cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Biological effects of the loss of homochirality in a multicellular organism
Creators: name: Banreti, Agnes
name: Bhattacharya, Shayon
name: Wien, Frank
name: Matsuo, Koichi
name: Refregiers, Matthieu
name: Meinert, Cornelia
name: Meierhenrich, Uwe J.
name: Hudry, Bruno
name: THOMPSON, DAMIEN
name: Noselli, Stéphane
Publisher: name: University of Limerick
Year: 2023

description: Homochirality is a fundamental feature of all known forms of life, maintaining biomolecules (amino-acids, proteins, sugars, nucleic acids) in one specific chiral form. While this condition is central to biology, the mechanisms by which the adverse accumulation of non-L-α-amino-acids in proteins lead to pathophysiological consequences remain poorly understood. To address how heterochirality build-up impacts organism’s health, we use chiral-selective in vivo assays to detect protein-bound non-L-α-amino acids (focusing on aspartate) and assess their functional significance in Drosophila. We find that altering the in vivo chiral balance creates a ‘heterochirality syndrome’ with impaired caspase activity, increased tumour formation, and premature death. Our work shows that preservation of homochirality is a key component of protein function that is essential to maintain homeostasis across the cell, tissue and organ level.
Undecidability of the Spectral Gap (short version)
Creators: name: Cubitt, Toby
name: Perez-Garcia, David
name: Wolf, Michael M.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: Other Condensed Matter (cond-mat.other)
subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: The spectral gap - the energy difference between the ground state and first excited state - is central to quantum many-body physics. Many challenging open problems, such as the Haldane conjecture, existence of gapped topological spin liquid phases, or the Yang-Mills gap conjecture, concern spectral gaps. These and other problems are particular cases of the general spectral gap problem: given a quantum many-body Hamiltonian, is it gapped or gapless? Here we prove that this is an undecidable problem. We construct families of quantum spin systems on a 2D lattice with translationally-invariant, nearest-neighbour interactions for which the spectral gap problem is undecidable. This result extends to undecidability of other low energy properties, such as existence of algebraically decaying ground-state correlations. The proof combines Hamiltonian complexity techniques with aperiodic tilings, to construct a Hamiltonian whose ground state encodes the evolution of a quantum phase-estimation algorithm followed by a universal Turing Machine. The spectral gap depends on the outcome of the corresponding Halting Problem. Our result implies that there exists no algorithm to determine whether an arbitrary model is gapped or gapless. It also implies that there exist models for which the presence or absence of a spectral gap is independent of the axioms of mathematics.
description: v2: published version. 7 pages, 3 figures. See long companion paper arXiv:1502.04573 (same title and authors) for full technical details. v3: Added supplementary material as ancilliary file (previously part of arXiv:1502.04573v2)
An Electronic Compendium of Extreme Functions for the Gomory--Johnson Infinite Group Problem
Creators: name: Köppe, Matthias
name: Zhou, Yuan
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optimization and Control (math.OC)
subject: Discrete Mathematics (cs.DM)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: In this note we announce the availability of an electronic compendium of extreme functions for Gomory--Johnson's infinite group problem. These functions serve as the strongest cut-generating functions for integer linear optimization problems. We also close several gaps in the literature.
description: 15 pages, 4 figures. Post-print (accepted manuscript) version, CC-BY-NC-ND
Szegö kernel asymptotics and Morse inequalities on CR manifolds with $S^1$ action
Creators: name: Hsiao, Chin-Yu
name: Li, Xiaoshan
Publisher: name: arXiv
Year: 2015
Subjects: subject: Complex Variables (math.CV)
subject: Differential Geometry (math.DG)
subject: FOS: Mathematics

description: Let $X$ be a compact connected CR manifold of dimension $2n-1, n\geq 2$. We assume that there is a transversal CR locally free $S^1$ action on $X$. Let $L^k$ be the $k$-th power of a rigid CR line bundle $L$ over $X$. Without any assumption on the Levi-form of $X$, we obtain a scaling upper-bound for the partial Szegő kernel on $(0,q)$-forms with values in $L^k$. After integration, this gives the weak Morse inequalities. By a refined spectral analysis, we also obtain the strong Morse inequalities in CR setting. We apply the strong Morse inequalities to show that the Grauert-Riemenschneider criterion is also true in the CR setting.
description: 34 pages, final version, to appear in the Asian Journal of Mathematics. arXiv admin note: text overlap with arXiv:1204.4810, arXiv:1401.6647
Decomposition of the nonabelian tensor product of Lie algebras via the diagonal ideal
Creators: name: Niroomand, P.
name: Johari, F.
name: Parvizi, M.
name: Russo, F. G.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Rings and Algebras (math.RA)
subject: FOS: Mathematics
subject: 17B30, 17B60, 17B99

