cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Solving Large-Scale Robust Stability Problems by Exploiting the Parallel Structure of Polya's Theorem
Creators: name: Kamyar, Reza
name: Peet, Matthew M.
name: Peet, Yulia
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optimization and Control (math.OC)
subject: FOS: Mathematics

description: In this paper, we propose a distributed computing approach to solving large-scale robust stability problems on the simplex. Our approach is to formulate the robust stability problem as an optimization problem with polynomial variables and polynomial inequality constraints. We use Polya's theorem to convert the polynomial optimization problem to a set of highly structured Linear Matrix Inequalities (LMIs). We then use a slight modification of a common interior-point primal-dual algorithm to solve the structured LMI constraints. This yields a set of extremely large yet structured computations. We then map the structure of the computations to a decentralized computing environment consisting of independent processing nodes with a structured adjacency matrix. The result is an algorithm which can solve the robust stability problem with the same per-core complexity as the deterministic stability problem with a conservatism which is only a function of the number of processors available. Numerical tests on cluster computers and supercomputers demonstrate the ability of the algorithm to efficiently utilize hundreds and potentially thousands of processors and analyze systems with 100+ dimensional state-space. The proposed algorithms can be extended to perform stability analysis of nonlinear systems and robust controller synthesis.
Reading between the Lines: Ambiguity and Interpretation in 'Lolita' by Vladimir Nabokov
Creators: name: Rewaa Ahmed Anwer
Publisher: name: Zenodo
Year: 2023

description: This paper investigates into the linguistic ambiguity found within "Lolita," shedding light on Nabokov's adept manipulation of language, particularly through the character of Humbert, in order to convey concealed meanings. It encourages readers to look beyond the superficial layer of language and unearth hidden subtleties. The complexities of the narrative arise from Humbert's unreliability as a narrator, sowing seeds of doubt regarding the events and compelling readers to navigate through multiple perspectives. This study provides valuable insights into Humbert's linguistic intricacies and their significance.
Vladimir masterfully employs a variety of ambiguity forms, including lexical, syntactic, semantic, linguistic, amphibolic, pragmatic, polysemic, and punctuation-based forms, to captivate readers and heighten the complexity of the characters. This intentional use of ambiguity challenges preconceptions, mirrors the characters' psyches, and underscores the novel's themes. The intricate interplay of these diverse forms of ambiguity enriches the enigmatic narrative structure of "Lolita," inviting readers to partake in a more profound analysis and fostering a deeper understanding of the characters and themes.
Prototyping 3D 'Smart' Textile Surfaces for Pervasive Computing Environments
Creators: name: Calder, Lynsey
name: Aylett, Ruth
name: Louchart, Sandy
name: Robertson, Sara
Publisher: name: FUTURESCAN
Year: 2019
Subjects: subject: 120306 Textile and Fashion Design
subject: FOS: Arts (arts, history of arts, performing arts, music)

description: Research paper presented at Futurescan 2: Collective Voices, Sheffield Hallam University, 10th-11th January 2013.

Futurescan 2: Collective Voices
Edited by Helena Britt, Sally Wade and Kerry WaltonDecember 2013ISBN: 978 1 907382 64 2
title: TUQR: A Topology Unaware QOS Routing Protocol for Manets
Creators: name: Zagli, Ibrahim
Publisher: name: Old Dominion University
publisherIdentifier: https://ror.org/04zjtrb98
publisherIdentifierScheme: ROR
Year: 2006

description: In this thesis, the main purpose is to design a new Quality of Service (QoS) Routing Protocol for Mobile ad-hoc Networks that improves packet delivery ratio in QoS constrained communication in comparison to current well known protocols by using distributed multi-path routing. To accomplish that, a new approach to the QoS routing in Mobile ad hoc Networks (MANET) is developed to reduce the effects of the distrustful environment of MANET by keeping a number of suitable paths as high as possible and distributing the decision mechanism among the nodes on the path.

In most current protocols that mainly evaluate and store the valid path information on unique nodes, in case of a problem on the path that the packet follows (like resource decreasing, or congestion), that packet simply drops. And it has to be re-sent by the originating node. And also, this problem has to be reported to the concerning node all the way back to prevent new packets from being sent over that path (obviously creating extra overhead and traffic load).

With those major problems in mind, the only way to reduce the possibility of a packet dropping case caused by wireless link status changes on the path in QoS Routing, is to give alternative way(s) to a packet (in case it is in trouble) while it is on its way. This can be done by assigning (distributing) path selection role to intermediate nodes. By this way, also in "Route Maintenance", there is no need to inform all nodes on the path towards the source node (decreasing the overhead).

The new approach uses on-demand route discovery. The source node or any other node has no idea about the path that will be followed by data packets. Instead, starting with the source node, each node just knows which neighbour(s) is capable of forwarding data packets to the given destination.

