cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Identification of catalytically active domain epitopes in neuraminidase protein of H9N2 subtype of avian influenza virus
Creators: name: Huang, Xiangyu
name: Cai, Yiqin
name: Yin, Guihu
name: Chen, Zili
name: Hu, Jianing
name: Gao, Zichen
name: Guo, Xinyu
name: Xiong, Fuqiang
name: Feng, Xiuli
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Evolutionary Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Hematology
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: Virology

description: H9N2 subtype of avian influenza virus (AIV) is primarily a bird virus, which is widespread in clinical avian disease, and reported in cases of human infection. As one of the surface proteins of AIV, the neuraminidase (NA) protein plays an important role mainly in viral budding. However, vaccine development and detection methods for NA of H9N2 AIVs are in urgent clinical need. In this study, a truncated NA gene (205–900 bp) was cloned from the NA sequence of H9N2 strain, and then expressed using pET-28a (+) vector. This purified recombinant NA protein was used to immunize BALB/c mice, and the monoclonal antibodies were screened through the indirect enzyme-linked immunosorbent assay (ELISA). Next, eight prokaryotic expression vectors were constructed for epitope identification. After cell fusion, three hybridoma cell lines producing the antibodies special to NA protein were screened by ELISA, western blotting, and indirect immunofluorescence; these were named 1B10, 2B6, and 5B2, respectively. Epitope scanning techniques were used to identify three B-cell epitopes recognized by these three monoclonal antibodies, 196KNATASIIYDGMLVD210, 210DSIGSWSKNIL220 and 221RTQESECVCI230. The subsequent homology analysis revealed the three epitopes were highly conserved in H9N2 AIV strains. The structural predictions of the antigenic epitopes indicated that all three epitopes were located in the catalytic region of NA. These results provide a basis for studying the function of the NA protein of H9N2 AIV and technical support for the development of a universal detection method based on anti-NA monoclonal antibodies.
Detailed methodology and additional results from Predicting 1-year in-stent restenosis in superficial femoral arteries through multi-scale computational modelling
Creators: name: Corti, Anna
name: Migliavacca, Francesco
name: Berceli, Scott A.
name: Chiastra, Claudio
Publisher: name: The Royal Society
Year: 2023
Subjects: subject: 60114 Systems Biology
subject: FOS: Biological sciences
subject: 110601 Biomechanics
subject: FOS: Health sciences
subject: Computational Biology

description: In-stent restenosis in superficial femoral arteries (SFAs) is a complex, multi-factorial and multi-scale vascular adaptation process whose thorough understanding is still lacking. Multi-scale computational agent-based modelling has recently emerged as a promising approach to decipher mechanobiological mechanisms driving the arterial response to the endovascular intervention. However, the long-term arterial response has never been investigated with this approach, although being of fundamental relevance. In this context, this study investigates the 1-year post-operative arterial wall remodelling in three patient-specific stented SFA lesions through a fully coupled multi-scale agent-based modelling framework. The framework integrates the effects of local haemodynamics and monocyte gene expression data on cellular dynamics through a bi-directional coupling of computational fluid dynamics simulations with an agent-based model of cellular activities. The framework was calibrated on the follow-up data at one month and six months of one stented SFA lesion and then applied to the other two lesions. The calibrated framework successfully captured (i) the high lumen area reduction occurring within the first post-operative month and (ii) the stabilization of the median lumen area from one-month to 1-year follow-ups in all the stented lesions, demonstrating the potentialities of the proposed approach for investigating patient-specific short- and long-term responses to endovascular interventions.
Many-body Green's function theory for electron-phonon interactions: the Kadanoff-Baym approach to spectral properties of the Holstein dimer
Creators: name: Säkkinen, N.
name: Peng, Y.
name: Appel, H.
name: van Leeuwen, R.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We present a Kadanoff-Baym formalism to study time-dependent phenomena for systems of interacting electrons and phonons in the framework of many-body perturbation theory. The formalism takes correctly into account effects of the initial preparation of an equilibrium state, and allows for an explicit time-dependence of both the electronic and phononic degrees of freedom. The method is applied to investigate the charge neutral and non-neutral excitation spectra of a homogeneous, two-site, two-electron Holstein model. This is an extension of a previous study of the ground state properties in the Hartree (H), partially self-consistent Born (Gd) and fully self-consistent Born (GD) approximations published in Ref. [arXiv:1403.2968]. We show that choosing a homogeneous ground state solution leads to unstable dynamics for a sufficiently strong interaction, and that allowing a symmetry-broken state prevents this. The instability is caused by the bifurcation of the ground state and understood physically to be connected with the bipolaronic crossover of the exact system. This mean-field instability persists in the partially self-consistent Born approximation but is not found for the fully self-consistent Born approximation. By understanding the stability properties, we are able to study the linear response regime by calculating the density-density response function by time-propagation. This functions amounts to a solution of the Bethe-Salpeter equation with a sophisticated kernel. The results indicate that none of the approximations is able to describe the response function during or beyond the bipolaronic crossover for the parameters investigated. Overall, we provide an extensive discussion on when the approximations are valid, and how they fail to describe the studied exact properties of the chosen model system.
description: 12 figures
Early Paleozoic intermediate igneous rocks in the Dunhuang Block, southern Central Asian Orogenic Belt: Geochronology, petrogenesis, and implications for tectonic evolution
Creators: name: Gan, Baoping
name: Diwu, Chunrong
name: Wang, Tingyi
name: Pei, Qiuming
name: Wang, Shiming
Publisher: name: Geological Society of London
Year: 2022
Subjects: subject: Geology
subject: FOS: Earth and related environmental sciences

