cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
WHO classification of tumours fifth edition: Evolving issues in the classification, diagnosis and prognostication of prostate cancer
Creators: name: Kench, James G
name: Amin, Mahul B
name: Berney, Daniel M
name: Compérat, Eva M
name: Cree, Ian A
name: Gill, Anthony J
name: Hartmann, Arndt
name: Menon, Santosh
name: Moch, Holger
name: Netto, George J
name: Raspollini, Maria R
name: Rubin, Mark A
name: Tan, Puay Hoon
name: Tsuzuki, Toyonori
name: Turajlic, Samra
name: van der Kwast, Theo H
name: Zhou, Ming
name: Srigley, John R
Publisher: name: The Francis Crick Institute
Year: 2022
Subjects: classificationCode: Tumour Biology
subject: Tumour Biology
classificationCode: Signalling & Oncogenes
subject: Signalling & Oncogenes
classificationCode: Genetics & Genomics
subject: Genetics & Genomics
classificationCode: Genome Integrity & Repair
subject: Genome Integrity & Repair
classificationCode: Computational & Systems Biology
subject: Computational & Systems Biology

description: The 5th edition of the WHO Classification of Tumours of the Urinary and Male Genital Systems encompasses several updates to the classification and diagnosis of prostatic carcinoma as well as incorporating advancements in assessment of its prognosis, including recent grading modifications. Some of the salient aspects include: 1) recognition that PIN-like carcinoma is not synonymous with a pattern of ductal carcinoma but better classified as a subtype of acinar adenocarcinoma; 2) a specific section on treatment-related neuroendocrine prostatic carcinoma in view of the tight correlation between androgen deprivation therapy and the development of prostatic carcinoma with neuroendocrine morphology, and the emerging data on lineage plasticity; 3) a terminology change of basal cell carcinoma to “adenoid cystic (basal cell) cell carcinoma” given the presence of an underlying MYB::NFIB gene fusion in many cases; 4) discussion of the current issues in the grading of acinar adenocarcinoma and the prognostic significance of cribriform growth patterns; and 5) more detailed coverage of intraductal carcinoma of prostate (IDC-P) reflecting our increased knowledge of this entity, while recommending the descriptive term atypical intraductal proliferation (AIP) for lesions falling short of IDC-P but containing more atypia than typically seen in high-grade prostatic intraepithelial neoplasia (HGPIN). Lesions previously regarded as cribriform patterns of HGPIN are now included in the AIP category. This review discusses these developments, summarising the existing literature, as well as the emerging morphological and molecular data that underpins the classification and prognostication of prostatic carcinoma.
MOESM3 of A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos
Creators: name: Troll, Christopher
name: Kapp, Joshua
name: Rao, Varsha
name: Harkins, Kelly
name: Cole, Charles
name: Naughton, Colin
name: Morgan, Jessica
name: Shapiro, Beth
name: Green, Richard
Publisher: name: figshare
Year: 2019
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Plant Biology

description: Additional file 3: Figure S1. Insert distribution for replicate libraries for H-69 and H-81. (docx 303â€‰kb)
Confinement versus Chiral Symmetry
Creators: name: Mocsy, Agnes
name: Sannino, Francesco
name: Tuominen, Kimmo
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We construct an effective Lagrangian which illustrates why color deconfines when chiral symmetry is restored in hot gauge theories with quarks in the fundamental representation. For quarks in the adjoint representation we show that while deconfinement and the chiral transition do not need to coincide, entanglement between them is still present. Extension to the chemical potential driven transition is discussed.
description: RevTeX 4, 4 pages, 1 eps figure, version to appear in PRL
Unsupervised Feature Learning in Remote Sensing
Creators: name: Reite, Aaron
name: Kangas, Scott
name: Steck, Zackery
name: Goley, Steven
name: Von Stroh, Jonathan
name: Forsyth, Steven
Publisher: name: arXiv
Year: 2019
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Machine Learning (cs.LG)
subject: Image and Video Processing (eess.IV)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: The need for labeled data is among the most common and well-known practical obstacles to deploying deep learning algorithms to solve real-world problems. The current generation of learning algorithms requires a large volume of data labeled according to a static and pre-defined schema. Conversely, humans can quickly learn generalizations based on large quantities of unlabeled data, and turn these generalizations into classifications using spontaneous labels, often including labels not seen before. We apply a state-of-the-art unsupervised learning algorithm to the noisy and extremely imbalanced xView data set to train a feature extractor that adapts to several tasks: visual similarity search that performs well on both common and rare classes; identifying outliers within a labeled data set; and learning a natural class hierarchy automatically.
Deformations of N=4 SYM and integrable spin chain models
Creators: name: Berenstein, David
name: Cherkis, Sergey A.
Publisher: name: arXiv
Year: 2004
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Beginning with the planar limit of N=4 SYM theory, we study planar diagrams for field theory deformations of N=4 which are marginal at the free field theory level. We show that the requirement of integrability of the full one loop dilatation operator in the scalar sector, places very strong constraints on the field theory, so that the only soluble models correspond essentially to orbifolds of N=4 SYM. For these, the associated spin chain model gets twisted boundary conditions that depend on the length of the chain, but which are still integrable. We also show that theories with integrable subsectors appear quite generically, and it is possible to engineer integrable subsectors to have some specific symmetry, however these do not generally lead to full integrability. We also try to construct a theory whose spin chain has quantum group symmetry SO_q(6) as a deformation of the SO(6) R-symmetry structure of N=4 SYM. We show that it is not possible to obtain a spin chain with that symmetry from deformations of the scalar potential of N=4 SYM. We also show that the natural context for these questions can be better phrased in terms of multi-matrix quantum mechanics rather than in four dimensional field theories.
description: 43 pages, Latex, 3 figures. v2: updated references, minor changes. v3: added one reference, minor changes
Robust Traffic Control Using a First Order Macroscopic Traffic Flow Model
Creators: name: Liu, Hao
name: Claudel, Christian
name: Machemehl, Randy
Publisher: name: arXiv
Year: 2020
Subjects: subject: Optimization and Control (math.OC)
subject: FOS: Mathematics

