cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Optimal observables and estimators for practical superresolution imaging
Creators: name: Sorelli, Giacomo
name: Gessner, Manuel
name: Walschaers, Mattia
name: Treps, Nicolas
Publisher: name: arXiv
Year: 2021
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Recent works identified resolution limits for the distance between incoherent point sources. However, it remains unclear how to choose suitable observables and estimators to reach these limits in practical situations. Here, we show how estimators saturating the Cramér-Rao bound for the distance between two thermal point sources can be constructed using an optimally designed observable in the presence of practical imperfections, such as misalignment, crosstalk and detector noise.
description: 6 pages, 4 figures. Comments are welcome
Healthcare Data for Clinical Practice Guideline of Psoriasis Patients in Phitsanulok
Creators: name: Wikunda  Limpiangkanan
name: Wichuda  Limpiangkanan
Publisher: name: Yala Rajabhat University
Year: 2011
Subjects: Psoriasis, Clinical Practice Guideline, Auto-immune disease

description: 2, 6, Journal of Yala Rajabhat University
Towards a closed differential aging formula in special relativity
Creators: name: Minguzzi, E.
Publisher: name: arXiv
Year: 2006
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: It is well known that the Lorentzian length of a timelike curve in Minkowski spacetime is smaller than the Lorentzian length of the geodesic connecting its initial and final endpoints. The difference is known as the 'differential aging' and its calculation in terms of the proper acceleration history of the timelike curve would provide an important tool for the autonomous spacetime navigation of non-inertial observers. I give a solution in 3+1 dimensions which holds whenever the acceleration is decomposed with respect to a lightlike transported frame (lightlike transport will be defined), the analogous and more natural problem for a Fermi-Walker decomposition being still open.
description: Latex2e, 6 pages, 1 figure, uses psfrag. Contribution to the Proceedings of The Spanish Relativity Meeting (ERE 2006), Palma de Mallorca, Spain September 4-8, 2006
Infrared properties of propagators in Landau-gauge pure Yang-Mills theory at finite temperature
Creators: name: Cucchieri, Attilio
name: Maas, Axel
name: Mendes, Tereza
Publisher: name: arXiv
Year: 2007
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: The finite-temperature behavior of gluon and of Faddeev-Popov-ghost propagators is investigated for pure SU(2) Yang-Mills theory in Landau gauge. We present nonperturbative results, obtained using lattice simulations and Dyson-Schwinger equations. Possible limitations of these two approaches, such as finite-volume effects and truncation artifacts, are extensively discussed. Both methods suggest a very different temperature dependence for the magnetic sector when compared to the electric one. In particular, a clear thermodynamic transition seems to affect only the electric sector. These results imply in particular the confinement of transverse gluons at all temperatures and they can be understood inside the framework of the so-called Gribov-Zwanziger scenario of confinement.
description: 25 pages, 14 figures, 2 tables, minor changes of typographical and design character, some minor errors corrected, version to appear in PRD
Winter recreational demand and multiple use in the Revelstoke/Golden region of British Columbia
Creators: name: Loewen, Kurt Gregory
Publisher: name: University of British Columbia
Year: 2009

description: The forestlands of Southeastern British Columbia are under multiple use pressures. Timber harvesting is the primary land use, but winter recreation is increasing. Questionnaire data and a Travel Cost Model were employed to determine daily consumer surplus of three recreational activities: helicopter skiing, commercial backcountry skiing and snowmobiling. Depending on which functional form is chosen, significant differences in consumer surplus calculations are apparent. Results from a simple linear program that maximizes social benefit from heli-skiing, commercial backcountry skiing and snowmobiling, suggest that commercial backcountry skiing should be favoured over the other two uses for a specified zone of conflict.
Holography and black holes in asymptotically flat FLRW
Creators: name: Enriquez-Rojo, Martin
name: Heckelbacher, Till
Publisher: name: arXiv
Year: 2021
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In this paper, we extend the treatment of asymptotically decelerating spatially flat FLRW spacetimes initiated in [1]. We show that a certain class of those metrics is ruled by the asymptotic algebra $\mathfrak{b}\mathfrak{m}\mathfrak{s}_s$, which belongs to a one-parameter family of deformations of $\mathfrak{b}\mathfrak{m}\mathfrak{s}$. Furthermore, we enlarge our ansatz to include $\text{Diff}(S^2)$ transformations whose asymptotic algebra $\mathfrak{g}\mathfrak{b}\mathfrak{m}\mathfrak{s}_s$ is a one parameter deformation of $\mathfrak{g}\mathfrak{b}\mathfrak{m}\mathfrak{s}$. Therefore, the holographic algebras $\mathfrak{b}\mathfrak{m}\mathfrak{s}_s$ and $\mathfrak{g}\mathfrak{b}\mathfrak{m}\mathfrak{s}_s$ in FLRW can be related to their flat counterparts through a cosmological holographic flow. Finally, we introduce a logarithmic ansatz in order to account for cosmological black holes, which does not generally satisfy the peeling property but preserves the asymptotic algebra.
description: 20+6 pages, matches the published version
Narrowband and ultranarrowband filters with electro-optic structurally chiral materials
Creators: name: Lakhtakia, Akhlesh
Publisher: name: arXiv
Year: 2006
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: When a circularly polarized plane wave is normally incident on a slab of a structurally chiral material with local $\bar{4}2m$ point group symmetry and a central twist defect, the slab can function as either a narrowband reflection hole filter for co-handed plane waves or an ultranarrowband transmission hole filter for cross-handed plane waves, depending on its thickness and the magnitude of the applied dc electric field. Exploitation of the Pockels effect significantly reduces the thickness of the slab.
description: To be published in: Asian Journal of Physics
Topological data analysis of C. elegans locomotion and behavior
Creators: name: Thomas, Ashleigh
name: Bates, Kathleen
name: Elchesen, Alex
name: Hartsock, Iryna
name: Lu, Hang
name: Bubenik, Peter
Publisher: name: arXiv
Year: 2021
Subjects: subject: Algebraic Topology (math.AT)
subject: Quantitative Methods (q-bio.QM)
subject: FOS: Mathematics
subject: FOS: Biological sciences
subject: 55N31 (Primary), 62R40 (Secondary)

