cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Methods for protein complex prediction and their contributions towards understanding the organization, function and dynamics of complexes
Creators: name: Srihari, Sriganesh
name: Yong, Chern Han
name: Patil, Ashwini
name: Wong, Limsoon
Publisher: name: arXiv
Year: 2015
Subjects: subject: Molecular Networks (q-bio.MN)
subject: FOS: Biological sciences
subject: 68

description: Complexes of physically interacting proteins constitute fundamental functional units responsible for driving biological processes within cells. A faithful reconstruction of the entire set of complexes is therefore essential to understand the functional organization of cells. In this review, we discuss the key contributions of computational methods developed till date (approximately between 2003 and 2015) for identifying complexes from the network of interacting proteins (PPI network). We evaluate in depth the performance of these methods on PPI datasets from yeast, and highlight challenges faced by these methods, in particular detection of sparse and small or sub- complexes and discerning of overlapping complexes. We describe methods for integrating diverse information including expression profiles and 3D structures of proteins with PPI networks to understand the dynamics of complex formation, for instance, of time-based assembly of complex subunits and formation of fuzzy complexes from intrinsically disordered proteins. Finally, we discuss methods for identifying dysfunctional complexes in human diseases, an application that is proving invaluable to understand disease mechanisms and to discover novel therapeutic targets. We hope this review aptly commemorates a decade of research on computational prediction of complexes and constitutes a valuable reference for further advancements in this exciting area.
description: 1 Table
Determination of protein-DNA binding constants and specificities from statistical analyses of single molecules: MutS-DNA interactions
Creators: name: Hsieh, Peggy
name: Erie, Dorothy A.
name: Du, Chunwei
name: Sass, Lauryn E.
name: Yang, Yong
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Atomic force microscopy (AFM) is a powerful technique for examining the conformations of protein–DNA complexes and determining the stoichiometries and affinities of protein–protein complexes. We extend the capabilities of AFM to the determination of protein–DNA binding constants and specificities. The distribution of positions of the protein on the DNA fragments provides a direct measure of specificity and requires no knowledge of the absolute binding constants. The fractional occupancies of the protein at a given position in conjunction with the protein and DNA concentrations permit the determination of the absolute binding constants. We present the theoretical basis for this analysis and demonstrate its utility by characterizing the interaction of MutS with DNA fragments containing either no mismatch or a single mismatch. We show that MutS has significantly higher specificities for mismatches than was previously suggested from bulk studies and that the apparent low specificities are the result of high affinity binding to DNA ends. These results resolve the puzzle of the apparent low binding specificity of MutS with the expected high repair specificities. In conclusion, from a single set of AFM experiments, it is possible to determine the binding affinity, specificity and stoichiometry, as well as the conformational properties of the protein–DNA complexes.
Pair of associated Schouten-van Kampen connections adapted to an almost contact B-metric structure
Creators: name: Manev, Mancho
Publisher: name: arXiv
Year: 2015
Subjects: subject: Differential Geometry (math.DG)
subject: FOS: Mathematics
subject: Primary 53C25, Secondary 53C07, 53C50, 53D15