description: Supplementary material.
On a parabolic Hamilton-Jacobi-Bellman equation degenerating at the boundary
Creators: name: Castorina, Daniele
name: Cesaroni, Annalisa
name: Rossi, Luca
Publisher: name: arXiv
Year: 2015
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: We derive the long time asymptotic of solutions to an evolutive Hamilton-Jacobi-Bellman equation in a bounded smooth domain, in connection with ergodic problems recently studied in \cite{bcr}. Our main assumption is an appropriate degeneracy condition on the operator at the boundary. This condition is related to the characteristic boundary points for linear operators as well as to the irrelevant points for the generalized Dirichlet problem, and implies in particular that no boundary datum has to be imposed. We prove that there exists a constant $c$ such that the solutions of the evolutive problem converge uniformly, in the reference frame moving with constant velocity $c$, to a unique steady state solving a suitable ergodic problem.
description: 12pp
Early Paleozoic intermediate igneous rocks in the Dunhuang Block, southern Central Asian Orogenic Belt: Geochronology, petrogenesis, and implications for tectonic evolution
Creators: name: Gan, Baoping
name: Diwu, Chunrong
name: Wang, Tingyi
name: Pei, Qiuming
name: Wang, Shiming
Publisher: name: Geological Society of London
Year: 2022
Subjects: subject: Geology
subject: FOS: Earth and related environmental sciences

description: Supplementary Fig S1.
Homogenizable structures and model completeness
Creators: name: Ahlman, Ove
Publisher: name: arXiv
Year: 2016
Subjects: subject: Logic (math.LO)
subject: FOS: Mathematics
subject: 03C10, 03C50, 03C52

description: A homogenizable structure $\mathcal{M}$ is a structure where we may add a finite amount of new relational symbols to represent some $\emptyset-$definable relations in order to make the structure homogeneous. In this article we will divide the homogenizable structures into different classes which categorize many known examples and show what makes each class important. We will show that model completeness is vital for the relation between a structure and the amalgamation bases of its age and give a necessary and sufficient condition for an $ω-$categorical model-complete structure to be homogenizable.
description: 20 pages. Proposition 3.4 is removed from the lates version since the proof contained an error, however no other results depend on it so the rest of the paper remain consistent
Recursive Sparse Point Process Regression with Application to Spectrotemporal Receptive Field Plasticity Analysis
Creators: name: Sheikhattar, Alireza
name: Fritz, Jonathan B.
name: Shamma, Shihab A.
name: Babadi, Behtash
Publisher: name: arXiv
Year: 2015
Subjects: subject: Neural and Evolutionary Computing (cs.NE)
subject: Systems and Control (eess.SY)
subject: Optimization and Control (math.OC)
subject: Applications (stat.AP)
subject: Computation (stat.CO)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Mathematics

description: We consider the problem of estimating the sparse time-varying parameter vectors of a point process model in an online fashion, where the observations and inputs respectively consist of binary and continuous time series. We construct a novel objective function by incorporating a forgetting factor mechanism into the point process log-likelihood to enforce adaptivity and employ $\ell_1$-regularization to capture the sparsity. We provide a rigorous analysis of the maximizers of the objective function, which extends the guarantees of compressed sensing to our setting. We construct two recursive filters for online estimation of the parameter vectors based on proximal optimization techniques, as well as a novel filter for recursive computation of statistical confidence regions. Simulation studies reveal that our algorithms outperform several existing point process filters in terms of trackability, goodness-of-fit and mean square error. We finally apply our filtering algorithms to experimentally recorded spiking data from the ferret primary auditory cortex during attentive behavior in a click rate discrimination task. Our analysis provides new insights into the time-course of the spectrotemporal receptive field plasticity of the auditory neurons.
A fractal classification of the drainage dynamics in thin liquid films
Creators: name: Tsekov, R.
name: Evstatieva, E.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: It is demonstrated that the dynamic structure is very important for the rate of drainage of a thin liquid film and it can be effectively taken into account by a dynamic fractal dimension. It is shown that the latter is a powerful tool for description of the film drainage and classifies all the known results from the literature. The obtained general expression for the thinning rate is a heuristic one and predicts variety of drainage models, which are even difficult to simulate in practice. It is a typical example of a scaling law, which explains the origin of the complicate dependence of the thinning rate on the film radius.
Early Paleozoic intermediate igneous rocks in the Dunhuang Block, southern Central Asian Orogenic Belt: Geochronology, petrogenesis, and implications for tectonic evolution
Creators: name: Gan, Baoping
name: Diwu, Chunrong
name: Wang, Tingyi
name: Pei, Qiuming
name: Wang, Shiming
Publisher: name: Geological Society of London
Year: 2022
Subjects: subject: Geology
subject: FOS: Earth and related environmental sciences

