cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Abnormal Type I Collagen Post-translational Modification and Crosslinking in a Cyclophilin B KO Mouse Model of Recessive Osteogenesis Imperfecta
Creators: name: Yamauchi, Mitsuo
name: Weis, MaryAnn
name: Kozloff, Kenneth M.
name: Perosky, Joseph E.
name: Perdivara, Irina
name: Eyre, David R.
name: Cabral, Wayne A.
name: Chang, Weizhong
name: Tomer, Kenneth B.
name: Marini, Joan C.
name: Terajima, Masahiko
name: Leikin, Sergey
name: Makareeva, Elena N.
name: Blissett, Angela R.
name: Mertz, Edward L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Cyclophilin B (CyPB), encoded by PPIB, is an ER-resident peptidyl-prolyl cis-trans isomerase (PPIase) that functions independently and as a component of the collagen prolyl 3-hydroxylation complex. CyPB is proposed to be the major PPIase catalyzing the rate-limiting step in collagen folding. Mutations in PPIB cause recessively inherited osteogenesis imperfecta type IX, a moderately severe to lethal bone dysplasia. To investigate the role of CyPB in collagen folding and post-translational modifications, we generated Ppib−/− mice that recapitulate the OI phenotype. Knock-out (KO) mice are small, with reduced femoral areal bone mineral density (aBMD), bone volume per total volume (BV/TV) and mechanical properties, as well as increased femoral brittleness. Ppib transcripts are absent in skin, fibroblasts, femora and calvarial osteoblasts, and CyPB is absent from KO osteoblasts and fibroblasts on western blots. Only residual (2–11%) collagen prolyl 3-hydroxylation is detectable in KO cells and tissues. Collagen folds more slowly in the absence of CyPB, supporting its rate-limiting role in folding. However, treatment of KO cells with cyclosporine A causes further delay in folding, indicating the potential existence of another collagen PPIase. We confirmed and extended the reported role of CyPB in supporting collagen lysyl hydroxylase (LH1) activity. Ppib−/− fibroblast and osteoblast collagen has normal total lysyl hydroxylation, while increased collagen diglycosylation is observed. Liquid chromatography/mass spectrometry (LC/MS) analysis of bone and osteoblast type I collagen revealed site-specific alterations of helical lysine hydroxylation, in particular, significantly reduced hydroxylation of helical crosslinking residue K87. Consequently, underhydroxylated forms of di- and trivalent crosslinks are strikingly increased in KO bone, leading to increased total crosslinks and decreased helical hydroxylysine- to lysine-derived crosslink ratios. The altered crosslink pattern was associated with decreased collagen deposition into matrix in culture, altered fibril structure in tissue, and reduced bone strength. These studies demonstrate novel consequences of the indirect regulatory effect of CyPB on collagen hydroxylation, impacting collagen glycosylation, crosslinking and fibrillogenesis, which contribute to maintaining bone mechanical properties.
D 8.1 – Plan for Communication actions
Creators: name: Severgnini, Michela
name: Grassi, Stefano Fabrizio
name: Oleari, Elettra
Publisher: name: Zenodo
Year: 2018
Subjects: communication
dissemination
plan
stakeholder
strategy
action plan

description: This document is primarily addressed to the project partners, and it is instrumental in Task 8.1 “Plan for Communication actions” and 8.2 “Plan for Exploitation and dissemination”. Its structure is the following: SARAS identity definition and templates creation Market and Stakeholder analysis and definition Communication & Dissemination strategy Action plan
Heterogeneous Mean Field for neural networks with short term plasticity
Creators: name: di Volo, Matteo
name: Burioni, Raffaella
name: Casartelli, Mario
name: Livi, Roberto
name: Vezzani, Alessandro
Publisher: name: arXiv
Year: 2014
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: We report about the main dynamical features of a model of leaky-integrate-and fire excitatory neurons with short term plasticity defined on random massive networks. We investigate the dynamics by a Heterogeneous Mean-Field formulation of the model, that is able to reproduce dynamical phases characterized by the presence of quasi-synchronous events. This formulation allows one to solve also the inverse problem of reconstructing the in-degree distribution for different network topologies from the knowledge of the global activity field. We study the robustness of this inversion procedure, by providing numerical evidence that the in-degree distribution can be recovered also in the presence of noise and disorder in the external currents. Finally, we discuss the validity of the heterogeneous mean-field approach for sparse networks, with a sufficiently large average in-degree.
Lifting the learning curve: personal academic training in La Trobe University arts foundation subjects
Creators: name: Schurholz, Hannah
name: Midford, Sarah
name: Roemhild, Julianne
name: James, Sara
Publisher: name: La Trobe
Year: 2023

description: Annual Students,Transitions, Achievement, Retention and Success (STARS) Conference (1st : 2015 : Melbourne)
Applying the simplest Kochen-Specker set for quantum information processing
Creators: name: Cañas, Gustavo
name: Arias, Mauricio
name: Etcheverry, Sebastián
name: Gómez, Esteban S.
name: Cabello, Adán
name: Xavier, Guilherme B.
name: Lima, Gustavo
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Kochen-Specker (KS) sets are key tools for proving some fundamental results in quantum theory and also have potential applications in quantum information processing. However, so far, their intrinsic complexity has prevented experimentalists from using them for any application. The KS set requiring the smallest number of contexts has been recently found. Relying on this simple KS set, here we report an input state-independent experimental technique to certify whether a set of measurements is actually accessing a preestablished quantum six-dimensional space encoded in the transverse momentum of single photons.