description: We prove a theorem of splitting for the nonabelian tensor product $L \otimes N$ of a pair $(L,N)$ of Lie algebras $L$ and $N$ in terms of its diagonal ideal $L \square N$ and of the nonabelian exterior product $L \wedge N$. A similar circumstance was described two years ago by the second author in the special case $N=L$. The interest is due to the fact that the size of $L \square N$ influences strongly the structure of $L \otimes N$. Another question, often related to the structure of $L \otimes N$, deals with the behaviour of the operator $\square$ with respect to the formation of free products. We answer with another theorem of splitting even in this case, noting some connections with the homotopy theory.
description: The published version contains some improvements
title: Fungi in the built environment: biodeterioration and bioprotection
titleType: Other
Creators: name: Zhao, Jiayue
Publisher: name: University of Dundee
Year: 2022

description: The built environment comprises all facilities and civil infrastructure systems, including buildings, transportation, energy and water supply, sewage, and communication systems. Fungi, are widespread microorganisms in rocks, stones, and artificial buildings, and can have profound impacts on the built environment. Fungal activities are well known for rock and mineral transformations resulting in bioweathering of such materials which can have profound cultural, social, and economic consequences. On the other hand, biomineralization abilities related to fungi-metal-mineral transformations also show application prospects in the built environment, such as acting as protective agents to building materials. This research aimed to explore the processes by which fungi interact with construction materials to understand their significance in biodeterioration or bioprotection important materials used in the built environment.
title: First generation Chinese migrants and their association with the development of Liverpool's Chinatown
Creators: name: Soon, Su-Chuin
Publisher: name: University of Liverpool Repository
Year: 2014

description: My research aims to provide an in-depth understanding of first generation Chinese migrants and their changing connection to Liverpool’s Chinatown. Liverpool’s Chinatown is used as an angle from which I study the Chinese community, a holistic appreciation of the evolution of Liverpool’s Chinatown is first warranted. There are therefore two components to my research. For the historical portion, research driven by archival sources from the 1700s to date was conducted. For the contemporary portion of the research, 68 in-depth qualitative interviews with first generation Chinese migrants across the socio-economic spectrum were undertaken. In the historical part of my thesis, I will show that the construction and re-constructions of Liverpool’s Chinatown is a product of white political domination and context-specific economic factors underlie the power assertions. In the contemporary part of my thesis, I will show that Liverpool’s Chinatown, as characterised by Chinese associations and Chinese cuisine, will persist but not flourish. Liverpool’s Chinatown is currently associated with a Chinese community that is fragmented within itself and segregated from mainstream society. This fragmentation and segregation are accentuated by technological advancements in our contemporary world. In studying the developmental pathways of Chinatowns, scholars have argued that they will eventually die out (Lee, 1949) or become theme parks manipulated by hegemonic social groups (Laguerre, 2000; Lai, 2009). These conclusions are drawn without considering the agency of first generation Chinese migrants. With a focus on first generation Chinese migrants and especially on the ordinary Chinese for the contemporary part of my thesis, the primary aim of my research on the Chinese community will supplement studies on ethnic minorities in Britain as Chinese is a relatively less studied group compared to South Asian and Black populations in Britain. As a secondary objective, my research will also plug a gap in the academic discourse on Chinatowns.
title: Online network intrusion detection system using temporal logic and stream data processing
Creators: name: Ahmed, Abdulbasit
Publisher: name: University of Liverpool Repository
Year: 2013

description: These days, the world are becoming more interconnected, and the Internet has dominated the ways to communicate or to do business. Network security measures must be taken to protect the organization environment. Among these security measures are the intrusion detection systems. These systems aim to detect the actions that attempt to compromise the confidentiality, availability, and integrity of a resource by monitoring the events occurring in computer systems and/or networks. The increasing amounts of data that are transmitted at higher and higher speed networks created a challenging problem for the current intrusion detection systems. Once the traffic exceeds the operational boundaries of these systems, packets are dropped. This means that some attacks will not be detected. In this thesis, we propose developing an online network based intrusion detection system by the combined use of temporal logic and stream data processing. Temporal Logic formalisms allow us to represent attack patterns or normal behaviour. Stream data processing is a recent database technology applied to flows of data. It is designed with high performance features for data intensive applications processing. In this work we develop a system where temporal logic specifications are automatically translated into stream queries that run on the stream database server and are continuously evaluated against the traffic to detect intrusions. The experimental results show that this combination was efficient in using the resources of the running machines and was able to detect all the attacks in the test data. Additionally, the proposed solution provides a concise and unambiguous way to formally represent attack signatures and it is extensible allowing attacks to be added. Also, it is scalable as the system can benefit from using more CPUs and additional memory on the same machine, or using distributed servers.
From a Challenge to an Opportunity
Creators: name: Gütte, Annelie Maja
name: Roggero, Matteo
Publisher: name: Humboldt-Universität zu Berlin
Year: 2022
Subjects: subject: sustainability
subject: socio-ecological systems
subject: "dark side" social capital
subject: Greece
subject: 577 Ökologie