description: There are introduced and studied a pair of associated Schouten-van Kampen affine connections adapted to the contact distribution and an almost contact B-metric structure generated by the pair of associated B-metrics and their Levi-Civita connections. By means of the constructed non-symmetric connections, the basic classes of almost contact B-metric manifolds are characterized. Curvature properties of the considered connections are obtained.
description: 12 pages
Faster quantitative real-time PCR protocols may lose sensitivity and show increased variability
Creators: name: Vahrson, Wolfgang
name: Hilscher, Chelsey
name: Dittmer, Dirk P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Quantitative real-time PCR has become the method of choice for measuring mRNA transcription. Recently, fast PCR protocols have been developed as a means to increase assay throughput. Yet it is unclear whether more rapid cycling conditions preserve the original assay performance characteristics. We compared 16 primer sets directed against Epstein–Barr virus (EBV) mRNAs using universal and fast PCR cycling conditions. These primers are of clinical relevance, since they can be used to monitor viral oncogene and drug-resistance gene expression in transplant patients and EBV-associated cancers. While none of the primers failed under fast PCR conditions, the fast PCR protocols performed worse than universal cycling conditions. Fast PCR was associated with a loss of sensitivity as well as higher variability, but not with a loss of specificity or with a higher false positive rate.
(400003) John Lindsay Adamson
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
N-methylpurine DNA glycosylase overexpression increases alkylation sensitivity by rapidly removing non-toxic 7-methylguanine adducts
Creators: name: Kelley, M. R.
name: Pachkowski, B. F.
name: Nakamura, J.
name: He, Y.
name: Rinne, M. L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Previous studies indicate that overexpression of N-methylpurine DNA glycosylase (MPG) dramatically sensitizes cells to alkylating agent-induced cytotoxicity. We recently demonstrated that this sensitivity is preceded by an increased production of AP sites and strand breaks, confirming that overexpression of MPG disrupts normal base excision repair and causes cell death through overproduction of toxic repair intermediates. Here we establish through site-directed mutagenesis that MPG-induced sensitivity to alkylation is dependent on enzyme glycosylase activity. However, in contrast to the sensitivity seen to heterogeneous alkylating agents, MPG overexpression generates no cellular sensitivity to MeOSO2(CH2)2-lexitropsin, an alkylator which exclusively induces 3-meA lesions. Indeed, MPG overexpression has been shown to increase the toxicity of alkylating agents that produce 7-meG adducts, and here we demonstrate that MPG-overexpressing cells have dramatically increased removal of 7-meG from their DNA. These data suggest that the mechanism of MPG-induced cytotoxicity involves the conversion of non-toxic 7-meG lesions into highly toxic repair intermediates. This study establishes a mechanism by which a benign DNA modification can be made toxic through the overexpression of an otherwise well-tolerated gene product, and the application of this principle could lead to improved chemotherapeutic strategies that reduce the peripheral toxicity of alkylating agents.
Persistent chimera states in nonlocally coupled phase oscillators
Creators: name: Suda, Yusuke
name: Okuda, Koji
Publisher: name: arXiv
Year: 2015
Subjects: subject: Adaptation and Self-Organizing Systems (nlin.AO)
subject: FOS: Physical sciences

description: Chimera states in the systems of nonlocally coupled phase oscillators are considered stable in the continuous limit of spatially distributed oscillators. However, it is reported that in the numerical simulations without taking such limit, chimera states are chaotic transient and finally collapse into the completely synchronous solution. In this paper, we numerically study chimera states by using the coupling function different from the previous studies and obtain the result that chimera states can be stable even without taking the continuous limit, which we call the persistent chimera state.
description: To be published in Physical Review E (Rapid Communication), 5 pages, 7 figures
Additional file 1 of Do education and living standard matter in breaking barriers to healthcare access among women in Bangladesh?
Creators: name: Sen, Kanchan Kumar
name: Nilima, Shahnaz
name: Zahura, Fatima-Tuz
name: Bari, Wasimul
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
classificationCode: 59999
subject: Environmental Sciences not elsewhere classified
classificationCode: 19999
subject: Mathematical Sciences not elsewhere classified
subject: Science Policy
classificationCode: 110309
subject: Infectious Diseases
subject: FOS: Health sciences

description: Supplementary Material 1
Appendix from Kinetics of surface growth with coupled diffusion and the emergence of a universal growth path.
Creators: name: Abi-Akl, Rami
name: Abeyaratne, Rohan
name: Cohen, Tal
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Mechanical Engineering
subject: FOS: Mechanical engineering
subject: 10599 Mathematical Physics not elsewhere classified
subject: FOS: Mathematics
subject: 19999 Mathematical Sciences not elsewhere classified

description: Appendix
The observation of photon echoes from evanescently coupled rare-earth ions in a planar waveguide
Creators: name: Marzban, Sara
name: Bartholomew, John G.
name: Madden, Stephen
name: Vu, Khu
name: Sellars, Matthew J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We report the measurement of the inhomogeneous linewidth, homogeneous linewidth and spin state lifetime of Pr3+ ions in a novel waveguide architecture. The TeO2 slab waveguide deposited on a bulk Pr3+:Y2SiO5 crystal allows the 3H4 - 1D2 transition of Pr3+ ions to be probed by the optical evanescent field that extends into the substrate. The 2 GHz inhomogeneous linewidth, the optical coherence time of 70 +- 5 us, and the spin state lifetime of 9.8 +- 0.3 s indicate that the properties of ions interacting with the waveguide mode are consistent with those of bulk ions. This result establishes the foundation for large, integrated and high performance rare-earth-ion quantum systems based on a waveguide platform.
description: 5 pages, 5 figures
Fallimento e arbitrato rituale. Profili di interrelazione e autonomia tra i due procedimenti
Creators: name: Baccaglini, Laura
Publisher: name: Universit� degli Studi di Trento
Year: 2018