description: We apply topological data analysis to the behavior of C. elegans, a widely-studied model organism in biology. In particular, we use topology to produce a quantitative summary of complex behavior which may be applied to high-throughput data. Our methods allow us to distinguish and classify videos from various environmental conditions and we analyze the trade-off between accuracy and interpretability. Furthermore, we present a novel technique for visualizing the outputs of our analysis in terms of the input. Specifically, we use representative cycles of persistent homology to produce synthetic videos of stereotypical behaviors.
description: 27 pages, 15 figures/tables
X-ray Hardness Variations as an Internal/External Shock Diagnostic
Creators: name: Butler, Nathaniel R.
name: Kocevski, Daniel
Publisher: name: arXiv
Year: 2007
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: The early, highly time-variable X-ray emission immediately following GRBs exhibits strong spectral variations that are unlike the temporally smoother emission which dominates after $t\sim 10^3$ s. The ratio of hard channel (1.3-10.0 keV) to soft channel (0.3-1.3 keV) counts in the Swift X-ray telescope provides a new measure delineating the end time of this emission. We define $T_{H}$ as the time at which this transition takes place and measure for 59 events a range of transition times that span $10^2$ s to $10^{4}$ s, on average 5 times longer than the prompt $T_{90}$ duration observed in the Gamma-ray band. It is very likely that the mysterious light curve plateau phase and the later powerlaw temporal evolution, both of which typically occur at times greater than $T_{H}$ and hence exhibit very little hardness ratio evolution, are both produced by external shocking of the surrounding medium and not by the internal shocks thought responsible for the earlier emission. We use the apparent lack of spectral evolution to discriminate against proposed models for the plateau phase emission. We favor energy injection scenarios with a roughly linearly increasing input energy versus time for six well sampled events with nearly flat light curves at $t\approx 10^3-10^4$s. Also, using the transition time $T_{H}$ as the delineation between the GRB and afterglow emission, we calculate that the kinetic energy in the afterglow shock is typically a factor of 10 lower than that released in the GRB. Lack of hardness variations in these three events may be due to a very highly relatavistic outflow or due to a very dense circumburst medium. There are a handful of rare cases of very late time $t>10^4$s hardness evolution, which may point to residual central engine activity at very late time.
description: 18 pages, 8 figures, 1 table, includes material removed from astro-ph/0612564 v1, Accepted to ApJ
Formation of Ionization-Cone Structures in Active Galactic Nuclei: II. Nonlinear Hydrodynamic Modelling
Creators: name: Afanasiev, V. L.
name: Dodonov, S. N.
name: Khrapov, S. S.
name: Moiseev, A. V.
name: Mustsevoy, V. V.
Publisher: name: arXiv
Year: 2007
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: In Part I of this paper we described an equilibrium model of a jet in the gravitational field corresponding to the rigid-rotation region of the galactic disk. We used linear stability analysis to find the waveguide-resonance instability of internal gravity waves due to the superreflection of these waves from the jet boundary. In this part of the paper, we perform nonlinear numerical 2D and 3D simulations of the development of this instability. We show that the shocks produced by this instability in the ambient medium of the jet are localized inside a cone with a large opening angle and are capable of producing features that are morphologically similar to those observed in galaxies with active nuclei (NGC 5252 for example).
description: 10 pages, 9 PS and 4 JPEG figures, published in Astrophysical Bulletin
Differentiation of Benign Vs. Malignant Colorectal Polyps Using Machine Learning Techniques: A Systematic Review and Meta-Analysis
Creators: name: Ernest E. Onuiri, Emmanuel Ikhioya, Kelechi C. Umeaka
Publisher: name: Zenodo
Year: 2024

