cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
title: High-performance computing for computational biology of the heart
Creators: name: McFarlane, Ross
Publisher: name: University of Liverpool Repository
Year: 2011

description: This thesis describes the development of Beatbox — a simulation environment for computational biology of the heart. Beatbox aims to provide an adaptable, approachable simulation tool and an extensible framework with which High Performance Computing may be harnessed by researchers. Beatbox is built upon the QUI software package, which is studied in Chapter 2. The chapter discusses QUI’s functionality and common patterns of use, and describes its underlying software architecture, in particular its extensibility through the addition of new software modules called ‘devices’. The chapter summarises good practice for device developers in the Laws of Devices. Chapter 3 discusses the parallel architecture of Beatbox and its implementation for distributed memory clusters. The chapter discusses strategies for domain decomposition, halo swapping and introduces an efficient method for exchange of data with diagonal neighbours called Magic Corners. The development of Beatbox’s parallel Input/Output facilities is detailed, and its impact on scaling performance discussed. The chapter discusses the way in which parallelism can be hidden from the user, even while permitting the runtime execution user-defined functions. The chapter goes on to show how QUI’s extensibility can be continued in a parallel environment by providing implicit parallelism for devices and defining Laws of Parallel Devices to guide third-party developers. Beatbox’s parallel performance is evaluated and discussed. Chapter 4 describes the extension of Beatbox to simulate anatomically realistic tissue geometry. Representation of irregular geometries is described, along with associated user controls. A technique to compute no-flux boundary conditions on irregular boundaries is introduced. The Laws of Devices are further developed to include irregular geometries. Finally, parallel performance of anatomically realistic meshes is evaluated.
title: Using personal development planning for career development with research scientists in sub-Saharan Africa
Creators: name: McCullough, Hazel
Publisher: name: University of Liverpool Repository
Year: 2011

description: This research study evaluated the use of Personal Development Planning (PDP) as a strategy to help a group of ten doctoral and fourteen postdoctoral research scientists, based in eight developing countries in Africa, enhance and progress their career development. To achieve this, a PDP system, with built-in tools and support systems was developed specifically for this purpose. Using an Action Research approach, within a framework adapted from Kirkpatrick’s “Four Levels of Evaluation” the research study evaluated the PDP system, tools and processes; and from lessons learned developed a transferable system and tools for future use with research scientists based in these and other developing countries in Africa. The study explored the following questions: (1) How do these research scientists feel about using PDP, the system and tools? (2) What is being done differently as a result of engaging with PDP – are there any learning gains, and are they applied in practice? (3) To what extent has PDP helped these research scientists feel confident about planning and managing their career development? (4) How far is it feasible to implement PDP more widely with other research scientists in Africa? Using both quantitative and qualitative data from the Group’s PDP documentation, questionnaires, nominal group technique, an online focus group discussion, and semi-structured interviews, the main study findings showed that overall the majority of the group felt that PDP made a positive contribution to helping them enhance and progress their career development; and was successful in helping them to feel confident about planning and managing their career development and progression. Given the focus and limited time, the study does not evaluate the broader impact that engagement with PDP might have on career progression. A longitudinal, follow up study would be needed to evaluate this aspect of PDP in relation to career development in Africa. The data showed that PDP is a concept that can be transferred successfully to developing country settings in Africa. It also indicated that, with the essential support elements of personal support, financial support, time and institutional support built into a PDP programme, it would be feasible to implement PDP with a similar group of research scientists in Africa. Further studies are needed to evaluate feasibility of implementing this strategy more widely in countries in Sub-Saharan Africa.
title: Searches for Higgs bosons in the di-tau decay channels at the ATLAS experiment
Creators: name: Leney, Katharine JC
Publisher: name: University of Liverpool Repository
Year: 2011

description: The search for the Higgs boson will be one of the primary tasks of the LHC. One of the most promising channels in the search for a low mass Higgs boson will be the scenario where the Higgs is produced via Vector Boson Fusion and subsequently decays to a pair of tau leptons. One of the dominant (and most complex) backgrounds to this analysis is expected to come from tt decays. Monte Carlo samples with a centre-of-mass energy of 14 TeV are used to investigate the contributions from different tt decay modes and to develop methods to reduce the contribution from this background process and improve the overall sensitivity of the analysis. A technique to estimate contributions from background processes when there are insufficient Monte Carlo samples available to calculate this directly is also presented. A low mass Standard Model Higgs boson will require at least 10 inverse femtobarns of data before a discovery (or exclusion) can be claimed, but extensions to the Standard Model that realise Supersymmetry predict that there should be three neutral Higgs bosons. The production cross-section is strongly enhanced and it is there- fore expected that competitive limits on an MSSM Higgs boson can be made using data from the 2010-2011 LHC data-taking period (1 inverse femtobarn expected with 7 TeV centre-of-mass collisions). A search strategy for an MSSM Higgs boson decaying to two taus is presented, focusing on ensuring analysis robustness during this early period. Comparisons with the first ATLAS data are also made.
Hidden dibaryons in one- and two-pion production in NN collisions
Creators: name: Platonova, M. N.
name: Kukulin, V. I.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: Processes of one- and two-pion production in $NN$ collisions are considered in connection with excitation of intermediate dibaryon resonances. In particular, relative contributions of the conventional meson-exchange and dibaryon excitation mechanisms in the reaction $pp \to d π^+$ are investigated in detail. Inclusion of the intermediate isovector dibaryon resonances is shown to essentially improve the description of experimental data for this reaction, provided the soft meson-baryon form factors consistent with $πN$ elastic scattering are used. Manifestation of the intermediate isoscalar and isovector dibaryons in the two-pion production processes is also studied. The role of the isovector dibaryon resonances in the reaction $pp \to pp ππ$ is discussed for the first time. An explanation of the observed strong differences between two-pion production cross sections in $pn$ and $pp$ collisions based in part on the analysis of dibaryon structure is suggested.
description: Version accepted for publication in Nuclear Physics A
Worte der Erinnerung an Johannes Naef, prakt. Arzt (1865-1914)
Creators: name: Sutz, Johannes
name: Spinner, Johannes
Publisher: name: Zentralbibliothek Zürich
Year: 1915
Subjects: subject: 610 Medizin und Gesundheit
subject: 920 Biografien, Genealogie, Insignien
subject: Nachruf
subject: Oberuzwil
subject: Sankt Gallen