description: Il libro indaga i rapporti tra fallimento e arbitrato rituale ed affronta il problema se, quando e come un giudizio arbitrale possa iniziare o proseguire nonostante l?apertura di una procedura di insolvenza a carico di una delle parti, quali effetti possano riconoscersi al lodo pronunciato prima dell?apertura del fallimento. Le riforme che negli ultimi lustri hanno interessato, a livello nazionale, sia il fallimento sia l?arbitrato, e la disciplina contenuta nel Reg. europeo n. 848/2015 in materia d?insolvenza transfrontaliera, rendono opportuna una rinnovata riflessione in argomento. Il tema � tutt?ora assai dibattuto, complice anche la mancanza di un intervento chiarificatore del legislatore (n� tale pu� considerarsi l?introduzione di una norma settoriale ed ambigua qual � l?art. 83-bis legge fall.). Numerose e rilevanti, sul piano dogmatico e pratico-applicativo, sono le questioni trattate nel presente lavoro: quando il curatore possa considerarsi vincolato alla convenzione arbitrale conclusa dal fallito, in bonis; come il contraddittorio debba essere ripristinato con il curatore quando il fallimento intervenga a giudizio arbitrale pendente; quando un lodo, pronunciato prima della dichiarazione di fallimento, possa considerarsi opponibile alla massa.
The amplification of risk in experimental diffusion chains
Creators: name: Moussaid, Mehdi
name: Brighton, Henry
name: Gaissmaier, Wolfgang
Publisher: name: arXiv
Year: 2015
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Social and Information Networks (cs.SI)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: Understanding how people form and revise their perception of risk is central to designing efficient risk communication methods, eliciting risk awareness, and avoiding unnecessary anxiety among the public. However, public responses to hazardous events such as climate change, contagious outbreaks, and terrorist threats are complex and difficult-to-anticipate phenomena. Although many psychological factors influencing risk perception have been identified in the past, it remains unclear how perceptions of risk change when propagated from one person to another and what impact the repeated social transmission of perceived risk has at the population scale. Here, we study the social dynamics of risk perception by analyzing how messages detailing the benefits and harms of a controversial antibacterial agent undergo change when passed from one person to the next in 10-subject experimental diffusion chains. Our analyses show that when messages are propagated through the diffusion chains, they tend to become shorter, gradually inaccurate, and increasingly dissimilar between chains. In contrast, the perception of risk is propagated with higher fidelity due to participants manipulating messages to fit their preconceptions, thereby influencing the judgments of subsequent participants. Computer simulations implementing this simple influence mechanism show that small judgment biases tend to become more extreme, even when the injected message contradicts preconceived risk judgments. Our results provide quantitative insights into the social amplification of risk perception, and can help policy makers better anticipate and manage the public response to emerging threats.
description: Published online in PNAS Early Edition (open-access): http://www.pnas.org/content/early/2015/04/14/1421883112
(400005) William Adamson
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
(400006) Thomas Adamson
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Pyrimido[1,2-a]-purin-10(3H)-one, M1G, is less prone to artifact than base oxidation
Creators: name: Upton, Patricia B.
name: Jeong, Yo Chan
name: Swenberg, James A.
name: Nakamura, Jun
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Pyrimido[1,2-a]-purin-10(3H)-one (M1G) is a secondary DNA damage product arising from primary reactive oxygen species (ROS) damage to membrane lipids or deoxyribose. The present study investigated conditions that might lead to artifactual formation or loss of M1G during DNA isolation. The addition of antioxidants, DNA isolation at low temperature or non-phenol extraction methods had no statistically significant effect on the number of M1G adducts measured in either control or positive control tissue samples. The number of M1G adducts in nuclear DNA isolated from brain, liver, kidney, pancreas, lung and heart of control male rats were 0.8, 1.1, 1.1, 1.1, 1.8 and 4.2 M1G/108 nt, respectively. In rat liver tissue, the mitochondrial DNA contained a 2-fold greater number of M1G adducts compared with nuclear DNA. Overall, the results from this study demonstrated that measuring M1G is a reliable way to assess oxidative DNA damage because the number of M1G adducts is significantly affected by the amount of ROS production, but not by DNA isolation procedures. In addition, this study confirmed that the background number of M1G adducts reported in genomic DNA could have been overestimated by one to three orders of magnitude in previous reports.
Dressed scalar propagator in a non-abelian background from the worldline formalism
Creators: name: Ahmadiniaz, Naser
name: Bastianelli, Fiorenzo
name: Corradini, Olindo
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We study the propagator of a colored scalar particle in the background of a non-abelian gauge field using the worldline formalism. It is obtained by considering the open worldline of a scalar particle with extra degrees of freedom needed to take into account the color charge of the particle, which we choose to be in the fundamental representation of the gauge group. Specializing the external gauge field to be given by a sum of plane waves, i.e. a sum of external gluons, we produce a master formula for the scalar propagator with an arbitrary number of gluons directly attached to the scalar line, akin to similar formulas derived in the literature for the case of the scalar particle performing a loop. Our worldline description produces at the same time the situation in which the particle has a color charge given by an arbitrarily chosen symmetric or antisymmetric tensor product of the fundamental.
description: 21 pages, 1 figure; title modified, discussion improved, references added, main results unchanged. Matches version published in PRD
Additional file 1 of Knowledge, attitude, and intended practice of abortion among pharmacy students in Thailand after the amendment of the Thai Abortion Law
Creators: name: Rongkapich, Ratthapong
name: Poolkumlung, Rada
name: Sinthuchai, Natchanika
name: Limsirorat, Phobsan
name: Chiemchaisri, Nattaporn
name: Santibenchakul, Somsook
name: Jaisamrarn, Unnop
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Science Policy

