Kohta
name: Dermer, Charles D.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Anisotropy in the arrival direction distribution of ultrahigh-energy cosmic rays (UHECRs) produced by powerful sources is numerically evaluated. We show that, taking account of the Galactic magnetic field, nondetection of significant anisotropy at $\approx 10^{19}$ eV at present and in future experiments imposes general upper limits on UHECR proton luminosity of steady sources as a function of source redshifts. The upper limits constrain the existence of typical steady sources in the local universe and limit the local density of $10^{19}$ eV UHECR sources to be $\gtrsim 10^{-3}$ Mpc$^{-3},$ assuming average intergalactic magnetic fields less than $10^{-9}$ G. This isotropy, which is stronger than measured at the highest energies, may indicate the transient generation of UHECRs. Our anisotropy calculations are applied for extreme high-frequency-peaked BL Lac objects 1ES 0229+200, 1ES 1101-232, and 1ES 0347-121, to test the UHECR-induced cascade model, in which beamed UHECR protons generate TeV radiation in transit from sources. While the magnetic-field structure surrounding the sources affects the required absolute cosmic-ray luminosity of the blazars, the magnetic-field structure surrounding the Milky Way directly affects the observed anisotropy. If both of the magnetic fields are weak enough, significant UHECR anisotropy from these blazars should be detectable by the Pierre Auger Observatory unless the maximum energy of UHECR protons is well below $10^{19}$ eV. Furthermore, if these are the sources of UHECRs above $10^{19}$ eV, a local magnetic structure surrounding the Milky Way is needed to explain the observed isotropy at $\sim 10^{19}$ eV, which may be incompatible with large magnetic structures around all galaxies for the UHECR-induced cascade model to work with reasonable jet powers.
description: 15 pages, 10 figures, accepted for publication in The Astrophysical Journal
Grover Search with Lackadaisical Quantum Walks
Creators: name: Wong, Thomas G.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The lazy random walk, where the walker has some probability of staying put, is a useful tool in classical algorithms. We propose a quantum analogue, the lackadaisical quantum walk, where each vertex is given $l$ self-loops, and we investigate its effects on Grover's algorithm when formulated as search for a marked vertex on the complete graph of $N$ vertices. For the discrete-time quantum walk using the phase flip coin, adding a self-loop to each vertex boosts the success probability from 1/2 to 1. Additional self-loops, however, decrease the success probability. Using instead the Ambainis, Kempe, and Rivosh (2005) coin, adding self-loops simply slows down the search. These coins also differ in that the first is faster than classical when $l$ scales less than $N$, while the second requires that $l$ scale less than $N^2$. Finally, continuous-time quantum walks differ from both of these discrete-time examples---the self-loops make no difference at all. These behaviors generalize to multiple marked vertices.
description: 16 pages, 7 figures; additional 2-page corrigendum
title: The role and origin of uterine natural killer cells in patients with unexplained recurrent miscarriage
Creators: name: Karam, Asiyah
Publisher: name: University of Liverpool Repository
Year: 2012

description: The aim of the study was to determine the role of uNK cells by looking at their numbers across three location sites, the epithelial edge, areas of low stromal cell density/oedema and peri-vascular stroma/spiral arteries. The universal NK cell marker, CD56 was used to identify uNK cells in the endometrium. The research determined whether uNK cells were the result of proliferation and differentiation of resident uNK cells or trafficking of pbNK cells. In addition, it was determined whether uNK cells play a part in spiral artery remodelling and trophoblast invasion and also the role they may play in RM. The hypothesis was tested using Immunohistochemical staining on serial sequential sections of endometrial tissue received from RM patients of extreme phenotype between LH + 5-9 days. Analysis was made on 20 RM patients, 10 patients were grouped as high uNK, defined as an uNK cell density value of ≥ 5% and 10 were grouped as low uNK, defined as an uNK cell density value of ≤ 2.5%. The endometrial samples were stained for the antibodies to CD56, KI67, NKp30, L-Selectin and CD16, uNK cell markers of proliferation, differentiation and trafficking. No association was found between RM and age. The high uNK density group had significantly higher levels for all the antibodies stained (P
title: ‘Minor-Attracted People’: Attitudes toward people attracted to prepubescent children and the impact on professionals.
Creators: name: Andreou, Stavroula
Publisher: name: University of Central Lancashire
Year: 2024

description: Minor-Attracted People (MAPs) have been found to experience higher stigma, negative attitudes, and misconceptions than other populations affecting their propensity to seek and find suitable treatment (Heron et al., 2021; Jahnke et al., 2015a; Jahnke & Hoyer, 2013; Jahnke et al., 2015b; Jara & Jeglic, 202; Stiels-Glenn, 2010). This research project aims to promote a better understanding of the attitudes, stigma and misconceptions towards MAPs and the impact of offence (offending, non-offending) and offence type (contact, non-contact), as well as the use of the terminology MAP among a sample of the public and professionals. Additionally, the purpose of this project is to provide insights into the associative stigma experienced by therapy providers working with MAPs, if any. The data for this project was collected through a systematic review of the literature using a Narrative Synthesis as well as through open-ended questions from a panel of experts using the Delphi method. The attitudes towards MAPs were found to be punitive by the public but more accepting by professionals. The level of stigma toward MAPs was found to be less in the professional sample than in the public. Misconceptions were found to exist in both samples. The terminology MAP was found to be useful and less stigmatising by therapy providers. Therapy providers reported that they experience stigmatisation due to their work with MAPs. These findings indicate the need for more specific training about minor-attraction and support for professionals, to enable more treatment opportunities available for MAPs. Additionally, the need for further research regarding the associative stigma experienced by professionals working with MAPs including different professional groups has been identified. Furthermore, the gap in the literature regarding the significance of the offence type (contact or non-contact) in influencing people’s attitudes, stigma, and misconceptions towards MAPs, remains and has been highlighted.