This approach, as a whole, tries to avoid being effected by wireless link status changes by reacting to them in a timely fashion, and keeps the packet on its way using all possible resources of the network. And simulation results are used to verify expected improvement in packet delivery ratio compared to selected protocols.
Homometry and direct-sum decompositions of lattice-convex sets
Creators: name: Averkov, Gennadiy
name: Langfeld, Barbara
Publisher: name: arXiv
Year: 2014
Subjects: subject: Metric Geometry (math.MG)
subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: 52C07, 05B10, 52B20, 52C05, 78A45

description: Two sets in $\mathbb{R}^d$ are called homometric if they have the same covariogram, where the covariogram of a finite subset $K$ of $\mathbb{R}^d$ is the function associating to each $u \in \mathbb{R}^d$ the cardinality of $K \cap (K+u)$. Understanding the structure of homometric sets is important for a number of areas of mathematics and applications. If two sets are homometric but do not coincide up to translations and point reflections, we call them nontrivially homometric. We study nontrivially homometric pairs of lattice-convex sets, where a set $K$ is called lattice-convex with respect to a lattice $\mathbb{M} \subseteq \mathbb{R}^d$ if $K$ is the intersection of $\mathbb{M}$ and a convex subset of $\mathbb{R}^d$. This line of research was initiated in 2005 by Daurat, Gérard and Nivat and, independently, by Gardner, Gronchi and Zong. All pairs of nontrivially homometric lattice-convex sets that have been known so far can essentially be written as direct sums $S \oplus T$ and $S \oplus (-T)$, where $T$ is lattice-convex, the underlying lattice~$\mathbb{M}$ is the direct sum of $T$ and some sublattice $\mathbb{L}$, and $S$ is a subset of $\mathbb{L}$. We study pairs of nontrivially homometric lattice-convex sets assuming this particular form and establish a necessary and a sufficient condition for the lattice-convexity of $S \oplus T$. This allows us to explicitly describe all nontrivially homometric pairs in dimension two, under the above assumption, and to construct examples of nontrivially homometric pairs of lattice-convex sets for each $d \ge 3$.
description: 30 pages,8 figures, Magma code
Managing Creative Conversations Between Designers and Consumers
Creators: name: Kalkreuter, Britta
name: Robb, David
name: Chantler, Mike
name: Padilla, Stefano
Publisher: name: FUTURESCAN
Year: 2019
Subjects: subject: 120306 Textile and Fashion Design
subject: FOS: Arts (arts, history of arts, performing arts, music)

description: Research paper presented at Futurescan 2: Collective Voices, Sheffield Hallam University, 10th-11th January 2013.

Futurescan 2: Collective Voices
Edited by Helena Britt, Sally Wade and Kerry WaltonDecember 2013ISBN: 978 1 907382 64 2
Reporting Corruption from within Papua New Guinea's Public Financial Management System
Creators: name: Watson, Amanda H A
name: Wiltshire, Colin
Publisher: name: Canberra, ACT: State, Society and Governance in Melanesia (SSGM), Research School of Pacific and Asian Studies, The Australian National University
Year: 2016

description: For Papua New Guinea (PNG) to achieve its development aspirations, effective utilisation of public expenditure is essential. However, significant weaknesses exist in its decentralised political, fiscal and administrative arrangements, which open up spaces for corruption. This paper explores the potential of technology-based corruption reporting in the midst of substantial fiscal and logistical pressures. The research was designed to be of practical assistance to those with an interest in innovative uses of technology, while also contributing to broader debates about the potential strategic use of mobile telephony in developing countries. As widespread mobile phone networks are relatively new in the Pacific region, the findings presented are the first to explore mobile phone use for corruption reporting in any detail, which helps to fill gaps in the literature regarding potential future opportunities. In PNG, public officials responsible for administering funds have lacked anonymous and accessible ways to report corrupt practices. In response, the PNG Department of Finance, with support from the Australian Government and the United Nations Development Program, has established a way for public officials working in the public financial management system to anonymously report cases of corruption through a mobile phone text messaging service. All reported cases are referred to the Internal Audit and Compliance Division in the Department of Finance for further investigation, in collaboration with relevant state authorities. This paper reports on this innovative approach to expand corruption reporting practices in PNG based on the experiences of public officials using this new reporting mechanism. Overall, the findings show that the service has been well utilised, with hundreds of ongoing investigations and several arrests. However, it is argued here that while the project is proving to be successful, its expansion should be very carefully and cautiously planned. The current context of PNG’s public financial management system is explained first, before the project is introduced. The paper presents the research design and findings, followed by a discussion of practical recommendations and implications for the domains of policy and theory. Finally, the conclusion presents suggestions for further research.
Sequence-Specific Biosensors Report Drug-Induced Changes in Epigenetic Silencing in Living Cells
Creators: name: Szpakowski, Sebastian
name: Huang, Xudong
name: Narayanaswamy, Rammohan
name: Fenn, Kathleen
name: Blancafort, Pilar
name: Lizardi, Paul M.
name: Costa, Jose
name: Sasaki, Clarence
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Treatment with demethylating drugs can induce demethylation and reactivation of abnormally silenced tumor suppressor genes in cancer cells, but it can also induce potentially deleterious loss of methylation of repetitive elements. To enable the observation of unwanted drug effects related to loss of methylation of repetitive DNA, we have developed a novel biosensor capable of reporting changes in DNA accessibility via luminescence, in living cells. The biosensor design comprises two independent modules, each with a polydactyl zinc finger domain fused to a half intein and to a split-luciferase domain that can be joined by conditional protein splicing after binding to adjacent DNA targets. We show that an artificial zinc finger design specifically targeting DNA sequences near the promoter region of the L1PA2 subfamily of Line-1 retroelements is able to generate luminescent signals, reporting loss of epigenetic silencing and increased DNA accessibility of retroelements in human cells treated with the demethylating drugs decitabine or 5-azacytidine.
Supplementary Table 1: Differential expressed genes (DEGs) of SEV vs MOD body conditionloss cows at week seven of calving. P ≤ 0.05 and |fold change| ≥ 1.5.
Creators: name: Alemu, Teshome
name: Duggavathi, Raj
Publisher: name: figshare
Year: 2023
Subjects: classificationCode: 300305
subject: Animal reproduction and breeding