description: Supplementary Material 1
Appendix from Kinetics of surface growth with coupled diffusion and the emergence of a universal growth path
Creators: name: Abi-Akl, Rami
name: Abeyaratne, Rohan
name: Cohen, Tal
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Mechanical Engineering
subject: FOS: Mechanical engineering
subject: 10599 Mathematical Physics not elsewhere classified
subject: FOS: Mathematics
subject: 19999 Mathematical Sciences not elsewhere classified

description: Appendix
(400002) Alice Lindsay Adamson
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Role of the N- and C-terminal extensions on the activity of mammalian mitochondrial translational initiation factor 3
Creators: name: Bhargava, Kalpana
name: Spremulli, Linda L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Mammalian mitochondrial translational initiation factor 3 (IF3mt) promotes initiation complex formation on mitochondrial 55S ribosomes in the presence of IF2mt, fMet-tRNA and poly(A,U,G). The mature form of IF3mt is predicted to be 247 residues. Alignment of IF3mt with bacterial IF3 indicates that it has a central region with 20–30% identity to the bacterial factors. Both the N- and C-termini of IF3mt have extensions of ∼30 residues compared with bacterial IF3. To examine the role of the extensions on IF3mt, deletion constructs were prepared in which the N-terminal extension, the C-terminal extension or both extensions were deleted. These truncated derivatives were slightly more active in promoting initiation complex formation than the mature form of IF3mt. Mitochondrial 28S subunits have the ability to bind fMet-tRNA in the absence of mRNA. IF3mt promotes the dissociation of the fMet-tRNA bound in the absence of mRNA. This activity of IF3mt requires the C-terminal extension of this factor. Mitochondrial 28S subunits also bind mRNA independently of fMet-tRNA or added initiation factors. IF3mt has no effect on the formation of these complexes and cannot dissociate them once formed. These observations have lead to a new model for the function of IF3mt in mitochondrial translational initiation.
Additional file 2 of Knowledge, attitude, and intended practice of abortion among pharmacy students in Thailand after the amendment of the Thai Abortion Law
Creators: name: Rongkapich, Ratthapong
name: Poolkumlung, Rada
name: Sinthuchai, Natchanika
name: Limsirorat, Phobsan
name: Chiemchaisri, Nattaporn
name: Santibenchakul, Somsook
name: Jaisamrarn, Unnop
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Science Policy

description: Supplementary Material 2
SU(N) Heisenberg model with multi-column representations
Creators: name: Okubo, Tsuyoshi
name: Harada, Kenji
name: Lou, Jie
name: Kawashima, Naoki
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: The $\mathrm{SU}(N)$ symmetric antiferromagnetic Heisenberg model with multi-column representations on the two-dimensional square lattice is investigated by quantum Monte Carlo simulations. For the representation of Young diagram with two columns, we confirm that a valence-bond solid order appears as soon as the Néel order disappears at $N = 10$ indicating no intermediate phase. In the case of the representation with three columns, there is no evidence for both of the Néel and the valence-bond solid ordering for $N\ge 15$. This is actually consistent with the large-$N$ theory, which predicts that the VBS state immediately follows the Néel state, because the expected spontaneous order is too weak to be detected.
description: 5 pages, 5 figures
Copyright as Monopoly: the Italian Fire under the Ashes
Creators: name: Caso, Roberto
name: Dore, Giulia
Publisher: name: Universit� degli studi di Trento
Year: 2016