description: REVTeX4, 5 pages, 5 figures
Compensated compactness: continuity in optimal weak topologies
Creators: name: Guerra, André
name: Raiţă, Bogdan
name: Schrecker, Matthew R. I.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Analysis of PDEs (math.AP)
subject: Functional Analysis (math.FA)
subject: FOS: Mathematics
subject: 49J45, 35E20, 42B30, 46E30

description: For $l$-homogeneous linear differential operators $\mathcal{A}$ of constant rank, we study the implication $v_j\rightharpoonup v$ in $X$ and $\mathcal{A} v_j\rightarrow \mathcal{A} v$ in $W^{-l}Y$ implies $F(v_j)\rightsquigarrow F(v)$ in $Z$, where $F$ is an $\mathcal{A}$-quasiaffine function and $\rightsquigarrow$ denotes an appropriate type of weak convergence. Here $Z$ is a local $L^1$-type space, either the space $\mathscr{M}$ of measures, or $L^1$, or the Hardy space $\mathscr{H}^1$; $X,\, Y$ are $L^p$-type spaces, by which we mean Lebesgue or Zygmund spaces. Our conditions for each choice of $X,\,Y,\,Z$ are sharp. Analogous statements are also given in the case when $F(v)$ is not a locally integrable function and it is instead defined as a distribution. In this case, we also prove $\mathscr{H}^p$-bounds for the sequence $(F(v_j))_j$, for appropriate $p<1$, and new convergence results in the dual of Hölder spaces when $(v_j)$ is $\mathcal{A}$-free and lies in a suitable negative order Sobolev space $W^{-β,s}$. The choice of these Hölder spaces is sharp, as is shown by the construction of explicit counterexamples. Some of these results are new even for distributional Jacobians.
description: 39 pages. New examples added to show optimality of Theorem D
Modeling Dynamic Component Interfaces
Creators: name: Huber, Franz
name: Rausch, Andreas
name: Rumpe, Bernhard
Publisher: name: arXiv
Year: 2014
Subjects: subject: Software Engineering (cs.SE)
subject: FOS: Computer and information sciences

description: We adopt a component model based on object-oriented systems, introducing the concepts of components and their structure. A component consists of a dynamically changing set of connected objects. Only some of these objects are interface objects, and are thus accessible from the environment. During the component lifetime not only the number of objects, but also that of interface objects, and their connections change. To describe this situation, we introduce component interface diagrams (CIDs)-an adaption of UML diagrams-as a notation to characterize interfaces of components, their structure, and their navigability. We show how CIDs can be used to describe the in-house developed Open Editor Framework (OEF). Finally, we give guidelines that allow to map components described with CIDs directly to several component technologies, like ActiveX, CORBA, or Java Beans
description: 13 pages, 5 figures
Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation
Creators: name: Chatterjee, Gautam
name: Gonzalez-Hilarion, Sara
name: Paulet, Damien
name: Hsueh, Yen-Ping
name: Coppée, Jean-Yves
name: Floyd-Averette, Anna
name: Gujja, Sharvari
name: Yadav, Vikas
name: Chow, Eve W. L.
name: Brunel, François
name: Ormerod, Kate L.
name: Moyrand, Frédérique
name: Lam, Woei
name: Mieczkowski, Piotr A.
name: Kozubowski, Lukasz
name: Jones, Steven
name: Bahn, Yong-Sun
name: Goldberg, Jonathan
name: Mesner, Larry D.
name: Ianiri, Giuseppe
name: Gaillardin, Claude
name: Janbon, Guilhem
name: Chen, Yuan
name: Byrnes, Edmond J.
name: Hamlin, Joyce L.
name: Mullapudi, Nandita
name: Marra, Marco
name: Gerik, Kimberly J.
name: Billmyre, R. Blake
name: Chen, Weidong
name: Hon, Chung-Chau
name: Kodira, Chinnappa D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. It occurs as two serotypes (A and D) representing two varieties (i.e. grubii and neoformans, respectively). Here, we sequenced the genome and performed an RNA-Seq-based analysis of the C. neoformans var. grubii transcriptome structure. We determined the chromosomal locations, analyzed the sequence/structural features of the centromeres, and identified origins of replication. The genome was annotated based on automated and manual curation. More than 40,000 introns populating more than 99% of the expressed genes were identified. Although most of these introns are located in the coding DNA sequences (CDS), over 2,000 introns in the untranslated regions (UTRs) were also identified. Poly(A)-containing reads were employed to locate the polyadenylation sites of more than 80% of the genes. Examination of the sequences around these sites revealed a new poly(A)-site-associated motif (AUGHAH). In addition, 1,197 miscRNAs were identified. These miscRNAs can be spliced and/or polyadenylated, but do not appear to have obvious coding capacities. Finally, this genome sequence enabled a comparative analysis of strain H99 variants obtained after laboratory passage. The spectrum of mutations identified provides insights into the genetics underlying the micro-evolution of a laboratory strain, and identifies mutations involved in stress responses, mating efficiency, and virulence.