description: The role of social capital for socio-ecological systems is undisputed. While fostering cooperation in some communities, however, social capital can also lead to tight social control and distrust towards outsiders and new practices, contributing to the persistence of undesirable, unsustainable practices. This paper explores the challenges emerging from the “dark side” of social capital for sustainability efforts in socio-ecological systems, raising the question how they can be addressed and overcome. It focuses on the case of Paros, Greece, where decades of mass tourism and conventional agriculture have put a heavy burden on the socio-ecological system. In the aftermath of the 2008-2011 crisis, returnees and newcomers leaving mainland Greece brought new ideas on how to reconcile the island’s economy, ecology, and society with one another. Interviews reveal how the specifics of social capital in Paros posed structural, cognitive, and relational challenges to their projects. Surprisingly, though, those challenges could be turned into opportunities to embed new projects on the island. Promoting sustainability in socioecological systems may thus be less a matter of creating more social capital, but one of tailoring interventions to the specific type of social capital available.
Supplementary Material for Histree: A Tree-Based Experiment History Tracking Tool for Jupyter Notebooks
Creators: name: Studtmann, Laurens
name: Aydin, Selin
name: Lichter, Horst
Publisher: name: Zenodo
Year: 2023

description: User feedback results and a demo Jupyter Notebook as supplementary material for our paper "Histree: A Tree-Based Experiment History Tracking Tool for Jupyter Notebooks".
title: Making sense of mental health difficulties through live reading: an interpretative phenomenological analysis of the experience of being in a reader group
Creators: name: Gray, Ellie
Publisher: name: University of Liverpool Repository
Year: 2014

description: Reader groups involve the reading aloud of complex literature by a skilled facilitator in a group setting, followed by group discussion in relation to the text. They are delivered to a wide variety of populations within both physical and mental health and social care services, across community, residential and inpatient settings. A limited body of existing literature indicates that reader groups can produce positive therapeutic effects to enhance mental health and well-being, but research thus far is largely based on pilot studies with small samples. Further investigation is warranted to explore the experience of reader groups from the perspective of individuals with mental health problems and to consider possible psychological mechanisms underpinning potential therapeutic effects, since this is the first psychological study to be conducted in this area. The aim of the current research was to explore the experience of being in a community reader group for people with mental health problems, and to consider how participation relates to making sense of life experiences and relationships, both inside and outside the group. Eight participants took part in semi-structured interviews, which were transcribed and analysed using Interpretative Phenomenological Analysis. Five master themes pertaining to participants’ experience of reader groups emerged: ‘Literature as an Intermediary Object’, ‘Boundaries and Rules of Engagement’, ‘Self as Valued, Worthy, Capable’, ‘Community and Togetherness in Relational Space’, and ‘Changing View of Self, World, Others’. The findings were discussed in relation to existing literature, to provide an indication of possible psychological mechanisms underpinning participants’ experiences of reader groups. Clinical implications of the current research were considered, particularly in terms of mental health service provision and access to alternative therapeutic activity, and suggestions were made for future research.
title: Model structure selection in powertrain calibration and control
Creators: name: Li, Zongyan
Publisher: name: University of Liverpool Repository
Year: 2013

description: This thesis develops and investigates the application of novel identification and structure identification techniques for I.C. engine systems. The legislated demand for reduced vehicle fuel consumption and emissions indicates that improved model-based dynamical engine calibration and control methods are required in place of the existing static set-point based mapping methods currently used in industry. The choice of structure of any dynamical engine model has significant consequences for the accuracy and the calibration/optimization time of engine systems. This thesis primarily addresses the issue of this structure selection. Linear models are well understood and relatively easy to implement however the modern I.C. engine is a highly nonlinear system which restricts the use of linear structures. Further the newer technologies required to achieve demanding fuel consumption and emission targets are increasingly more complex and nonlinear. The selection of appropriate nonlinear model regressor terms presents a combinatorial explosion problem which must be solved for accurate engine system modelling. In this thesis, two systematic nonlinear model structure selection techniques, namely stepwise regression with F-statistics and orthogonal least squares method with error reduction ratio, are accordingly investigated. SISO algebraic NARMAX engine models are then established in simulation studies with these methods and demonstrate the effectiveness of the approach. The thesis also investigates the development and application of multi-modelling techniques and the expansion of the model structure selection techniques to the identification of the local models terms within the multi-model structures for the engine. Based on the en- gine operating regions, novel multi-model networks can be established and several alternative multi-modelling techniques, such as LOLIMOT, Neural Network, Gaussian and log-sigmoid function weighted multi-models, for the multi-model engine system identification are explored and compared. An experimental validation of the methods is given by a black box identification of SISO engine models which are developed purely from the experimental engine test data sets. The results demonstrate that the multi-model structure selection techniques can be successfully applied on the engine systems, and that the multi-modelling techniques give good model accuracy and that good modelling efficiency can also be achieved. The outcome is a set of techniques for the efficient development of accurate nonlinear black-box models which can be acquired from experimental dynamometer test-bed data which should assist in the dynamic control of future advanced technology engine systems.
title: Mechanistic Insights into Changes in Blood Flow Following Application of Intermittent Negative Pressure
titleType: Other
Creators: name: McIntosh, Jody
Publisher: name: University of Dundee
Year: 2022