description: This essay provides an overview of some research that is in its early stages. The principal purpose of the authors is to understand whether, in a Continental European legal system such as the Italian one ? traditionally led by a strong historical and normative vision of copyright (or author?s right) as natural right and nowadays influenced by the EU propertization trend ? it is yet possible to foresee a different approach that is prone to interpreting the exclusivity of copyright in terms of monopoly. The latter approach, to some extent, might in fact be more relevant to restricting copyright protection by limiting the exclusive rights (ius excludendi alios) while supporting the public interest. Besides, the vision of ?copyright as monopoly? seems in particular to play an overriding role within the digital context, where property is less apt in terms of the promotion and sharing of knowledge and, on the contrary, monopolistic jeopardy is sensibly flourishing.
Il fascino discreto degli indicatori: quale impatto sull?Universit�? = The discreet charm of the indicators: which impact on the University?
Creators: name: Pascuzzi, Giovanni
Publisher: name: Universit� degli studi di Trento. Facolt� di giurisprudenza
Year: 2017

description: In the last years Italian Universities were attracted by the logic of the indicators.I list the indicators today used to assess the Italian Universities. Then I show the consequences of the massive use of the indicators.
La parola mitigata: usi reticenti, Spie linguistiche del 'non dire'
Creators: name: Dallabrida, Sara
Publisher: name: Universit� degli Studi di Trento - Dipartimento di Lettere e Filosofia
Year: 2016

description: Il contributo � centrato su alcune strategie mitigatorie, grazie alle quali � possibile attenuare un atto linguistico allo scopo di preservare la faccia del parlante ed evitare potenziali conflitti interazionali. Attraverso una serie di esempi, estrapolati da contesti diversi e contrassegnati dalla volont� di non dire, o comunque di dire il meno possibile, sono analizzate come forme di non detto strategico alcune mosse retorico-linguistiche che rendono vago il contenuto di un determinato enunciato e oscurano l?impegno personale rispetto a ci� che viene detto.
(400004) Isabella Lindsay Adamson
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Mathematical analyses and supplementary figures from The social evolution of sleep: sex differences, intragenomic conflicts and clinical pathologies.
Creators: name: Faria, Gonçalo S.
name: Varela, Susana A. M.
name: Gardner, Andy
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: 60801 Animal Behaviour
subject: 10202 Biological Mathematics
subject: FOS: Mathematics

description: In this file, you can find the mathematical analyses of the work and its supplementary figures.
La repressione dei crimini internazionali tra diritto di autodeterminazione dei popoli e affermazione della statualit�. / Die Repression der internationalen Verbrechen zwischen dem Recht auf Selbstbestimmung der V�lker und der Behauptung der Staatlichkeit.
Creators: name: Nesi, Giuseppe
Publisher: name: Universit� di Trento. Facolt� di Giurisprudenza
Year: 2015