description: Colorectal polyps are critical markers for colorectal cancer (CRC), and distinguishing between benign and malignant polyps is essential for early diagnosis and treatment. This systematic review and meta-analysis assess the performance of machine learning techniques in accurately differentiating benign from malignant colorectal polyps. The review examines recent research that integrates advanced technologies, including computer-aided diagnosis (CADx) systems and deep learning models, particularly convolutional neural networks (CNNs). These machine learning techniques show great promise in analyzing histopathological images, identifying subtle patterns and characteristics that may be overlooked by traditional methods. Additionally, the integration of optical coherence tomography (OCT) with CADx systems enhances tissue structure interpretation, leading to more precise diagnoses. By synthesizing data from multiple studies, this review highlights the significant advancements in CRC diagnosis and the potential for improved patient outcomes through the application of machine learning techniques.
"ASRNI QARITGAN KUN" ROMANIDA OBRAZLAR MA'NAVIY-RUHIY OLAMINING QIYOSIY TAHLILI
Creators: name: Abdugapparova, Shodiyona
Publisher: name: Zenodo
Year: 2024

description: Chingiz Aytmatov oʻzining ilk romani “Asrni qaritgan kun” romani bilan adabiyot ixlosmandlarining qalbidan chuqurroq joy olishga muvaffaq boʻldi. Roman avval rus tilida yozilib (“Boʻronli bekat”, 1980)[1], keyin qirg‘iz tiliga tarjima qilingan. Shundan soʻng adib ijodida  roman pallasi boshlandi(Suvon Meli) va “Qiyomat”, “Kassandra tamg‘asi”, “Mangu qalliq” kabi romanlari dunyo yuzini koʻrdi.  Romanda qalamga olingan inson va tabiat, jamiyat va inson, insoniy qadriyatlar va zamonaviy talqinlar oʻzaro bog‘lanib, bir-biriga chirmashib ketgan, janr jihatidan juda murakkab ushbu asar yozuvchiga ayricha bir muvaffaqiyat olib kelganligini ta’kidlash joiz.
Semi-Dirac and Weyl Fermions in Transition Metal Oxides
Creators: name: Mohanta, Narayan
name: Ok, Jong Mok
name: Zhang, Jie
name: Miao, Hu
name: Dagotto, Elbio
name: Lee, Ho Nyung
name: Okamoto, Satoshi
Publisher: name: arXiv
Year: 2021
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We show that a class of compounds with $I$4/$mcm$ crystalline symmetry hosts three-dimensional semi-Dirac fermions. Unlike the known two-dimensional semi-Dirac points, the degeneracy of these three-dimensional semi-Dirac points is not lifted by spin-orbit coupling due to the protection by a nonsymmorphic symmetry -- screw rotation in the $a-b$ plane and a translation along the $c$ axis. This crystalline symmetry is found in tetragonal perovskite oxides, realizable in thin films by epitaxial strain that results in a$^0$a$^0$c$^-$-type octahedral rotation. Interestingly, with broken time-reversal symmetry, two pairs of Weyl points emerge from the semi-Dirac points within the Brillouin zone, and an additional lattice distortion leads to enhanced intrinsic anomalous Hall effect. The ability to tune the Berry phase by epitaxial strain can be useful in novel oxide-based electronic devices.
Analytical and semianalytical tools to determine the topological character of Shiba chains
Creators: name: Sedlmayr, Nicholas
name: Kaladzhyan, Vardan
name: Bena, Cristina
Publisher: name: arXiv
Year: 2021
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We introduce three new analytical and semi-analytical tools that allow one to determine the topological character of impurity Shiba chains. The analytical methods are based on calculating the effective Green's function of an infinite embedded chain using the T-matrix formalism and describing the chain as a {\it line impurity}. We thus provide a solution to the longstanding size-effects problem affecting the only general alternative method, the numerical tight-binding analysis. As an example we consider a chain of magnetic impurities deposited on an s-wave superconducting substrate with Rashba spin-orbit and we calculate its topological phase diagram as a function of the magnetic impurity strength and the chemical potential. We find a perfect agreement between all our new techniques and a numerical analysis.
The influence of Reliability of the Bank's Services on Organizational Performance at Stanbic Bank, Mbarara City Branch
Creators: name: Asiimwe Emmanuel, Murangira Martin, Begumisa Bernard
Publisher: name: Zenodo
Year: 2024