description: Enthält: Rede bei der Bestattung von Johannes Naef, med. pract. in Weggis gehalten im Krematorium St. Gallen am 21. November 1914 von Johannes Sutz, Pfarrer am St. Peter in Zürich; Letzter Gruss an seinen lieben Freund Johannes Naef von Johannes Spinner, Pfarrer in Zürich-Oberstrass gesprochen in Weggis am 6. Dezember 1914
Gestion de crise - Présentation de l'outil Ogéric mis en place par la DEAL Guadeloupe
Creators: name: SCHERZL, Namik
Publisher: name: Zenodo
Year: 2023
Subjects: G2OI
Grand Observatoire de l'Océan Indien
Direction Général de la Sécurité Civile
Union des Comores
SIG
Risques Naturels
Gestion de crise
Risques technologiques

description: Présentation réalisée dans le cadre de l'atelier sur le traitement d'images aériennes et géospatiales auprès des partenaires de la Direction Générale de la Sécurité Civile de l'Union des Comores. L'objectif de cette présentation était de favoriser les échanges sur la thématique des risques naturels, et plus particulièrement sur les outils SIG permettant de mieux comprendre le risque, d'améliorer les capacités de gestion des crises et la résilience des populations.
description: Presentation given as part of the workshop on aerial and geospatial image processing for partners of the Union of the Comoros' General Directorate for Civil Security. The aim of this presentation was to encourage discussion on the subject of natural hazards and, more specifically, on GIS tools that can be used to understand risk, increase crisis management capacity and improve people's resilience.
description: Le Projet Grand Observatoire de l'Océan IndienLe Projet G2OI avait pour objectif principal de valoriser les données de recherche de la région de l'Océan Indien. Le projet a collaboré avec différents partenaires afin de pérenniser les données qui ont été acquises dans le cadre de divers projets.
Des ateliers ont été organisés avec le réseau de partenaires afin de leur fournir des outils libres et gratuits leur permettant d'acquérir, valoriser, publier et pérenniser les données.
title: Assessing entomological and parasitaemia prevalence to monitor a malaria control programme in Zambezia, Mozambique
Creators: name: Abilio, Ana
Publisher: name: University of Liverpool Repository
Year: 2011