description: Since the 1930’s, intermittent negative pressure (INP) has been tested as a means of treating vascular diseases. Recently, the literature has indicated that INP can be used to reduce pain and facilitate wound healing in patients with peripheral arterial disease (PAD) however the physiological mechanism behind these clinical benefits remains unclear. The aim of this study was to evaluate the physiological effects of INP application, in particular vascular function, in both healthy and diseased physiology. Three study groups were assessed: healthy volunteers, PAD patients and volunteers suffering from cold hypersensitivity. INP was applied to participants using the Flow-Ox device with applies a negative pressure of -40mmHg in intermittent cycles of 10 seconds negative pressure followed by 7 seconds of no pressure. Vascular function was evaluated through assessment of blood perfusion and endothelial function using full field laser speckle contrast imaging. Systemic effects of INP on vascular function was tested by measuring arterial stiffness, in particular augmentation index and pulse wave velocity. Blood samples were collected to assess blood inflammatory and oxidative stress markers. In patients suffering from PAD, clinical markers including ankle-brachial pressure index and pain score were also evaluated. This study demonstrated that after one session of INP application, cutaneous blood perfusion and endothelial function local to the site of INP application improves in PAD patients but not in healthy physiology. Further, patients reported a significantly lower pain score after up to 8 weeks of INP application compared to baseline. No other significant findings were recorded for any other the other assessments. As microvascular function is severely impaired in PAD, the potential of using INP as a novel treatment modality capable of improving microvascular circulation and function with benefits in reducing pain and wound healing warrants further investigation.
title: Staphylococcal responses to antimicrobial skin lipids
Creators: name: Moran, Josephine
Publisher: name: University of Liverpool Repository
Year: 2015

description: Antimicrobial lipids on skin are proposed to form a barrier against microbial colonisation. Skin lipids, such as unsaturated fatty acids and sphingosines, cause membrane permeabilisation and/or proton motive force disruption . These lipids may be crucial in determining the diversity and degree of staphylococcal skin colonisation. Specifically, antimicrobial lipids may inhibit skin colonisation by Staphylococcus aureus while permitting the growth of Staphylococcus epidermidis. Here it was shown that skin fatty acids sapienic acid and linoleic acid are more active against S. aureus than S. epidermidis. This supports a role for fatty acids in the prevention of S. aureus skin colonisation. The most anti-staphylococcal skin lipid tested was D-sphingosine; no differences in resistance levels between S. aureus and S. epidermidis to D-sphingosine were observed. The genetic response and basis for resistance to skin antimicrobial lipids of S. epidermidis and S. aureus was investigated using next generation sequencing. The transcriptomic response of both species to sapienic acid was determined using RNA-Seq. Additionally, S. epidermidis and S. aureus were passaged in sapienic acid or D-sphingosine. Isolates with increased lipid resistance after passaging were genome sequenced, and mutations associated with increased resistance were characterised. From these approaches, several genes and pathways potentially involved in the responses of both species to skin lipids became apparent. These components included cell wall biosynthesis, transport and production of small molecules, ammonia production, albumin binding proteins and putative lipid efflux pumps. Cellular components identified as specifically involved in S. aureus resistance to sapienic acid included capsule and staphyloxanthin biosynthesis. Cellular components involved specifically in S. epidermidis resistance to sapienic acid were also speculatively identified, though the functions of these components were not resolved. This study has increased our understanding of staphylococcal molecular interactions with host antimicrobial lipids, which could lead to applications in the design of novel antimicrobial compounds.
Wess-Zumino-Witten Terms in Graphene Landau Levels
Creators: name: Lee, Junhyun
name: Sachdev, Subir
Publisher: name: arXiv
Year: 2014
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We consider the interplay between the antiferromagnetic and Kekulé valence bond solid orderings in the zero energy Landau levels of neutral monolayer and bilayer graphene. We establish the presence of Wess-Zumino-Witten terms between these orders: this implies that their quantum fluctuations are described by the deconfined critical theories of quantum spin systems. We present implications for experiments, including the possible presence of excitonic superfluidity in bilayer graphene.
description: 5 pages, 2 figures. Supplemental material added (v3)
title: An analysis of the implementation of horizontal collaboration to enhance performance in the logistics industry
Creators: name: Everington, Lucy
Publisher: name: University of Liverpool Repository
Year: 2013