description: Traffic control is at the core of research in transportation engineering because it is one of the best practices for reducing traffic congestion. It has been shown in recent years that the traffic control problem involving Lighthill-Whitham-Richards (LWR) model can be formulated as a Linear Programming (LP) problem given that the corresponding initial conditions and the model parameters in the fundamental diagram are fixed. However, the initial conditions can be uncertain when studying actual control problems. This paper presents a stochastic programming formulation of the boundary control problem involving chance constraints, to capture the uncertainty in the initial conditions. Different objective functions are explored using this framework, and case studies for both a single highway link and a small network are conducted. In addition, the optimal results are validated with Monte Carlo simulation.
description: Published on IEEE Transactions on Intelligent Transportation Systems
Additional file of A simple Bayesian estimate of direct RNAi gene regulation events from differential gene expression profiles
Creators: name: Wilson, Paul A
name: Plucinski, Mathew
Publisher: name: figshare
Year: 2021
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 60506 Virology
subject: Computational Biology

description: Additional file of A simple Bayesian estimate of direct RNAi gene regulation events from differential gene expression profiles
Halting planet migration by photoevaporation from the central source
Creators: name: Matsuyama, Isamu
name: Johnstone, Doug
name: Murray, Norman
Publisher: name: arXiv
Year: 2003
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: The recent discovery of Jupiter-mass planets orbiting at a few AU from their stars compliments earlier detections of massive planets on very small orbits. The short period orbits strongly suggest that planet migration has occurred, with the likely mechanism being tidal interactions between the planets and the gas disks out of which they formed. The newly discovered long period planets, together with the gas giant planets in our solar system, show that migration is either absent or rapidly halted in at least some systems. We propose a mechanism for halting type-II migration at several AU in a gas disk. Photoevaporation of the disk by irradiation from the central star can produce a gap in the disk at a few AU, preventing planets outside the gap from migrating down to the star. This would result in an excess of systems with planets at or just outside the photoevaporation radius.
description: 12 pages, 3 figures, accepted for publication by ApJ Letters
MOESM2 of A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos
Creators: name: Troll, Christopher
name: Kapp, Joshua
name: Rao, Varsha
name: Harkins, Kelly
name: Cole, Charles
name: Naughton, Colin
name: Morgan, Jessica
name: Shapiro, Beth
name: Green, Richard
Publisher: name: figshare
Year: 2019
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Cancer
subject: Hematology

description: Additional file 2: Table S2. All ofther human cfDNA libraries NGS statistics. (docx 16â€‰kb)
Defeating Opaque Predicates Statically through Machine Learning and Binary Analysis
Creators: name: Tofighi-Shirazi, Ramtine
name: Asăvoae, Irina
name: Elbaz-Vincent, Philippe
name: Le, Thanh-Ha
Publisher: name: arXiv
Year: 2019
Subjects: subject: Cryptography and Security (cs.CR)
subject: Machine Learning (cs.LG)
subject: Programming Languages (cs.PL)
subject: Symbolic Computation (cs.SC)
subject: FOS: Computer and information sciences