description: Oggetto dello scritto � il rapporto tra repressione dei crimini internazionali, creazione di uno Stato e principio di autodeterminazione dei popoli. In primo luogo, si esamina l?impatto della giustizia penale internazionale rispetto allo Stato e a entit� che aspirano a essere riconosciute come Stati, e come la posizione da questi assunta rispetto alla giustizia penale internazionale possa rafforzare o indebolire situazioni territoriali incerte o poco definite. Sono poi esaminate le posizioni di quegli Stati che criticano la giustizia penale internazionale poich� essa avrebbe conseguenze negative, tra l?altro, sul diritto all?autodeterminazione. A tal proposito lo scritto si sofferma in particolare sulle modalit� di attivazione della Corte penale internazionale in Africa per comprendere meglio come si � configurato (o come � stato percepito) in quel contesto geografico il rapporto tra autodeterminazione dei popoli e giustizia penale internazionale. The work centers on the repression of international crimes, the creation of States and the principle of self-determination. Firstly, the impact of international criminal justice on the process of creation of States and entities willing to become States is analyzed; their attitude has repercussions on the strengthening or weakening of uncertain or undefined territorial situations. Furthermore, the position of States that criticize international criminal justice because it would have negative consequences on the principle of self-determination is also examined. In this regard, the article focuses on the trigger mechanisms of the International Criminal Court in Africa in order to understand how the relationship between international criminal justice and self-determination is shaped (or has been perceived) in that area.
A specific loop in human DNA polymerase mu allows switching between creative and DNA-instructed synthesis
Creators: name: Blanco, Luis
name: McElhinny, Stephanie A.Nick
name: Ramsden, Dale
name: Juárez, Raquel
name: Ruiz, José F.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Human DNA polymerase mu (Polμ) is a family X member that has terminal transferase activity but, in spite of a non-orthodox selection of the template information, displays its maximal catalytic efficiency in DNA-templated reactions. As terminal deoxynucleotidyl transferase (TdT), Polμ has a specific loop (loop1) that could provide this enzyme with its terminal transferase activity. When loop1 was deleted, human Polμ lacked TdT activity but improved DNA-binding and DNA template-dependent polymerization. Interestingly, when loop1 from TdT was inserted in Polμ (substituting its cognate loop1), the resulting chimaera displayed TdT activity, preferentially inserting dGTP residues, but had a strongly reduced template-dependent polymerization activity. Therefore, a specialized loop in Polμ, that could adopt alternative conformations, appears to provide this enzyme with a dual capacity: (i) template independency to create new DNA information, in which loop1 would have an active role by acting as a ‘pseudotemplate’; (ii) template-dependent polymerization, in which loop1 must allow binding of the template strand. Recent in vivo and in vitro data suggest that such a dual capacity could be advantageous to resolve microhomology-mediated end-joining reactions.
A Simple Method for Finding the Scattering Coefficients of Quantum Graphs
Creators: name: Cottrell, Seth S.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantum walks are roughly analogous to classical random walks, and like classical walks they have been used to find new (quantum) algorithms. When studying the behavior of large graphs or combinations of graphs it is useful to find the response of a subgraph to signals of different frequencies. In so doing we can replace an entire subgraph with a single vertex with frequency dependent scattering coefficients. In this paper a simple technique for quickly finding the scattering coefficients of any quantum graph will be presented. These scattering coefficients can be expressed entirely in terms of the characteristic polynomial of the graph's time step operator. Moreover, with these in hand we can easily derive the "impulse response" which is the key to predicting the response of a graph to any signal. This gives us a powerful set of tools for rapidly understanding the behavior of graphs or for reducing a large graph into its constituent subgraphs regardless of how they are connected.
description: 43 pages. 10 figures. Presented at the APS March Meeting 2015
Matson, S. W. & Robertson, A. B. The UvrD helicase and its modulation by the mismatch repair protein MutL. Nucleic Acids Res. 34, 4089-4097
Creators: name: Robertson, Adam B.
name: Matson, Steven W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: UvrD is a superfamily I DNA helicase with well documented roles in excision repair and methyl-directed mismatch repair (MMR) in addition to poorly understood roles in replication and recombination. The MutL protein is a homodimeric DNA-stimulated ATPase that plays a central role in MMR in
Geomorphological characterisation and Spectroscopy analysis of the Gusev and Jezero craters on Mars: Landing sites of NASA's Mars exploration missions.
Creators: name: Anangonó-Tutasig, Ronny Steveen
name: Fernández Menéndez, Susana
name: Diez Alonso, Enrique
name: De Cos Juez, Francisco Javier
Publisher: name: Zenodo
Year: 2022
Subjects: Mars
Crater
Mapping
Gusev
Jezero
Geomorphological

description: Gusev Crater, landing site of the MER-A mission, and Jezero Crater, site of the Mars2020 mission, were possibly two past fluvial-lacustrine systems, and have therefore been of great interest to understand the past of Mars. The study of terrestrial analogues is important to know the possible origin of these morphologies observed on Mars.
(4268) Archibald Sword Rodger
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Memoria della guerra: fonti scritte e orali al servizio della storia e della linguistica
Creators: name: Baggio, Serenella
Publisher: name: Universit� degli Studi di Trento
Year: 2016