description: This thesis examines the extent to which horizontal collaboration is being undertaken in the logistics industry, the different ways horizontal collaboration is being implemented in the logistics industry and the performance enhancements that can be achieved by logistics companies through horizontal collaboration partnerships. Research into the subject of horizontal collaboration has only in the past 5 years gained enough momentum and support to become a topic in its own right, rather than a footnote to research on vertical collaboration. For this reason existing research on the topic has been confined to a small number of areas and very little literature exists on comparing the performance enhancements of different types of horizontal collaboration. This research involved a large-scale survey to investigate general patterns and perceptions of horizontal collaboration in the logistics industry and following that a number of case studies were undertaken to gain in-depth knowledge of how horizontal collaboration can be successfully undertaken. The results from these were then developed into a set of guidelines which can be used by logistics companies implementing horizontal collaboration by providing information on issues such as problems that can be addressed using horizontal collaboration, necessary partner requirements, necessary internal requirements, duration and formality of the collaboration, benefits, risks and obstacles for each of the four main types of horizontal collaboration being undertaken in the logistics industry. Horizontal collaboration was found to be a wide-spread practice in the UK Logistics industry across companies of all sizes and types. The most common form of horizontal collaboration is ‘shared services’, however, ‘joint ventures’ are perceived to be the most effective form of collaboration.
Location-domination and matching in cubic graphs
Creators: name: Foucaud, Florent
name: Henning, Michael A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Combinatorics (math.CO)
subject: FOS: Mathematics

description: A dominating set of a graph $G$ is a set $D$ of vertices of $G$ such that every vertex outside $D$ is adjacent to a vertex in $D$. A locating-dominating set of $G$ is a dominating set $D$ of $G$ with the additional property that every two distinct vertices outside $D$ have distinct neighbors in $D$; that is, for distinct vertices $u$ and $v$ outside $D$, $N(u) \cap D \neq N(v) \cap D$ where $N(u)$ denotes the open neighborhood of $u$. A graph is twin-free if every two distinct vertices have distinct open and closed neighborhoods. The location-domination number of $G$, denoted $γ_L(G)$, is the minimum cardinality of a locating-dominating set in $G$. Garijo, Gonzalez and Marquez [Applied Math. Computation 249 (2014), 487--501] posed the conjecture that for $n$ sufficiently large, the maximum value of the location-domination number of a twin-free, connected graph on $n$ vertices is equal to $\lfloor \frac{n}{2} \rfloor$. We propose the related (stronger) conjecture that if $G$ is a twin-free graph of order $n$ without isolated vertices, then $γ_L(G)\leq \frac{n}{2}$. We prove the conjecture for cubic graphs. We rely heavily on proof techniques from matching theory to prove our result.
description: 16 pages; 4 figures
A category mistake in observational claims regarding ultrashort-lived unstable particles
Creators: name: Cabbolet, Marcoen J. T. F.
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Physics (physics.gen-ph)
subject: History and Philosophy of Physics (physics.hist-ph)
subject: FOS: Physical sciences

description: The physics literature contains many claims that ultrashort-lived unstable particles, such as a Higgs boson, have been observed. These claims are a matter of applying the $5σ$-convention in particle physics. This paper, however, shows that by applying this $5σ$-convention a category mistake is made, by which a pure reasoning is passed off as an observation. Not only are these two fundamentally different primitive notions at the very basis of science, but the pure reasoning in question is also weaker than an observation: what we have in each case is that the existence of the ultrashort-lived unstable particle is inferred to the best explanation, but that does absolutely not merit the stronger claim that the particle in question has been "observed". Consequently, the observational claims in question will thus have to be dismissed as overstatements. On a general note, this demonstrates that the empirical support for the Standard Model of particle physics is significantly less than hitherto thought.
description: 6 pages, 2 figures; this version is a proof that the $5 \sigma$-convention in particle physics is by itself inadequate for observational claims; the previous version, a conference paper with criticism on the $5\sigma$-convention from the perspective of existing philosophical literature, has been made available at philpapers.org
Central limit theorem for reducible and irreducible open quantum walks
Creators: name: Sadowski, Przemysław
name: Pawela, Łukasz
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: In this work we aim at proving central limit theorems for open quantum walks on $\mathbb{Z}^d$. We study the case when there are various classes of vertices in the network. Furthermore, we investigate two ways of distributing the vertex classes in the network. First we assign the classes in a regular pattern. Secondly, we assign each vertex a random class with a uniform distribution. For each way of distributing vertex classes, we obtain an appropriate central limit theorem, illustrated by numerical examples. These theorems may have application in the study of complex systems in quantum biology and dissipative quantum computation.
description: 20 pages, 4 figures
title: Does G-quadruplex DNA have a functional role in regulation of the transcriptome?
Creators: name: Myers, Paul
Publisher: name: University of Liverpool Repository
Year: 2015