description: This study investigates the relationship between customer service and organizational performance at Stanbic Bank's Mbarara City Branch. Employing a case study design, the research utilized questionnaires and interviews to collect data. Descriptive statistics, including frequencies, means, and regression analysis, were used to analyze the variables. The findings reveal a positive correlation between the reliability of bank services and organizational performance, indicating that a one-unit increase in service reliability is associated with a 5.32-unit increase in organizational performance. The low p-value (<0.001) confirms the statistical significance of this relationship. The study concludes that reliable bank services are crucial for organizational performance. Recommendations include strengthening regulatory frameworks to encourage financial institutions to prioritize service reliability and investing in staff training programs to enhance service quality.
Echoes of a Hidden Valley at Hadron Colliders
Creators: name: Strassler, Matthew J.
name: Zurek, Kathryn M.
Publisher: name: arXiv
Year: 2006
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We consider examples of ``hidden-valley'' models, in which a new confining gauge group is added to the standard model. Such models often arise in string constructions, and elsewhere. The resulting (electrically-neutral) bound states can have low masses and long lifetimes, and could be observed at the LHC and Tevatron. Production multiplicities are often large. Final states with heavy flavor are common; lepton pairs, displaced vertices and/or missing energy are possible. Accounting for LEP constraints, we find LHC production cross-sections typically in the 1-100 fb range, though they can be larger. It is possible the Higgs boson could be discovered at the Tevatron through rare decays to the new particles.
description: 5 pages, 5 figures (v2: minor improvements, one added reference, no substantial changes)
An Arc of Young Stars in the Halo of M82
Creators: name: Davidge, T. J.
Publisher: name: arXiv
Year: 2008
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: The properties of the brightest resolved stars in an arc that was originally identified by Sun et al. (2005) and is located in the extraplanar regions of M82 are discussed. The stars form an elongated structure that is traced over a projected area of 3.0 x 0.8 kpc. The integrated brightness is M_V ~ -11, while the total stellar mass is between 3 x 10^5 and 2 x 10^6 solar masses. If there is only foreground extinction then the youngest stars have a metallicity Z > 0.008 and an age log(tyears) ~ 7.75; thus, the youngest stars formed at roughly the same time as stars in tidal features that are associated with other M81 Group galaxies. If the arc is dispersing then it will deposit young, chemically enriched stars into the M82 halo.
description: 11 pages including 3 postscript figures; accepted for publication in ApJ (Letters)
Six Myths on the Virial Theorem for Interstellar Clouds
Creators: name: Ballesteros-Paredes, Javier
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: It has been paid little or no attention to the implications that turbulent fragmentation has on the validity of at least six common assumptions on the Virial Theorem (VT), which are: (i) the only role of turbulent motions within a cloud is to provide support against collapse, (ii) the surface terms are negligible compared to the volumetric ones, (iii) the gravitational term is a binding source for the clouds, (iv) the sign of the second-time derivative of the moment of inertia determines whether the cloud is contracting or expanding, (v) interstellar clouds are in Virial Equilibrium (VE), and (vi) Larson's (1981) relations are the observational proof that clouds are in VE. Interstellar clouds cannot fulfill these assumptions, however, because turbulent fragmentation will induce flux of mass, moment and energy between the clouds and their environment, and will favor local collapse while may disrupt the clouds within a dynamical timescale. It is argued that, although the observational and numerical evidence suggests that interstellar clouds are not in VE, the so-called ``Virial Mass'' estimations, which actually should be called ``energy-equipartition mass'' estimations, are good order-of magnitude estimations of the actual mass of the clouds just because observational surveys will tend to detect interstellar clouds appearing to be close to energy equipartition. However, since clouds are actually out of VE, as suggested by asymmetrical line profiles, they should be transient entities. These results are compatible with observationally-based estimations for rapid star formation. , and call into question the models for the star formation efficiency based on clouds being in VE.
description: Accepted by MNRAS. 9 pages, no figures
Additional file 2 of Changes in transcriptomic and metabolomic profiles of morphotypes of Ophiocordyceps sinensis within the hemocoel of its host larvae, Thitarodes xiaojinensis
Creators: name: Li, Miaomiao
name: Meng, Qian
name: Zhang, Huan
name: Shu, Ruihao
name: Zhao, Yanni
name: Wu, Peipei
name: Li, Xuan
name: Zhou, Guiling
name: Qin, Qilian
name: Zhang, Jihong
Publisher: name: figshare
Year: 2020
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Plant Biology

description: Additional file 2: Figure S1. Principal component analysis of the RNA-Seq data. Figure S2. Analysis of DEGs between two adjacent stages. Figure S3. KEGG enrichment analysis for differentially expressed genes (DEGs). Figure S4. PLS-DA score plot and validation plots of the metabolic profiling results.
Bold Diagrammatic Monte Carlo: When Sign Problem is Welcome
Creators: name: Prokof'ev, Nikolay
name: Svistunov, Boris
Publisher: name: arXiv
Year: 2007
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We introduce a Monte Carlo scheme for sampling bold-line diagrammatic series specifying an unknown function in terms of itself. The range of convergence of this bold(-line) diagrammatic Monte Carlo (BMC) is significantly broader than that of a simple iterative scheme for solving integral equations. With BMC technique, a moderate "sign problem" turns out to be an advantage in terms of the convergence of the process. For an illustrative example, we solve one-particle s-scattering problem. As an important application, we obtain T-matrix for a fermipolaron (one spin-down particle interacting with the spin-up fermionic sea).
description: 4 pages, 2 figures, revtex4
The development of VLSI implementation-related neural network training algorithms
Creators: name: Li, Gang
Publisher: name: University of British Columbia
Year: 2009