Observations on the ground running spider Hirriusa arenacea (Lawrence, 1927) from South Africa (Araneae: Philodromidae)
Creators: name: Dippenaar-Schoeman, A.S.
name: Webb, P.
Publisher: name: Zenodo
Year: 2024

description: Hirriusa arenacea is a Southern African spider described by Lawrence (1927) as Hirrius arenaceus from Namibia. They are small ground-running spiders frequently encountered in sandy areas on the soil surface. Information on their general morphology, behaviour, and distribution in South Africa, as well as photographs of live specimens, is provided.
Disruption of SUMO-Specific Protease 2 Induces Mitochondria Mediated Neurodegeneration
Creators: name: Yu, H.-M. Ivy
name: Cheng, Jr-Gang
name: Hsu, Wei
name: Chiu, Shang-Yi
name: Fu, Jiang
name: Mirando, Anthony J.
name: Maruyama, Eri O.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Post-translational modification of proteins by small ubiquitin-related modifier (SUMO) is reversible and highly evolutionarily conserved from yeasts to humans. Unlike ubiquitination with a well-established role in protein degradation, sumoylation may alter protein function, activity, stability and subcellular localization. Members of SUMO-specific protease (SENP) family, capable of SUMO removal, are involved in the reversed conjugation process. Although SUMO-specific proteases are known to reverse sumoylation in many well-defined systems, their importance in mammalian development and pathogenesis remains largely elusive. In patients with neurodegenerative diseases, aberrant accumulation of SUMO-conjugated proteins has been widely described. Several aggregation-prone proteins modulated by SUMO have been implicated in neurodegeneration, but there is no evidence supporting a direct involvement of SUMO modification enzymes in human diseases. Here we show that mice with neural-specific disruption of SENP2 develop movement difficulties which ultimately results in paralysis. The disruption induces neurodegeneration where mitochondrial dynamics is dysregulated. SENP2 regulates Drp1 sumoylation and stability critical for mitochondrial morphogenesis in an isoform-specific manner. Although dispensable for development of neural cell types, this regulatory mechanism is necessary for their survival. Our findings provide a causal link of SUMO modification enzymes to apoptosis of neural cells, suggesting a new pathogenic mechanism for neurodegeneration. Exploring the protective effect of SENP2 on neuronal cell death may uncover important preventive and therapeutic strategies for neurodegenerative diseases.
A new functional flow equation for Einstein-Cartan quantum gravity
Creators: name: Harst, Ulrich
name: Reuter, Martin
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We construct a special-purpose functional flow equation which facilitates non-perturbative renormalization group (RG) studies on theory spaces involving a large number of independent field components that are prohibitively complicated using standard methods. Its main motivation are quantum gravity theories in which the gravitational degrees of freedom are carried by a complex system of tensor fields, a prime example being Einstein-Cartan theory, possibly coupled to matter. We describe a sequence of approximation steps leading from the functional RG equation of the Effective Average Action to the new flow equation which, as a consequence, is no longer fully exact on the untruncated theory space. However, it is by far more "user friendly" when it comes to projecting the abstract equation on a concrete (truncated) theory space and computing explicit beta-functions. The necessary amount of (tensor) algebra reduces drastically, and the usually very hard problem of diagonalizing the pertinent Hessian operator is sidestepped completely. In this paper we demonstrate the reliability of the simplified equation by applying it to a truncation of the Einstein-Cartan theory space. It is parametrized by a scale dependent Holst action, depending on a O(4) spin-connection and the tetrad as the independent field variables. We compute the resulting RG flow, focusing in particular on the running of the Immirzi parameter, and compare it to the results of an earlier computation where the exact equation had been applied to the same truncation. We find consistency between the two approaches and provide further evidence for the conjectured non-perturbative renormalizability (asymptotic safety) of quantum Einstein-Cartan gravity. We also investigate a duality symmetry relating small and large values of the Immirzi parameter which is displayed by the beta-functions in absence of a cosmological constant.
description: 111 pages, 27 figures
The Black Hole Mass Scale of Classical and Pseudo Bulges in Active Galaxies
Creators: name: Ho, Luis C.
name: Kim, Minjin
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: The mass estimator used to calculate black hole (BH) masses in broad-line active galactic nuclei (AGNs) relies on a virial coefficient (the "$f$ factor") that is determined by comparing reverberation-mapped (RM) AGNs with measured bulge stellar velocity dispersions against the $M_{\rm BH}-σ_*$ relation of inactive galaxies. It has recently been recognized that only classical bulges and ellipticals obey a tight $M_{\rm BH}-σ_*$ relation; pseudobulges have a different zero point and much larger scatter. Motivated by these developments, we reevaluate the $f$ factor for RM AGNs with available $σ_*$ measurements, updated H$β$ RM lags, and new bulge classifications based on detailed decomposition of high-resolution ground-based and space-based images. Separate calibrations are provided for the two bulge types, whose virial coefficients differ by a factor of $\sim 2$: $f=6.3\pm1.5$ for classical bulges and ellipticals and $f = 3.2\pm0.7$ for pseudobulges. The structure and kinematics of the broad-line region, at least as crudely encoded in the $f$ factor, seems to related to the large-scale properties or formation history of the bulge. Lastly, we investigate the bulge stellar masses of the RM AGNs, show evidence for recent star formation in the AGN hosts that correlates with Eddington ratio, and discuss the potential utility of the $M_{\rm BH}-M_{\rm bulge}$ relation as a more promising alternative to the conventionally used $M_{\rm BH}-σ_*$ relation for future refinement of the virial mass estimator for AGNs.
