cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Harmonic analysis on Lagrangian manifolds of integrable Hamiltonian systems
Creators: name: Bernatska, Julia
name: Holod, Petro
Publisher: name: arXiv
Year: 2013
Subjects: subject: Mathematical Physics (math-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences
subject: 22E47, 22E70, 81R05

description: For an integrable Hamiltonian system we construct a representation of the phase space symmetry algebra over the space of functions on a Lagrangian manifold. The representation is a result of the canonical quantization of the integrable system in terms of separation variables. The variables are chosen in such way that a half of them parameterizes the Lagrangian manifold, which coincides with the Liouville torus of the integrable system. The obtained representation is indecomposable and non-exponentiated.
description: 13 pages, XIVth International Conference 'Geometry, Integrability and Quantization', June 8-13, 2012, Varna, Bulgaria
Additional file 2 of Adaptations of evidence-based trauma-focused interventions for children and adolescents: a systematic review
Creators: name: Lange, Brittany C. L.
name: Nelson, Ashley
name: Lang, Jason M.
name: Stirman, Shannon Wiltsey
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 2. Search Strategy.
Dynamic renormalization group analysis of propagation of elastic waves in two-dimensional heterogeneous media
Creators: name: Sepehrinia, Reza
name: Bahraminasab, Alireza
name: Sahimi, Muhammad
name: Tabar, M. Reza Rahimi
Publisher: name: arXiv
Year: 2013
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: We study localization of elastic waves in two-dimensional heterogeneous solids with randomly distributed Lamé coefficients, as well as those with long-range correlations with a power-law correlation function. The Matin-Siggia-Rose method is used, and the one-loop renormalization group (RG) equations for the the coupling constants are derived in the limit of long wavelengths. The various phases of the coupling constants space, which depend on the value $ρ$, the exponent that characterizes the power-law correlation function, are determined and described. Qualitatively different behaviors emerge for $ρ<1$ and $ρ>1$. The Gaussian fixed point (FP) is stable (unstable) for $ρ<1$ ($ρ>1$). For $ρ<1$ there is a region of the coupling constants space in which the RG flows are toward the Gaussian FP, implying that the disorder is irrelevant and the waves are delocalized. In the rest of the disorder space the elastic waves are localized. We compare the results with those obtained previously for acoustic wave propagation in the same type of heterogeneous media, and describe the similarities and differences between the two phenomena.
description: 13 pages, 4 figures
Proactive bottleneck performance analysis in parallel computing using openMP
Creators: name: Rajput, Vibha
name: Katiyar, Alok
Publisher: name: arXiv
Year: 2013
Subjects: subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: Performance (cs.PF)
subject: FOS: Computer and information sciences

description: The aim of parallel computing is to increase an application performance by executing the application on multiple processors. OpenMP is an API that supports multi platform shared memory programming model and shared-memory programs are typically executed by multiple threads. The use of multi threading can enhance the performance of application but its excessive use can degrade the performance. This paper describes a novel approach to avoid bottlenecks in application and provide some techniques to improve performance in OpenMP application. This paper analyzes bottleneck performance as bottleneck inhibits performance. Performance of multi threaded applications is limited by a variety of bottlenecks, e.g. critical sections, barriers and so on. This paper provides some tips how to avoid performance bottleneck problems. This paper focuses on how to reduce overheads and overall execution time to get better performance of application.
description: 8 Pages,6 figure
MONAPipe: Modular Natural Language Processing Pipeline for Digital Humanities
Creators: name: Florian Barth
name: Yannic Bracke
name: José Calvo Tello
name: George Dogaru
name: Tillmann Dönicke
name: Keli Du
name: Stefan E. Funk
name: Philippe Genet
name: Mathias Göbel
name: Lennart Keller
name: Daniel Kurzawe
name: Ubbo Veentjer
name: Lukas Weimer
Publisher: name: Zenodo
Year: 2023
Subjects: Natural Language Processing
Research Data
Digital Humanities

description: Dieses Poster wurde auf dem Text+-Plenary (27.-29. September 2023) in Göttingen vorgestellt und ist der Task Area "Collections" und "Infrastructure Operations" zugeordnet.

Die Natural Language Processing Pipeline MONAPipe wird gemeinschaftlich von den beteiligten Partnern in Text+ für die Anwendung im Bereich der digitalen Geisteswissenschaften entwickelt. MONAPipe basiert auf spaCy und nutzt dessen System der "Custom Components" zur Integration eigener Entwicklungen. Zudem verfügt MONAPipe über ein eigenes auf Universal Dependencies basierendes Sprachmodell für das Deutsche. Im vorliegenden Poster werden eigene Komponenten und Implementierungen (blau) gegenüber den in spaCy integrierten (rot) vorgestellt.
Improving Smartphone Battery Life Utilizing Device-to-device Cooperative Relays Underlaying LTE Networks
Creators: name: Ta, Tuan
name: Baras, John S.
name: Zhu, Chenxi
Publisher: name: arXiv
Year: 2014
Subjects: subject: Networking and Internet Architecture (cs.NI)
subject: FOS: Computer and information sciences