description: Malaria vector control interventions in Africa are currently being scaled up in order to attain universal access and appropriate coverage. The aim is to reduce or interrupt disease transmission, and to reach long term goals of malaria elimination and eradication. Currently, in Mozambique the main methods of vector control are indoor residual spraying and long-lasting insecticidal nets. The selection of insecticide resistance is a major concern for the national malaria control programme and its partners, as both these interventions rely on insecticides. This study was designed to evaluate the impact of IRS and ITN programmes implemented in Zambézia province,Mozambique on malaria transmission, through monitoring the vector species abundance,sporozoite rate and insecticide susceptibility. The impact on malaria was measured through parasite prevalence studies. Anopheles gambiae complex and An. funestus group mosquitoes were collected in 23 sentinel sites established in 7 districts in Zambézia province, using windows exit traps. These collections were used to assess abundance, sporozoite rate and transmission index and mouth aspiration catches of females were used for insecticide resistance assays. Identification of An. gambiae s.l and An. funestus s.l and sporozoite detection from the head/thorax were performed using polymerase chain reaction. Plasmodium falciparum prevalence in children aged between 1 and 15 years was assessed using ICT™ malaria rapid diagnostic tests. Annual prevalence was calculated the changes in susceptibility and malaria prevalence in subsequent survey periods compared. Anopheles gambiae s.s, An. arabiensis and An. funestus were the only known malaria vectors found in the study area. Anopheles gambiae and An. funestus were most abundant. Anopheles gambiae s.s and An. funestus were confirmed to be vectors of malaria transmission in the area and the sporozoite rate for both were ranging from 4.1 % and 2.3 % in 2006 to 2007 to 1 % to 0 % in 2009-2010 respectively. No infected An.arabiensis were detected. After several IRS rounds with DDT from 2006 to 2009 there was a significant reduction in mosquito abundance and sporozoite rates (P
Lagrangian Formulation for Particle Interpretations of Quantum Mechanics: Single-Particle Case
Creators: name: Sutherland, Roderick
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: A Lagrangian description is presented which can be used in conjunction with particle interpretations of quantum mechanics. A special example of such an interpretation is the well-known Bohm model. The Lagrangian density introduced here also contains a potential for guiding the particle. The advantages of this description are that the field equations and the particle equations of motion can both be deduced from a single Lagrangian density expression and that conservation of energy and momentum are assured. After being developed in a general form, this Lagrangian formulation is then applied to the special case of the Bohm model as an example. It is thereby demonstrated that such a Lagrangian description is compatible with the predictions of quantum mechanics.
description: 12 pages
Magnetic properties of spin-1/2 Fermi gases with ferromagnetic interaction
Creators: name: Wang, Baobao
name: Qin, Jihong
name: Guo, Huaiming
Publisher: name: arXiv
Year: 2014
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We investigate the magnetic properties of spin-$1/2$ charged Fermi gases with ferromagnetic coupling via mean-field theory, and find the interplay among the paramagnetism, diamagnetism and ferromagnetism. Paramagnetism and diamagnetism compete with each other. When increasing the ferromagnetic coupling the spontaneous magnetization occurs in a weak magnetic field. The critical ferromagnetic coupling constant of the paramagnetic phase to ferromagnetic phase transition increases linearly with the temperature. Both the paramagnetism and diamagnetism increase when the magnetic field increases. It reveals the magnetization density $\bar M$ increases firstly as the temperature increases, and then reaches a maximum. Finally the magnetization density $\bar M$ decreases smoothly in the high temperature region. The domed shape of the magnetization density $\bar M$ variation is different from the behavior of Bose gas with ferromagnetic coupling. We also find the curve of susceptibility follows the Curie-Weiss law, and for a given temperature the susceptibility is directly proportional to the Landé factor.
description: 7 pages, 7 figures
INVESTIGATING GERMINATING SEEDS AS OXYGEN SCAVENGERS IN HERMETIC STORAGE: IMPLICATIONS FOR INSECT MORTALITY
Creators: name: Lamsal, Gunakeshari
Publisher: name: Purdue University Graduate School
Year: 2023
Subjects: classificationCode: 309999
subject: Other agricultural, veterinary and food sciences not elsewhere classified

description: Hermetic storage systems have gained global popularity for their ability to minimize stored product losses by depleting oxygen. However, relying solely on insects to deplete oxygen in hermetic storage, when this process takes longer, can result in (further) damage to stored commodities. This study was conducted to investigate: (i) the potential of four different germinating seeds (soybean, rice, cowpea, and corn) in scavenging oxygen within hermetic storage systems; (ii) the impact of container volume and the number of germinating seeds on oxygen depletion; and (iii) the effects of germinating seeds on insect mortality and grain quality. Among the crops tested, cowpea, during their fourth, fifth, and sixth germination stages (T4, T5, and T6), depleted oxygen below 5% within 12 hours. The fourth stage of cowpea (T4) was identified as a potential oxygen scavenger due to its shorter germination time and ease of handling. Moreover, increasing the number of germinating seeds resulted in a faster initial rate of oxygen depletion in all-sized jars. Doubling both the volume of the jars and the number of germinating seeds had a similar rate of oxygen depletion. Additionally, an equation was derived to predict the required number of germinating seeds based on data from different numbers of seed and container volume combinations. Relative humidity levels increased to approximately 90% when empty jars were used but remained consistent at 40% when the jars were filled with grains. Furthermore, using 10, 20, and 30 germinating cowpea seeds with stored grains and insects, oxygen levels were reduced below 5% at different time intervals. Complete adult mortality of C. maculatus was achieved within 3-5 days of exposure, depending upon the number of germinating seeds. 20 and 30 seeds achieved complete mortality within 72 hours, while 10 seeds required 120 hours. As the number of germinating seeds increased, egg counts decreased, and moisture content significantly increased in the treatment involving 30 seeds. Furthermore, no adult emerged after 96 and 120 hours of exposure to normoxia for the 30 and 20 seed treatments, respectively. However, in the 10 seeds treatment, a small percentage of adults (0.29%) did emerge even after 120 hours of exposure.
title: Agents with a human touch: modeling of human rationality in agent systems
Creators: name: Nawwab, Fahd Saud
Publisher: name: University of Liverpool Repository
Year: 2011