description: Supplementary Table 1: Differential expressed genes (DEGs) of SEV vs MOD body condition loss cows at week seven of calving. P ≤ 0.05 and |fold change| ≥ 1.5.Cows were monitored for body condition score (BCS, 5-point scale) during the transition period (3 weeks before to 7 weeks after calving) and were classified as Moderate (MOD, < 0.75 units) or Severe (SEV, ≥ 0.75 units) loss groups. Liver biopsies were collected at Week 7 for trascriptome analysis (N=3 per group).
Interplay between DNA polymerases β and λ in repair of oxidation DNA damage in chicken DT40 cells
Creators: name: Nakamura, Jun
name: Arakawa, Hiroshi
name: Prasad, Rajendra
name: Sonoda, Eiichiro
name: Wilson, Samuel H.
name: Buerstedde, Jean-Marie
name: Tano, Keizo
name: Asagoshi, Kenjiro
name: Takeda, Shunichi
name: Braithwaite, Elena K.
name: Watanabe, Masami
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: DNA polymerase λ (Pol λ) is a DNA polymerase β (Pol β)-like enzyme with both DNA synthetic and 5'-deoxyribose-5'-phosphate lyase domains. Resent biochemical studies implicated Pol λ as a backup enzyme to Pol ß in the mammalian base excision repair (BER) pathway. To examine the interrelationship between Pol λ and Pol ß in BER of DNA damage in living cells, we disrupted the genes for both enzymes either singly or in combination in the chicken DT40 cell line and then characterized BER phenotypes. Disruption of the genes for both polymerases caused hypersensitivity to H2O2-induced cytotoxicity, whereas the effect of disruption of either polymerase alone was only modest. Similarly, BER capacity in cells after H2O2 exposure was lower in Pol β−/−/Pol λ−/− cells than in Pol β−/−, wild-type and Pol λ−/− cells, which were equivalent. These results suggest that these polymerases can complement for one another in counteracting oxidative DNA damage. Similar results were obtained in assays for in vitro BER capacity using cell extracts. With MMS-induced cytotoxicity, there was no significant effect on either survival or BER capacity from Pol λ gene disruption. A strong hypersensitivity and reduction in BER capacity was observed for Pol β−/−/Pol λ−/− and Pol β−/− cells, suggesting that Pol β had a dominant role in counteracting alkylation DNA damage in this cell system.
Awaken: Contemporary Fashion and Textile Interpretation of Archival Material
Creators: name: Britt, Helena
name: Stephen-Cran, Jimmy
name: Bremner, Elaine
Publisher: name: FUTURESCAN
Year: 2019
Subjects: subject: 120306 Textile and Fashion Design
subject: FOS: Arts (arts, history of arts, performing arts, music)

description: Research paper presented at Futurescan 2: Collective Voices, Sheffield Hallam University, 10th-11th January 2013.

Futurescan 2: Collective Voices
Edited by Helena Britt, Sally Wade and Kerry WaltonDecember 2013ISBN: 978 1 907382 64 2
Projections of planar sets in well-separated directions
Creators: name: Orponen, Tuomas
Publisher: name: arXiv
Year: 2015
Subjects: subject: Classical Analysis and ODEs (math.CA)
subject: FOS: Mathematics

description: First, let $K \subset B(0,1) \subset \mathbb{R}^{2}$ be a set with $\mathcal{H}_{\infty}^{1}(K) \sim 1$, and write $π_{e}(K)$ for the orthogonal projection of $K$ into the line spanned by $e \in S^{1}$. For $1/2 \leq s < 1$, write $$E_{s} := \{e : N(π_{e}(K),δ) \leq δ^{-s}\}, $$ where $N(A,r)$ is the $r$-covering number of the set $A$. It is well-known -- and essentially due to R. Kaufman -- that $N(E_{s},δ) \lessapprox δ^{-s}$. Using the polynomial method, I prove that $$ N(E_{s},r) \lessapprox \min\left\{δ^{-s}\left(\fracδ{r}\right)^{1/2},r^{-1}\right\}, \quad δ\leq r \leq 1.$$ I construct examples showing that the exponents in the bound are sharp for $δ\leq r \leq δ^{s}$. The second theorem concerns projections of $1$-Ahlfors-David regular sets. Let $A \geq 1$ and $1/2 \leq s < 1$ be given. I prove that, for $p = p(A,s) \in \mathbb{N}$ large enough, the finite set of unit vectors $S_{p} := \{e^{2πi k/p} : 0 \leq k < p\}$ has the following property. If $K \subset B(0,1)$ is non-empty and $1$-Ahlfors-David regular with regularity constant at most $A$, then $$\frac{1}{p} \sum_{e \in S_{p}} N(π_{e}(K),δ) \geq δ^{-s}$$ for all small enough $δ> 0$. In particular, $\overline{\dim}_{\text{B}} π_{e}(K) \geq s$ for some $e \in S_{p}$.
description: 20 pages, 3 figures. v5: Corrected typos and updated references. To appear in Adv. Math
Highly tunable ultra-narrow-resonances with optical nano-antenna phased arrays in the infrared
Creators: name: Li, Shi-Qiang
name: Zhou, Wei
name: Guo, Peijun
name: Buchholz, D. Bruce
name: Qiu, Ziwei
name: Ketterson, John B.
name: Ocola, Leonidas E.
name: Sakoda, Kazuaki
name: Chang, Robert P. H.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We report our recent development in pursuing high Quality-Factor (high-Q factor) plasmonic resonances, with vertically aligned two dimensional (2-D) periodic nanorod arrays. The 2-D vertically aligned nano-antenna array can have high-Q resonances varying arbitrarily from near infrared to terahertz regime, as the antenna resonances of the nanorod are highly tunable through material properties, the length of the nanorod, and the orthogonal polarization direction with respect to the lattice surface,. The high-Q in combination with the small optical mode volume gives a very high Purcell factor, which could potentially be applied to various enhanced nonlinear photonics or optoelectronic devices. The 'hot spots' around the nanorods can be easily harvested as no index-matching is necessary. The resonances maintain their high-Q factor with the change of the environmental refractive index, which is of great interest for molecular sensing.
description: 8 pages, appears in Proc. SPIE 9163, Plasmonics: Metallic Nanostructures and Their Optical Properties XII, 91630R (September 10, 2014)
The Good Life - Designing for Sustainable Luxury
Creators: name: Marr, Anne
Publisher: name: FUTURESCAN
Year: 2019
Subjects: subject: 120306 Textile and Fashion Design
subject: FOS: Arts (arts, history of arts, performing arts, music)