description: The utility of smartphones has been limited to a great extent by their short battery life. In this work, we propose a new approach to prolonging smartphone battery life. We introduce the notions of "valueless" and "valued battery", as being the available battery when the user does or does not have access to a power source, respectively. We propose a cooperative system where users with high battery level help carry the traffic of users with low battery level. Our scheme helps increase the amount of valued battery in the network, thus it reduces the chance of users running out of battery early. Our system can be realized in the form of a proximity service (ProSe) which utilizes a device-to-device (D2D) communication architecture underlaying LTE. We show through simulations that our system reduces the probability of cellular users running out of battery before their target usage time (probability of outage). Our simulator source code is made available to the public.
description: Accepted at IEEE ICC 2014
Performance of simulated annealing in p-spin glasses
Creators: name: Krzakala, Florent
name: Zdeborova, Lenka
Publisher: name: arXiv
Year: 2013
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: We perform careful numerical simulations of slow Monte-Carlo annealings in the dense 3-body spin glass model and compare with the predictions from different theories: thresholds states, isocomplexity, following state. We conclude that while isocomplexity and following state both provide excellent agreement the numerical data, the influence of threshold states -- that is still the most commonly considered theory -- can be excluded from our data.
description: 7 pages, 7 figures, International Meeting on "Inference, Computation, and Spin Glasses" (ICSG2013), Sapporo, Japan
Constraining the two-Higgs doublet models with the LHC data
Creators: name: Ilisie, Victor
Publisher: name: arXiv
Year: 2013
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The recent discovery of a Standard Model-like boson with mass of about 126 GeV seems to be the first direct information on the electroweak symmetry breaking mechanism. Using the available experimental data from the LHC and Tevatron we study the implications on the parameter space of the Two-Higgs Doublet Model extension of the Standard Model. The generic structure of the Aligned Two-Higgs Doublet model is imposed in the Yukawa sector; also the models with discrete $\mathcal{Z}_2$ symmetries are analyzed.
description: 7 pages, 5 figures, 2013 EPS Conference Proceedings, v2: minor corrections made, references updated
Enchodelus georgensis Eliava, Tskitishvili & Bagaturia 2006
Creators: name: Elshishka, Milka
name: Mladenov, Aleksandar
name: Altash, Stela
name: Álvarez-Ortega, Sergio
name: Peña-Santiago, Reyes
name: Peneva, Vlada
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Nematoda
Enoplea
Dorylaimida
Nordiidae
Enchodelus
Enchodelus georgensis

description: Enchodelus georgensis Eliava, Tskitishvili & Bagaturia, 2006
Enchodelus georgensis Eliava, Tskitishvili & Bagaturia, 2006; Eliava et al. (2006) BLR: https://doi.org/10.5281/zenodo.11003168
Enchodelus georgensis; Peña-Santiago (2021 b): 207 BLR: https://doi.org/10.5281/zenodo.11193694
Distribution
Enchodelus georgensis is found only from the Palearctic, with a single report from Georgia (type habitat: deciduous forest, moss, firry forest, soil - Eliava et al. (2006)).
description: Published as part of Elshishka, Milka, Mladenov, Aleksandar, Altash, Stela, Álvarez-Ortega, Sergio, Peña-Santiago, Reyes & Peneva, Vlada, 2024, Cyber catalogue and revision of the nematode genus Enchodelus (Dorylaimida, Nordiidae), pp. e 126315 in Biodiversity Data Journal 12 on page e126315, DOI: 10.3897/BDJ.12.e126315
Exploring the Challenges and Future Expansion Opportunities of Wine & Kitchen during Pandemic
Creators: name: Lee, Kuan-Huei
name: Lim, Tze-Hin Jawn
name: Jun Long, Toh
Publisher: name: Applied Learning Conference 2022
Year: 2023
Subjects: Hospitality management
Small business organisation and management