description: 2014, ApJ, 789, 17
Single-particle vs. pair superfluidity in a bilayer system of dipolar bosons
Creators: name: Macia, A.
name: Astrakharchik, G. E.
name: Mazzanti, F.
name: Giorgini, S.
name: Boronat, J.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: We consider the ground state of a bilayer system of dipolar bosons, where dipoles are oriented by an external field in the direction perpendicular to the parallel planes. Quantum Monte Carlo methods are used to calculate the ground-state energy, the one-body and two-body density matrix, and the superfluid response as a function of the separation between layers. We find that by decreasing the interlayer distance for fixed value of the strength of the dipolar interaction, the system undergoes a quantum phase transition from a single-particle to a pair superfluid. The single-particle superfluid is characterized by a finite value of both the atomic condensate and the super-counterfluid density. The pair superfluid phase is found to be stable against formation of many-body cluster states and features a gap in the spectrum of elementary excitations.
description: 4 figures
Cosmological Consequences of Initial State Entanglement
Creators: name: Albrecht, Andreas
name: Bolis, Nadia
name: Holman, R.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We explore the cosmological consequences of having the fluctuations of the inflaton field entangled with those of another scalar, within the context of a toy model consisting of non-interacting, minimally coupled scalars in a fixed de Sitter background. We find that despite the lack of interactions in the Lagrangian, the initial state entanglement modifies the mode equation for the inflaton fluctuations and thus can induce changes in cosmological observables. These effects are examined for a variety of choices of masses and we find that they can be consistent with the requirement that the back reaction of the modified state not affect the inflationary phase while still giving rise to observable effects in the power spectrum. Our results suggest that more realistic extensions of the ideas explored here beyond the simple toy model may lead to interesting observable effects.
description: 17 pages, 5 figures
Eliminating Both Canonical and Short-Patch Mismatch Repair in Drosophila melanogaster Suggests a New Meiotic Recombination Model
Creators: name: Crown, K. Nicole
name: McMahan, Susan
name: Sekelsky, Jeff
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: In most meiotic systems, recombination is essential to form connections between homologs that ensure their accurate segregation from one another. Meiotic recombination is initiated by DNA double-strand breaks that are repaired using the homologous chromosome as a template. Studies of recombination in budding yeast have led to a model in which most early repair intermediates are disassembled to produce noncrossovers. Selected repair events are stabilized so they can proceed to form double-Holliday junction (dHJ) intermediates, which are subsequently resolved into crossovers. This model is supported in yeast by physical isolation of recombination intermediates, but the extent to which it pertains to animals is unknown. We sought to test this model in Drosophila melanogaster by analyzing patterns of heteroduplex DNA (hDNA) in recombination products. Previous attempts to do this have relied on knocking out the canonical mismatch repair (MMR) pathway, but in both yeast and Drosophila the resulting recombination products are complex and difficult to interpret. We show that, in Drosophila, this complexity results from a secondary, short-patch MMR pathway that requires nucleotide excision repair. Knocking out both canonical and short-patch MMR reveals hDNA patterns that reveal that many noncrossovers arise after both ends of the break have engaged with the homolog. Patterns of hDNA in crossovers could be explained by biased resolution of a dHJ; however, considering the noncrossover and crossover results together suggests a model in which a two-end engagement intermediate with unligated HJs can be disassembled by a helicase to a produce noncrossover or nicked by a nuclease to produce a crossover. While some aspects of this model are similar to the model from budding yeast, production of both noncrossovers and crossovers from a single, late intermediate is a fundamental difference that has important implications for crossover control.
A late-Holocene Aboriginal hearth from Point Nepean, Victoria, Australia: Maximising insights from minimal impacts
Creators: name: Thomas, David
name: Turnbull, Dan
name: Stephenson, Birgitta
name: Carah, Xavier
name: Phillips, Oona
name: Coombes, Barry
name: Archaeology Program, La Trobe University
Publisher: name: La Trobe
Year: 2023

description: Blank
A Note on Semantics (with an Emphasis on UML)
Creators: name: Rumpe, Bernhard
Publisher: name: arXiv
Year: 2014
Subjects: subject: Software Engineering (cs.SE)
subject: FOS: Computer and information sciences

description: This note clarifies the concept of syntax and semantics and their relationships. Today, a lot of confusion arises from the fact that the word "semantics" is used in different meanings. We discuss a general approach at defining semantics that is feasible for both textual and diagrammatic notations and discuss this approach using an example formalization. The formalization of hierarchical Mealy automata and their semantics definition using input/output behaviors allows us to define a specification, as well as an implementation semantics. Finally, a classification of different approaches that fit in this framework is given. This classification may also serve as guideline when defining a semantics for a new language.