description: Research paper presented at Futurescan 2: Collective Voices, Sheffield Hallam University, 10th-11th January 2013.

Futurescan 2: Collective Voices
Edited by Helena Britt, Sally Wade and Kerry WaltonDecember 2013ISBN: 978 1 907382 64 2
A comparison of BRCT domains involved in nonhomologous end-joining: Introducing the solution structure of the BRCT domain of polymerase lambda
Creators: name: Mueller, Geoffrey A.
name: Ramsden, Dale A.
name: DeRose, Eugene F.
name: Havener, Jody M.
name: Pedersen, Lars C.
name: Moon, Andrea F.
name: London, Robert E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Three of the four family X polymerases, DNA polymerase λ, DNA polymerase µ, and TdT have been associated with repair of double-strand DNA breaks by nonhomologous end-joining. Their involvement in this DNA repair process requires an N-terminal BRCT domain that mediates interaction with other protein factors required for recognition and binding of broken DNA ends. Here we present the NMR solution structure of the BRCT domain of DNA polymerase λ, completing the structural portrait for this family of enzymes. Analysis of the overall fold of the polymerase λ BRCT domain reveals structural similarity to the BRCT domains of polymerase µ and TdT, yet highlights some key sequence and structural differences that may account for important differences in the biological activities of these enzymes and their roles in nonhomologous end-joining. Mutagenesis studies indicate that the conserved Arg57 residue of Pol λ plays a more critical role for binding to the XRCC4-Ligase IV complex than its structural homolog in Pol µ, Arg43. In contrast, the hydrophobic Leu60 residue of Pol λ contributes less significantly to binding than the structurally homologous Phe46 residue of Pol µ. A third leucine residue involved in the binding and activity of Pol µ, is nonconservatively replaced by a glutamine in Pol λ (Gln64) and, based on binding and activity data, is apparently unimportant for Pol λ interactions with the NHEJ complex. In conclusion, both the structure of the Pol λ BRCT domain and its mode of interaction with the other components of the NHEJ complex significantly differ from the two previously studied homologs, Pol µ and TdT.
title: Website boundary detection via machine learning
Creators: name: Alshukri, Ayesh
Publisher: name: University of Liverpool Repository
Year: 2013

description: This thesis describes research undertaken in the field of web data mining. More specifically this research is directed at investigating solutions to the Website Boundary Detection (WBD) problem. WBD is the problem of identifying the collection of all web pages that are part of a single website, which is an open problem. Potential solutions to WBD can be beneficial with respect to tasks such as archiving web content and the automated construction of web directories. A pre-requisite to any WBD approach is that of a definition of a website. This thesis commences with a discussion of previous definitions of a website, and subsequently proposes a definition of a website which is used with respect to the WBD solution approaches presented later in this thesis. The WBD problem may be addressed in either the static or the dynamic context. Both are considered in this thesis. Static approaches require all web page data to be available a priori in order to make a decision on what pages are within a website boundary. While dynamic approaches make decisions on portions of the web data, and incrementally build a representation of the pages within a website boundary. There are three main approaches to the WBD problem presented in this thesis; the first two are static approaches, and the final one is a dynamic approach. The first static approach presented in this thesis concentrates on the types of features that can be used to represent web pages. This approach presents a practical solution to the WBD problem by applying clustering algorithms to various combinations of features. Further analysis investigates the ``best'' combination of features to be used in terms of WBD performance. The second static approach investigates graph partitioning techniques based on the structural properties of the web graph in order to produce WBD solutions. Two variations of the approach are considered, a hierarchical graph partitioning technique, and a method based on minimum cuts of flow networks. The final approach for the evaluation of WBD solutions presented in this research considers the dynamic context. The proposed dynamic approach uses both structural properties and various feature representations of web pages in order to incrementally build a website boundary as the pages of the web graph are traversed. The evaluation of the approaches presented in this thesis was conducted using web graphs from four academic departments hosted by the University of Liverpool. Both the static and dynamic approaches produce appropriate WBD solutions, however. The reported evaluation suggests that the dynamic approach to resolving the WBD problem offers additional benefits over a static approach due to the lower resource cost of gathering and processing typically smaller amounts of web data.
From Counterfeit to Counter
Creators: name: Armstrong, Angela
Publisher: name: FUTURESCAN
Year: 2019
Subjects: subject: 120306 Textile and Fashion Design
subject: FOS: Arts (arts, history of arts, performing arts, music)

description: Research paper presented at Futurescan 2: Collective Voices, Sheffield Hallam University, 10th-11th January 2013.