description: Supplementary tables S1–S4.
Chiral plasmon in gapped Dirac systems
Creators: name: Kumar, Anshuman
name: Nemilentsau, Andrei
name: Fung, Kin Hung
name: Hanson, George
name: Fang, Nicholas X.
name: Low, Tony
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We study the electromagnetic response and surface electromagnetic modes in a generic gapped Dirac material under pumping with circularly polarized light. The valley imbalance due to pumping leads to a net Berry curvature, giving rise to a finite transverse conductivity. We discuss the appearance of nonreciprocal chiral edge modes, their hybridization and waveguiding in a nanoribbon geometry, and giant polarization rotation in nanoribbon arrays.
Early Paleozoic intermediate igneous rocks in the Dunhuang Block, southern Central Asian Orogenic Belt: Geochronology, petrogenesis, and implications for tectonic evolution
Creators: name: Gan, Baoping
name: Diwu, Chunrong
name: Wang, Tingyi
name: Pei, Qiuming
name: Wang, Shiming
Publisher: name: Geological Society of London
Year: 2022
Subjects: subject: Geology
subject: FOS: Earth and related environmental sciences

description: Supplementary Fig S2.
Porphyra umbilicalis Kutzing 1843
Creators: name: Dumilag, Richard V.
name: Aguinaldo, Zae-Zae A.
name: Mintu, Cynthia B.
name: Quinto, Myrna P.
name: Ame, Evelyn C.
name: Andres, Rolando C.
name: Monotilla, Wilberto D.
name: Yap, Sandra L.
name: Cao, Ernelea P.
name: Vital, Pierangeli G.
name: Fontanilla, Ian Kendrich C.
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Plantae
Rhodophyta
Bangiophyceae
Bangiales
Bangiaceae
Porphyra
Porphyra umbilicalis

description: Porphyra umbilicalis Kützing (1843: 383) [Ang et al. 2014: 23]
 Type: BM No. 000769632, Easdale, Argyll, Scotland (from the back of a limpet), 23.vii.1998, colls. J. Brodie & P. K. Hayes, with a cox 1 sequence (Genbank accession number: DQ442891) reported in Robba et al. (2006)
Philippine record of distribution: Manila Bay.
 Note: Ulva umbilicalis Linnaeus (1753: 1163) is currently recognized as the basionym of Po. umbilicalis (Brodie et al. 2008). The reduction of the Philippine record of U. umbilicalis to Po. umbilicalis (Ang et al. 2014) is unsubstantiated. The only Philippine specimen identified as U. umbilicalis was collected from Manila Bay by Blanco (1837, 1845, 1879). The same material used by the former was later described by Martens (1868: 47) as Zonaria gymnospora, now Padina gymnospora (Kützing) Sonder (1871: 47). Later, Merill (1905, 1918) identified Blanco’s material as Padina australis Hauck (1887: 44). The current accepted taxonomic name for Blanco’s U. umbilicalis specimen is P. australis, whose distribution is common throughout the Philippines (Silva et al. 1987).
description: Published as part of Dumilag, Richard V., Aguinaldo, Zae-Zae A., Mintu, Cynthia B., Quinto, Myrna P., Ame, Evelyn C., Andres, Rolando C., Monotilla, Wilberto D., Yap, Sandra L., Cao, Ernelea P., Vital, Pierangeli G. & Fontanilla, Ian Kendrich C., 2017, A review of the current taxonomic status of foliose Bangiales (Rhodophyta) in the Philippines, pp. 47-59 in Phytotaxa 312 (1) on page 51, DOI: 10.11646/phytotaxa.312.1.3, http://zenodo.org/record/13701704
Discrete gene replication events drive coupling between the cell cycle and circadian clocks
Creators: name: Paijmans, Joris
name: Bosman, Mark
name: Wolde, Pieter Rein ten
name: Lubensky, David K.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Molecular Networks (q-bio.MN)
subject: FOS: Biological sciences

description: Many organisms possess both a cell cycle to control DNA replication and a circadian clock to anticipate changes between day and night. In some cases, these two rhythmic systems are known to be coupled by specific, cross-regulatory interactions. Here, we use mathematical modeling to show that, additionally, the cell cycle generically influences circadian clocks in a non-specific fashion: The regular, discrete jumps in gene-copy number arising from DNA replication during the cell cycle cause a periodic driving of the circadian clock, which can dramatically alter its behavior and impair its function. A clock built on negative transcriptional feedback either phase locks to the cell cycle, so that the clock period tracks the cell division time, or exhibits erratic behavior. We argue that the cyanobacterium Synechococcus elongatus has evolved two features that protect its clock from such disturbances, both of which are needed to fully insulate it from the cell cycle and give it its observed robustness: a phosphorylation-based protein modification oscillator, together with its accompanying push-pull read-out circuit that responds primarily to the ratios of the different phosphoforms, makes the clock less susceptible to perturbations in protein synthesis; and the presence of multiple, asynchronously replicating copies of the same chromosome diminishes the effect of replicating any single copy of a gene.
description: 21 pages, 5 figures
Congruence subgroups and Enriques surface automorphisms
Creators: name: Allcock, Daniel
Publisher: name: arXiv
Year: 2016
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14J28, 20F55