description: After gaining extensive knowledge, community recognition, and proven experience over his lengthy career, William Seah founded his company, Wine & Gourmet Factory, in August 2017. The company had performed well, operating its first restaurant at Bukit Pasoh peacefully until 2021, where the devasting impacts of the COVID-19 pandemic led to its closure. William opened Wine & Kitchen together with Sally Seow just before the closure of the first restaurant (i.e., December 2020) at the considerably more accessible location of Somerset and operated with an adapted business model. As a result, William now has the opportunity to open his next outlet and enter regional countries. Notwithstanding, several business challenges exist and are presented in this case study. If you were William and Sally, what would you do to overcome them and expand your business?
Additional file 3 of Adaptations of evidence-based trauma-focused interventions for children and adolescents: a systematic review
Creators: name: Lange, Brittany C. L.
name: Nelson, Ashley
name: Lang, Jason M.
name: Stirman, Shannon Wiltsey
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 3. Study Quality.
A Bose-condensed, simultaneous dual species Mach-Zehnder atom interferometer
Creators: name: Kuhn, C. C. N.
name: McDonald, G. D.
name: Hardman, K. S.
name: Bennetts, S.
name: Everitt, P. J.
name: Altin, P. A.
name: Debs, J. E.
name: Close, J. D.
name: Robins, N. P.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Atomic Physics (physics.atom-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: This paper presents the first realisation of a simultaneous $^{87}$Rb -$^{85}$Rb Mach-Zehnder atom interferometer with Bose-condensed atoms. A number of ambitious proposals for precise terrestrial and space based tests of the Weak Equivalence Principle rely on such a system. This implementation utilises hybrid magnetic-optical trapping to produce spatially overlapped condensates with a duty cycle of 20s. A horizontal optical waveguide with co-linear Bragg beamsplitters and mirrors is used to simultaneously address both isotopes in the interferometer. We observe a non-linear phase shift on a non-interacting $^{85}$Rb interferometer as a function of interferometer time, $T$, which we show arises from inter-isotope scattering with the co-incident $^{87}$Rb interferometer. A discussion of implications for future experiments is given.
description: 7 pages, 5 figures. The authors welcome comments and feedback on this manuscript
First results of proton antiproton annihilation into a pion pair at large scattering angles within the handbag approach
Creators: name: Goritschnig, Alexander T.
name: Kofler, Stefan
name: Schweiger, Wolfgang
Publisher: name: arXiv
Year: 2013
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We propose to describe the process $ p ~ \bar{p} \rightarrow π^+ ~ π^-$ in a perturbative, QCD motivated framework in which a hard $ud \, \bar{u} \bar{d} \rightarrow d \, \bar{d} $ annihilation factorizes from soft transition distribution amplitudes. We advocate that the scale allowing for this factorization is the large transverse momentum transfer. In our simplified model, in which the proton is considered as a (scalar)diqark-quark system, a transition distribution amplitude describes the non-perturbative transition of the proton to the meson by emission of a scalar, isoscalar $ ud $-diquark and absorption of an antiquark (analogously for $ \bar{p} \rightarrow π^- $). We model the transition distribution amplitudes as an overlap of light-cone wave functions and present first results for the differential cross section. This process will be measured by the $ \bar{\mbox{P}}$ANDA experiment at GSI-FAIR.
description: FAIR NExt generation ScientistS 2013 (FAIRNESS 2013) CNUM: C13-09-16.2
Constraining dark matter capture and annihilation cross sections by searching for neutrino signature from the Earth core
Creators: name: Lee, Fei-Fan
name: Lin, Guey-Lin
name: Tsai, Yue-Lin Sming
Publisher: name: arXiv
Year: 2013
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We study the sensitivity of IceCube/DeepCore detector to dark matter annihilations in the Earth core. We focus on annihilation modes $χχ\to ν\barν, \, τ^+ τ^-, \, b \bar{b}$, and $W^+W^-$. Both track and cascade events are considered in our analysis. By fixing the dark matter annihilation cross section $\langle σ\upsilon\rangle$ at some nominal values, we study the sensitivity of IceCube/DeepCore detector to dark matter spin-independent cross section $σ_p^{\rm SI}$ for $m_χ$ ranging from few tens of GeV to 10 TeV. This sensitivity is compared with the existing IceCube 79-string constraint on the same cross section, which was obtained by searching for dark matter annihilations in the Sun. We compare this sensitivity to dark matter direct detection results as well, in particular the XENON100 (2012) limit and the parameter regions preferred by DAMA and CRESST-II experiments. We also present IceCube/DeepCore sensitivity to $\langle σ\upsilon \rangle$ as a function of $m_χ$ by fixing $σ_p^{\rm SI}$ at XENON100 (2012) and XENON1T limits, respectively. This sensitivity is compared with the preferred dark matter parameter range derived from the combined fitting to PAMELA and AMS02 positron fraction data. We conclude that the search for dark matter annihilations in the Earth core provides competitive constraints on $σ_p^{\rm SI}$ and $\langle σ\upsilon \rangle$ in the case of low-mass dark matter. Particularly, the expected constraint on $\sigsip$ for 5 years of data taking in IceCube/DeepCore is more stringent than the current IceCube 79-string limit mentioned above.
description: 23 pages, 8 figures
Beam-beam Effects of 'Gear-changing' in Ring-Ring Colliders
Creators: name: Hao, Yue
name: Litvinenko, Vladimir N.
name: Ptitsyn, Vadim
Publisher: name: arXiv
Year: 2013
Subjects: subject: Accelerator Physics (physics.acc-ph)
subject: FOS: Physical sciences

description: In ring-ring colliders, the collision frequency determines the bunch structures, e.g. the time between the bunches in both rings should be identical. Because of relatively low relativistic speed of the hadron beam in sub-TeV hadron-hadron- and electron-ions-colliders, scanning the hadron beam's energy would require either a change in the circumference of one of the rings, or a switching of the bunch (harmonic) number in a ring. The later would cause so-called 'gear-changing', i.e. the change of the colliding bunches turn by turn. In this article, we study the difficulties in beam dynamics in this 'gear-changing' scheme.
Additional file 1 of Experiences and consequences of phasing out substances of concern in a multinational healthcare company
Creators: name: Ujaczki, Éva
name: Stark-Rogel, Véronique
name: Olbrich, Martin
name: Fuetsch, Michaela
name: Backmann, Jan
Publisher: name: figshare
Year: 2022
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Computational Biology

description: Additional file 1: Table S1. Lists of substances (of concern) issued by states and international organisations. Table S2. Company initiatives to identify, list and track current and upcoming chemicals of concern. Figure S1. Molecular formulas of balovaptan, taselisib, ipatasertib and fenebrutinib
The cosmological evolution of the cosmological plasma with interpartial scalar interaction. I. The canonic formulation of classical scalar interaction
Creators: name: Ignat'ev, Yu. G.
Publisher: name: arXiv
Year: 2013
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: On the basis of Hamilton a formalism the dynamic equations of movement scalar charged particles in a classical scalar field are formulated. Unlike earlier published works of the author the model with zero own weight of particles is considered. Linear integrals of movement are found and ambiguity of communication between kinematic speed and an impulse of particles is specified.
description: 8 pages
A Prediction Model for System Testing Defects using Regression Analysis
Creators: name: Suffian, Muhammad Dhiauddin Mohamed
name: Ibrahim, Suhaimi
Publisher: name: arXiv
Year: 2014
Subjects: subject: Software Engineering (cs.SE)
subject: FOS: Computer and information sciences
subject: 68N30