description: Artificial neural networks are systems composed of interconnected simple computing units known as artificial neurons which simulate some properties of their biological counterparts. They have been developed and studied for understanding how brains function, and for computational purposes. Two kinds of architecture of Neural Network Models( NNMs) are the most popular, Recurrent and Feed-forward. The recurrent model (Hopfield network) is one of the simplest NNMs. It is specially designed as a Content Addressable Memory (CAM). The feed-forward models include Perceptron and multilayer perceptrons. They have been proved to be useful in many applications. Two parts are included in this thesis. In part 1, recurrent models are investigated and a novel digital CMOS VLSI implementation scheme is proposed. Synaptic matrix construction rules (training rules) for the proposed model were simulated on SUN work stations. Three widely accepted training rules are simulated and compared, the Hebb's rule, the Projection rule and the Simplex method. A coding scheme, named "dilution", is applied to the three training rules. Both Dilution Coding Hebb's rule and Dilution Coding Projection rule were verified to exhibit good performance. In part 2 of the thesis, feed-forward models are introduced. Variations of the BP algorithm are developed together with the considerations of hardware implementations. The proposed DPT (Delta Pre-Training) method can speed up BP training and can also reduce the probability of getting trapped in a local minima. The implementation of the DPT method will not increase the complexity of VLSI design.
Unveiling the $K_1(1270)$ double-pole structure in the $\bar{B}\to J/ψρ\bar{K}$ and $\bar{B}\to J/ψ\bar{K}^*π$ decays
Creators: name: Dias, J. M.
name: Toledo, G.
name: Roca, L.
name: Oset, E.
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: By looking at the pseudoscalar-vector meson spectra in the $\bar{B}\to J/ψρ\bar{K}$ and $\bar{B}\to J/ψ\bar{K}^*π$ weak decays, we theoretically investigate the double-pole structure of the $K_1(1270)$ resonance by using the Chiral Unitary approach to account for the final state interactions between the pseudoscalar and vector mesons. The $K_1(1270)$ resonance appears as dynamically generated through these interactions in coupled channels and influence the shape of the invariant mass distributions under consideration. We show how those shapes are affected by the $K_1(1270)$ double-pole structure to confront the results from our model with future experiments that might investigate the $PV$ spectra in these decays.
description: 26 pages, 12 figures, and 2 Tables. Manuscript published in PRD
From Fastq to Drug Recommendation – Automated Cancer Report Generation using OncoRep & Omics Pipe
Creators: name: Meißner, Tobias
name: Fisch, Kathleen M
name: Gioia, Louis
name: Su, Andrew I
Publisher: name: F1000Research
Year: 2015

description: Next generation sequencing allows us to study cancer in a large scale and in multiple dimensions. This provides in-depth insight into tumor pathogenesis on the individual patient level, paving the path to precision medicine. The advent of precision medicine introduces a shift in how cancer patients will be treated in the future, away from the one drug – one disease paradigm towards the idea of bringing the right drug to the right patient.
Challenges that arise with this paradigm shift are i) High-throughput, automated, parallel, and reproducible processing and analysis of sequencing data in the n-of-1 setting, ii) extracting, integrating, interpreting and reporting relevant information from various layers of omics data iii) integrating omics data with drug databases, (iv) presenting the information in an understandable and timely manner to provide clinically relevant and actionable targets to the clinician and tumor board, and (v) creating a transparent, open-source, community framework for enabling community curation of best practices and algorithms, and reproducible analysis pipelines in a move towards standardizing next generation sequencing analysis for patient care.

To address these challenges, we present an automated cancer reporting framework based on two open- source platforms, OncoRep and Omics Pipe. OncoRep is an RNAseq-based n-of-1 reporting tool for cancer patients that has been integrated into Omics Pipe, a community-based framework that enables reproducibility by curating and automating best practice omics data analysis pipelines. We have applied this framework to breast cancer patients in an n-of-1 setting. RNA-seq was performed for each patient and the fastq files were processed and analyzed using Omics Pipe, generating expression data, variants and fusions based on published methods. OncoRep was incorporated as a custom pipeline in Omics Pipe to perform prospective molecular classification, detect altered genes and pathways, identify gene fusion events and clinically actionable mutations, and to report suitable drugs based on identified actionable targets. Omics Pipe automates these analyses and keeps a detailed record of the analyses and parameters used to ensure reproducibility. OncoRep integrates and visualizes the data in an approachable html based interactive report as well as a PDF based summary report, providing the clinician and tumor board with an approachable report to guide the treatment decision making process. We hope with our contribution to enhance transparency and reproducibility of next generation sequencing analysis and clinical reporting, which will be needed for moving this technology into routine clinical practice.
CIViC: Crowdsourcing the Clinical Interpretation of Variants in Cancer
Creators: name: Griffith, Malachi
name: Spies, Nicholas
name: Kilannin Krysiak
name: McMichael, Josh
name: Coffman, Adam
name: Ainscough, Benjamin
name: Bilski, Rachel
name: Eldred, James
name: Larson, David
name: Walker, Jason
name: Wilson, Richard
name: Mardis, Elaine
name: Obi Griffith
Publisher: name: F1000Research
Year: 2015