description: We present a new approach that bridges binary analysis techniques with machine learning classification for the purpose of providing a static and generic evaluation technique for opaque predicates, regardless of their constructions. We use this technique as a static automated deobfuscation tool to remove the opaque predicates introduced by obfuscation mechanisms. According to our experimental results, our models have up to 98% accuracy at detecting and deob-fuscating state-of-the-art opaque predicates patterns. By contrast, the leading edge deobfuscation methods based on symbolic execution show less accuracy mostly due to the SMT solvers constraints and the lack of scalability of dynamic symbolic analyses. Our approach underlines the efficiency of hybrid symbolic analysis and machine learning techniques for a static and generic deobfuscation methodology.
Paradoxical whole genome DNA methylation dynamics of 5’aza-deoxycytidine in chronic low-dose exposure in mice
Creators: name: Mathia Colwell
name: Wanner, Nicole M.
name: Drown, Chelsea
name: Drown, Melissa
name: Dolinoy, Dana C.
name: Faulk, Christopher
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Decitabine (5-aza-2ʹdeoxycytidine; DAC) is a DNA methyltransferase inhibitor used to hypomethylate the epigenome. Current dosing regimens of DAC for use in mice vary widely and their hypomethylating ability has not been robustly characterized, despite reliable results of hypomethylation of the epigenome with cell lines in vitro and tissue specificity in vivo. We investigated the effects on the DNA methylome and gene expression within mice exposed to chronic low doses of DAC ranging from 0 to 0.35 mg/kg over a period of 7 weeks without causing toxicity. Our dose paradigm resulted in no cytotoxic effects within target tissues, although testes weight and sperm concentration significantly reduced as dose increased (p-value <0.05). By whole genome bisulphite sequencing (WGBS), we identify tissue and dose-specific differentially methylated CpGs (DMCs) and regions (DMRs) in testes and liver. Testes methylation is more sensitive to DAC exposure when compared to liver, cortex, and hippocampus. Gene expression was dysregulated in testes and liver, targeting non-specific pathways as dose increases. Together our data suggest DNA methylation and gene expression are disrupted by in vivo DAC treatment in a non-uniform manner contrary to expectations, and that no dose level or regimen is sufficient to cause systemic hypomethylation in whole mice.
Exotic baryons with charm number $\pm1$ from Skyrme model
Creators: name: Wu, Bin
name: Ma, Bo-Qiang
Publisher: name: arXiv
Year: 2004
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: Nuclear Experiment (nucl-ex)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We illustrate the exotic SU(3) baryon sub-multiplets in the SU(4) baryon multiplets predicted from the flavor SU(4) collective-coordinate quantization, and investigate the exotic states with charm number $C=\pm1$ up to leading order of $1/N_c$ under chiral $SU(3)_L\times SU(3)_R$ symmetry and the heavy quark limit from bound state approach. We find that there exist the $\bar{15}$-plets and 24-plets with C=1 and the $\bar{6}$-plets, 15-plets and $15^{\prime}$-plets with $C=-1$ bounded in this approach, qualitatively consistent with predictions from the flavor SU(4) collective-coordinate quantization. By fitting one unique parameter of leading SU(3) flavor symmetry breaking term with the mass difference between $Ξ_c$ and $Σ_c$ and up to $O(m_Q^0N_c^{-1})$, we give all the average masses of baryons in $\bar{6}$-plet and 15-plet. Several general relations of these masses without any parameter are also introduced.
description: 13 pages, 2 figures. Errs in figures corrected. To appear in PRD
MOESM1 of A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos
Creators: name: Troll, Christopher
name: Kapp, Joshua
name: Rao, Varsha
name: Harkins, Kelly
name: Cole, Charles
name: Naughton, Colin
name: Morgan, Jessica
name: Shapiro, Beth
name: Green, Richard
Publisher: name: figshare
Year: 2019
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Hematology