description: This research describes the initial effort of building a prediction model for defects in system testing carried out by an independent testing team. The motivation to have such defect prediction model is to serve as early quality indicator of the software entering system testing and assist the testing team to manage and control test execution activities. Metrics collected from prior phases to system testing are identified and analyzed to determine the potential predictors for building the model. The selected metrics are then put into regression analysis to generate several mathematical equations. Mathematical equation that has p-value of less than 0.05 with R-squared and R-squared (adjusted) more than 90% is selected as the desired prediction model for system testing defects. This model is verified using new projects to confirm that it is fit for actual implementation.
description: 14 pages, 12 figures and 3 tables. e-ISSN: 2251-7545
Host Proteins Interacting with the Moloney Murine Leukemia Virus Integrase: Multiple Transcriptional Regulators and Chromatin Binding Factors
Creators: name: Studamire, Barbara
name: Goff, Stephen P.
Publisher: name: Columbia University
Year: 2008
Subjects: Virology
Oncology
Biochemistry

description: Background
A critical step for retroviral replication is the stable integration of the provirus into the genome of its host. The viral integrase protein is key in this essential step of the retroviral life cycle. Although the basic mechanism of integration by mammalian retroviruses has been well characterized, the factors determining how viral integration events are targeted to particular regions of the genome or to regions of a particular DNA structure remain poorly defined. Significant questions remain regarding the influence of host proteins on the selection of target sites, on the repair of integration intermediates, and on the efficiency of integration.

Results
We describe the results of a yeast two-hybrid screen using Moloney murine leukemia virus integrase as bait to screen murine cDNA libraries for host proteins that interact with the integrase. We identified 27 proteins that interacted with different integrase fusion proteins. The identified proteins include chromatin remodeling, DNA repair and transcription factors (13 proteins); translational regulation factors, helicases, splicing factors and other RNA binding proteins (10 proteins); and transporters or miscellaneous factors (4 proteins). We confirmed the interaction of these proteins with integrase by testing them in the context of other yeast strains with GAL4-DNA binding domain-integrase fusions, and by in vitro binding assays between recombinant proteins. Subsequent analyses revealed that a number of the proteins identified as Mo-MLV integrase interactors also interact with HIV-1 integrase both in yeast and in vitro.

Conclusion
We identify several proteins interacting directly with both MoMLV and HIV-1 integrases that may be common to the integration reaction pathways of both viruses. Many of the proteins identified in the screen are logical interaction partners for integrase, and the validity of a number of the interactions are supported by other studies. In addition, we observe that some of the proteins have documented interactions with other viruses, raising the intriguing possibility that there may be common host proteins used by different viruses. We undertook this screen to identify host factors that might affect integration target site selection, and find that our screens have generated a wealth of putative interacting proteins that merit further investigation.
Enchodelus hopedoroides Altherr 1963
Creators: name: Elshishka, Milka
name: Mladenov, Aleksandar
name: Altash, Stela
name: Álvarez-Ortega, Sergio
name: Peña-Santiago, Reyes
name: Peneva, Vlada
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Nematoda
Enoplea
Dorylaimida
Nordiidae
Enchodelus
Enchodelus hopedoroides

description: Enchodelus hopedoroides Altherr, 1963
Enchodelus (Enchodelus) hopedoroides Altherr, 1963 (Ahmad & Jairajpuri, 1980); Ahmad and Jairajpuri (1980) BLR: https://doi.org/10.5281/zenodo.8144934
Enchodelus hopedoroides Altherr, 1963; Altherr (1963) BLR: https://doi.org/10.5281/zenodo.8117912
Enchodelus hopedoroides; Eliava and Eliashvily (1990): 57, 98 BLR: https://doi.org/10.5281/zenodo.11003031
Enchodelus hopedoroides; Guerrero et al. (2008 a) BLR: https://doi.org/10.5281/zenodo.8114882
Enchodelus hopedoroides; Peña-Santiago (2021 b): 207 BLR: https://doi.org/10.5281/zenodo. 11191895
Distribution
Enchodelus hopedoroides is a part of Palearctic nematode fauna, reported only from Europe: Switzerland (type habitat: subalpine forest, Calamagrostis villosa (Chaix) Gmel., grasses, 2170 m a. s. l. - Altherr (1963)) and Spain (wet meadow, 2800 m a. s. l. - Guerrero et al. (2008 a)).
Taxon discussion
This species was originally described by Altherr (1963) in Switzerland. Later, Guerrero et al. (2008 a) re-examined its type material and studied Iberian specimens.
description: Published as part of Elshishka, Milka, Mladenov, Aleksandar, Altash, Stela, Álvarez-Ortega, Sergio, Peña-Santiago, Reyes & Peneva, Vlada, 2024, Cyber catalogue and revision of the nematode genus Enchodelus (Dorylaimida, Nordiidae), pp. e 126315 in Biodiversity Data Journal 12 on page e126315, DOI: 10.3897/BDJ.12.e126315
Additional file 10 of Epigenetic machinery is functionally conserved in cephalopods
Creators: name: Macchi, Filippo
name: Edsinger, Eric
name: Sadler, Kirsten C.
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 10: Figure S6. Structural modelling of DNMT1 and UHRF1. A. 3D structure of the BAH1, BAH2 and CTD domains of DNMT1 in M. musculus. B. 3D model of BAH1, BAH2 and CTD domains of DNMT1_OCTBM in O. bimaculoides. C. 3D structure of SRA domain of UHRF1 in M. musculus. D. 3D model of SRA domain of UHRF1_OCTBM in O. bimaculoides.
Retarded Fields of Null Particles and the Memory Effect
Creators: name: Tolish, Alexander
name: Wald, Robert M.
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We consider the retarded solution to the scalar, electromagnetic, and linearized gravitational field equations in Minkowski spacetime, with source given by a particle moving on a null geodesic. In the scalar case and in the Lorenz gauge in the electromagnetic and gravitational cases, the retarded integral over the infinite past of the source does not converge as a distribution, so we cut off the null source suitably at a finite time $t_0$ and then consider two different limits: (i) the limit as the observation point goes to null infinity at fixed $t_0$, from which the ``$1/r$'' part of the fields can be extracted and (ii) the limit $t_0 \to - \infty$ at fixed ``observation point.'' The limit (i) gives rise to a ``velocity kick'' on distant test particles in the scalar and electromagnetic cases, and it gives rise to a ``memory effect'' (i.e., a permanent change in relative separation of two test particles) in the linearized gravitational case, in agreement with previous analyses. Although the second limit does not exist for the Lorenz gauge potentials in the electromagnetic and linearized gravitational cases, we obtain a well defined distributional limit for the electromagnetic field strength and for the linearized Riemann tensor. In the gravitational case, this limit agrees with the Aichelberg-Sexl solution, but there is no ``memory effect'' associated with this limiting solution. This strongly suggests that the memory effect---including nonlinear memory effect of Christodoulou---should not be interpreted as arising simply from the passage of (effective) null stress energy to null infinity but rather as arising from a ``burst of radiation'' associated with the creation of the null stress-energy (as in case (i) above) or, more generally, with radiation present in the spacetime that was not ``produced'' by the null stress-energy.
description: 19 pages
Bank Permata Syariah dan Konvensional: Studi Pustaka (Library Research) dan Bibliometrik VOSviewer
Creators: name: Prayogi, Adha Herfian
name: Budianto, Eka Wahyu Hestya
name: Dewi, Nindi Dwi Tetria
Publisher: name: Zenodo
Year: 2023
Subjects: Bank Permata Syariah dan Konvensional
Studi Pustaka
Bibliometrik
VOSviewer