description: 21 pages, 2 figures
Effects of Bone Types on Bone Remodeling of a Dental Implant: A Review of the Literature
Creators: name: Pimduen Rungsiyakull
Publisher: name: Faculty of Dentistry, Chiang Mai University
Year: 2021
Subjects: bone density
bone quality
peri-implant bone
type of bone

description: Chiang Mai Dental Journal, 42, 2, 13-19
Sub-diffractional nanopatterning and nanocharacterization of silk fibroin using tip-enhanced near-field optics
Creators: name: Lee, Woonsoo
Publisher: name: The University of Texas at Austin
Year: 2020
Subjects: Silk protein
Fibroin
s-SNOM
Near-field lithography
SPL

description: Mid-IR scattering-type scanning near-field optical microscope (s-SNOM) has extended spatial resolution of vibrational microscopy and spectroscopy to ~10 nm, over two orders of magnitude better than one-half-wavelength diffraction limit. Concentrated near-field light can also be used for creating features with nanoscopic precision. This dissertation documents the development of a novel nanopatterning approach based on s-SNOM that can be used to pattern sub-diffractional, dual-tone, and grayscale nanostructures onto ultra-thin silk fibroin film. This approach is named tip-enhanced near-field infrared nanolithography (TNINL). TNINL was conceived with the aim of combining nano-characterization capabilities of s-SNOM with the lithography potential of tip-enhanced near-field optics. This dissertation examines the potential of s-SNOM as a basic tool for closed-loop lithography, a versatile nanopatterning platform with inherent feedback to optimize the writing process. In this context, the use of silk is advantageous because silk interface well with both biotic and abiotic interfaces. In addition, its strength, robustness, cytocompatibility, biocompatibility, biodegradability, and tunable water-solubility make silk favorable functional substrate for various nanofabricated devices. In the development of TNINL, various approaches for patterning silk with s-SNOM were conceived and tested. Nanoscale features were patterned and characterized in-situ, revealing both topographical and conformational modifications. System input parameters were empirically and analytically studied, and a thermomechanical patterning mechanism was proposed. A versatile patterning capability is demonstrated, and potential applications are investigated
Genome-Wide Diet-Gene Interaction Analyses for Risk of Colorectal Cancer
Creators: name: Jiao, Shuo
name: Slattery, Martha L.
name: Chang-Claude, Jenny
name: Casey, Graham
name: Lin, Yi
name: Caan, Bette J.
name: Chan, Andrew T.
name: Rosse, Stephanie A.
name: Carlson, Christopher S.
name: Giovannucci, Edward L.
name: Figueiredo, Jane C.
name: Hsu, Li
name: Fortini, Barbara
name: Berndt, Sonja I.
name: Chanock, Stephen J.
name: Campbell, Peter T.
name: Haile, Robert W.
name: Cotterchio, Michelle
name: Gallinger, Steven
name: Hayes, Richard B.
name: Duggan, David
name: Le Marchand, Loic
name: Zanke, Brent W.
name: Newcomb, Polly A.
name: Brenner, Hermann
name: Baron, John A.
name: Wu, Kana
name: Lemire, Mathieu
name: Curtis, Keith R.
name: Harrison, Tabitha A.
name: Gong, Jian
name: Hutter, Carolyn M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Dietary factors, including meat, fruits, vegetables and fiber, are associated with colorectal cancer; however, there is limited information as to whether these dietary factors interact with genetic variants to modify risk of colorectal cancer. We tested interactions between these dietary factors and approximately 2.7 million genetic variants for colorectal cancer risk among 9,287 cases and 9,117 controls from ten studies. We used logistic regression to investigate multiplicative gene-diet interactions, as well as our recently developed Cocktail method that involves a screening step based on marginal associations and gene-diet correlations and a testing step for multiplicative interactions, while correcting for multiple testing using weighted hypothesis testing. Per quartile increment in the intake of red and processed meat were associated with statistically significant increased risks of colorectal cancer and vegetable, fruit and fiber intake with lower risks. From the case-control analysis, we detected a significant interaction between rs4143094 (10p14/near GATA3) and processed meat consumption (OR = 1.17; p = 8.7E-09), which was consistently observed across studies (p heterogeneity = 0.78). The risk of colorectal cancer associated with processed meat was increased among individuals with the rs4143094-TG and -TT genotypes (OR = 1.20 and OR = 1.39, respectively) and null among those with the GG genotype (OR = 1.03). Our results identify a novel gene-diet interaction with processed meat for colorectal cancer, highlighting that diet may modify the effect of genetic variants on disease risk, which may have important implications for prevention.
Crossover from 2D ferromagnetic insulator to wide bandgap quantum anomalous Hall insulator in ultra-thin MnBi2Te4
Creators: name: Trang, Chi Xuan
name: Li, Qile
name: Yin, Yuefeng
name: Hwang, Jinwoong
name: Akhgar, Golrokh
name: Di Bernardo, Iolanda
name: Grubišić-Čabo, Antonija
name: Tadich, Anton
name: Fuhrer, Michael S.
name: Mo, Sung- Kwan
name: Medhekar, Nikhil
name: Edmonds, Mark T.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Intrinsic magnetic topological insulators offer low disorder and large magnetic bandgaps for robust magnetic topological phases operating at higher temperatures. By controlling the layer thickness, emergent phenomena such as the Quantum Anomalous Hall (QAH) effect and axion insulator phases have been realised. These observations occur at temperatures significantly lower than the Neel temperature of bulk MnBi2Te4, and measurement of the magnetic energy gap at the Dirac point in ultra-thin MnBi2Te4 has yet to be achieved. Critical to achieving the promise of this system is a direct measurement of the layer-dependent energy gap and verifying whether the gap is magnetic in the QAH phase. Here we utilise temperature dependent angle-resolved photoemission spectroscopy to study epitaxial ultra-thin MnBi2Te4. We directly observe a layer dependent crossover from a 2D ferromagnetic insulator with a bandgap greater than 780 meV in one septuple layer (1 SL) to a QAH insulator with a large energy gap (>100 meV) at 8 K in 3 and 5 SL MnBi2Te4. The QAH gap is confirmed to be magnetic in origin, as it abruptly diminishes with increasing temperature above 8 K. The direct observation of a large magnetic energy gap in the QAH phase of few-SL MnBi2Te4 is promising for further increasing the operating temperature of QAH materials.