description: We give conceptual proofs of some results on the automorphism group of an Enriques surface X, for which only computational proofs have been available. Namely, there is an obvious upper bound on the image of Aut(X) in the isometry group of X's numerical lattice, and we establish a lower bound for the image that is quite close to this upper bound. These results apply over any algebraically closed field, provided that X lacks nodal curves, or that all its nodal curves are (numerically) congruent to each other mod 2. In this generality these results were originally proven by Looijenga and Cossec-Dolgachev, developing earlier work of Coble.
description: Minor corrections, and a terminology change: "nodal class"--->"nodality class"
On the power of message passing for learning on graph-structured data
Creators: name: Fey, Matthias
Publisher: name: TU Dortmund
Year: 2022
Subjects: subject: Graph neural networks
subject: Deep learning
subject: 004
subject: Graph
subject: Deep Learning

description: This thesis proposes novel approaches for machine learning on irregularly structured input data such as graphs, point clouds and manifolds. Specifically, we are breaking up with the regularity restriction of conventional deep learning techniques, and propose solutions in designing, implementing and scaling up deep end-to-end representation learning on graph-structured data, known as Graph Neural Networks (GNNs). GNNs capture local graph structure and feature information by following a neural message passing scheme, in which node representations are recursively updated in a trainable and purely local fashion. In this thesis, we demonstrate the generality of message passing through a unified framework suitable for a wide range of operators and learning tasks. Specifically, we analyze the limitations and inherent weaknesses of GNNs and propose efficient solutions to overcome them, both theoretically and in practice, e.g., by conditioning messages via continuous B-spline kernels, by utilizing hierarchical message passing, or by leveraging positional encodings. In addition, we ensure that our proposed methods scale naturally to large input domains. In particular, we propose novel methods to fully eliminate the exponentially increasing dependency of nodes over layers inherent to message passing GNNs. Lastly, we introduce PyTorch Geometric, a deep learning library for implementing and working with graph-based neural network building blocks, built upon PyTorch.
Pyropia suborbiculata J. E. Sutherland, H. G. Choi, M. S. Hwang
Creators: name: Dumilag, Richard V.
name: Aguinaldo, Zae-Zae A.
name: Mintu, Cynthia B.
name: Quinto, Myrna P.
name: Ame, Evelyn C.
name: Andres, Rolando C.
name: Monotilla, Wilberto D.
name: Yap, Sandra L.
name: Cao, Ernelea P.
name: Vital, Pierangeli G.
name: Fontanilla, Ian Kendrich C.
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Plantae
Rhodophyta
Bangiophyceae
Bangiales
Bangiaceae
Pyropia
Pyropia suborbiculata

description: Pyropia suborbiculata (Kjellman) J.E.Sutherland, H.G.Choi, M.S.Hwang & W.A. Nelson in Sutherland et al.
 2011: 1145 [Cordero 1974: 138, 1977: 37, 1979: 23, 1980: 39, 1984: 86, 2008: 51; Trono & Fortes 1980: 67, 1982: 149; Ganzon-Fortes 1981: 22; Marcos-Agngarayngay 1984a: 19, 1984b: 124; Tungpalan 1984: 140; Masuda et al. 1991: 377; Monotilla & Notoya 2004: 323; Ame et al. 2010: 55]
Type: UPS, Goto, Nagasaki Prefecture, Japan, 25.v.1881, coll. J. V. Petersen
Philippine record of distribution: Cavite (Corregidor Is.), Ilocos Norte (Burgos), Cagayan (Palaui Is., Sta. Ana).
 Note: Sequenced materials of Py. tanegashimensis (Dumilag et al. 2016) suggest that records of specimens previously known as Py. suborbiculata from Palaui Is., Cagayan (Cordero 1974) may have been misidentified. Cordero (1977) described conspecific specimens from Ilocos Norte to display “no mark of taxonomic differences” from those found in the former site. Molecular analysis on foliose Bangiales specimens collected from the similar site reported in Monotilla & Notoya (2004), i.e., Burgos, Ilocos Norte, have indicated the presence only of Py. acanthophora (Dumilag & Aguinaldo 2017). Although Py. suborbiculata is widely distributed throughout Asian waters (Yoshida 1998; Monotilla & Notoya 2004; Tsutsui et al. 2005) and is known to have been introduced to the Atlantic United States, New Zealand, Canary Islands, Brazil and Iberian Peninsula (Broom et al. 2002 and references therein; Milstein & Oliviera 2005; Vergès et al. 2013), its presence in the Philippines is yet to be confirmed until actual materials are sequenced.
description: Published as part of Dumilag, Richard V., Aguinaldo, Zae-Zae A., Mintu, Cynthia B., Quinto, Myrna P., Ame, Evelyn C., Andres, Rolando C., Monotilla, Wilberto D., Yap, Sandra L., Cao, Ernelea P., Vital, Pierangeli G. & Fontanilla, Ian Kendrich C., 2017, A review of the current taxonomic status of foliose Bangiales (Rhodophyta) in the Philippines, pp. 47-59 in Phytotaxa 312 (1) on page 52, DOI: 10.11646/phytotaxa.312.1.3, http://zenodo.org/record/13701704
Three-dimensional photonic Dirac points stabilized by point group symmetry
Creators: name: Wang, HaiXiao
name: Xu, Lin
name: Chen, HuanYang
name: Jiang, Jian-Hua
Publisher: name: arXiv
Year: 2016
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We discover a pair of stable 3D Dirac points, 3D photonic analog of graphene, in all-dielectric photonic crystals using structures commensurate with nano-fabrication for visible-frequency photonic applications. The Dirac points carry nontrivial $Z_2$ topology and emerge for a large range of material parameters in hollow cylinder hexagonal photonic crystals. From Kramers theorem and group theory, we find that only the $C_6$ symmetry lead to point group symmetry stabilized Dirac points in 3D all-dielectric photonic crystals. {The Dirac points are characterized using ${\vec k}\cdot{\vec P}$ theory for photonic bands in combination with symmetry analysis. Breaking inversion symmetry splites the Dirac points into Weyl points. The physical properties and experimental consequences of Dirac points are also studied. The Dirac points are found to be robust against parameter tuning and weak disorders.
description: 12 pages, 13 figures. Published version
Supplementary Figures from Cx43 can form functional channels at the nuclear envelope and modulate gene expression in cardiac cells
Creators: name: Martins-Marques, Tania
name: Witschas, Katja
name: Ribeiro, Ilda
name: Zuzarte, Mónica
name: Catarino, Steve
name: Ribeiro-Rodrigues, Teresa
name: Caramelo, Francisco
name: Aasen, Trond
name: Carreira, Isabel Marques
name: Goncalves, Lino
name: Leybaert, Luc
name: Girao, Henrique
Publisher: name: The Royal Society
Year: 2023
Subjects: Biochemistry and Cell Biology not elsewhere classified