description: Penelitian ini bertujuan untuk memetakan topik penelitian seputar Bank Permata Syariah dan Konvensional dengan pendekatan kualitatif, yang bersifat studi pustaka (library research). Teknik pengumpulan data dengan: pertama, membuka sofware Perish/Harzing, lalu mencari jurnal berdasarkan kategori title words berkata kunci "Bank Permata Syariah dan Konvensional" dalam kurun waktu seluruh tahun. Kedua, mengumpulkan data judul jurnal dalam Microsoft Excel, dan mengidentifikasi judul jurnal yang ganda. Ketiga, mengunduh file berformat RIS (Research Information Systems) dan PDF (Portable Document Format) dari seluruh jurnal yang telah dikumpulkan datanya. Keempat, memasukkan file data RIS ke dalam software Mendeley Dekstop. Teknik analisis data dengan memetakan topik penelitian seputar Bank Permata Syariah dan Konvensional berdasarkan jurnal-jurnal yang telah dikumpulkan. Hasil penelitian menunjukkan bahwa terdapat 6 pemetaan topik penelitian menggunakan studi pustaka seputar Bank Permata Syariah dan Konvensional, yaitu: (1) Kinerja keuangan; (2) Kinerja karyawan; (3) Perilaku nasabah; (4) Produk pembiayaan/kredit; (5) Bank Permata Unit Usaha Syariah; dan (6) Isu-isu lainnya. Implikasi dan kontribusi penelitian ini adalah pemetaan topik-topik penelitian seputar Bank Permata Syariah dan Konvensional, baik yang sering ataupun jarang diteliti oleh peneliti, sehingga peneliti lainnya dapat mengetahui kekosongan penelitian dalam topik ini.
Enchodelus hopedorus Thorne 1939
Creators: name: Elshishka, Milka
name: Mladenov, Aleksandar
name: Altash, Stela
name: Álvarez-Ortega, Sergio
name: Peña-Santiago, Reyes
name: Peneva, Vlada
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Nematoda
Enoplea
Dorylaimida
Nordiidae
Enchodelus
Enchodelus hopedorus