Identification of a Regulatory Variant That Binds FOXA1 and FOXA2 at the CDC123/CAMK1D Type 2 Diabetes GWAS Locus
Creators: name: Mohlke, Karen L.
name: Gaulton, Kyle J.
name: Cannon, Maren E.
name: Vadlamudi, Swarooparani
name: Fogarty, Marie P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Many of the type 2 diabetes loci identified through genome-wide association studies localize to non-protein-coding intronic and intergenic regions and likely contain variants that regulate gene transcription. The CDC123/CAMK1D type 2 diabetes association signal on chromosome 10 spans an intergenic region between CDC123 and CAMK1D and also overlaps the CDC123 3′UTR. To gain insight into the molecular mechanisms underlying the association signal, we used open chromatin, histone modifications and transcription factor ChIP-seq data sets from type 2 diabetes-relevant cell types to identify SNPs overlapping predicted regulatory regions. Two regions containing type 2 diabetes-associated variants were tested for enhancer activity using luciferase reporter assays. One SNP, rs11257655, displayed allelic differences in transcriptional enhancer activity in 832/13 and MIN6 insulinoma cells as well as in human HepG2 hepatocellular carcinoma cells. The rs11257655 risk allele T showed greater transcriptional activity than the non-risk allele C in all cell types tested. Using electromobility shift and supershift assays we demonstrated that the rs11257655 risk allele showed allele-specific binding to FOXA1 and FOXA2. We validated FOXA1 and FOXA2 enrichment at the rs11257655 risk allele using allele-specific ChIP in human islets. These results suggest that rs11257655 affects transcriptional activity through altered binding of a protein complex that includes FOXA1 and FOXA2, providing a potential molecular mechanism at this GWAS locus.
Which Irrigant Should be used for Vital Pulp Therapy in Permanent Teeth? : A Review of the Literature
Creators: name: Nattakan Chaipattanawan
Publisher: name: Faculty of Dentistry, Chiang Mai University
Year: 2021
Subjects: chlorhexidine
ethylenediamine tetra-acetic acid
irrigant
saline solution
sodium hypochlorite
vital pulp therapy

description: Chiang Mai Dental Journal, 42, 2, 20-31
KDM6 Demethylase Independent Loss of Histone H3 Lysine 27 Trimethylation during Early Embryonic Development
Creators: name: Magnuson, Terry
name: Starmer, Joshua
name: Shpargel, Karl B.
name: Pohlers, Michael
name: Yee, Della
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: The early mammalian embryo utilizes histone H3 lysine 27 trimethylation (H3K27me3) to maintain essential developmental genes in a repressive chromatin state. As differentiation progresses, H3K27me3 is removed in a distinct fashion to activate lineage specific patterns of developmental gene expression. These rapid changes in early embryonic chromatin environment are thought to be dependent on H3K27 demethylases. We have taken a mouse genetics approach to remove activity of both H3K27 demethylases of the Kdm6 gene family, Utx (Kdm6a, X-linked gene) and Jmjd3 (Kdm6b, autosomal gene). Male embryos null for active H3K27 demethylation by the Kdm6 gene family survive to term. At mid-gestation, embryos demonstrate proper patterning and activation of Hox genes. These male embryos retain the Y-chromosome UTX homolog, UTY, which cannot demethylate H3K27me3 due to mutations in catalytic site of the Jumonji-C domain. Embryonic stem (ES) cells lacking all enzymatic KDM6 demethylation exhibit a typical decrease in global H3K27me3 levels with differentiation. Retinoic acid differentiations of these ES cells demonstrate loss of H3K27me3 and gain of H3K4me3 to Hox promoters and other transcription factors, and induce expression similar to control cells. A small subset of genes exhibit decreased expression associated with reduction of promoter H3K4me3 and some low-level accumulation of H3K27me3. Finally, Utx and Jmjd3 mutant mouse embryonic fibroblasts (MEFs) demonstrate dramatic loss of H3K27me3 from promoters of several Hox genes and transcription factors. Our results indicate that early embryonic H3K27me3 repression can be alleviated in the absence of active demethylation by the Kdm6 gene family.