Futurescan 2: Collective Voices
Edited by Helena Britt, Sally Wade and Kerry WaltonDecember 2013ISBN: 978 1 907382 64 2
Rethinking the Designer's Role: The Challenge of Unfinished Knitwear Design
Creators: name: Holroyd, Amy Twigger
Publisher: name: FUTURESCAN
Year: 2019
Subjects: subject: 120306 Textile and Fashion Design
subject: FOS: Arts (arts, history of arts, performing arts, music)

description: Research paper presented at Futurescan 2: Collective Voices, Sheffield Hallam University, 10th-11th January 2013.

Futurescan 2: Collective Voices
Edited by Helena Britt, Sally Wade and Kerry WaltonDecember 2013ISBN: 978 1 907382 64 2
Catalytic mechanism of human DNA polymerase λ with Mg2+ and Mn2+ from ab initio quantum mechanical/molecular mechanical studies
Creators: name: Cisneros, G. Andrés
name: García-Díaz, Miguel
name: Kunkel, Thomas A.
name: Perera, Lalith
name: Pedersen, Lee G.
name: Bebenek, Katarzyna
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: DNA polymerases play a crucial role in the cell cycle due to their involvement in genome replication and repair. Understanding the reaction mechanism by which these polymerases carry out their function can provide insights into these processes. Recently, the crystal structures of human DNA polymerase λ (Polλ) have been reported both for pre- and post- catalytic complexes (García-Díaz et al., DNA Repair, 3, 1333, 2007). Here we employ the pre-catalytic complex as a starting structure for the determination of the catalytic mechanism of Polλ using ab initio quantum mechanical/molecular mechanical methods. The reaction path has been calculated using Mg2+ and Mn2+ as the catalytic metals. In both cases the reaction proceeds through a two step mechanism where the 3′-OH of the primer sugar ring is deprotonated by one of the conserved Asp residues (D490) in the active site before the incorporation of the nucleotide to the nascent DNA chain. A significant charge transfer is observed between both metals and some residues in the active site as the reaction proceeds. The optimized reactant and product structures agree with the reported crystal structures. In addition, the calculated reaction barriers for both metals are close to experimentally estimated barriers. Energy decomposition analysis to explain individual residue contributions suggests that several amino acids surrounding the active site are important for catalysis. Some of these residues, including R420, R488 and E529, have been implicated in catalysis by previous mutagenesis experiments on the homologous residues on Polβ. Furthermore, Polλ residues R420 and E529 found to be important from the energy decomposition analysis, are homologous to residues R183 and E295 in Polβ, both of which are linked to cancer. In addition, residues R386, E391, K422 and K472 appear to have an important role in catalysis and could be a potential target for mutagenesis experiments. There is partial conservation of these residues across the Pol X family of DNA polymerases.
On the difference of torus geometry between hidden and non-hidden broad line active galactic nuclei
Creators: name: Ichikawa, Kohei
name: Packham, Christopher
name: Almeida, Cristina Ramos
name: Ramos, Andres Asensio
name: Alonso-Herrero, Almudena
name: Gonzalez-Martin, Omaira
name: Lopez-Rodriguez, Enrique
name: Ueda, Yoshihiro
name: Diaz-Santos, Tanio
name: Elitzur, Moshe
name: Hoenig, Sebastian F.
name: Imanishi, Masatoshi
name: Levenson, Nancy A.
name: Mason, Rachel E.
name: Perlman, Eric S.
name: Alsip, Crystal D.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present results from the fitting of infrared (IR) spectral energy distributions of 21 active galactic nuclei (AGN) with clumpy torus models. We compiled high spatial resolution ($\sim 0.3$--$0.7$ arcsec) mid-IR $N$-band spectroscopy, $Q$-band imaging and nuclear near- and mid-IR photometry from the literature. Combining these nuclear near- and mid-IR observations, far-IR photometry and clumpy torus models, enables us to put constraints on the torus properties and geometry. We divide the sample into three types according to the broad line region (BLR) properties; type-1s, type-2s with scattered or hidden broad line region (HBLR) previously observed, and type-2s without any published HBLR signature (NHBLR). Comparing the torus model parameters gives us the first quantitative torus geometrical view for each subgroup. We find that NHBLR AGN have smaller torus opening angles and larger covering factors than those of HBLR AGN. This suggests that the chance to observe scattered (polarized) flux from the BLR in NHBLR could be reduced by the dual effects of (a) less scattering medium due to the reduced scattering volume given the small torus opening angle and (b) the increased torus obscuration between the observer and the scattering region. These effects give a reasonable explanation for the lack of observed HBLR in some type-2 AGN.
description: 13 pages, 5 figures, accepted for publication in ApJ
The histone methylase Set2p and the histone deacetylase Rpd3p repress meiotic recombination at the HIS4 meiotic recombination hotspot in Saccharomyces cerevisiae
Creators: name: Mieczkowski, Piotr
name: Strahl, Brian D.
name: Rinella, Erica
name: Merker, Jason D.
name: Shibata, Yoichiro
name: Bouck, David C.
name: Dominska, Margaret
name: Petes, Thomas D.
name: Greenwell, Patricia W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: The rate of meiotic recombination in the yeast Saccharomyces cerevisiae varies widely in different regions of the genome with some genes having very high levels of recombination (hotspots). A variety of experiments done in yeast suggest that hotspots are a feature of chromatin structure rather than a feature of primary DNA sequence. We examined the effects of mutating a variety of enzymes that affect chromatin structure on the recombination activity of the well-characterized HIS4 hotspot including the Set2p and Dot1p histone methylases, the Hda1p and Rpd3p histone deacetylases, the Sin4p global transcription regulator, and a deletion of one of the two copies of the genes encoding histone H3–H4. Loss of Set2p or Rpd3p substantially elevated HIS4 hotspot activity, and loss of Hda1p had a smaller stimulatory effect; none of the other alterations had a significant effect. The increase of HIS4 hotspot activity in set2 and rpd3 strains is likely to be related to the recent finding that histone H3 methylation by Set2p directs deacetylation of histones by Rpd3p.
Anapole moment of the lightest neutralino in the cMSSM
Creators: name: Cabral-Rosetti, Luis G.
name: Mondragón, Myriam
name: Reyes-Pérez, Esteban
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We study the anapole moment of the lightest neutralino in the constrained Minimal Supersymmetric Standard Model (cMSSM). The electromagnetic anapole is the only allowed electromagnetic form factor for Majorana fermions, such as the neutralino. Since the neutralino is the LSP in many versions of the MSSM and therefore a candidate for dark matter, its characterization through its electromagnetic properties is important both for particle physics and for cosmology. We perform a scan in the parameter space of the cMSSM and find that the anapole moment is different from zero albeit very small ($< 10^{-3}$ GeV$^{-2}$). Combined with experimental constraints like the Higgs mass and the DM relic density, the allowed region of parameter space lies within the reach of future direct DM searches. Thus, the anapole moment could be used as a complementary constraint when studying the parameter space of the cMSSM and other similar models.
description: 22 pages, 13 figures. arXiv admin note: substantial text overlap with arXiv:1206.5052
Futurescan 2: Collective Voices - Author Details
Creators: name: Figshare Admin Futurescan
Publisher: name: FUTURESCAN
Year: 2019
Subjects: subject: 120306 Textile and Fashion Design
subject: FOS: Arts (arts, history of arts, performing arts, music)