description: The landscape of the genomics of tumorigenesis has been systematically surveyed in recent years, identifying thousands of potential cancer-driving alterations. However, few resources exist to facilitate prioritization and interpretation of these alterations in a clinical context. Interpreting the events from even a single case requires both extensive bioinformatics expertise as well as an understanding of cancer biology and clinical paradigms. This interpretation step now represents a significant bottleneck, preventing the realization of personalized medicine. To this end, we present CIViC (www.civicdb.org) as a forum for the clinical interpretation of variants in cancer. We believe that to succeed, such a resource must be comprehensive, current, community-based and above all, open-access. CIViC allows curation of structured evidence coupled with free-form discussion for user-friendly interpretation of clinical actionability of genomic alterations.
Additional file 4 of Genome-wide identification, and phylogenetic and expression profiling analyses, of XTH gene families in Brassica rapa L. and Brassica oleracea L.
Creators: name: Wu, Di
name: Liu, Anqi
name: Qu, Xiaoyu
name: Liang, Jiayi
name: Song, Min
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 4. Structure-based sequence alignment of BraXTHs and PttXET16A. Sequences were aligned using ClustalX and generated by ESPript [70]. The secondary structure elements indicated above the alignment are those of PttXET16A, Populus tremula × tremuloides XET16A (AF515607), whose structure has been experimentally determined [45]. Blue frames indicate conserved residues, white letters in red boxes indicate strict identity, and red letters in white boxes indicate similarity. The predicted α-helices and β-strands are represented by spirals and horizontal arrows, respectively.
The singular field used to calculate the self-force on non-spinning and spinning particles
Creators: name: Messaritaki, Eirini
Publisher: name: arXiv
Year: 2007
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The singular field of a point charge has recently been described in terms of a new Green's function of curved spacetime. This singular field plays an important role in the calculation of the self-force acting upon the particle. We provide a method for calculating the singular field and a catalog of expansions of the singular field associated with the geodesic motion of monopole and dipole sources for scalar, electromagnetic and gravitational fields. These results can be used, for example, to calculate the effects of the self-force acting on a particle as it moves through spacetime.
description: 14 pages; addressed referee's comments; published in PhysRevD
CIViC: Crowdsourcing the Clinical Interpretation of Variants in Cancer
Creators: name: Griffith, Malachi
Publisher: name: F1000Research
Year: 2015

description: The landscape of the genomics of tumorigenesis has been systematically surveyed in recent years, identifying thousands of potential cancer-driving alterations. However, few resources exist to facilitate prioritization and interpretation of these alterations in a clinical context. Interpreting the events from even a single case requires both extensive bioinformatics expertise as well as an understanding of cancer biology and clinical paradigms. This interpretation step now represents a significant bottleneck, preventing the realization of personalized medicine. To this end, we present CIViC (www.civicdb.org) as a forum for the clinical interpretation of variants in cancer. We believe that to succeed, such a resource must be comprehensive, current, community-based and above all, open-access. CIViC allows curation of structured evidence coupled with free-form discussion for user-friendly interpretation of clinical actionability of genomic alterations.
The Effect of Stationary Axisymmetric Spacetimes in Interferometric Visibility
Creators: name: Basso, Marcos L. W.
name: Maziero, Jonas
Publisher: name: arXiv
Year: 2021
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: In this manuscript, we consider a scenario in which a spin-1/2 quanton goes through a superposition of co-rotating and counter-rotating geodetic circular paths, which play the role of the paths of a Mach-Zehnder interferometer in a stationary and axisymmetric spacetime. Since the spin of the particle plays the role of a quantum clock, as the quanton moves in a superposed path it gets entangled with the momentum (or the path), and this will cause the interferometric visibility (or the internal quantum coherence) to drop, since, in stationary axisymmetric spacetimes there is a difference in proper time elapsed along the two trajectories. However, as we show here, the proper time of each path will couple to the corresponding local Wigner rotation, and the effect in the spin of the superposed particle will be a combination of both. Besides, we discuss a general framework to study the local Wigner rotations of spin-1/2 particles in general stationary axisymmetric spacetimes for circular orbits.
description: 11 pages, 4 figures. arXiv admin note: text overlap with arXiv:2101.06320
Revealing drivers and risks for power grid frequency stability with explainable AI
Creators: name: Kruse, Johannes
name: Schäfer, Benjamin
name: Witthaut, Dirk
Publisher: name: arXiv
Year: 2021
Subjects: subject: Systems and Control (eess.SY)
subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Physical sciences

description: Stable operation of the electrical power system requires the power grid frequency to stay within strict operational limits. With millions of consumers and thousands of generators connected to a power grid, detailed human-build models can no longer capture the full dynamics of this complex system. Modern machine learning algorithms provide a powerful alternative for system modelling and prediction, but the intrinsic black-box character of many models impedes scientific insights and poses severe security risks. Here, we show how eXplainable AI (XAI) alleviates these problems by revealing critical dependencies and influences on the power grid frequency. We accurately predict frequency stability indicators (such as RoCoF and Nadir) for three major European synchronous areas and identify key features that determine the power grid stability. Load ramps, specific generation ramps but also prices and forecast errors are central to understand and stabilize the power grid.
description: 26 pages, 19 figures; updated comments; this is the initially submitted version, for the final version see journal link
Topological Superconductivity and Superfluidity
Creators: name: Qi, Xiao-Liang
name: Hughes, Taylor L.
name: Raghu, Srinivas
name: Zhang, Shou-Cheng
Publisher: name: arXiv
Year: 2008
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: We construct time reversal invariant topological superconductors and superfluids in two and three dimensions which are analogous to the recently discovered quantum spin Hall and three-d $Z_2$ topological insulators respectively. These states have a full pairing gap in the bulk, gapless counter-propagating Majorana states at the boundary, and a pair of Majorana zero modes associated with each vortex. We show that the time reversal symmetry naturally emerges as a supersymmetry, which changes the parity of the fermion number associated with each time-reversal invariant vortex. In the presence of external T-breaking fields, non-local topological correlation is established among these fields, which is an experimentally observable manifestation of the emergent supersymmetry.
description: 5 pages, 3 figures
Portable workflow and tool descriptions with the CWL (Common Workflow Language)
Creators: name: Amstutz, Peter
name: Nebojša Tijanić
name: Soiland-Reyes, Stian
name: Kern, John
name: Stojanovic, Luka
name: Pierce, Tim
name: Chilton, John
name: Mikheev, Maxim
name: Lampa, Samuel
name: Ménager, Hervé
name: Frazer, Scott
name: Malladi, Venkat Sai
name: Crusoe, Michael R.
Publisher: name: F1000Research
Year: 2015