Cooling Techniques for Trapped Ions
Creators: name: Segal, Daniel M.
name: Wunderlich, Christof
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: This book chapter gives an introduction to, and an overview of, methods for cooling trapped ions. The main addressees are researchers entering the field. It is not intended as a comprehensive survey and historical account of the extensive literature on this topic. We present the physical ideas behind several cooling schemes, outline their mathematical description, and point to relevant literature useful for a more in-depth study of this topic.
description: Part of the Proceedings of the Les Houches Winter School on the Physics with Trapped Charged Particles held in January 2012. References updated in mid 2012
Mechanism of Suppression of Chromosomal Instability by DNA Polymerase POLQ
Creators: name: Takata, Kei-ichi
name: Hensley, Sean C.
name: Bylund, Göran O.
name: Wyatt, David W.
name: Johansson, Erik
name: Ramsden, Dale A.
name: Tomida, Junya
name: Mu, Yunxiang
name: Yousefzadeh, Matthew J.
name: McBride, Kevin M.
name: Wood, Richard D.
name: Doublié, Sylvie
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Although a defect in the DNA polymerase POLQ leads to ionizing radiation sensitivity in mammalian cells, the relevant enzymatic pathway has not been identified. Here we define the specific mechanism by which POLQ restricts harmful DNA instability. Our experiments show that Polq-null murine cells are selectively hypersensitive to DNA strand breaking agents, and that damage resistance requires the DNA polymerase activity of POLQ. Using a DNA break end joining assay in cells, we monitored repair of DNA ends with long 3′ single-stranded overhangs. End joining events retaining much of the overhang were dependent on POLQ, and independent of Ku70. To analyze the repair function in more detail, we examined immunoglobulin class switch joining between DNA segments in antibody genes. POLQ participates in end joining of a DNA break during immunoglobulin class-switching, producing insertions of base pairs at the joins with homology to IgH switch-region sequences. Biochemical experiments with purified human POLQ protein revealed the mechanism generating the insertions during DNA end joining, relying on the unique ability of POLQ to extend DNA from minimally paired primers. DNA breaks at the IgH locus can sometimes join with breaks in Myc, creating a chromosome translocation. We found a marked increase in Myc/IgH translocations in Polq-defective mice, showing that POLQ suppresses genomic instability and genome rearrangements originating at DNA double-strand breaks. This work clearly defines a role and mechanism for mammalian POLQ in an alternative end joining pathway that suppresses the formation of chromosomal translocations. Our findings depart from the prevailing view that alternative end joining processes are generically translocation-prone.
Supernova SN 2012dn: A spectroscopic clone of SN 2006gz
Creators: name: Chakradhari, N. K.
name: Sahu, D. K.
name: Srivastav, S.
name: Anupama, G. C.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We present optical and UV analysis of the luminous type Ia supernova SN 2012dn covering the period $\sim -$11 to +109 days with respect to the $B$ band maximum, that occurred on JD 2456132.89 $\pm$ 0.19, with an apparent magnitude of $m_{B}^\text{max}$ = 14.38 $\pm$ 0.02. The absolute magnitudes at maximum in $B$ and $V$ bands are $M_{B}^\text{max} = -19.52 \pm 0.15$ and $M_{V}^\text{max} = -19.42 \pm 0.15$, respectively. SN 2012dn is marginally luminous compared to normal type Ia supernovae. The peak bolometric luminosity of $\log L_\text{bol}^\text{max} = 43.27 \pm 0.06$ erg s$^{-1}$ suggests that $0.82 \pm 0.12$ M$_\odot$ of $^{56}$Ni was synthesized in the explosion. The decline rate $Δm_{15}(B)_\text{true}= 0.92 \pm 0.04$ mag is lower than that of normal type Ia supernovae, and similar to the luminous SN 1991T. However, the photometric and spectroscopic behaviour of SN 2012dn is different from that of SN 1991T. Early phase light curves in $R$ and $I$ bands are very broad. The $I$ band peak has a plateau-like appearance similar to the super-Chandra SN 2009dc. Pre-maximum spectra show clear evidence of C\,{\sc ii} 6580 Å\, line, indicating the presence of unburned materials. The velocity evolution of C\,{\ sc ii} line is peculiar. Except for the very early phase ($\sim-$13 d), the C\,{\sc ii} line velocity is lower than the velocity estimated using the Si\,{\sc ii} line. During the pre-maximum and close to maximum phase, to reproduce observed shape of the spectra, the synthetic spectrum code {\sc syn++} needs significantly higher blackbody temperature than those required for normal type Ia events. The photospheric velocity evolution and other spectral properties are similar to those of the carbon-rich SN 2006gz.
description: Accepted for publication in MNRAS, 19 pages, 20 figures
Valence Bond Phases in $S=1/2$ Kane-Mele-Heisenberg Model
Creators: name: Zare, Mohammad H.
name: Mosadeq, Hamid
name: Shahbazi, Farhad
name: Jafari, S. A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The phase diagram of Kane-Mele-Heisenberg (KMH) model in classical limit~\cite{zare}, contains disordered regions in the coupling space, as the result of to competition among different terms in the Hamiltonian, leading to frustration in finding a unique ground state. In this work we explore the nature of these phase in the quantum limit, for a $S=1/2$. Employing exact diagonalization (ED) in $S_z$ and nearest neighbor valence bond (NNVB) bases, bond and plaquette valence bond mean field theories, We show that the disordered regions are divided into ordered quantum states in the form of plaquette valence bond crystal(PVBC) and staggered dimerized (SD) phases.