description: Supplementary Figures 1-8
Pyropia acanthophora M. C. Oliveira, D. Milstein & E. C. Oliveira
Creators: name: Dumilag, Richard V.
name: Aguinaldo, Zae-Zae A.
name: Mintu, Cynthia B.
name: Quinto, Myrna P.
name: Ame, Evelyn C.
name: Andres, Rolando C.
name: Monotilla, Wilberto D.
name: Yap, Sandra L.
name: Cao, Ernelea P.
name: Vital, Pierangeli G.
name: Fontanilla, Ian Kendrich C.
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Plantae
Rhodophyta
Bangiophyceae
Bangiales
Bangiaceae
Pyropia
Pyropia acanthophora

description: Pyropia acanthophora (E.C.Oliveira & Coll) M.C.Oliveira, D.Milstein & E.C.Oliveira in Sutherland et al. 2011:
 1142 [Rivera 2014, Dumilag & Aguinaldo 2017]
Type: SPF 5170, Ubatuba, São Paulo, Brazil, 25.x.1973, colls. E. C. Oliveira & J. Coll
Philippine record of distribution: Camiguin Is., Ilocos Norte (Burgos, Pagudpud), Cagayan (Aparri, Claveria, Sta. Praxedes, Sta. Ana), Pamocton Island.
 Note: Confirmed Py. acanthophora materials from the Philippines include populations with multiple haplotypes that are closely associated to other native conspecifics found in the Indo-Pacific region. So far, Py. acanthophora is the most widely distributed foliose Bangiales in the Philippines. Phylogenetic and haplotype analyses showed that populations from thirteen sites in the northern Philippines showed high genetic variation characteristic of endemic populations. The genetic structure of Philippine populations of Py. acanthophora exhibited a chaotic patchiness pattern wherein populations displayed highly site-exclusive haplotypes with wide genetic variability but lacked corresponding local geographic patterns (Dumilag & Aguinaldo 2017).
description: Published as part of Dumilag, Richard V., Aguinaldo, Zae-Zae A., Mintu, Cynthia B., Quinto, Myrna P., Ame, Evelyn C., Andres, Rolando C., Monotilla, Wilberto D., Yap, Sandra L., Cao, Ernelea P., Vital, Pierangeli G. & Fontanilla, Ian Kendrich C., 2017, A review of the current taxonomic status of foliose Bangiales (Rhodophyta) in the Philippines, pp. 47-59 in Phytotaxa 312 (1) on page 53, DOI: 10.11646/phytotaxa.312.1.3, http://zenodo.org/record/13701704
Contribution to Financial Modeling and Financial Forecasting
Creators: name: Ebrahimabadi, Rouhollah
Publisher: name: London South Bank University
Year: 2022