description: All DNA transactions involving overtwisting or undertwisting of the double helix alter the topological state of DNA, yielding distortions known as DNA supercoiling or DNA torsional stress. Under conditions of negative supercoiling susceptible sequences within B-form DNA may be transformed to stable, non-B-DNA structures such as G-quadruplex. G-quadruplex DNA has the potential to create or destroy transcription factor binding sites or influence nucleosome positioning and so may contribute to gene regulation, making it an attractive therapeutic target. Although in vitro and in silico studies support the notion that G-quadruplex is regulatory, a compelling in vivo demonstration of G-quadruplex function is lacking. Using computational and experimental approaches previously developed to identify DNA segments that actually adopt non-B DNA conformations in vivo, I have identified sequences with a high probability of secondary structure formation. Identified sequences are located in the promoters of three genes central to cancer biology where much of the work in G-Quadruplex has been focused. I have expanded this focus into the field of neuroscience by identifying a further three sequences in the promoters of genes implicated in a range of neurological disorders. Preliminary biochemical analysis of these regions assessed methylation status and transcription factor binding profiles corresponding to a dynamic model of G-quadruplex formation at the well characterised CT element in the c-MYC promoter. In order to provide definitive structure function analysis of G-quadruplex I designed a gene editing strategy to reengineer the well characterized CT element of c-MYC. The initial strategy used AAV- targeting vectors to introduce strategic mutations that destabilize G-quadruplex DNA conformations in the CT element of c-MYC in the HCT-116 cell line via homologous recombination. In parallel to these structure-destabilizing mutations, neutral base changes were targeted to the 5´-UTRs of the targeted alleles, distinguishing them from their respective unmodified homologous partners. qPCR and ChIP analysis of the relative expression and factor binding profiles of targeted and wild-type alleles will enable a definitive structure function analysis of basal or induced expression; determining whether these secondary structures have a functional role in regulating gene expression and the factors involved. Low targeting efficiencies of the AAV gene editing strategy prompted me combine the recent technology of the CRISPR-Cas system with traditional AAV targeting to produce a highly efficient, high fidelity and streamlined approach to gene editing.
Lipid emulsion therapy during management of the critically-ill poisoned patient: a prospective cohort study
Creators: name: Levine, Michael
name: Brent, Jeffrey
name: Wiegand, Timothy
name: Maguire, Bryan
name: Cohen, Neta
name: Vaerrier, David
name: Beuhler, Michael
name: Leikin, Jerrold B.
name: Ganetsky, Michael
name: Stellpflug, Samuel
name: Ruha, Anne-Michelle
name: Carey, Jennifer
name: Geib, Ann-Jeannette
name: Cao, Dazhe James
name: Kleinschmidt, Kurt
name: Vohra, Rais
name: Riley, Brad D.
name: Moore, Phillip
name: Schwarz, Evan
name: Neavyn, Mark
name: Rusyniak, Daniel E.
name: Greene, Spencer
name: Nogar, Joshua
name: Manini, Alex
name: Wermuth, Mary
name: Pizon, Anthony
name: Hendrickson, Robert G.
name: Griswold, Matthew
name: Aldy, Kim
name: Wax, Paul
name: Spyres, Meghan Beth
name: Campleman, Sharan
name: Macdonald, Erin
name: Finkelstein, Yaron
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Medicine
Cell Biology
Pharmacology
Biotechnology
Chemical Sciences not elsewhere classified
Science Policy
Hematology

description: Despite conflicting data, intravenous lipid emulsion has emerged as a potential antidote. The “lipid sink” theory suggests that following intravenous administration of lipid, lipophilic drugs are sequestered in the vascular compartment, thereby reducing their tissue concentrations. This study sought to determine if survival is associated with the intoxicant’s degree of lipophilicity. We reviewed all cases in the Toxicology Investigators Consortium’s lipid sub-registry between May 2012 through December 2018. Information collected included demographics, exposure circumstances, clinical course, management, disposition, and outcome. The primary outcome was survival after lipid emulsion therapy. Survival was stratified by the log of the intoxicant’s octanol-water partition coefficient. We also assessed the association between intoxicant lipophilicity and an increase in systolic blood pressure after lipid emulsion administration. We identified 134 patients, including 81 (60.4%) females. The median age was 40 years (interquartile range 21-75). One hundred and eight (80.6%) patients survived, including 45 (33.6%) with cardiac arrest during their intoxication. Eighty-two (61.2%) were hypotensive, and 98 (73.1%) received mechanical ventilation. There was no relationship between survival and the log of the partition coefficient of the intoxicant on linear analysis (P = 0.89) or polynomial model (P = 0.10). Systolic blood pressure increased in both groups. The median (interquartile range) systolic blood pressure before lipid administration was 68 (60-78) mmHg for those intoxicants with a log partition coefficient < 3.6 compared with 89 (76-104) mmHg after lipid administration. Among those drugs with a log partition coefficient > 3.6, the median (interquartile range) was 69 (60-84) mmHg before lipid and 89 (80-96) mmHg after lipid administration. Most patients in this cohort survived. Lipophilicity was not correlated with survival or the observed changes in blood pressure. The study did not address the efficacy of lipid emulsion.
title: The role of Heparin-binding proteins in normal pancreas and acute pancreatitis
Creators: name: Nunes, Quentin
Publisher: name: University of Liverpool Repository
Year: 2015