description: Additional file 1: Table S1. SRSLY human cfDNA libraries NGS statistics. (docx 15â€‰kb)
Long-term stabilization of carrier envelope phases of mid-infrared pulses for the precise detection of phase-sensitive responses to electromagnetic waves
Creators: name: Yamakawa, T.
name: Sono, N.
name: Kitao, T.
name: Morimoto, T.
name: Kida, N.
name: Miyamoto, T.
name: Okamoto, H.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We report a newly designed mid-infrared-pump visible-probe measurement system, which can measure phase-sensitive responses to a mid-infrared pulse along the oscillating electromagnetic field. In this system, the pump light is a phase-locked mid-infrared pulse with temporal width of 100 fs, which is produced via difference frequency generation (DFG) from two idler pulses of two optical parametric amplifiers (OPAs) that are excited by the same Ti:sapphire regenerative amplifier. The probe pulse is a visible pulse with temporal width of 9 fs, and it is generated from a custom-built non-collinear OPA. By measuring the electric-field waveforms of mid-infrared pump pulses with electro-optic sampling and evaluating their carrier envelope phase (CEP) and the temporal positions of their envelopes relative to ultrashort visible probe pulses, we are able to perform double feedback corrections that eliminate both the following sources of drift. The CEP drift in mid-infrared pulses originating from fluctuations in the difference of optical-path lengths of the two idler pulses before the DFG is corrected by inserting a wedge plate in one idler path, and the drift in pump-probe delay times due to fluctuations in the difference of the overall optical-path lengths of the pump and probe pulses is corrected with mechanical delay lines. In this double-feedback system, the absolute carrier phase of mid-infrared pulses can be fixed within 200 mrad and errors in the measurement of phase-sensitive responses can be reduced to within 1 fs over a few tens of hours.
description: 17 pages including 4 figures (Supplementary materials: 4 pages including no figures)
Supplementary document for Nanophotonic supercontinuum based mid-infrared dual-comb spectroscopy - 4729854.pdf
Creators: name: Guo, Hairun
name: Weng, Wenle
name: Liu, Junqiu
name: Yang, Fan
name: Hänsel, Wolfgang
name: Brès, Camille-Sophie
name: Holzwarth, Ronald
name: Thevenaz, Luc
name: Kippenberg, Tobias
Publisher: name: Optica Publishing Group
Year: 2020
Subjects: Uncategorized

description: Supplemental information to the manuscript
Nodal quasiparticles and classical phase fluctuations in d-wave superconductors
Creators: name: Samokhin, K. V.
name: Mitrovic, B.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We show that the nodal quasiparticles have significant effect on the classical phase fluctuations in a quasi-two-dimensional d-wave superconductor. They give rise to singularities in the temperature behavior of some of the coupling constants in the phase-only effective action. One of the consequences is that the classical XY-model is not adequate for the description of the superconducting fluctuations in d-wave superconductors at low temperatures.
description: 4 pages
Under what conditions does the bar model support mathematical problem solving of two-step, real-life, word problems for autistic students?
Creators: name: Thompson, Shaun Martin
Publisher: name: University of Leicester
Year: 2022
Subjects: Uncategorized