description: Will it be possible to create a self-aware and reasoning entity that has the capacity for decision making similar to that we ascribe to human beings? Modern agent systems, although used today in various applications wherever intelligence is required, are not ready for applications where human rationalities are usually the only option in making important decisions in critical or sensitive situations. This thesis is a contribution to this area: a decision-making methodology is introduced to address the different characteristics that an agent should have in order to be better trusted with such critical decisions. The work begins with a study of philosophy in the literature (Chapter 2), which reveals that trust is based on emotions and faith in performance. The study concludes that a trustworthy decision has five main elements: it considers options and their likely effects; it predicts how the environment and other agents will react to decisions; it accounts for short- and long-term goals through planning; it accounts for uncertainties and working with incomplete information; and, finally, it considers emotional factors and their effects. The first four elements address decision making as a product of "beliefs"; the last addresses it as a product of "emotions". A complete discussion of these elements is provided in Section 2.1. This thesis is divided into two main parts: the first treats trust as a product of beliefs and the second treats trust as a product of emotions. The first part builds the decision-making methodology based on argumentation through a five-step approach where first the problem situation representing the actions available to the agent and their likely consequences is formulated. Next, arguments to perform these actions are constructed by instantiating an argumentation scheme designed to justify actions in terms of the values and goals they promote. These arguments are then subjected to a series of critical questions to identify possible counter arguments so that all the options and their weaknesses have been identified. Preferences are accommodated by organising the resulting arguments into an Argumentation Framework (we use Value-Based Argumentation [VAF] for this approach). Arguments acceptable to the agents will be identified through the ranking of the agent's values, which may differ from agent to agent. In the second part (Chapters 5 and 6), this methodology is extended to account for emotions. Emotions are generated based on whether other agents relevant to the situation support or frustrate the agent's goals and values; the emotional attitude toward the other agents then influences the ranking of the agent's values and, hence, influences the decision. In Chapters 4 and 6, the methodology is illustrated through an example study. This example has been implemented and tested on a software program. The experimental data and some screen shots are also given in the appendix.
Multi-brid DBI Inflation
Creators: name: Khoeini-Moghaddam, Salomeh
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: It is shown that it is possible to apply $δ\cN$ to some special non-canonic cases. We extended the multi-brid idea to the multi-field separable model with a non-canonical kinetic term, mainly the DBI model. Assuming a specific surface for the end of inflation and introducing new fields, enable us to find an explicit expression for the number of e-folds in terms of the new fields. By using $δ$N formalism, we arrived at the cosmological parameters. We considered the DBI model for two different limits, viz., speed limit and constant sound speed.
description: improved version
title: Structural aspects of talin regulation through Rap1A signalling
Creators: name: Zacharchenko, Thomas
Publisher: name: University of Liverpool Repository
Year: 2014

description: At the nascent focal adhesion, GTPase Rap1A recruits the adaptor protein RIAM (Rap1 Interacting Adaptor Molecule), and RIAM recruits the scaffold protein talin facilitating integrin activation (Lee et al., 2009). As the nascent adhesion matures, actin linkages are strengthened via recruitment of the talin-actin bridging protein vinculin. In vivo data shows that RIAM is not found in mature focal adhesions; furthermore RIAM and vinculin occupy the same binding sites within talin (Goult et al., 2013). This thesis shows that RIAM-talin interaction is synergistic, with multiple domains simultaneously contributing to the binding. Vinculin and RIAM compete for talin, providing a mechanism of RIAM displacement by vinculin as adhesions mature. The interactions are thus characterised by a range biophysical techniques. SHARPIN (Shank associated RH-domain interacting Protein) potentially competes with talin for integrin binding (Rantala et al., 2011). SHARPIN interaction with the synaptic protein SHANK3 (SH3 and multiple ankyrin repeat domains protein 3) may provide a mechanism for SHANK3 recruitment to the adhesion (Lim et al., 2001). This thesis solves the structure of the SHANK N-terminal domain that contains the SHARPIN binding region. The structure shows the presence of a previously uncharacterised RA (Ras-association) domain that packs against the following ankyrin repeat domain. We show the RA domain binds with high affinity to the GTPase-Rap1A. Rap1A-SHANK could provide a negative feedback pathway for integrin regulation in adhesion. In the course of adhesion maturation multiple proteins are recruited to the adhesion complex; these proteins facilitate linkages to the actomyosin contractile machinery. One such protein is DLC1 (Deleted in Liver Cancer 1); DLC1 contains an LD-like motif that is homologues to the LD domains of the adhesion protein paxillin (Brown et al., 1996). This LD-like motif is responsible for tumour suppressor function and binding to talin (Li et al., 2011; Cao et al., 2012). In this thesis we characterise the talin-DLC1 interaction using X-ray crystallography, and suggest mutations to disrupt the interaction in cell experiments.
Topology of the Grünbaum-Hadwiger-Ramos hyperplane mass partition problem
Creators: name: Blagojevic, Pavle V. M.
name: Frick, Florian
name: Haase, Albert
name: Ziegler, Günter M.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Algebraic Topology (math.AT)
subject: FOS: Mathematics
subject: 55N25, 51M20, 52A35, 55R20

description: In 1960 Grünbaum asked whether for any finite mass in $\mathbb{R}^d$ there are $d$ hyperplanes that cut it into $2^d$ equal parts. This was proved by Hadwiger (1966) for $d\le3$, but disproved by Avis (1984) for $d\ge5$, while the case $d=4$ remained open. More generally, Ramos (1996) asked for the smallest dimension $Δ(j,k)$ in which for any $j$ masses there are $k$ affine hyperplanes that simultaneously cut each of the masses into $2^k$ equal parts. At present the best lower bounds on $Δ(j,k)$ are provided by Avis (1984) and Ramos (1996), the best upper bounds by Mani-Levitska, Vrećica \& Živaljević (2006). The problem has been an active testing ground for advanced machinery from equivariant topology. We give a critical review of the work on the Grünbaum--Hadwiger--Ramos problem, which includes the documentation of essential gaps in the proofs for some previous claims. Furthermore, we establish that $Δ(j,2)= \frac12(3j+1)$ in the cases when $j-1$ is a power of $2$, $j\ge5$.
description: Revised version, Transactions of the Amer. Math. Soc., in print
title: Scrape-off layer ion temperature measurements on MAST by retarding field energy analyser
Creators: name: Elmore, Sarah
Publisher: name: University of Liverpool Repository
Year: 2014