description: Bioinformatics workflow platforms provide provenance tracking, execution and data management, repeatability, and an environment for data exploration and visualization. Example F/OSS bioinformatics workflow platforms include Arvados, Galaxy, Mobyle, iPlant DiscoveryEnvironment, Apache Taverna and Yabi. Each one presently represent workflows using different vocabularies and formats, and adding new tools requires different procedures for each system.

Neither the description of the workflows nor the descriptions of the tools that power them are usable outside of the platforms they were written for. This results in duplicated effort, reduced reusability, and impedes collaboration.

Three engineers (Peter Amstutz, John Chilton, and Nebojsa Tijanic) from leading bioinformatics platform teams (Curoverse, Galaxy Team, and Seven Bridges Genomics) and a tool author (Michael R. Crusoe / khmer project) started working together at the BOSC 2014 Codefest with an initial focus on developing a portable means of representing, sharing and invoking command line tools which was then the basis for portable workflow descriptions. The group placed high value on re-using existing formats and ontologies; they governed themselves with a lazy consensus / do-ocracy approach.

On March 31st, 2015 the group released their second draft of the Common Workflow Language specification. The serialized form is a YAML document that is validated by an Apache Avro schema and can be interpreted as an RDF graph using JSON-LD. The documents are also valid Wf4Ever 'wfdesc' descriptions after a simple transformation. Future drafts will include the use of the EDAM ontology to describe the tools enabling discovery via the ELIXIR tool registry].

Seven Bridges Genomics, the Galaxy Project, and the organization behind Arvados (Curoverse) have started to implement support for the Common Workflow Language, with interest from other projects and organizations like Apache Taverna, BioDatomics and the Broad Institute. Developers on the Galaxy Team are exploring adding CWL tool description support with plans to add support for the CWL workflow descriptions. Tool authors and other community members will benefit as they will only have to describe their tool and workflow interfaces once. This will enable scientists, researchers and other analysts to share their workflows and pipelines in an interoperable and yet human readable manner.
ОТВЕТСТВЕННОСТЬ ЗА НАРУШЕНИЕ ПРИРОДООХРАННОГО ЗАКОНОДАТЕЛЬСТВА
Creators: name: Карабаева, Зумрат
name: Набиева, Ситора
Publisher: name: Zenodo
Year: 2024

description: Преступления в области экологии – преступления против природопользования и защиты окружающей среды.  Экология – это социальное состояние, связывающее человека с природой.  Такая зависимость, в свою очередь, может привести к нарушениям в результате противоправного поведения.  Подобные нарушения являются причиной преступлений в сфере экологии.
Rare Events Detected with a Bulk Acoustic Wave High Frequency Gravitational Wave Antenna
Creators: name: Goryachev, Maxim
name: Campbell, William M.
name: Heng, Ik Siong
name: Galliou, Serge
name: Ivanov, Eugene N.
name: Tobar, Michael E.
Publisher: name: arXiv
Year: 2021
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: High Energy Physics - Experiment (hep-ex)
subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences

description: This work describes the operation of a High Frequency Gravitational Wave detector based on a cryogenic Bulk Acoustic Wave (BAW) cavity and reports observation of rare events during 153 days of operation over two seperate experimental runs (Run 1 and Run 2). In both Run 1 and Run 2 two modes were simultaneously monitored. Across both runs, the 3rd overtone of the fast shear mode (3B) operating at 5.506 MHz was monitored, while in Run 1 the second mode was chosen to be the 5th OT of the slow shear mode (5C) operating at 8.392 MHz. However, in Run 2 the second mode was selected to be closer in frequency to the first mode, and chosen to be the 3rd overtone of the slow shear mode (3C) operating at 4.993 MHz. Two strong events were observed as transients responding to energy deposition within acoustic modes of the cavity. The first event occurred during Run 1 on the 12/05/2019 (UTC), and was observed in the 5.506 MHz mode, while the second mode at 8.392 MHz observed no event. During Run 2, a second event occurred on the 27/11/2019(UTC) and was observed by both modes. Timing of the events were checked against available environmental observations as well as data from other detectors. Various possibilities explaining the origins of the events are discussed.
description: 4 pages, 4 figures
Biopython Project Update – 2015
Creators: name: Rodrigues, João
name: Antão, Tiago
name: Cock, Peter
name: Wibowo Arindrarto
name: Talevich, Eric
name: Hoon, Michiel De
Publisher: name: F1000Research
Year: 2015