description: The current PhD thesis explores the key conditions (factors) associated with mathematical problem solving amongst autistic pupils, with a focus on the use and application of the bar model. Previous research within mathematical problem solving identifies an uneven range of profiles amongst the autistic population. Furthermore, a lack of empirical evidence exists as to the success and best classroom practice within mathematical problem solving for this group of pupils. Previous studies identify individual conditions likely to be influential on mathematical problem solving, the aim of the current study was to explore the combinations of these conditions with respect to successful word problem solving amongst autistic pupils. Although the bar model is becoming more widely adopted within mathematics teaching and learning, there remains a paucity of empirical research around the conditions associated with its success. The research questions are answered through the exploratory use of qualitative comparative analysis (QCA) in small-N (N=9), educational research. Through the use of pupil discussions and observations of mathematical problem solving and teacher interviews, the analysis of individual conditions and configurations of conditions giving rise to successful mathematical word problem solving are explored. The findings from the study identify mathematical attainment and pupils’ self-perception of their own mathematical ability to be significant in mathematical problem solving. Through further analysis, the impact of the executive functions, particularly working memory and attention, are identified, along with the importance of pupils’ conceptual understanding within mathematical problem solving. The study suggests that teachers pay particular attention to the broader profiles of autistic pupils within the mathematics classroom and consider carefully the balance of procedural and conceptual teaching and learning, particularly when utilising the bar model. Through a range of data analysis techniques, the study provides encouraging data to advocate the use of QCA in small-N, educational research.
Salinomycin inhibits epigenetic modulator EZH2 to enhance death receptors in colon cancer stem cells
Creators: name: Anup Kumar Singh
name: Ayushi Verma
name: Akhilesh Singh
name: Arya, Rakesh Kumar
name: Shrankhla Maheshwari
name: Priyank Chaturvedi
name: Nengroo, Mushtaq Ahmad
name: Saini, Krishan Kumar
name: Achchhe Lal Vishwakarma
name: Singh, Kavita
name: Jayanta Sarkar
name: Datta, Dipak
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Drug resistance is one of the trademark features of Cancer Stem Cells (CSCs). We and others have recently shown that paucity of functional death receptors (DR4/5) on the cell surface of tumour cells is one of the major reasons for drug resistance, but their involvement in the context of in CSCs is poorly understood. By harnessing CSC specific cytotoxic function of salinomycin, we discovered a critical role of epigenetic modulator EZH2 in regulating the expression of DRs in colon CSCs. Our unbiased proteome profiler array approach followed by ChIP analysis of salinomycin treated cells indicated that the expression of DRs, especially DR4 is epigenetically repressed in colon CSCs. Concurrently, EZH2 knockdown demonstrated increased expression of DR4/DR5, significant reduction of CSC phenotypes such as spheroid formation in-vitro and tumorigenic potential in-vivo in colon cancer. TCGA data analysis of human colon cancer clinical samples shows strong inverse correlation between EZH2 and DR4. Taken together, this study provides an insight about epigenetic regulation of DR4 in colon CSCs and advocates that drug-resistant colon cancer can be therapeutically targeted by combining TRAIL and small molecule EZH2 inhibitors.
The statistical mechanics of networks
Creators: name: Park, Juyong
name: Newman, M. E. J.
Publisher: name: arXiv
Year: 2004
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: We study the family of network models derived by requiring the expected properties of a graph ensemble to match a given set of measurements of a real-world network, while maximizing the entropy of the ensemble. Models of this type play the same role in the study of networks as is played by the Boltzmann distribution in classical statistical mechanics; they offer the best prediction of network properties subject to the constraints imposed by a given set of observations. We give exact solutions of models within this class that incorporate arbitrary degree distributions and arbitrary but independent edge probabilities. We also discuss some more complex examples with correlated edges that can be solved approximately or exactly by adapting various familiar methods, including mean-field theory, perturbation theory, and saddle-point expansions.
description: 15 pages, 4 figures
MOESM1 of Modelling the evolution of cognitive styles
Creators: name: Liedtke, Jannis
name: Fromhage, Lutz
Publisher: name: figshare
Year: 2019
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified

description: Additional file 1: Figure S1. Predation prevents the emergence of fast exploration strategy. Figure S2. Predation hinders co-existence. Figure S3. Predation can also induce co-existence. Figure S4. Influence of behavioural traits on cognitive traits and vice versa.
Modelling the M*-SFR relation at high redshift: untangling factors driving biases in the intrinsic scatter measurement
Creators: name: Curtis-Lake, E.
name: Chevallard, J.
name: Charlot, S.
name: Sandles, L.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present a method to self-consistently propagate M$_{*}$ and SFR ($Ψ$) uncertainties onto intercept, slope and intrinsic scatter estimates for a simple model of the main sequence of star forming galaxies where $Ψ= α+ β$M$_{*} + \mathcal{N}(0,σ)$. From simple idealised models set up with broad-band photometry from NIRCam filters at $z\sim5$, we test the method and compare to methods in the literature. Simplifying the $Ψ$ estimate by basing it on dust-corrected MUV can help to reduce the impact of template set degeneracies on slope and intercept estimates, but act to bias the intrinsic scatter estimate. We find that broad-band fluxes alone cannot constrain the contribution from emission lines, implying that strong priors on the emission-line contribution are required if no medium-band constraints are available. Therefore at high redshifts, where emission lines contribute a higher fraction of the broad-band flux, photometric fitting is sensitive to $Ψ$ variations on short ($\sim$ 10 Myr) timescales. Priors on age imposed with a constant (or rising) star formation history (SFH) do not allow one to investigate a possible dependence of $σ$ on M$_{*}$ at high redshifts. Delayed exponential SFHs have less constrained priors, but do not account for $Ψ$ variations on short timescales, a problem if $σ$ increases due to stochasticity of star formation. A simple SFH with current star formation decoupled from the previous history is appropriate. We show that, for simple exposure-time calculations assuming point sources, with low levels of dust, we should be able to obtain unbiased estimates of the main sequence down to log(M/M$_{\odot}$) $\sim$ 8 at $z\sim5$ with the James Webb Space Telescope while allowing for stochasticity of star formation.
description: MNRAS published
Line profile variations in classical Cepheids. Evidence for non-radial pulsations?
Creators: name: Kovtyukh, V. V.
name: Andrievsky, S. M.
name: Luck, R. E.
name: Gorlova, N. I.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We have investigated line profiles in a large sample of Cepheid spectra, and found four stars that show unusual (for Cepheids) line profile structure (bumps or/and asymmetries). The profiles can be phase dependent but the behavior persists over many cycles. The asymmetries are unlikely to be due to the spectroscopic binarity of these stars or the specific velocity field in their atmospheres caused by shock waves. As a preliminary hypothesis, we suggest that the observed features on the line profiles in the spectra of X Sgr, V1334 Cyg, EV Sct and BG Cru can be caused by the non-radial oscillations. It is possible that these non-radial oscillations are connected to resonances between the radial modes (3.2, 7.5 or 10.0 days).
description: Accepted by A&A
Additional file 10 of A simple Bayesian estimate of direct RNAi gene regulation events from differential gene expression profiles
Creators: name: Wilson, Paul A
name: Plucinski, Mathew
Publisher: name: figshare
Year: 2020
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 60506 Virology
subject: Computational Biology