description: This thesis consists of three chapters. Each chapter is independent research that is conducted during my study. This research is concentrated on financial time series modeling and forecasting. On first chapter, the research aims to prove that any abnormal behavior in debt level is a signal of future unexpected return for firms that is listed in indexes in this study, hence it is a signal to buy. In order to prove this theory multiple indexes from around the world were taken into consideration. This behavior is consistent in most of indexes around the word. The second chapter investigate the effect of United State president speech on value of United State Currency in Foreign Exchange Rate market. In this analysis it is shown that during the time the president is delivering a speech there is distinctive changes in USD value and volatility in global markets. This chapter implies that this effect cannot be captured by linear models, and the impact of the presidential speech is short term. Finally, the third chapter which is the major research of this thesis, suggest two new methods that potentially enhance the financial time series forecasting. Firstly, the new ARMA-RNN model is presented. The suggested model is inheriting the process of Autoregressive Moving Average model which is extensively studied, and train a recurrent neural network based on it to benefit from unique ability of ARMA model as well as strength and nonlinearity of artificial neural network. Secondly the research investigates the use of different frequency of data for input layer to predict the same data on output layer. In other words, artificial neural networks are trained on higher frequency data to predict lower frequency. Finally, both stated method is combined to achieve more superior predictive model.
Necessary conditions for an AdS-type instability
Creators: name: Menon, Dhanya S.
name: Suneeta, Vardarajan
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In this work, we analyze the necessary conditions for a nonlinear AdS-type instability in the gravity-scalar field system. In particular, we discuss the necessary conditions for a cascade of energy to higher modes by applying results in KAM theory. Our analytical framework explains numerical observations of instability of spacetimes even when the spectrum is only asymptotically resonant, and the fact that a minimum field amplitude is needed to trigger it. Our framework can be applied for similar stability analyses of fields in (locally) asymptotically AdS spacetimes. We illustrate this with the example of the AdS soliton. Further, we conjecture on the possible reasons for quasi-periodic behaviour observed in perturbations of AdS spacetime. Certain properties of the eigenfunctions of the linear system dictate whether there will be localization in space leading to black hole formation. These properties are examined using the asymptotics of Jacobi polynomials. Finally we discuss recent results on the AdS instability in Einstein-Gauss-Bonnet gravity in light of our work.
description: 31 pages, version to appear in Physical Review D
Supplementary material to: “The media composition as a crucial element in high throughput metabolic network reconstruction"
Creators: name: Borer, Benedict
name: Magnúsdóttir, Stefanía
Publisher: name: The Royal Society
Year: 2023
Subjects: subject: 60114 Systems Biology
subject: FOS: Biological sciences
subject: 60113 Synthetic Biology
subject: Computational Biology

description: In recent years, metagenome-assembled genomes (MAGs) have provided glimpses into the intra- and interspecies genetic diversity and interactions that form the bases of complex microbial communities. High-throughput reconstruction of genome-scale metabolic networks (GEMs) from MAGs is a promising avenue to disentangle the myriad trophic interactions stabilizing these communities. However, high-throughput reconstruction of GEMs relies on accurate gap filling of metabolic pathways using automated algorithms. Here, we systematically explore how the media composition (specification of the available nutrients and metabolites) during gap filling influences the resulting GEMs concerning predicted auxotrophies for fully sequenced model organisms and environmental isolates. We expand this analysis by using 106 MAGs from the same species with differing quality. We find that although the completeness of MAGs influences the fraction of gap-filled reactions, the media composition plays the dominant role in the accurate prediction of auxotrophies that form the basis of myriad community interactions. We propose that constraining the media composition for gap filling through both experimental approaches and computational approaches will increase the reliability of high-throughput reconstruction of genome-scale metabolic models from MAGs and paves the way for culture independent prediction of trophic interactions in complex microbial communities.
Supplementary Figures from Cx43 can form functional channels at the nuclear envelope and modulate gene expression in cardiac cells
Creators: name: Martins-Marques, Tania
name: Witschas, Katja
name: Ribeiro, Ilda
name: Zuzarte, Mónica
name: Catarino, Steve
name: Ribeiro-Rodrigues, Teresa
name: Caramelo, Francisco
name: Aasen, Trond
name: Carreira, Isabel Marques
name: Goncalves, Lino
name: Leybaert, Luc
name: Girao, Henrique
Publisher: name: The Royal Society
Year: 2023
Subjects: Cell Biology

description: Supplementary Figures 1-8
Kim and Hu (2023) Onggi - Supplemental Material.pdf from Onggi’s permeability to carbon dioxide accelerates kimchi fermentation
Creators: name: Kim, Soohwan
name: Hu, David L.
Publisher: name: The Royal Society
Year: 2023
Subjects: subject: Biophysics
subject: 110601 Biomechanics
subject: FOS: Health sciences
subject: 10202 Biological Mathematics
subject: FOS: Mathematics