description: Enchodelus hopedorus (Thorne, 1929) Thorne, 1939
Dorylaimellus hopedorus Thorne, 1929; Thorne (1929) BLR: https://doi.org/10.5281/zenodo.10797322
Enchodelus (Enchodelus) hopedorus (Thorne, 1929) Thorne, 1939
Enchodelus (Enchodelus) hopedorus; Ahmad and Jairajpuri (1980) BLR: https://doi.org/10.5281/zenodo.8144934
Enchodelus (Enchodelus) hopedorus; Choi et al. (1997) BLR: https://doi.org/10.5281/zenodo.10822468
Enchodelus hopedorus (Thorne, 1929) Thorne, 1939; Thorne (1939) BLR: https://doi.org/10.5281/zenodo.11003129
Enchodelus hopedorus; Brzeski (1963 a) BLR: https://doi.org/10.5281/zenodo.10869685
Enchodelus hopedorus; Zullini (1973) BLR: https://doi.org/10.5281/zenodo.10845257
Enchodelus hopedorus; Andrássy (1978): 116 [list]
Enchodelus hopedorus; Winiszewska-Slipinska (1987) BLR: https://doi.org/10.5281/zenodo.10854938
Enchodelus hopedorus; Eliava and Eliashvily (1990): 58, 98 BLR: https://doi.org/10.5281/zenodo.11003031
Enchodelus hopedorus; Guerrero and Peňa-Santiago (2007) BLR: https://doi.org/10.5281/zenodo.8111780
Enchodelus hopedorus; Peña-Santiago (2021 b): 207 BLR: https://doi.org/10.5281/zenodo.11194191
Distribution
A member of Holarctic nematode fauna, reported from: USA (type habitat: roots of alpine plants and moss, 4344 m a. s. l. - Thorne (1929) / deciduous forests - Johnson et al. (1972)), North America (freshwater habitats - Esser and Buckingham (1987)), Georgia (Eliava and Eliashvily (1990)), Korea (Pinus densiflora Siebold & Zucc. - Choi et al. (1997)) and Poland (Sphagnum spp. - Brzeski (1963 a) / oak-hornbeam forest litter and peat bog litter - Winiszewska-Slipinska (1987)), as well as from the high Himalaya, which form part of the boundary between the Palearctic and Indomalayan Regions: Nepal (soil from Rhododendron spp., Betula utilis D. Don, Abies sp., 4100 m a. s. l. - Zullini (1973)).
Taxon discussion
After its original description in the USA, this species was recorded from different locations in Europe and Asia. Guerrero et al. (2008 a) raised doubts regarding the identity of non-American material, with the possible exception of Polish material studied by Winiszewska-Slipinska (1987), which might belong to other species.
description: Published as part of Elshishka, Milka, Mladenov, Aleksandar, Altash, Stela, Álvarez-Ortega, Sergio, Peña-Santiago, Reyes & Peneva, Vlada, 2024, Cyber catalogue and revision of the nematode genus Enchodelus (Dorylaimida, Nordiidae), pp. e 126315 in Biodiversity Data Journal 12 on page e126315, DOI: 10.3897/BDJ.12.e126315
A Khovanov type invariant derived from an unoriented HQFT for links in thickened surfaces
Creators: name: Tagami, Keiji
Publisher: name: arXiv
Year: 2013
Subjects: subject: Geometric Topology (math.GT)
subject: FOS: Mathematics
subject: 57M25, 57M27

description: Two link diagrams on compact surfaces are strongly equivalent if they are related by Reidemeister moves and orientation preserving homeomorphisms of the surfaces. They are stably equivalent if they are related by the two previous operations and adding or removing handles. Turaev and Turner constructed a link homology for each stable equivalence class by applying an unoriented topological quantum field theory (TQFT) to a geometric chain complex similar to Bar-Natan's one. In this paper, by using an unoriented homotopy quantum field theory (HQFT), we construct a link homology for each strong equivalence class. Moreover, our homology yields an invariant of links in the oriented I-bundle of a compact surface.
description: 24 pages, 17 figures
MassBank Europe - Progress Report 2023
Creators: name: Schulze, Tobias
name: Neumann, Steffen
name: Stravs, Michael
name: Meier, Rene
name: Schymanski, Emma L.
Publisher: name: Zenodo
Year: 2023
Subjects: MassBank
NORMAN Association

description: Presentation given on an online non-target screening cross-working group meeting of the NORMAN Association on 07 November 2023.
Enchodelus longispiculus Guerrero, Liebanas & Pena-Santiago 2008
Creators: name: Elshishka, Milka
name: Mladenov, Aleksandar
name: Altash, Stela
name: Álvarez-Ortega, Sergio
name: Peña-Santiago, Reyes
name: Peneva, Vlada
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Nematoda
Enoplea
Dorylaimida
Nordiidae
Enchodelus
Enchodelus longispiculus

description: Enchodelus longispiculus Guerrero, Liébanas & Peña-Santiago, 2008
Enchodelus longispiculus Guerrero, Liébanas & Peña-Santiago, 2008; Guerrero et al. (2008 a) BLR: https://doi.org/10.5281/zenodo.8114886
Enchodelus longispiculus; Ciobanu et al. (2010 b) BLR: https://doi.org/10.5281/zenodo.8111641
Enchodelus longispiculus; Pedram et al. (2011) BLR: https://doi.org/10.5281/zenodo.8114668
Enchodelus longispiculus; Peña-Santiago (2021 b): 207-208 BLR: https://doi.org/10.5281/zenodo. 11191897
Distribution
A typical member of Palearctic nematode fauna: Spain (type habitat: wet meadow, 2925 m a. s. l., other microhabitats: gorse scrubland and wet meadows, 2590-2700 m a. s. l. - Guerrero et al. (2008 a)), Iran (rhizosphere of grasses - Pedram et al. (2011)) and Romania (beech forest, cliff vegetation, grassland, 400-2000 m a. s. l. - Ciobanu et al. (2010 b)).
Taxon discussion
Originally described from Spain, this species was later recorded in Romania and Iran. Pedram et al. (2011) provided its first molecular characterisation, based on the 18 S rDNA, ITS and partial 5.8 S gene.
description: Published as part of Elshishka, Milka, Mladenov, Aleksandar, Altash, Stela, Álvarez-Ortega, Sergio, Peña-Santiago, Reyes & Peneva, Vlada, 2024, Cyber catalogue and revision of the nematode genus Enchodelus (Dorylaimida, Nordiidae), pp. e 126315 in Biodiversity Data Journal 12 on page e126315, DOI: 10.3897/BDJ.12.e126315
Transcript, gene and gene set integration analysis using network biology.
Creators: name: Conceição, Izabela
name: Queiroz, Lúcio
Publisher: name: F1000 Research Limited
Year: 2020