description: Nel volume studiosi di varie discipline storiche (storia contemporanea, paleografia, etnomusicologia, storia della lingua italiana) si confrontano sul tema delle fonti della Grande Guerra indicando percorsi di ricerca innovativi, dal recupero della memoria indiretta con inchieste di storia orale all?esplorazione di corpora e archivi pubblici e privati ancora poco noti. Accanto alle testimonianze del vissuto di guerra l?eccezionalit� di quell?evento � testimoniata dallo sviluppo delle scienze sociali favorito dalla mobilit� di guerra e dalle strutture concentrazionarie; dobbiamo ad etno-antropologi e a dialettologi alla ricerca della psicologia dei popoli la possibilit� di sentire le voci registrate dei soldati che recitano e cantano e di leggere le loro lettere.
Phytome: a platform for plant comparative genomics
Creators: name: Hartmann, Stefanie
name: Phillips, Jason
name: Vision, Todd J.
name: Lu, Dihui
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Phytome is an online comparative genomics resource that can be applied to functional plant genomics, molecular breeding and evolutionary studies. It contains predicted protein sequences, protein family assignments, multiple sequence alignments, phylogenies and functional annotations for proteins from a large, phylogenetically diverse set of plant taxa. Phytome serves as a glue between disparate plant gene databases both by identifying the evolutionary relationships among orthologous and paralogous protein sequences from different species and by enabling cross-references between different versions of the same gene curated independently by different database groups. The web interface enables sophisticated queries on lineage-specific patterns of gene/protein family proliferation and loss. This rich dataset is serving as a platform for the unification of sequence-anchored comparative maps across taxonomic families of plants. The Phytome web interface can be accessed at the following URL: . Batch homology searches and bulk downloads are available upon free registration.
Orbital Arrangements and Magnetic Interactions in the Quasi-One-Dimensional Cuprates ACuMoO_4(OH) (A = Na, K)
Creators: name: Nawa, Kazuhiro
name: Yajima, Takeshi
name: Okamoto, Yoshihiko
name: Hiroi, Zenji
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: A new spin-1/2 quasi-one-dimensional antiferromagnet KCuMoO_4(OH) is prepared by the hydrothermal method. The crystal structures of KCuMoO_4(OH) and the already-known Na-analogue, NaCuMoO_4(OH), are isotypic, comprising chains of Cu^{2+} ions in edge-sharing CuO_4(OH)_2 octahedra. Despite the structural similarity, their magnetic properties are quite different because of the different arrangements of d_{x2-y2} orbitals carrying spins. For NaCuMoO_4(OH), d_{x2-y2} orbitals are linked by superexchange couplings via two bridging oxide ions, which gives a ferromagnetic nearest-neighbor interaction J_1 of -51 K and an antiferromagnetic next-nearest-neighbor interaction J_2 of 36 K in the chain. In contrast, a staggered d_{x2-y2} orbital arrangement in KCuMoO_4(OH) results in superexchange couplings via only one bridging oxide ion, which makes J_1 antiferromagnetic as large as 238 K and J_2 negligible. This comparison between the two isotypic compounds demonstrates an important role of orbital arrangements in determining the magnetic properties of cuprates.
description: 7 pages, 5 figures published to Inorg. Chem. (2015)
Replication fork regression in repetitive DNAs
Creators: name: Roy, Debasmita
name: Griffith, Jack D.
name: Fouché, Nicole
name: Özgür, Sezgin
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Among several different types of repetitive sequences found in the human genome, this study has examined the telomeric repeat, necessary for the protection of chromosome termini, and the disease-associated triplet repeat (CTG)·(CAG)n. Evidence suggests that replication of both types of repeats is problematic and that a contributing factor is the repetitive nature of the DNA itself. Here we have used electron microscopy to investigate DNA structures formed at replication forks on large model DNAs containing these repeat sequences, in an attempt to elucidate the contributory effect that these repetitive DNAs may have on their replication. Visualization of the DNA revealed that there is a high propensity for a paused replication fork to spontaneously regress when moving through repetitive DNAs, and that this results in a four-way chickenfoot intermediate that could present a significant block to replication in vivo, possibly leading to unwanted recombination events, amplifications or deletions.
(400000) John Lindsay Adamson
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Additional file 3 of Knowledge, attitude, and intended practice of abortion among pharmacy students in Thailand after the amendment of the Thai Abortion Law
Creators: name: Rongkapich, Ratthapong
name: Poolkumlung, Rada
name: Sinthuchai, Natchanika
name: Limsirorat, Phobsan
name: Chiemchaisri, Nattaporn
name: Santibenchakul, Somsook
name: Jaisamrarn, Unnop
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Science Policy

description: Supplementary Material 3
Mathematical analyses and supplementary figures from The social evolution of sleep: sex differences, intragenomic conflicts and clinical pathologies
Creators: name: Faria, Gonçalo S.
name: Varela, Susana A. M.
name: Gardner, Andy
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: 60801 Animal Behaviour
subject: 10202 Biological Mathematics
subject: FOS: Mathematics