description: Acute pancreatitis (AP) is a leading cause for hospitalisation and has significant quality of life implications for the patient and cost implications for the National Health Service. Although most episodes of AP are mild and self-limiting, the severe form of the disease is associated with a high mortality. In the absence of definitive treatment, management is mainly supportive. There is an urgent need to develop more effective biomarkers and drugs to manage AP. Genome-wide studies have demonstrated that proteins that bind to heparin (HBPs) form highly interconnected networks which are functionally important in health and disease. It was hypothesized that this is true in the pancreas and in AP. Testing this hypothesis, using mRNA as a proxy for protein, it was shown that HBPs constitute an important extracellular sub-proteome within the normal pancreas and in major pancreatic diseases that is likely to provide a rich repository of potential biomarkers and drug targets. Building upon this work, a proteomic analysis of HBPs in normal pancreas (NP) and in caerulein-induced mouse AP was undertaken. This has more than doubled the number of HBPs to 883, with 460 new HBPs identified. These may represent the most interconnected set of extracellular proteins and therefore with the greatest regulatory potential. Non canonical HBPs such as NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFA9, NDUFA10, NDUFA9 and NDUFA10 were identified and found to be underexpressed in AP as compared to NP. These may have potential moonlighting roles, not previously known. By virtue of being extracellular and binding to heparin, HBPs are accessible and are potential biomarkers and drug targets in AP. In addition to identifying existing biomarkers in AP such as pancreatic amylase, a number of HBPs with biomarkers potential such as HRG, CD14 and FN1 were identified and need further investigation. HBPs such as SERPINC1, VEGFA and PIP5K1C need further evaluation in drug development. These along with modified heparins, heparin mimetics and matrix therapy in AP provide exciting areas for future research.
title: Developing a culturally sensitive formative feedback model for medical education in an ethnically diverse environment: a Sri Lankan case study
titleType: Other
Creators: name: Sathaananthan, Thillainathan
Publisher: name: University of Dundee
Year: 2022

description: Learner-centered feedback is one of the most powerful influences in learning and achievement. However specific literature on feedback for culturally diverse environments, such as Sri Lanka is lacking. By addressing this problem, I aimed to enhance learning and teaching in medical schools. The objective was to explore and develop a culturally sensitive feedback guidance model for Medical Education.

This qualitative, ethnographic, case study of the ethnically diverse Eastern University, Sri Lanka (EUSL) was emergent in design. Staff and students of EUSL represent predominantly three different ethnicities, Sinhala, Tamil and Muslim.

Piloting highlighted the dominance of deficit thinking, which was mediated by the introduction of an Appreciative Inquiry framework.

Data gathering utilised observation of learning conversations and semi structured interviews with three types of stakeholders, students, faculty and policy makers. Continuous ongoing analysis and iterative literature searching illuminated the value of an anthropological perspective to define “culture” and contextual power dynamics.  Planned thematic analysis was usefully supplemented by discourse analysis in order to reduce uncritical imposition of western concepts.

Findings identified under-problematization of feedback practices, unaddressed cultural and historical complexities and evidence of espoused claims, alongside interest and willingness to develop a model to address the post-colonial challenges from overly simplistic hegemonic “west is best” assumptions. Non-WEIRD (Westernised, Educated, Industrialised, Rich and Democratic) countries e.g. Sri Lanka can benefit from WEIRD evidence-based theories such as dialogic feedback and learner transitions best when informed by and adapted to local cultural practices and knowledge.

A key outcome is a blueprint for co-adaptation of western theories and co-construction of locally effective Formative Assessment mechanisms and feedback practices. The cSEEFAR (culturally Sensitive, Effective and Efficient, Formative Assessment Relationships) blueprint model is a comma rather than a full stop, an opportunity to contribute to global understandings and facilitate increased praxis between theorized accounts of formative assessment and sensitive best practice for Sri Lanka.
title: Stochastic models for the spread of infectious diseases on finite contact networks: exact results and representations
Creators: name: Wilkinson, Robert
Publisher: name: University of Liverpool Repository
Year: 2015