description: Differential expression analysis is problematic due to the vast amount of differentially expressed genes that arise and the challenging task of correlating these genes with a concise biological function or molecular pathway. Multiple gene set enrichment methods (GSE) were developed aiming to solve that problem. However, frequently, enrichment analysis results in hundreds of enriched gene sets, because many genes participate in multiple cellular processes or multiple sets describe associated pathways.
Another issue in most expression data analyses is that they are performed in a gene-level manner only. Although, a gene can produce multiple different coding and non-coding transcripts through alternative splicing, a process present in all multicellular eukaryotes. This causes gene-level summarised quantification to sometimes lead to incorrect conclusions about the contribution of a gene in a biological process. Therefore, integrating transcript-level expression could provide invaluable insights into the effective contribution of a given gene.
Networks have been previously used to visualize gene expression data and gene set integration. Nevertheless, not to also explore the relationships between genes and their isoforms. Here we present a workflow to produce and interpret those types of networks.
Starting with expression data in gene and transcript level, we correlate the differentially expressed transcripts with its genes and perform enrichment analysis using the transcripts fold-change, applying Bioconductor packages such as fgsea, topGO, GAGE. Followed by R packages tidygraph and ggraph to interconnect the relations between pathways, related genes, and the transcript isoforms from those genes, marking the isoform types and the direction of their expression, network properties and structure can then be integrated into several other network science analyses. The final network forms an intuitive and functional visualization for GSE and transcript enrichment results, and its topology could bring insights into transcript function, non-coding presence and integration between gene sets, helping unravel transcriptomic signatures.
Additional file 13 of Epigenetic machinery is functionally conserved in cephalopods
Creators: name: Macchi, Filippo
name: Edsinger, Eric
name: Sadler, Kirsten C.
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 13: Figure S7. Original uncropped images of Slot blot in Fig. 3A. A. Blots containing biological replicate 1 and used for quantification. B. Blots containing replicate 2 and run with water used to prepare all samples and solutions.
Professional Development for an Evolving Earth Science Workforce
Creators: name: Downs, Robert R.
name: Chen, Robert S.
Publisher: name: Columbia University
Year: 2014
Subjects: subject: Management
subject: Geology
subject: FOS: Earth and related environmental sciences

description: The EarthCube community is faced with various challenges, opportunities, and choices for enabling Earth science. Technology is evolving rapidly and new tools and techniques are being created and enhanced to enable community members to do more individually and collaboratively. Workforce development opportunities can assist community members in their efforts to improve their capabilities and knowledge. A panel will describe workforce development opportunities that are available for the Earth science community and engage in a discussion with the audience on how the EarthCube community can improve by leveraging these opportunities.
systemPipeR: a generic workflow environment federates R with command-line software
Creators: name: Cassol, Daniela
name: Zhang, Le
name: Ponmathi Ramasamy
name: Mosher, Gordon
name: Girke, Thomas
Publisher: name: F1000 Research Limited
Year: 2020

description: The systemPipeR project provides a suite of R/Bioconductor packages for designing, building, and running end-to-end analysis workflows on local machines, HPC clusters and cloud systems, while generating at the same time publication quality analysis reports. Pre-configured workflow templates are provided for a wide range of omics applications. The package allows to choose for each workflow step the optimal R or command-line software, customize workflows, and design entirely new ones while taking advantage of central community S4 classes of the Bioconductor ecosystem. Thus, it serves as a federation hub for integrating both R and command-line based software, that makes efficient use of existing software without limiting users to tools from a single community project. The most substantial new features we have added recently to systemPipeR include but are not limited to the following enhancements. First, a graphical workflow management interface has been added allowing users to: visualize workflow designs in different graphical layouts; execute workflows step-wise or entirely; monitor their run status while tracking all metadata associated with a project, and subsequently generate both scientific and technical status reports. Second, a workflow control class (S4) has been added allowing users to execute single or any number of complex workflow steps with a single R command, such as runWF(sys[1:3]), or using pipes (%>%). Third, a Shiny interface has been created to support interactive graphics in workflow reports. This includes interactive visualization of various statistical results and workflow topologies. Finally, we have made many improvements to systemPipeR’s command-line interface based on CWL (Common Workflow Language). In contrast to other CWL-based interfaces, systemPipeR is unique by implementing most of CWL’s functionalities in R rather than just providing a wrapper tool for them. This way users can render, debug, and run all command-line definitions within efficiently designed S4 workflow container classes.
The Legacy of Ken Wilson
Creators: name: Cardy, John
Publisher: name: arXiv
Year: 2013
Subjects: subject: History and Philosophy of Physics (physics.hist-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: This is a brief account of the legacy of Ken Wilson in statistical physics, high energy physics, computing and education.
description: Written version of a talk given at the Ken Wilson Memorial Session, StatPhys 25, Seoul, July 2013. To appear in the conference proceedings in J. Stat. Mech
Additional file 14 of Epigenetic machinery is functionally conserved in cephalopods
Creators: name: Macchi, Filippo
name: Edsinger, Eric
name: Sadler, Kirsten C.
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 14: Figure S8. Pattern of DNA methylation identified by WGBS and RRBS in octopus tissues. A. Table describing the number and relative percentage of CpGs covered in the O. bimaculoides genome by each technique and sample analyzed. CpGs were classified based on the percentage of methylation as methylated (> 80%) or not methylated (< 20%). B. Scaled violin plot of CpGs identified by WGBS and RRBS in Supra E and Sub E brain and in one whole-body 30 dpf hatchling. Box-and-whisker inside violin plots have a center line at the median, lower and upper hinges correspond to first and third quartiles, and whiskers extend from hinges to largest or smallest values no further than 1.5 × IQR (inter-quartile range), while data beyond the end of the whiskers are outlying points that are plotted individually. Numbers on the lines indicate the percent of CpGs that are detected as >80% methylated. C. Scatter plot of DNA methylation levels of common CpGs across Supra Esophageal (Supra E) and Hatchlings. Dot color represents DNA methylation levels in Sub Esophageal (Sub E) and size of the dots indicates scaled proportion of CpGs represented by each dot. D. Scatter plot of DNA methylation levels of common CpGs across Sub Esophageal (Sub E) and Hatchlings. Dot color represents DNA methylation levels in Supra Esophageal (Supra E) and size of the dots indicates scaled proportion of CpGs represented by each dot.
The hemagglutinin mutation E391K of pandemic 2009 influenza revisited
Creators: name: Radomski, Jan P.
name: Płoński, Piotr
name: Zagórski-Ostoja, Włodzimierz
Publisher: name: arXiv
Year: 2013
Subjects: subject: Genomics (q-bio.GN)
subject: Populations and Evolution (q-bio.PE)
subject: FOS: Biological sciences