description: Author details for Futurescan 2: Collective Voices, Sheffield Hallam University, 10th-11th January 2013.

Futurescan 2: Collective Voices
Edited by Helena Britt, Sally Wade and Kerry WaltonDecember 2013ISBN: 978 1 907382 64 2
Main-Sequence Effective Temperatures from a Revised Mass-Luminosity Relation Based on Accurate Properties
Creators: name: Eker, Z.
name: Soydugan, F.
name: Soydugan, E.
name: Bilir, S.
name: Gokce, E. Yaz
name: Steer, I.
name: Tuysuz, M.
name: Senyuz, T.
name: Demircan, O.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: The mass-luminosity (M-L), mass-radius (M-R) and mass-effective temperature ($M-T_{eff}$) diagrams for a subset of galactic nearby main-sequence stars with masses and radii accurate to $\leq 3\%$ and luminosities accurate to $\leq 30\%$ (268 stars) has led to a putative discovery. Four distinct mass domains have been identified, which we have tentatively associated with low, intermediate, high, and very high mass main-sequence stars, but which nevertheless are clearly separated by three distinct break points at 1.05, 2.4, and 7$M_{\odot}$ within the mass range studied of $0.38-32M_{\odot}$. Further, a revised mass-luminosity relation (MLR) is found based on linear fits for each of the mass domains identified. The revised, mass-domain based MLRs, which are classical ($L \propto M^α$), are shown to be preferable to a single linear, quadratic or cubic equation representing as an alternative MLR. Stellar radius evolution within the main-sequence for stars with $M>1M_{\odot}$ is clearly evident on the M-R diagram, but it is not the clear on the $M-T_{eff}$ diagram based on published temperatures. Effective temperatures can be calculated directly using the well-known Stephan-Boltzmann law by employing the accurately known values of M and R with the newly defined MLRs. With the calculated temperatures, stellar temperature evolution within the main-sequence for stars with $M>1M_{\odot}$ is clearly visible on the $M-T_{eff}$ diagram. Our study asserts that it is now possible to compute the effective temperature of a main-sequence star with an accuracy of $\sim 6\%$, as long as its observed radius error is adequately small (<1%) and its observed mass error is reasonably small (<6%).
description: 57 pages, including 12 figures and 7 tables, accepted for publication in Astronomical Journal
Activity of ribonucleotide reductase helps determine how cells repair DNA double strand breaks
Creators: name: Roberts, Steven A.
name: Havener, Jody M.
name: Burkhalter, Martin D.
name: Ramsden, Dale A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Mammalian cells can choose either nonhomologous end joining (NHEJ) or homologous recombination (HR) for repair of chromosome breaks. Of these two pathways, HR alone requires extensive DNA synthesis and thus abundant synthesis precursors (dNTPs). We address here if this differing requirement for dNTPs helps determine how cells choose a repair pathway. Cellular dNTP pools are regulated primarily by changes in ribonucleotide reductase activity. We show that an inhibitor of ribonucleotide reductase (hydroxyurea) hypersensitizes NHEJ-deficient cells, but not wild type or HR-deficient cells, to chromosome breaks introduced by ionizing radiation. Hydroxyurea additionally reduces the frequency of irradiated cells with a marker for an early step in HR, Rad51 foci, consistent with reduced initiation of HR under these conditions. Conversely, promotion of ribonucleotide reductase activity protects NHEJ-deficient cells from ionizing radiation. Importantly, promotion of ribonucleotide reductase activity also increases usage of HR in cells proficient in both NHEJ and HR at a targeted chromosome break. Activity of ribonucleotide reductase is thus an important factor in determining how mammalian cells repair broken chromosomes. This may explain in part why G1/G0 cells, which have reduced ribonucleotide reductase activity, rely more on NHEJ for DSB repair.
title: Synthesis, characterisation and single molecule conductance measurements of organic molecules
Creators: name: Brooke, Carly
Publisher: name: University of Liverpool Repository
Year: 2013