description: Authors’ original file for figure 6
MOESM5 of A case report of a 40-year-old woman with endomyocardial fibrosis in a non-tropical area: from initial presentation to high urgent heart transplantation
Creators: name: Wagner, Gernot
name: Haumer, Markus
name: Poelzl, Gerhard
name: Wiedemann, Dominik
name: Kliegel, Andreas
name: Ullrich, Robert
name: Gartlehner, Gerald
name: Zuckermann, Andreas
name: MÃ¼ller, Ludwig
name: Mayr, Harald
name: Moertl, Deddo
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Computational Biology

description: Additional file 5. Still image of left ventriculography, right anterior oblique (RAO) view.
The Variability of Sagittarius A* at Centimeter Wavelengths
Creators: name: Herrnstein, R. M.
name: Zhao, J. -H.
name: Bower, G. C.
name: Goss, W. M.
Publisher: name: arXiv
Year: 2004
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We present the results of a 3.3-year project to monitor the flux density of Sagittarius A* at 2.0, 1.3, and 0.7 cm with the VLA. The fully calibrated light curves for Sgr A* at all three wavelengths are presented. Typical errors in the flux density are 6.1%, 6.2%, and 9.2% at 2.0, 1.3, and 0.7 cm, respectively. There is preliminary evidence for a bimodal distribution of flux densities, which may indicate the existence of two distinct states of accretion onto the supermassive black hole. At 1.3 and 0.7 cm, there is a tail in the distribution towards high flux densities. Significant variability is detected at all three wavelengths, with the largest amplitude variations occurring at 0.7 cm. The rms deviation of the flux density of Sgr A* is 0.13, 0.16, and 0.21 Jy at 2.0, 1.3, and 0.7 cm, respectively. During much of this monitoring campaign, Sgr A* appeared to be relatively quiescent compared to results from previous campaigns. At no point during the monitoring campaign did the flux density of Sgr A* more than double its mean value. The mean spectral index of Sgr A* is alpha=0.20+/-0.01, with a standard deviation of 0.14. The spectral index appears to depend linearly on the observed flux density at 0.7 cm with a steeper index observed during outbursts. This correlation is consistent with the expectation for outbursts that are self-absorbed at wavelengths of 0.7 cm or longer and inconsistent with the effects of simple models for interstellar scintillation. Much of the variability of Sgr A*, including possible time lags between flux density changes at the different wavelengths, appears to occur on time scales less than the time resolution of our observations (8 days). Future observations should focus on the evolution of the flux density on these time scales.
description: 16 pages, 10 figures, accepted for publication in AJ
Similarity transformation of the electronic Schrödinger equation via Jastrow factorisation
Creators: name: Cohen, Aron J.
name: Luo, Hongjun
name: Guther, Kai
name: Dobrautz, Werner
name: Tew, David P.
name: Alavi, Ali
Publisher: name: arXiv
Year: 2019
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Other Condensed Matter (cond-mat.other)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: By expressing the electronic wavefunction in an explicitly-correlated (Jastrow-factorised) form, a similarity-transformed effective Hamiltonian can be derived. The effective Hamiltonian is non-Hermitian and contains three-body interactions. The resulting ground-state eigenvalue problem can be solved projectively using a stochastic configuration-interaction formalism. Our approach permits use of highly flexible Jastrow functions, which we show to be effective in achieving extremely high accuracy, even with small basis sets. Results are presented for the total energies and ionisation potentials of the first-row atoms, achieving accuracy within a mH of the basis-set limit, using modest basis sets and computational effort.
description: 6 pages, 1 figure
A unified framework for X-shaped radio galaxies
Creators: name: Garofalo, David
name: Joshi, Ravi
name: Yang, Xiaolong
name: Singh, Chandra B.
name: North, Max
name: Hopkins, Matthew
Publisher: name: arXiv
Year: 2019
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We propose a radically different picture for X-shaped radio galaxies compared to existing models as transition objects between cold mode accreting low spinning retrograde black holes and low spinning prograde black holes. The model explains their smaller average black hole masses, their general aversion for cluster compared to isolated environments, the negligible difference in spectral index between primary and secondary jets despite a time difference in their formation, their absence among the most powerful radio quasars and radio galaxies, and their connection to the elusive FRI quasar class, among others. The key to their formation is cold gas accretion onto Schwarzschild black holes.
description: 15 pages, 8 figures, Accepted for publication in the Astrophysical Journal
A novel CpG-methylation-based nomogram predicts survival in colorectal cancer
Creators: name: Xiaokang Wang
name: Danwen Wang
name: Jinfeng Liu
name: Maohui Feng
name: Xiongzhi Wu
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer

description: Aberrant DNA methylation is significantly associated with the prognosis of patients with colorectal cancer (CRC). Therefore, the aim of this study was to develop a CpG-methylation-based nomogram for prognostic prediction in CRC. First, 378 CRC patients with methylation data from The Cancer Genome Atlas were randomly divided into training cohort (n = 249) and test cohort (n = 129). A multistep screening strategy was performed to identify six CpG sites that were significantly associated with overall survival in the training cohort. Then, Cox regression modelling was performed to construct a prognostic signature based on the candidate CpG sites. The six-CpG signature successfully separated patients into high-risk and low-risk groups in both training and test cohorts, and its performance was superior to that of previously published methylation markers (P P P
MOESM1 of Two-year longitudinal survey reveals high genetic diversity of Schistosoma mansoni with adult worms surviving praziquantel treatment at the start of mass drug administration in Uganda
Creators: name: Faust, Christina
name: Crotti, Marco
name: Arinaitwe Moses
name: Oguttu, David
name: Aidah Wamboko
name: Adriko, Moses
name: Adekanle, Elizabeth
name: Kabatereine, Narcis
name: Edridah Tukahebwa
name: Norton, Alice
name: Gower, Charlotte
name: Webster, Joanne
name: Lamberton, Poppy
Publisher: name: figshare
Year: 2019
Subjects: subject: Space Science
subject: Medicine
subject: Pharmacology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Additional file 1: Text S1. Additional methods. Table S1. Travel distances between schools. Table S2. Summary of infrapopulations (individuals) sampled at each timepoint (listed as weeks since start of study). Table S3. Microsatellite loci utilized in this study. Text S2. Additional results. Table S4. Comparison of genetic diversity at the seven microsatellite loci used in the study. Table S5. Proportion infected at pre- and post-treatment. Table S6. Infection intensity between pre- and post-treatment timepoints. Table S7. Summary of infrapopulation phenotyped. Table S8. Frequency of miracidia isolated per individual from relative timepoints. Table S9. Frequency of full-sibling miracidia belonging to a family structure (including singletons) per individual. Table S10. Analysis of molecular variance (AMOVA) for Schistosoma mansoni. Figure S1. Parasite structure through time. Figure S2. Trees of phenotype data. Figure S3. Phylogenies of infrapopulations from individual children sampled over time (continued from Fig.Â 5). Figure S4. Pairwise FST between each school and timepoint. Figure S5. Population differentiation by village. Figure S6. Clustering by discriminant analysis of principal components (DAPC).
Impossibility of spontaneously breaking local symmetries and the sign problem
Creators: name: Splittorff, K.
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Elitzur's theorem stating the impossibility of spontaneous breaking of local symmetries in a gauge theory is reexamined. The existing proofs of this theorem rely on gauge invariance as well as positivity of the weight in the Euclidean partition function. We examine the validity of Elitzur's theorem in gauge theories for which the Euclidean measure of the partition function is not positive definite. We find that Elitzur's theorem does not follow from gauge invariance alone. We formulate a general criterion under which spontaneous breaking of local symmetries in a gauge theory is excluded. Finally we illustrate the results in an exactly solvable two dimensional abelian gauge theory.
description: Latex 6 pages
Additional file 11 of A simple Bayesian estimate of direct RNAi gene regulation events from differential gene expression profiles
Creators: name: Wilson, Paul A
name: Plucinski, Mathew
Publisher: name: figshare
Year: 2020
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 60506 Virology
subject: Computational Biology

description: Authors’ original file for figure 7
Interaction Effects of Dust and Water Deficit Stresses on Growth and Physiology of Persian Oak (Quercus Brantii Lindl.)
Creators: name: Yaghmaei, Leila
name: Jafari, Reza
name: Soltani, Saeid
name: Eshghizadeh, Hamid Reza
name: Jahanbazy, Hassan
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Space Science
subject: Medicine
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified

description: Understanding the relationship between factors affecting the decline of Zagros forests can elucidate many challenges associated with sustainable and effective forest management. Therefore, this study aimed to investigate the interaction effects of simulated dust (0, 20, 40 and 60 g/m2) using dust simulator at three times (April, July and October 2016) and irrigation regimes (−0.3 and −0.9 MPa of soil water potential as control and water deficit treatments) on morpho-physiological characteristics of one- and three-year-old seedlings of Persian Oak (Quercus brantii Lindl) in the Research Field of Isfahan University of Technology in Iran. Results showed that dust stress significantly increased physical damage at 15 and 30 days, proline content and concentration of soluble carbohydrates under both irrigation regimes. Dust stress at 60 g/m2 level significantly decreased relative water content, leaf area, membrane stability index, plant height and consequently shoot fresh and dry weights under both irrigation regime. Under water deficit stress, corresponding reduction in shoot dry weight was 37.9%, 51.6% and 67.2% in one-year-old seedlings and 38.3%, 53.2% and 63.3% in three-year-old seedlings at 20, 40, and 60 g/m2dust treatments, respectively. In general, the results revealed that water stress exacerbated the stress caused by dusting.
Little Hierarchy, Little Higgses, and a Little Symmetry
Creators: name: Cheng, Hsin-Chia
name: Low, Ian
Publisher: name: arXiv
Year: 2004
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Little Higgs theories are an attempt to address the little hierarchy problem, i.e., the tension between the naturalness of the electroweak scale and the precision measurements showing no evidence for new physics up to 5-10 TeV. In little Higgs theories, the Higgs mass-squareds are protected to the one-loop order from the quadratic divergence. This allows the cutoff to be raised up to \~10 TeV, beyond the scales probed by the precision data. However, strong constraints can still arise from the contributions of the new TeV scale particles and hence re-introduces the fine-tuning problem. In this paper we show that a new symmetry, denoted as T-parity, under which all heavy gauge bosons and scalar triplets are odd, can remove all the tree-level contributions to the electroweak observables and therefore makes the little Higgs theories completely natural. The T-parity can be manifestly implemented in a majority of little Higgs models by following the most general construction of the low energy effective theory a la Callan, Coleman, Wess and Zumino. In particular, we discuss in detail how to implement the T-parity in the littlest Higgs model based on SU(5)/SO(5). The symmetry breaking scale f can be even lower than 500 GeV if the contributions from the unknown UV physics at the cutoff are somewhat small. The existence of $T$-parity has drastic impacts on the phenomenology of the little Higgs theories. The T-odd particles need to be pair-produced and will cascade down to the lightest T-odd particle (LTP) which is stable. A neutral LTP gives rise to missing energy signals at the colliders which can mimic supersymmetry. It can also serve as a good dark matter candidate.
description: 20 pages, 2 figures, RevTeX; v2: Yukawa sector in the SU(5)/SO(5) model slightly modified. Also added comments on the Dirac mass term for the fermionic doublet partner; v3: clarifying comments on the modified Yukawa sector. version to appear on JHEP
ASNM Datasets: A Collection of Network Traffic Features for Testing of Adversarial Classifiers and Network Intrusion Detectors
Creators: name: Homoliak, Ivan
name: Hanacek, Petr
Publisher: name: arXiv
Year: 2019
Subjects: subject: Cryptography and Security (cs.CR)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: In this paper, we present three datasets that have been built from network traffic traces using ASNM features, designed in our previous work. The first dataset was built using a state-of-the-art dataset called CDX 2009, while the remaining two datasets were collected by us in 2015 and 2018, respectively. These two datasets contain several adversarial obfuscation techniques that were applied onto malicious as well as legitimate traffic samples during the execution of particular TCP network connections. Adversarial obfuscation techniques were used for evading machine learning-based network intrusion detection classifiers. Further, we showed that the performance of such classifiers can be improved when partially augmenting their training data by samples obtained from obfuscation techniques. In detail, we utilized tunneling obfuscation in HTTP(S) protocol and non-payload-based obfuscations modifying various properties of network traffic by, e.g., TCP segmentation, re-transmissions, corrupting and reordering of packets, etc. To the best of our knowledge, this is the first collection of network traffic metadata that contains adversarial techniques and is intended for non-payload-based network intrusion detection and adversarial classification. Provided datasets enable testing of the evasion resistance of arbitrary classifier that is using ASNM features.