description: Phylogenetic analyses based on small to moderately sized sets of sequential data lead to overestimating mutation rates in influenza hemagglutinin (HA) by at least an order of magnitude. Two major underlying reasons are: the incomplete lineage sorting, and a possible absence in the analyzed sequences set some of key missing ancestors. Additionally, during neighbor joining tree reconstruction each mutation is considered equally important, regardless of its nature. Here we have implemented a heuristic method optimizing site dependent factors weighting differently 1st, 2nd, and 3rd codon position mutations, allowing to extricate incorrectly attributed sub-clades. The least squares regression analysis of distribution of frequencies for all mutations observed on a partially disentangled tree for a large set of unique 3243 HA sequences, along all nucleotide positions, was performed for all mutations as well as for non-equivalent amino acid mutations: in both cases demonstrating almost flat gradients, with a very slight downward slope towards the 3'-end positions. The mean mutation rates per sequence per year were 3.83*10^-4 for the all mutations, and 9.64*10^-5 for the non-equivalent ones.
description: 23 pages with figures (5 in main text, 3 in supplementary materials)
annoFuse: An R Package to Annotate and Prioritize RNA Fusions
Creators: name: Krutika S. Gaonkar
name: Komal S.  Rathi
name: Payal Jain
name: Yuankun Zhu
name: Chimicles, Nicholas A.
name: Naqvi, Ammar S.
name: Brown, Miguel A.
name: Zhang, Bo
name: Storm, Phillip B.
name: Marris, John M.
name: Resnick, Adam C.
name: Pichai Raman
name: Taroni, Jaclyn N.
name: Rokita, Jo Lynne
Publisher: name: F1000 Research Limited
Year: 2020

description: Gene fusion events are a significant source of somatic variation across adult and pediatric cancers and have provided some of the most effective clinically relevant therapeutic targets, yet computational algorithms for fusion detection from RNA sequencing data show low overlap of predictions across methods. In addition, events such as polymerase read-throughs, mis-mapping due to gene homology, and fusions occurring in healthy normal tissue require stringent filtering, making it difficult for researchers and clinicians to discern gene fusions that might be true underlying oncogenic drivers of a tumor and in some cases, appropriate targets for therapy. Here, we present annoFuse, an R package developed to annotate and identify biologically-relevant expressed gene fusions, along with highlighting recurrent novel fusions in a given cohort. We applied annoFuse to STAR-Fusion and Arriba results for 1,028 pediatric brain tumor samples provided as part of the Open Pediatric Brain Tumor Atlas (OpenPBTA) Project. First, we used FusionAnnotator to identify and filter “red flag” fusions found in healthy tissues or in gene homology databases. Using annoFuse, we filtered out fusions known to be artifactual and retained high-quality fusion calls. Second, we prioritized and captured known and putative oncogenic driver fusions previously reported in TCGA or fusions containing gene partners that are known oncogenes, tumor suppressor genes, COSMIC genes, or transcription factors. Using the PFAM database, we defined fusions containing kinases and annotated each for domain retention. Fusions can be plotted to visualize breakpoints by transcript with domain annotation. Finally, we determined recurrent fusions across the OpenPBTA cohort and recurrently-fused genes within each histology.
cytomapper: Visualization of highly multiplexed imaging cytometry data in R
Creators: name: Eling, Nils
name: Damond, Nicolas
name: Hoch, Tobias
name: Bodenmiller, Bernd
Publisher: name: F1000 Research Limited
Year: 2020

description: Highly multiplexed imaging cytometry acquires the single-cell expression of selected proteins in a spatially-resolved fashion. Pixel-intensities represent the spatial distributions of feature expression with highest resolution. Furthermore, after segmentation, expression values or cell-level metadata (e.g. cell-type information) can be visualized on segmented cell areas. The cytomapper package allows 1. the visualization of pixel-level information across multiple channels, 2. displaying of cell-level information (expression and/or metadata) on segmentation masks and 3. provides a Shiny application to gate and visualize cells on images.
The Elusive Quest for Political Stability: Diverging Approaches by the United States, Russia, and China in Central Asia and Beyond
Creators: name: Cooley, Alexander A.
Publisher: name: Columbia University
Year: 2013
Subjects: subject: Political science
subject: FOS: Political science
subject: Asians
subject: International relations

description: The seeming growing call to maintain political stability in Central Asia masks fundamental differences in how the United States, Russia and China approach the practices of conflict-resolution, governance and political practice in the region. Stability, and how to achieve it, have different meanings to these external patrons, while securing it remains elusive in this volatile region.