description: Since ancient times, Korean chefs have fermented foods in an onggi, a traditional earthenware vessel. The porous structure of the onggi mimics the loose soil where lactic acid bacteria is naturally found. This permeability has been purported to facilitate the growth of lactic acid bacteria, but the details of the process remain poorly understood. In this combined experimental and theoretical study, we ferment salted Napa cabbage in onggi and hermetic glassware and measure the time course of carbon dioxide concentration, which is a signature of fermentation. We present a mathematical model for carbon dioxide generation rate during fermentation using the onggi’s gas permeability as a free parameter. Our model provides a good fit for the data, and we conclude that porous walls help the onggi to ‘exhale’ carbon dioxide, lowering internal levels to those favoured by lactic acid bacteria. The positive pressure inside the onggi and the constant outflow through its walls act as a safety valve for bacteria growth by blocking the entry of external contaminants without mechanical components. We hope this study draws attention to the work of traditional artisans and inspires energy-efficient methods for fermenting and storing food products.
Spin-orbital and spin Kondo effects in parallel coupled quantum dots
Creators: name: Krychowski, D.
name: Lipinski, S.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Strong electron correlations and interference effects are discussed in parallel-coupled single-level and orbitally doubly degenerate quantum dots. The finite-U mean-field slave boson approach is used to study many-body effects. The analysis is carried out in a wide range of parameter space including both atomic-like and molecular-like Kondo regimes and taking into account various perturbations, like interdot tunneling, interdot interaction, mixing of the electrode channels and exchange interaction. We also discuss the influence of singularities of electronic structure and the impact of polarization of electrodes. Special attention is paid to potential spintronic applications of these systems showing how current polarization can be controlled by adjusting interference conditions and correlations by gate voltage. Simple proposals of double dot spin valve and bipolar electrically tunable spin filter are presented.
description: 14 pages, 16 figures
Pyropia tanegashimensis N. Kikuchi & E. Fujiyoshi
Creators: name: Dumilag, Richard V.
name: Aguinaldo, Zae-Zae A.
name: Mintu, Cynthia B.
name: Quinto, Myrna P.
name: Ame, Evelyn C.
name: Andres, Rolando C.
name: Monotilla, Wilberto D.
name: Yap, Sandra L.
name: Cao, Ernelea P.
name: Vital, Pierangeli G.
name: Fontanilla, Ian Kendrich C.
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Plantae
Rhodophyta
Bangiophyceae
Bangiales
Bangiaceae
Pyropia
Pyropia tanegashimensis

description: Pyropia tanegashimensis (Shinmura) N.Kikuchi & E.Fujiyoshi in Sutherland et al. 2011: 1145 [Dumilag et al.
2016]
Type: Kagoshima Prefectural Fisheries Experimental Station (Shinmura no. 19731), Iseki, Tanegashima, Kagoshima Prefecture, Japan, 29.ix.1971, coll. I. Shinmura
Philippine record of distribution: Palaui Is., (Sta. Ana, Cagayan).
 Note: The infrequently reported Pyropia tanegashimensis was described for the first time in the Philippines, viz. Palaui Is., Sta. Ana, Cagayan (Dumilag et al. 2016). The morphological characteristics and phylogenetic affinity of Philippine Py. tanegashimensis among other related Pyropia species were explored. The frequently misidentified Py. suborbiculata that was previously reported from the same site has been confirmed as Py. tanegashimensis based on comparative analyses of plastid rbc L and mitochondrial COI-5 P gene sequences. Phylogenetic analysis revealed that Philippine populations of Py. tanegashimensis are endemic and are distinct from the known endemic populations from Japan and to the introduced strain found in Brazil.
description: Published as part of Dumilag, Richard V., Aguinaldo, Zae-Zae A., Mintu, Cynthia B., Quinto, Myrna P., Ame, Evelyn C., Andres, Rolando C., Monotilla, Wilberto D., Yap, Sandra L., Cao, Ernelea P., Vital, Pierangeli G. & Fontanilla, Ian Kendrich C., 2017, A review of the current taxonomic status of foliose Bangiales (Rhodophyta) in the Philippines, pp. 47-59 in Phytotaxa 312 (1) on page 53, DOI: 10.11646/phytotaxa.312.1.3, http://zenodo.org/record/13701704
Impact Angle Control of Interplanetary Shock Geoeffectiveness: A Statistical Study
Creators: name: Oliveira, D. M.
name: Raeder, J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Space Physics (physics.space-ph)
subject: FOS: Physical sciences

description: We present a survey of interplanetary (IP) shocks using Wind and ACE satellite data from January 1995 to December 2013 to study how IP shock geoeffectiveness is controlled by IP shock impact angles. A shock list covering one and a half solar cycle is compiled. The yearly number of IP shocks is found to correlate well with the monthly sunspot number. We use data from SuperMAG, a large chain with more than 300 geomagnetic stations, to study geoeffectiveness triggered by IP shocks. The SuperMAG SML index, an enhanced version of the familiar AL index, is used in our statistical analysis. The jumps of the SML index triggered by IP shock impacts on the Earth's magnetosphere is investigated in terms of IP shock orientation and speed. We find that, in general, strong (high speed) and almost frontal (small impact angle) shocks are more geoeffective than inclined shocks with low speed. The strongest correlation (correlation coefficient R = 0.70) occurs for fixed IP shock speed and varying the IP shock impact angle. We attribute this result, predicted previously with simulations, to the fact that frontal shocks compress the magnetosphere symmetrically from all sides, which is a favorable condition for the release of magnetic energy stored in the magnetotail, which in turn can produce moderate to strong auroral substorms, which are then observed by ground based magnetometers.
description: 8 pages, 5 figures, Journal of Geophysical Research (2015)
A Usage Comparison for Print and Electronic Books in the University of North Carolina at Chapel Hill
Creators: name: Fernandez, Michael
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003
Subjects: Use studies--Electronic books
College and university libraries--Book collections
College and university libraries--Collection development