description: Knowledge of the ion temperature (Ti) is important for tokamaks when determining plasma parameters from diagnostics which require knowledge of the ion and electron temperature (Te) and also because ions of high energy could damage plasma facing components by sputtering on high power devices. In the tokamak edge there are limited data for Ti, however the few existing measurements show that, beyond the confined plasma, Ti > Te, unlike in the confined plasma where ions and electrons are thermal coupled. A measurement technique using retarding field energy analyser(RFEA) probes to measure Ti has been implemented on the Mega Amp Spherical Tokamak (MAST) to allow measurements at the midplane and also at the divertor target which are two key areas in the scrape-off layer (SOL) plasma. Measurements in ohmic low confinement (L-mode) plasma discharges have shown that Ti ≈ 2Te at the midplane, while Ti ≈ Te at the target. Additionally heated L-mode plasmas have shown that Ti can be greater than Te at the divertor target. In inter-ELM high confinement (H-mode) plasmas, Ti is often found to be higher than Te, with extremes in high power plasmas of Ti/Te ≈ 3 at the target. Initial measurements of the temperature of ions released by an average ELM show that Ti reduces with distance from the strike point at the target. The measured upper limit on Ti in an average ELM reduces from 60 eV to 30 eV over ∼ 4 cm radially at the target. Measurements made by the target RFEA during ELMs show peak Ti ∼ 35 eV compared to peak Te measurements by Langmuir probes of ∼ 25 eV. These initial measurements of Ti agree with modelling of the ELM evolution in the SOL which show hot electrons arriving at the target before the remaining particles released by the ELM. Measurements by RFEA probes are subject to a correction in the presence of parallel flows in the SOL. It has been found from modelling of the MAST SOL that measurements made by the target RFEA should be multiplied by a correction factor between 0.65 and 0.7. Although this reduces the ratios measured of Ti/Te, measurements in inter-ELM H-mode and additionally heated L-mode plasmas would still show Ti > Te at the target. In ohmic L-mode plasmas, however, the reduction in Ti would mean Ti
Spherically symmetric conformal gravity and "gravitational bubbles"
Creators: name: Berezin, V. A.
name: Dokuchaev, V. I.
name: Eroshenko, Yu. N.
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The general structure of the spherically symmetric solutions in the Weyl conformal gravity is described. The corresponding Bach equations are derived for the special type of metrics, which can be considered as the representative of the general class. The complete set of the pure vacuum solutions is found. It consists of two classes. The first one contains the solutions with constant two-dimensional curvature scalar of our specific metrics, and the representatives are the famous Robertson--Walker metrics. One of them we called the "gravitational bubbles", which is compact and with zero Weyl tensor. Thus, we obtained the pure vacuum curved space-times (without any material sources, including the cosmological constant) what is absolutely impossible in General Relativity. Such a phenomenon makes it easier to create the universe from "nothing". The second class consists of the solutions with varying curvature scalar. We found its representative as the one-parameter family. It appears that it can be conformally covered by the thee-parameter Mannheim--Kazanas solution. We also investigated the general structure of the energy-momentum tensor in the spherical conformal gravity and constructed the vectorial equation that reveals clearly some features of non-vacuum solutions. Two of them are explicitly written, namely, the metrics à la Vaidya, and the electrovacuum space-time metrics.
description: 20 pages, published version
PAPER-64 Constraints on Reionization: The 21cm Power Spectrum at z=8.4
Creators: name: Ali, Zaki S.
name: Parsons, Aaron R.
name: Zheng, Haoxuan
name: Pober, Jonathan C.
name: Liu, Adrian
name: Aguirre, James E.
name: Bradley, Richard F.
name: Bernardi, Gianni
name: Carilli, Chris L.
name: Cheng, Carina
name: DeBoer, David R.
name: Dexter, Matthew R.
name: Grobbelaar, Jasper
name: Horrell, Jasper
name: Jacobs, Daniel C.
name: Klima, Pat
name: MacMahon, David H. E.
name: Maree, Matthys
name: Moore, David F.
name: Razavi, Nima
name: Stefan, Irina I.
name: Walbrugh, William P.
name: Walker, Andre
Publisher: name: arXiv
Year: 2015
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: In this paper, we report new limits on 21cm emission from cosmic reionization based on a 135-day observing campaign with a 64-element deployment of the Donald C. Backer Precision Array for Probing the Epoch of Reionization (PAPER) in South Africa. This work extends the work presented in Parsons et al. (2014) with more collecting area, a longer observing period, improved redundancy-based calibration, optimal fringe-rate filtering, and improved power-spectral analysis using optimal quadratic estimators. The result is a new $2σ$ upper limit on $Δ^{2}(k)$ of (22.4 mK)$^2$ in the range $0.15 < k < 0.5h\ {\rm Mpc}^{-1}$ at $z = 8.4$. This represents a three-fold improvement over the previous best upper limit. As we discuss in more depth in a forthcoming paper (Pober et al. 2015, in prep), this upper limit supports and extends previous evidence against extremely cold reionization scenarios. We conclude with a discussion of implications for future 21cm reionization experiments, including the newly funded Hydrogen Epoch of Reionization Array (HERA). $\textbf{The limits presented in this paper have been retracted: The erratum can be found in Appendix A.}$
description: Updated manuscript with an erratum in appendix A
Direct observation of Higgs mode oscillations in the pump-probe photoemission spectra of electron-phonon mediated superconductors
Creators: name: Kemper, A. F.
name: Sentef, M. A.
name: Moritz, B.
name: Freericks, J. K.
name: Devereaux, T. P.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: Using the non-equilibrium Keldysh formalism, we solve the equations of motion for electron-phonon superconductivity, including an ultrafast pump field. We present results for time-dependent photoemission spectra out of equilibrium which probes the dynamics of the superconducting gap edge. The partial melting of the order by the pump field leads to oscillations at twice the melted gap frequency, a hallmark of the Higgs or amplitude mode. Thus the Higgs mode can be directly excited through the nonlinear effects of an electromagnetic field and detected without any additional symmetry breaking.
$2-$Killing Vector Fields on Warped Product Manifolds
Creators: name: Shenawy, Sameh
name: Unal, Bulent
Publisher: name: arXiv
Year: 2014
Subjects: subject: Differential Geometry (math.DG)
subject: FOS: Mathematics