description: The use of single molecules to construct electronic devices is an exciting prospect, and one that has long provided a driving force for research in the area of molecular scale electronics. In order for this emerging field to advance a deep understanding of the fundamental mechanisms that govern electron conduction at the molecular level is imperative. Recent developments in areas such as scanning tunnelling microscopy, have facilitated the determination of the electrical properties of single molecules tethered between two metallic contacts. The analysis and potentially tailoring of structure-property relationships is hugely important and could lead to new and unforeseen applications for this emerging field. The work presented herein details two major studies. The first is an investigation of the transport properties of a series of analogous molecules, which consist of a single benzene ring sandwiched between two alkyl chains of varying length. Prior to the work in this thesis one such molecule, and various substituted analogues thereof, had shown behaviour similar to what would be expected of a molecular equivalent of a double tunnelling barrier. The data presented here demonstrates a remarkably low dependence of this system on molecular length; this result contradicts the behaviour expected of a coherent transport mechanism. Moreover, the study of the orbital energies and densities of these molecules provides further evidence of a mechanism of conduction that is very different to that previously suggested for this system. The second study centres around the investigation of the conductance behaviour of 4,4’-bipyridine and some substituted analogues thereof; this study is presented in two parts. The first details attempts to synthesise planar analogues of 4,4’-bipyridine, as well the synthesis and reactivity of novel substituted bipyridines. The second part reports conductance data, electrochemical studies and theoretical calculations of properties of these molecules. The data presented provides new information regarding the relationship between electronic structure and conductance behaviour in this type of system.
Tyrosyl-DNA phosphodiesterase and the repair of 3′-phosphoglycolate-terminated DNA double-strand breaks
Creators: name: Lin, Peck-Sun
name: Povirk, Lawrence F.
name: Akopiants, Konstantin
name: Mohapatra, Susovan
name: Valerie, Kristoffer
name: Ramsden, Dale A.
name: Zhou, Tong
name: Lees-Miller, Susan P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Although tyrosyl-DNA phosphodiesterase (TDP1) is capable of removing blocked 3′ termini from DNA double-strand break ends, it is uncertain whether this activity plays a role in double-strand break repair. To address this question, affinity-tagged TDP1 was overexpressed in human cells and purified, and its interactions with end joining proteins were assessed. Ku and DNA-PKcs inhibited TDP1-mediated processing of 3′-phosphoglycolate double-strand break termini, and in the absence of ATP, ends sequestered by Ku plus DNA-PKcs were completely refractory to TDP1. Addition of ATP restored TDP1-mediated end processing, presumably due to DNA-PK-catalyzed phosphorylation. Mutations in the 2609–2647 Ser/Thr phosphorylation cluster of DNA-PKcs only modestly affected such processing, suggesting that phosphorylation at other sites was important for rendering DNA ends accessible to TDP1. In human nuclear extracts, about 30% of PG termini were removed within a few hours despite very high concentrations of Ku and DNA-PKcs. Most such removal was blocked by the DNA-PK inhibitor KU-57788, but ~5% of PG termini were removed in the first few minutes of incubation even in extracts preincubated with inhibitor. The results suggest that despite an apparent lack of specific recruitment of TDP1 by DNA-PK, TDP1 can gain access to and can process blocked 3′ termini of double-strand breaks before ends are fully sequestered by DNA-PK, as well as at a later stage after DNA-PK autophosphorylation. Following cell treatment with calicheamicin, which specifically induces double-strand breaks with protruding 3′-PG termini, TDP1-mutant SCAN1 (spinocerebellar ataxia with axonal neuropathy) cells exhibited a much higher incidence of dicentric chromosomes, as well as higher incidence of chromosome breaks and micronuclei, than normal cells. This chromosomal hypersensitivity, as well as a small but reproducible enhancement of calicheamicin cytotoxicity following siRNA-mediated TDP1 knockdown, suggests a role for TDP1 in repair of 3′-PG double-strand breaks in vivo.
Partially user-irrepressible sequence sets and conflict-avoiding codes
Creators: name: Lo, Yuan-Hsun
name: Wong, Wing Shing
name: Fu, Hung-Lin
Publisher: name: arXiv
Year: 2014
Subjects: subject: Information Theory (cs.IT)
subject: Combinatorics (math.CO)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics
subject: 94B25, 94C15, 05B10