description: This study compares library usage of monographs in both print and electronic formats at the University of North Carolina at Chapel Hill. The purpose of the study was to assess the value of comparing usage statistics for collection development as well as to evaluate how subject areas affected user preference for the print or electronic format. For this study, a sample of thirty titles was taken in ten separate subject categories. The number of usages was aggregated for UNC's print collection and their netLibrary collection of electronic books for each of the ten categories. Comparing the usage data, the overall trend showed that on the average, print books were used more than their electronic counterparts. Within the different subject categories, comparative usage varied, with some subjects having higher usages of electronic books and others having higher usage of print books.
Fully quantum fluctuation theorems
Creators: name: Aberg, Johan
Publisher: name: arXiv
Year: 2016
Subjects: subject: Quantum Physics (quant-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: Systems that are driven out of thermal equilibrium typically dissipate random quantities of energy on microscopic scales. Crooks fluctuation theorem relates the distribution of these random work costs with the corresponding distribution for the reverse process. By an analysis that explicitly incorporates the energy reservoir that donates the energy, and the control system that implements the dynamic, we here obtain a quantum generalization of Crooks theorem that not only includes the energy changes in the reservoir, but the full description of its evolution, including coherences. This approach moreover opens up for generalizations of the concept of fluctuation relations. Here we introduce `conditional' fluctuation relations that are applicable to non-equilibrium systems, as well as approximate fluctuation relations that allow for the analysis of autonomous evolution generated by global time-independent Hamiltonians. We furthermore extend these notions to Markovian master equations, implicitly modeling the influence of the heat bath.
description: Published version
Melting and Mixing States of the Earth's Mantle after the Moon-Forming Impact
Creators: name: Nakajima, Miki
name: Stevenson, David J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: The Earth's Moon is thought to have formed by an impact between the Earth and an impactor around 4.5 billion years ago. This impact could have been so energetic that it could have mixed and homogenized the Earth's mantle. However, this view appears to be inconsistent with geochemical studies that suggest that the Earth's mantle was not mixed by the impact. Another plausible outcome is that this energetic impact melted the whole mantle, but the extent of mantle melting is not well understood even though it must have had a significant effect on the subsequent evolution of the Earth's interior and atmosphere. To understand the initial state of the Earth's mantle, we perform giant impact simulations using smoothed particle hydrodynamics (SPH) for three different models: (a) standard: a Mars-sized impactor hits the proto-Earth, (b) fast-spinning Earth: a small impactor hits a rapidly rotating proto-Earth, and (c) sub-Earths: two half Earth-sized planets collide. We use two types of equations of state (MgSiO3 liquid and forsterite) to describe the Earth's mantle. We find that the mantle remains unmixed in (a), but it may be mixed in (b) and (c). The extent of mixing is most extensive in (c). Therefore, (a) is most consistent and (c) may be least consistent with the preservation of the mantle heterogeneity, while (b) may fall between. We determine that the Earth's mantle becomes mostly molten by the impact in all of the models. The choice of the equations of state does not affect these outcomes. Additionally, our results indicate that entropy gains of the mantle materials by a giant impact cannot be predicted well by the Rankine-Hugoniot equations. Moreover, we show that the mantle can remain unmixed on a Moon-forming timescale if it does not become mixed by the impact.
description: Accepted for publication in EPSL
Potier et al. owls binocular_ Electronic-supplementary-materials from Binocular field configuration in owls: the role of foraging ecology
Creators: name: POTIER, Simon
name: Roulin, Alexandre
name: Martin, Graham R.
name: Portugal, Steven J.
name: Bonhomme, Vincent
name: Bouchet, Thierry
name: de Romans, Romuald
name: Meyrier, Eva
name: Kelber, Almut
Publisher: name: The Royal Society
Year: 2023
Subjects: Neurosciences not elsewhere classified

description: Supplementary analyses
Meron deconfinement in the quantum Hall bilayer at intermediate distances
Creators: name: Milovanovic, M. V.
name: Dobardzic, E.
name: Papic, Z.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Quantum Hall bilayer phase diagram with respect to interlayer distance bears a remarkable similarity with phase diagrams of strongly correlated systems as a function of doping, with magnetic ordering on the one end and Fermi-liquid-like behaviour on the other. Moreover, it has been suggested [PRL 101, 176803 (2008)] that a BCS correlated state of composite fermions with p-wave pairing may exist in the intermediate region. In the same region, an exact diagonalization study in the torus geometry [PRB 69, 045319 (2004)] pointed out the existence of state(s) with pseudospin spiraling order. Here we reconcile these two descriptions of the intermediate state by considering the underlying bosonic representation of the composite fermion paired state in the long distance limit, and by performing extensive exact diagonalizations on the torus. We argue that the spiraling states belong to the manifold of degenerate ground state(s), and are a consequence of Bose condensation of the quasiparticles (with critical algebraic correlations) at non-zero momenta in the two pseudospin states. The spiraling states, generated in this way as spin-textures, can be identified with meron-antimeron constructions. Thus, merons -- the fractionally charged vortex excitations of the XY magnetically ordered state -- constitute some of the topological sectors. It follows that merons are deconfined in the intermediate state, and allow for a smooth transition between the magnetically ordered and Fermi-liquid-like phases, in which they are bound in pairs.
description: 14 pages, 7 figures