description: The present article provides a study of $2-$Killing vector fields on warped product manifolds as well as characterization of this structure on standard static and generalized Robertson-Walker space-times. Some conditions for a $2-$Killing vector field on a warped product manifold to be parallel are obtained. Moreover, some results on the curvature of a warped product manifolds in terms of $2-$Killing vector fields are derived. Finally, we apply our results to describe $2-$Killing vector fields of some well known warped product space-time models.
description: 13 pages, no figures
D8.2 - Market and stakeholder analysis
Creators: name: ENGIE
name: ENGINEERING INGEGNERIA INFORMATICA SPA
name: MINSAIT
name: SAMPOL INGENIERIA Y OBRAS
Publisher: name: Zenodo
Year: 2023
Subjects: IoT market
Big data
Customer segments
Market drivers
Key stakeholder
Engagement strategies

description: The deliverable D8.2 lies under the scope of work package WP8- Business Models and Exploitation. Its content is based on the work of the Task 8.1 - Project Impact Assessment, led by ENGIE. It presents a market and stakeholder analysis concerning PLATOON tools. The main objective of this deliverable is to identify attractiveness of big data platforms to support the launch of business exploitation activities resulting from the R&D project PLATOON.
title: Rapid removal of TACC3–ch-TOG–clathrin from kinetochore fibres during mitosis
Creators: name: Cheeseman, Liam
Publisher: name: University of Liverpool Repository
Year: 2014

description: The mitotic spindle is required to accurately separate the two duplicated copies of the genome between the two daughter cells. Errors that occur during this process can lead to aneuploidy, a hallmark of cancer. Some microtubules of the spindle are bundled by inter-microtubule bridges to form kinetochore fibres (K-fibres), which are responsible for pulling the sister chromatids apart. Previous work has identified one type of inter- microtubule bridge, composed of three proteins: TACC3, ch-TOG and clathrin. These TACC3–ch-TOG–clathrin crosslinkers are important for accurate mitosis and were found to contribute to K-fibre stability. However, these studies used RNAi-mediated depletion to study the functions of these proteins at metaphase. RNAi-mediated depletion is slow, and it is therefore difficult to separate the roles of the proteins at early mitosis versus metaphase. For instance, the depletion phenotype at metaphase may have been due to the absence of the protein at metaphase, or to the assembly of a defective mitotic spindle in early mitosis. Here, knocksideways (KS) was used to deplete TACC3 in under 5 minutes from fully assembled spindle at metaphase, and trap the protein on the external membrane of mitochondria. TACC3 KS also caused the rerouting of both ch-TOG and clathrin, without affecting other spindle proteins. This depletion was supported by a concomitant reduction of inter-microtubule bridge frequency in K-fibres. When TACC3 KS was performed at early mitosis, cells displayed severe delays in aligning chromosomes. When TACC3 KS was performed at metaphase following a normal prometaphase, anaphase onset was delayed. In these cells, Mad2 on a subset of kinetochores indicated that the spindle checkpoint was active, and K-fibre tension was reduced. However, both a cold-stable K-fibre assay and electron microscopy analysis of K-fibres indicated that there was no significant loss of K-fibre microtubules, even after prolonged removal at metaphase. Furthermore, TACC3 KS at metaphase significantly altered kinetochore microdynamics and reduced spindle length. These results indicate that TACC3–ch-TOG–clathrin crosslinkers are important for mitotic spindle assembly, but not for K-fibre stability at metaphase. However, the complex is required for K-fibre function at metaphase, satisfaction of the spindle checkpoint, most likely by maintenance of K-fibre tension.
title: Understanding the mechanisms of UFMylation
titleType: Other
Creators: name: Peter, Joshua
Publisher: name: University of Dundee
Year: 2022