description: In this paper we give a partial shift version of user-irrepressible sequence sets and conflict-avoiding codes. By means of disjoint difference sets, we obtain an infinite number of such user-irrepressible sequence sets whose lengths are shorter than known results in general. Subsequently, the newly defined partially conflict-avoiding codes are discussed.
description: 13 pages, 4 figures, 3 tables. Published in Designs, Codes and Cryptography
Futurescan 2: Collective Voices - Acknowledgements
Creators: name: Figshare Admin Futurescan
Publisher: name: FUTURESCAN
Year: 2019
Subjects: subject: 120306 Textile and Fashion Design
subject: FOS: Arts (arts, history of arts, performing arts, music)

description: Acknowledgements for Futurescan 2: Collective Voices, Sheffield Hallam University, 10th-11th January 2013.

Futurescan 2: Collective Voices
Edited by Helena Britt, Sally Wade and Kerry WaltonDecember 2013ISBN: 978 1 907382 64 2
title: Irreconcilable differences : the unhappy marriage of Federal and State policy in the Welfare-to-Work programmes of the United States
Creators: name: Aldcroft, Julie
Publisher: name: University of Liverpool Repository
Year: 2023

description: In 1996, the United States Personal Responsibility and Work Opportunity Reconciliation Act (PRWORA) changed Aid for Families with Dependent Children (AFDC) from a program which gave single mothers on welfare some possibility of staying at home to raise small children, into TANF (Temporary Assistance for Needy Families), which established 60 month lifetime limit on financial support. Whilst continuing further the trend to devolve control to the states, this new approach mandated self-sufficiency via work, or work via welfare to work programmes, as the ultimate goal for everyone physically and mentally able to be self-sufficient. This thesis explores the possibility for welfare reform and its related programmes to create successes for the most disaffected.
Diffusion Estimation Over Cooperative Multi-Agent Networks With Missing Data
Creators: name: Gholami, Mohammad Reza
name: Jansson, Magnus
name: Ström, Erik G.
name: Sayed, Ali H.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Statistics Theory (math.ST)
subject: Systems and Control (eess.SY)
subject: FOS: Mathematics
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: In many fields, and especially in the medical and social sciences and in recommender systems, data are gathered through clinical studies or targeted surveys. Participants are generally reluctant to respond to all questions in a survey or they may lack information to respond adequately to some questions. The data collected from these studies tend to lead to linear regression models where the regression vectors are only known partially: some of their entries are either missing completely or replaced randomly by noisy values. In this work, assuming missing positions are replaced by noisy values, we examine how a connected network of agents, with each one of them subjected to a stream of data with incomplete regression information, can cooperate with each other through local interactions to estimate the underlying model parameters in the presence of missing data. We explain how to adjust the distributed diffusion through (de)regularization in order to eliminate the bias introduced by the incomplete model. We also propose a technique to recursively estimate the (de)regularization parameter and examine the performance of the resulting strategy. We illustrate the results by considering two applications: one dealing with a mental health survey and the other dealing with a household consumption survey.
description: To appear in IEEE Transactions on Signal and Information Processing Over Networks
title: Hafnium oxide-based dielectrics by atomic layer deposition
Creators: name: King, Peter
Publisher: name: University of Liverpool Repository
Year: 2013

description: In 2007 there was an important change in the architecture of nanotransistors - the building blocks of modern logic and memory devices. This change was from utilising thermally grown silicon dioxide as a dielectric to so-called high-_ hafnium oxide dielectrics grown by atomic layer deposition. The _rst production logic devices of this era used a hafnium oxide dielectric layer deposited by thermal atomic layer deposition; using HfCl4 and H2O as the precursors. Present day fabrication makes use of hafnium oxide-based atomic-layer-deposited dielectric _lms. The latest nanotransistor devices utilise a third generation hafnium oxide-based dielectric material. This thesis examines hafnium oxide-based thin _lm dielectric materials prepared by thermal atomic layer deposition on silicon substrates. Speci_cally the enhancement of the dielectric response of hafnium oxide by the addition of other elements is examined. Two ternary materials systems were deposited by thermal atomic layer deposition and analysed: titanium-hafnium oxide and cerium-hafnium oxide. Hafnium oxide _lms were deposited to be used as measurement benchmarks. Cerium oxide _lms were also deposited and analysed in their own right as potential dielectric layers. The hafnium oxide and both ternary deposition experiments used (MeCp)2Hf(OMe)(Me) as the hafnium precursor. The titanium-hafnium oxide growth used Ti(iOPr)4 as a titanium source and the cerium oxide and cerium-hafnium oxide work utilised Ce(mmp)4 as a cerium source. Post-deposition specimen sets consisted of an as-deposited sample, a sample spike-annealed in N2 at 850 _C and a sample annealed for 30 minutes at 500 _C. These annealing regimes were performed to mimic typical gate-_rst and gate-last transistor processing steps. The compositions and thicknesses of the _lms were measured using medium energy ion scattering. The structure of the _lms was analysed by X-ray di_raction and Raman spectroscopy. Capacitance-voltage and current density- _eld measurements were taken from fabricated MOS capacitor specimens to assess the dielectric response of the _lms. X-ray di_raction and Raman measurements showed that un-doped HfO2 had monoclinic crystallinity as-deposited and after the two annealing regimes. The dielectric constant and leakage current density, 17 and 1.7_10