description: In this file, you can find the mathematical analyses of the work and its supplementary figures.
(400001) Ann Lees
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
RosettaDesign server for protein design
Creators: name: Kuhlman, Brian
name: Liu, Yi
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: The RosettaDesign server identifies low energy amino acid sequences for target protein structures (). The client provides the backbone coordinates of the target structure and specifies which residues to design. The server returns to the client the sequences, coordinates and energies of the designed proteins. The simulations are performed using the design module of the Rosetta program (RosettaDesign). RosettaDesign uses Monte Carlo optimization with simulated annealing to search for amino acids that pack well on the target structure and satisfy hydrogen bonding potential. RosettaDesign has been experimentally validated and has been used previously to stabilize naturally occurring proteins and design a novel protein structure.
Quantum theory as a description of robust experiments: derivation of the Pauli equation
Creators: name: De Raedt, Hans
name: Katsnelson, Mikhail I.
name: Donker, Hylke C.
name: Michielsen, Kristel
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: It is shown that the Pauli equation and the concept of spin naturally emerge from logical inference applied to experiments on a charged particle under the conditions that (i) space is homogeneous (ii) the observed events are logically independent, and (iii) the observed frequency distributions are robust with respect to small changes in the conditions under which the experiment is carried out. The derivation does not take recourse to concepts of quantum theory and is based on the same principles which have already been shown to lead to e.g. the Schrödinger equation and the probability distributions of pairs of particles in the singlet or triplet state. Application to Stern-Gerlach experiments with chargeless, magnetic particles, provides additional support for the thesis that quantum theory follows from logical inference applied to a well-defined class of experiments.
description: Accepted for publication in Ann. Phys. arXiv admin note: text overlap with arXiv:1303.4574
Inhibition of MDR1 expression with altritol-modified siRNAs
Creators: name: Van Aerschot, Arthur
name: Juliano, Rudolph L.
name: Fisher, Michael
name: Xu, Dong
name: Abramov, Mikhail
name: Herdewijn, Piet
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: Altritol-modified nucleic acids (ANAs) support RNA-like A-form structures when included in oligonucleotide duplexes. Thus altritol residues seem suitable as candidates for the chemical modification of siRNAs. Here we report that ANA-modified siRNAs targeting the MDR1 gene can exhibit improved efficacy as compared to unmodified controls. This was particularly true of ANA modifications at or near the 3′ end of the sense or antisense strands, while modification at the 5′ end of the antisense strand resulted in complete loss of activity. Multiple ANA modifications within the sense strand were also well tolerated. Duplexes with ANA modifications at appropriate positions in both strands were generally more effective than duplexes with one modified and one unmodified strand. Initial evidence suggests that the loss of activity associated with ANA modification of the 5′-antisense strand may be due to reduced phosphorylation at this site by cellular kinases. Treatment of drug resistant cells with MDR1-targeted siRNAs resulted in reduction of P-glycoprotein (Pgp) expression, parallel reduction in MDR1 message levels, increased accumulation of the Pgp substrate rhodamine 123, and reduced resistance to anti-tumor drugs. Interestingly, the duration of action of some of the ANA-modified siRNAs was substantially greater than that of unmodified controls. These observations suggest that altritol modifications may be helpful in developing siRNAs with enhanced pharmacological effectiveness.
Le parole dopo la morte. Forme e funzioni della retorica funeraria nella tradizione greca e romana
Creators: name: Pepe, Cristina
name: Moretti, Gabriella
Publisher: name: Universit� degli studi di Trento. Dipartimento di Lettere e Filosofia
Year: 2015

description: Fin dall?Antichit�, alla parola � stato assegnato il compito di accompagnare il delicato e cruciale momento della morte. Il presente volume, che raccoglie gli Atti del Convegno Internazionale Le parole dopo la morte: forme e funzioni della retorica funeraria nella tradizione greca e romana, propone una riflessione sulle espressioni verbali che nel mondo antico erano legate al lutto e ai suoi riti e, in particolare, su quelle forme che conobbero un?esplicita codificazione in ambito retorico-letterario: dal threnos all?epigramma, dall?orazione funebre alla consolatio. L?approccio proposto punta l?attenzione non solo sugli aspetti caratteristici e distintivi di ciascuna di queste forme, ma anche, in una prospettiva pi� ampia, sulle tendenze e le funzioni che le accomunano nella loro natura di ?parole dopo la morte?.