description: Ubiquitin-fold modifier 1 (UFM1) is one of the recently discovered members of the Ubiquitin-like protein (Ubl) family. With a similar three-dimensional structure to Ubiquitin, UFM1 is covalently conjugated to lysine residues on target proteins, by a process called UFMylation. Protein UFMylation is emerging as a novel protein quality control system with functions focused on ER (Endoplasmic Reticulum) Phagy and Ribosomal Quality Control (RQC). Central to this modification system is the E3 ligase UFL1(UFM1 E3 Ligase 1) which is responsible for the conjugation of UFM1 onto its key target proteins predominantly on the Ribosome and ER membrane. With almost a decade passed, the precise mechanism by which UFM1 is conjugated onto substrate proteins is not understood. Here, in my PhD, I focused on developing biochemical tools to systematically characterize the key players involved in the ligation of UFM1 onto substrate proteins. I discover that UFL1 is an inactive enzyme on its own and is tightly regulated by two of its prominent binding partners namely, UFBP1 and CDK5RAP3. I show that UFL1 binds to UFBP1 to form an active E3 ligase complex. CDK5RAP3, on the other hand, functions as a regulatory module whose interaction with UFL1/UFBP1 complex, results in inhibition of UFMylation in vitro.
Existence of 2-parameter crossings, with applications
Creators: name: Williams, Jonathan D.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Geometric Topology (math.GT)
subject: FOS: Mathematics

description: A Morse 2-function is a generic smooth map from a manifold M of arbitrary finite dimension to a surface B. Its critical set maps to an immersed collection of cusped arcs in B. The aim of this paper is to explain exactly when it is possible to move these arcs around in B by a homotopy and to give a library of examples when M is a closed 4-manifold. The last two sections give applications to the theory of crown diagrams of smooth 4-manifolds.
description: accepted version
title: Synthesis and characterisation of layered hydroxy anion exchange materials
Creators: name: McIntyre, Laura J
Publisher: name: University of Liverpool Repository
Year: 2011

description: This thesis concerns the synthesis and characterisation of layered hydroxy anion exchange materials. The incorporation of rare-earth cations into these materials offers the potential to combine the optical, magnetic and catalytic properties of the lanthanides with the flexibility of intercalation hosts. A review of the literature surrounding intercalation chemistry and materials is presented in Chapter 1. Here the synthesis, structure and anion exchange reactions of layered hydroxides and their applications in the fields of catalysis, separation science, polymer additives and biological storage and delivery are discussed. Chapter 2 describes the hydrothermal synthesis and anion exchange capacity of new anion exchange host lattices containing the smaller lanthanide cations, with the composition Ln2(OH)5NO3•1.5H2O (Ln = Y, Gd - Lu), with Gd marking a limiting cation radius. Anion exchange reactions are facile with a wide range of organic carboxylates and sulfonates and investigations into their selectivity and optical properties have been carried out. This family has also been expanded to include Ln2(OH)5X•1.5H2O (X = Cl, Br; Ln = Y, Dy, Er, Yb) and crystal structures for orthorhombic and monoclinic Yb2(OH)5Cl•1.5H2O are reported. The findings of a time-resolved in situ X-ray powder diffraction study form the basis of Chapter 3. Three different phases with the layer composition [Yb2(OH)5]+; Yb2(OH)5NO3•1.5H2O d = 9.2 Å (1), Yb2(OH)5NO3•2H2O d = 9.4 Å (2) and Yb2(OH)5NO3•H2O d = 8.5 Å (3) were observed and shown to ultimately transform to a 3D structure Yb4O(OH)9NO3 d = 8.0 Å (4). Single crystal structures are given for phases 2 and 3, and the structure of 4 has been refined. The effects of temperature and metal concentration on phase formation have been investigated and compared with ex situ results. A full kinetic analysis is presented including the activation energy for the formation of phase 2. The values extracted indicate that the mechanism of crystallisation is phase boundary controlled. In Chapter 4 the room temperature precipitation synthesis of a related family of anion exchange host lattices with the composition, Ln2(OH)5NO3•H2O (Ln = Y, Eu–Er) and MgAl layered double hydroxides incorporating the precious metals Ru and Pd are discussed. Details of synthetic routes to the novel materials described and the methods of characterisation used are given in Chapter 5.
Top-pair production and decay at NLO matched with parton showers
Creators: name: Campbell, John M.
name: Ellis, R. Keith
name: Nason, Paolo
name: Re, Emanuele
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: We present a next-to-leading order (NLO) calculation of $t\bar{t}$ production in hadronic collisions interfaced to shower generators according to the POWHEG method. We start from an NLO result from previous work, obtained in the zero width limit, where radiative corrections to both production and decays are included. The POWHEG interface required an extension of the POWHEG BOX framework, in order to deal with radiation from the decay of resonances. This extension is fully general (i.e. it can be applied in principle to any process considered in the zero width limit), and is here applied for the first time. In order to perform a realistic simulation, we introduce finite width effects using different approximations, that we validated by comparing with published exact NLO results. We have interfaced our POWHEG code to the PYTHIA8 shower Monte Carlo generator. At this stage, we dealt with novel issues related to the treatment of resonances, especially with regard to the initial scale for the shower that needs to be set appropriately. This procedure affects, for example, the fragmentation function of the b quark, that we have studied with particular attention. We believe that the tool presented here improves over previous generators for all aspects that have to do with top decays, and especially for the study of issues related to top mass measurements that involve B hadrons or b jets. The work presented here also constitutes a first step towards a fully consistent matching of NLO calculations involving intermediate resonances decaying into coloured particles, with parton showers.
description: Minor changes: improved few sentences, added 1 explanatory figure in sec. 1. Now it matches the version published in JHEP
Stochastic Modelling with Randomised Markov Bridges
Creators: name: Macrina, Andrea
name: Sekine, Jun
Publisher: name: arXiv
Year: 2014
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics

description: We consider the filtering problem of estimating a hidden random variable $X$ by noisy observations. The noisy observation process is constructed by a randomised Markov bridge (RMB) $(Z_t)_{t\in [0,T]}$ of which terminal value is set to $Z_T=X$. That is, at the terminal time $T$, the noise of the bridge process vanishes and the hidden random variable $X$ is revealed. We derive the explicit filtering formula, governing the dynamics of the conditional probability process, for a general RMB. It turns out that the conditional probability is given by a function of current time $t$, the current observation $Z_t$, the initial observation $Z_0$, and the a priori distribution $ν$ of $X$ at $t=0$. As an example for an RMB we explicitly construct the skew-normal randomised diffusion bridge and show how it can be utilised to extend well-known commodity pricing models and how one may propose novel stochastic price models for financial instruments linked to greenhouse gas emissions.
description: 36 pages, 5 figures
PRADclass: Multi-pronged Gleason grade-informed computational strategy identifies consensus biomarker features of prostate adenocarcinoma that predict aggressive cancer
Creators: name: Palaniappan, Ashok
name: Balraj, Alex S
name: Muthamilselvan, Sangeetha
Publisher: name: figshare
Year: 2023
Subjects: classificationCode: 310201
subject: Bioinformatic methods development
classificationCode: 310202
subject: Biological network analysis
classificationCode: 310204
subject: Genomics and transcriptomics
classificationCode: 310208
subject: Translational and applied bioinformatics
classificationCode: 321102
subject: Cancer diagnosis
classificationCode: 321103
subject: Cancer genetics
classificationCode: 321109
subject: Predictive and prognostic markers

description: Supplementary material to: Balraj AS, Muthamilselvan S, Raja R, & Palaniappan A. PRADclass: Multi-pronged Gleason grade-informed computational strategy identifies consensus biomarker features of prostate adenocarcinoma that signify aggressive cancer (2023)
 Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, 613401, India.
title: Local crystal structure of Bi-based perovskites solved by RMC modeling
Creators: name: Szczecinski, Robert
Publisher: name: University of Liverpool Repository
Year: 2014

description: The local structure investigation by Reverse Monte Carlo modeling and comparison to average crystallographic structure of Bi-based perovskite materials are presented in this thesis. This novel technique using neutron total scattering is applied in search of possible short-range correlations between atoms to understand complex structure of these materials. Chapter One gives an introduction into perovskite structure and its properties. Chapter Two describes the difference between periodic and aperiodic crystals, which average crystallographic structure has been adopted by materials presented in this thesis. It also describes the total scattering and Pair Distribution Functions used in Reverse Monte Carlo modeling. The next chapters describe the local and average structure investigated during this thesis. Chapter Three describes the local and average perovskite structure of BiTi3/8Fe1/4Mg3/8O3 at various temperatures, where local structure analysis revealed particular displacements and correlations of A site and B site cations not captured by average crystallographic structure. Chapter Four compares local structure derived from RMC modeling and average incommensurate and commensurate crystallographic structures of Bi2Mn4/3Ni2/3O6 at room and high temperatures respectively, demonstrating importance of recognizing the length-scale of the probe used for structural characterization. Chapter Five describes the work on BiFe0.6Mn0.4O3 perovskite which was investigated by traditional crystallography to determine the modulated behavior and distorted structure of this material. The last Chapter 6 contains main conclusions from all experimental chapters.
On the Multiple Covering Densities of Triangles
Creators: name: Sriamorn, Kirati
name: Wetayawanich, Akanat
Publisher: name: arXiv
Year: 2014
Subjects: subject: Metric Geometry (math.MG)
subject: Number Theory (math.NT)
subject: FOS: Mathematics

description: Given a convex disk $K$ and a positive integer $k$, let $\vartheta_T^k(K)$ and $\vartheta_L^k(K)$ denote the $k$-fold translative covering density and the $k$-fold lattice covering density of $K$, respectively. Let $T$ be a triangle. In a very recent paper, K. Sriamorn proved that $\vartheta_L^k(T)=\frac{2k+1}{2}$. In this paper, we will show that $\vartheta_T^k(T)=\vartheta_L^k(T)$.