description: Mathematical models for the spread of infectious diseases between living organisms are crucial to humanity's endeavour to understand and control its environment. The threat posed by communicable diseases is great. For example, the 1918 flu pandemic resulted in the deaths of over 50 million people and the HIV/AIDS pandemic is still under way with 2.3 million new cases in 2012. Mathematical models allow us to make predictions about the likelihood, impact and time scale of possible epidemics, and to devise effective intervention programmes, e.g. mass vaccination. This thesis considers various stochastic models of disease propagation which utilise the concept of a finite contact (social) network. For such models, we investigate ways in which important information can be extracted without a full mathematical `solution' (often unavailable) or numerous time consuming simulations (often inefficient and uninformative). For example, we consider the probability that a large scale outbreak will occur when a single infected individual is introduced to a susceptible population, and the expected number of infected individuals at time t. Although we focus on the context of epidemiology, the models under investigation are elementary and will be applicable to other domains, such as the spread of computer viruses, the spread of ideas, chemical reactions, and interacting particle systems.
Doob--Martin boundary of Rémy's tree growth chain
Creators: name: Evans, Steven N.
name: Grübel, Rudolf
name: Wakolbinger, Anton
Publisher: name: arXiv
Year: 2014
Subjects: subject: Probability (math.PR)
subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: 60J50, 60J10, 68W40

description: Rémy's algorithm is a Markov chain that iteratively generates a sequence of random trees in such a way that the $n^{\mathrm{th}}$ tree is uniformly distributed over the set of rooted, planar, binary trees with $2n+1$ vertices. We obtain a concrete characterization of the Doob--Martin boundary of this transient Markov chain and thereby delineate all the ways in which, loosely speaking, this process can be conditioned to "go to infinity" at large times. A (deterministic) sequence of finite rooted, planar, binary trees converges to a point in the boundary if for each $m$ the random rooted, planar, binary tree spanned by $m+1$ leaves chosen uniformly at random from the $n^{\mathrm{th}}$ tree in the sequence converges in distribution as $n$ tends to infinity -- a notion of convergence that is analogous to one that appears in the recently developed theory of graph limits. We show that a point in the Doob--Martin boundary may be identified with the following ensemble of objects: a complete separable $\mathbb{R}$-tree that is rooted and binary in a suitable sense, a diffuse probability measure on the $\mathbb{R}$-tree that allows us to make sense of sampling points from it, and a kernel on the $\mathbb{R}$-tree that describes the probability that the first of a given pair of points is below and to the left of their most recent common ancestor while the second is below and to the right. The Doob--Martin boundary corresponds bijectively to the set of extreme points of the closed convex set of normalized nonnegative harmonic functions, in other words, the minimal and full Doob--Martin boundaries coincide. These results are in the spirit of the identification of graphons as limit objects in the theory of graph limits.
description: Compared to version 3, which was published in Ann. Probab. 45 (2017), 225-277, this version has the additional Section 9, which corrects Remark 5.20 and the proof of Lemma 5.3, and amends Definition 5.8
title: ‘A sea-change’: representations of the marine in Jacobean drama and visual culture
Creators: name: Shmygol, Maria
Publisher: name: University of Liverpool Repository
Year: 2015

description: This thesis is concerned with exploring different forms of Jacobean drama and performances that span across different sites, from the commercial stages of London, to the civic pageants that took place on the Thames and in the City, and the court entertainments held at Whitehall Palace. My research necessarily casts a wide net over its subject matter in order to illustrate how these different modes of performance engage with representations of the marine through the technologies available to them, whether poetic, material, or both. While the sea had long been a receptacle for literary and poetic attention and can repeatedly be found as the stronghold of adventure, wonder, danger, and exile in the English narrative tradition, it is specifically at the beginning of the seventeenth century that the sea takes a hold of the literary imagination with particular force. The cultural, political, and economic predominance of the marine in early modern England found numerous means of expression in drama, where the different facets of marine identity and occupation create on-stage marine spaces. The thesis elucidates how these modes of performance often invoke and exploit the dramatic potential of the marine and its commercial, political, and iconographical meanings. Commercial drama, written for a pre-proscenial stage, realises the marine through language and metaphor, appealing to a collective imaginary in bodying forth the limitless watery expanses on which the action takes place. This imaginative embodiment finds a very different—and indeed a more material—means of expression in civic drama and the court masque, where the extensive and elaborate pageant devices and stage machinery were largely indebted to and shaped by continental theatrical design. The material means of expressing the marine that are found in the civic performances and the court masques discussed in this study necessitates a consideration of European trends in theatre design and the decorative arts. In looking to visual and material culture this thesis explicates the interdependence between different modes of creating on-stage marine spaces and the ways in which the material presence inflects both language and action in Jacobean drama.
Decaying light particles in the SHiP experiment: Signal rate estimates for hidden photons
Creators: name: Gorbunov, D.
name: Makarov, A.
name: Timiryasov, I.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: For the extension of the Standard Model with light hidden photons we present preliminary estimates of the signal rate expected at the recently proposed fixed target SHiP experiment exploiting the CERN SPS beam of 400 GeV protons.
description: 6 pages, 5 figures; journal version with the typo in the equation below eq. (2) corrected; results are not affected