description: 8 pages, 9 figures, 52 references
Pairing in half-filled Landau level
Creators: name: Wang, Zhiqiang
name: Mandal, Ipsita
name: Chung, Suk Bum
name: Chakravarty, Sudip
Publisher: name: arXiv
Year: 2014
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: Pairing of composite fermions in half-filled Landau level state is reexamined by solving the BCS gap equation with full frequency dependent current-current interactions. Our results show that there can be a \emph{continuous} transition from the Halperin-Lee-Read state to a chiral odd angular momentum Cooper pair state for short-range contact interaction. This is at odds with the previously established conclusion of first order pairing transition, in which the low frequency effective interaction was assumed for the entire frequency range. We find that even if the low frequency effective interaction is repulsive, it is compensated by the high frequency regime, which is attractive. We construct the phase diagrams and show that $\ell=1$ angular momentum channel is quite different from higher angular momenta $\ell\ge 3$. Remarkably, the full frequency dependent analysis applied to the bilayer Hall system with a total filling fraction $ν=\frac{1}{2}+\frac{1}{2}$ is quantitatively changed from the previously established results but not qualitatively.
description: 9 pages,7 figures
Developing the UML as a Formal Modelling Notation
Creators: name: Evans, Andy
name: France, Robert
name: Lano, Kevin
name: Rumpe, Bernhard
Publisher: name: arXiv
Year: 2014
Subjects: subject: Software Engineering (cs.SE)
subject: FOS: Computer and information sciences

description: The Unified Modeling Language (UML) is rapidly emerging as a de-facto standard for modelling OO systems. Given this role, it is imperative that the UML have a well- defined, fully explored semantics. Such semantics is required in order to ensure that UML concepts are precisely stated and defined. In this paper we describe and motivate an approach to formalizing UML in which formal specification techniques are used to gain insight into the semantics of UML notations and diagrams. We present work carried out by the Precise UML (PUML) group on the development of a precise semantic model for UML class diagrams. The semantic model is used as the basis for a set of diagrammatical transformation rules, which enable formal deductions to be made about UML class diagrams. It is also shown how these rules can be used to verify whether one class diagram is a valid refinement (design) of another. Because these rules are presented at the diagrammatical level, it will be argued that UML can be successfully used as a formal modelling tool without the notational complexities that are commonly found in formal specification techniques.
description: 12 pages, 0 figures. arXiv admin note: substantial text overlap with arXiv:1409.6919
Mediation Analysis Demonstrates That Trans-eQTLs Are Often Explained by Cis-Mediation: A Genome-Wide Analysis among 1,800 South Asians
Creators: name: Chen, Lin S.
name: Esko, Tonu
name: Kibriya, Muhammad G.
name: Westra, Harm-Jan
name: Roy, Shantanu
name: Franke, Lude
name: Rahaman, Ronald
name: Tong, Lin
name: Islam, Tariqul
name: Pierce, Brandon L.
name: Baron, John A.
name: Argos, Maria
name: Rahman, Mahfuzar
name: Jasmine, Farzana
name: Paul-Brutus, Rachelle
name: Zaman, Rakibuz
name: Ahsan, Habibul
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: A large fraction of human genes are regulated by genetic variation near the transcribed sequence (cis-eQTL, expression quantitative trait locus), and many cis-eQTLs have implications for human disease. Less is known regarding the effects of genetic variation on expression of distant genes (trans-eQTLs) and their biological mechanisms. In this work, we use genome-wide data on SNPs and array-based expression measures from mononuclear cells obtained from a population-based cohort of 1,799 Bangladeshi individuals to characterize cis- and trans-eQTLs and determine if observed trans-eQTL associations are mediated by expression of transcripts in cis with the SNPs showing trans-association, using Sobel tests of mediation. We observed 434 independent trans-eQTL associations at a false-discovery rate of 0.05, and 189 of these trans-eQTLs were also cis-eQTLs (enrichment P<0.0001). Among these 189 trans-eQTL associations, 39 were significantly attenuated after adjusting for a cis-mediator based on Sobel P<10-5. We attempted to replicate 21 of these mediation signals in two European cohorts, and while only 7 trans-eQTL associations were present in one or both cohorts, 6 showed evidence of cis-mediation. Analyses of simulated data show that complete mediation will be observed as partial mediation in the presence of mediator measurement error or imperfect LD between measured and causal variants. Our data demonstrates that trans-associations can become significantly stronger or switch directions after adjusting for a potential mediator. Using simulated data, we demonstrate that this phenomenon is expected in the presence of strong cis-trans confounding and when the measured cis-transcript is correlated with the true (unmeasured) mediator. In conclusion, by applying mediation analysis to eQTL data, we show that a substantial fraction of observed trans-eQTL associations can be explained by cis-mediation. Future studies should focus on understanding the mechanisms underlying widespread cis-mediation and their relevance to disease biology, as well as using mediation analysis to improve eQTL discovery.
Observations on the black-faced huntsman spider Olios correvoni nigrifrons Lawrence, 1928 from Southern Africa (Araneae: Sparassidae)
Creators: name: Dippenaar-Schoeman, A.S.
name: Eichhoff, A.
name: Christiaan, R.
Publisher: name: Zenodo
Year: 2024

description: Olios correvoni Lessert, 1921 is an African endemic species described from Tanzania and the subspecies Olios correvoni nigrifrons was described by Lawrence, 1928 from Namibia. The subspecies is also known from South Africa and Botswana. It is a nocturnal spider that wanders at night searching for prey. During the day, they are found in silk retreats made in different microhabitats. Observations on their general morphology, behaviour, and distribution with photographs of live specimens are provided.