description: The Biopython Project is a long-running distributed collaborative effort, supported by the Open Bioinformatics Foundation, which develops a freely available Python library for biological computation. We present here details of the latest Biopython release – version 1.65. New features include: extended Bio.KEGG and Bio.Graphics modules to support the KEGG REST API, as well as parsing, representing, and drawing KGML pathways; inclusion of the new NCBI genetic code table 24 (Pterobranchia Mitochondrial) and corresponding translation functionality in Bio.Data; improvements to Bio.SeqIO (parse and index_db methods) and Bio.SearchIO (hit retrieval using alternative IDs); and a rewritten Bio.SeqUtils.MeltingTemp with additional methods to calculate oligonucleotide melting temperatures. Additionally, we continued our efforts to abide by the PEP8 coding style guidelines, namely using lowercase module names in new experimental modules. We are currently preparing a new release – version 1.66 – that will feature additional improvements to the Bio.KEGG and Bio.Graphics modules (support for transparency in KGML pathways), extended support for the ``abi'' format in Bio.SeqIO, miscellaneous improvements to the test suite, and further adherence to PEP8. In addition, our participation in Google Summer of Code 2014 had Evan Parker adding lazy-parsing support for Bio.SeqIO. The additions are currently under review and should soon be integrated. Finally, complementary to these developments, we created a new repository for Docker containers. The included containers support both Python versions 2 & 3 and install all of Biopython's dependencies. They are, therefore, useful for development, but also for teaching due to the inclusion of IPython Notebooks.
Measurement of phi_3 with Dalitz plot analysis of B+ -> D(*)K(*)+ decay
Creators: name: The Belle Collaboration
name: Poluektov, A.
Publisher: name: arXiv
Year: 2006
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: We present a measurement of the unitarity triangle angle phi_3 using a Dalitz plot analysis of the K0_S pi+ pi- decay of the neutral D meson from the B+- -> D(*)K(*)+- process. The method employs the interference between D0 and D0bar to extract the angle phi_3, strong phase Delta and the ratio r of suppressed and allowed amplitudes. We apply this method to a 357 fb-1 data sample collected by the Belle experiment. The analysis uses three modes: B+ -> DK+, B+ -> D*K+ with D* -> Dpi0, and B+ -> DK*+ with K*+ -> K0_S pi+, as well as the corresponding charge-conjugate modes. From a combined maximum likelihood fit to the three modes, we obtain phi_3=53+15-18(stat)+-3(syst)+-9(model) degrees. The corresponding two standard deviation interval is 8
description: 18 pages, 6 figures, 7 tables. To be submitted to Phys. Rev. D
Complexity as a holographic probe of strong cosmic censorship
Creators: name: Alishahiha, Mohsen
name: Banerjee, Souvik
name: Kames-King, Joshua
name: Loos, Emma
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Based on reasonable assumptions, we propose a new expression for Lloyd's bound, which confines the complexity growth of charged black holes. We then revisit holographic complexity for charged black branes in the presence of a finite cutoff. Using the proposed Lloyd's bound we find a relation between the UV and the behind the horizon cutoff. This is found to be consistent with the factorization of the partition function at leading order in large N. We argue that the result may be thought of as a holographic realization of strong cosmic censorship.
description: 26 pages, 2 figures, Published version
Prioritization of structural variants based on known biological information
Creators: name: Chapman, Brad
Publisher: name: F1000Research
Year: 2015

description: High-throughput human resequencing characterizes whole genome changes with the goal of linking variations to disease, drug responses or other phenotypes. The primary challenge following sensitive and precise variant detection is prioritizing the large number of results in the context of previously known biological information. This is especially problematic for samples that are not well explained by short variations like single nucleotide polymorphisms (SNPs) or small insertions and deletions. In these cases, structural variations such as larger insertions, deletions, rearrangments or copy number variations (CNVs) provide additional sources of causative variability. However, detecting structural variations from short reads is challenging, so biologists must search through a noisier dataset to find potentially relevant mutations for additional investigation.

We'll discuss an approach to help prioritize structural variations using pre-existing biological information. The approach is general and only reliant on inputs that link known mutations to genomic position, allowing incorporation of custom BED or VCF files into analyses. In this talk, we'll emphasize using public databases like COSMIC (), ClinVar () and CIViC () to evaluate cancer samples. We overlay known variants with existing annotations on genes, domains and other genome elements from Ensembl. Regions with pre-existing changes that match those found in BED files of structural variants are reported along with supporting information. We'll discuss practical examples of how this helps improve our ability to utilize structural changes in analysis of tumor variant calls.

The implementation is part of bcbio (), which provides a configuration file and command line interface for running variant analysis on distributed machines. We have an open development community which contributed to our current cancer calling support (). We actively develop and support bcbio and hope to grow the community of users who both contribute and use it for answering biological questions.