cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Literature on applied machine learning in metagenomic classification : A scoping review
Creators: name: Tonkovic, Petar
name: Kalajdziski, Slobodan A.
name: Zdravevski, Eftim
name: Lameski, Petre
name: Corizzo, Roberto
name: Pires, Ivan Miguel
name: Garcia, Nuno M.
name: Lončar-Turukalo, Tatjana
name: Trajkovik, Vladimir
Publisher: name: American University
Year: 2023

description: Applied machine learning in bioinformatics is growing as computer science slowly invades all research spheres. With the arrival of modern next-generation DNA sequencing algorithms, metagenomics is becoming an increasingly interesting research field as it finds countless practical applications exploiting the vast amounts of generated data. This study aims to scope the scientific literature in the field of metagenomic classification in the time interval 2008–2019 and provide an evolutionary timeline of data processing and machine learning in this field. This study follows the scoping review methodology and PRISMA guidelines to identify and process the available literature. Natural Language Processing (NLP) is deployed to ensure efficient and exhaustive search of the literary corpus of three large digital libraries: IEEE, PubMed, and Springer. The search is based on keywords and properties looked up using the digital libraries’ search engines. The scoping review results reveal an increasing number of research papers related to metagenomic classification over the past decade. The research is mainly focused on metagenomic classifiers, identifying scope specific metrics for model evaluation, data set sanitization, and dimensionality reduction. Out of all of these subproblems, data preprocessing is the least researched with considerable potential for improvement.
Additional file 2 of Transcriptome shifts triggered by vitamin A and SCD genotype interaction in Duroc pigs
Creators: name: Solé, Emma
name: González-Prendes, Rayner
name: Oliinychenko, Yelyzaveta
name: Tor, Marc
name: Ros-Freixedes, Roger
name: Estany, Joan
name: Pena, Ramona N.
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2.
Soja: 14 Impfmittel im Test
Creators: name: Recknagel, J.
name: Butz, A.
Publisher: name: Zenodo
Year: 2022

description: Einen Artikel in der Top agrar Suedplus. Am LTZ Augustenberg wurden Impfmittel für Soja drei Jahre lang an drei Orten geprüft. Die Unterschiede in der Wirkung waren zum Teil erheblich.
A General Volatility Framework and the Generalised Historical Volatility Estimator
Creators: name: Bollen, Bernard
name: Inder, Brett
name: Bollen, Bernard
name: Inder, Brett
Publisher: name: Unknown
Year: 1998
Subjects: Research Methods/ Statistical Methods

description: This study proposes a new approach to the estimation of the time series properties of daily volatility in financial markets. The estimation technique is a two stage procedure which initially estimates the volatility of any particular trading day from intraday data. This procedure is implemented over a number of trading days to produce a series of daily volatility estimates. A general volatility framework is also developed and the series of daily volatility estimates can be put into this framework to estimate the time series properties of daily volatility. Furthermore, with this new approach it is shown that the time series properties of daily volatility can be modelled in a wide range of functional forms, including those functional forms which capture asymmetric information effects.
Spatial correlations of trapped 1d bosons in an optical lattice
Creators: name: Kollath, C.
name: Schollwöck, U.
name: von Delft, J.
name: Zwerger, W.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We investigate a quasi-one dimensional system of trapped cold bosonic atoms in an optical lattice by using the density matrix renormalization group to study the Bose-Hubbard model at T=0 for experimentally realistic numbers of lattice sites. It is shown that a properly rescaled one-particle density matrix characterizes superfluid versus insulating states just as in the homogeneous system. For typical parabolic traps we also confirm the widely used local density approach for describing correlations in the limit of weak interaction. Finally, we note that the superfluid to Mott-insulating transition is seen most directly in the half width of the interference peak.
Bulk properties and flow
Creators: name: Xu, Zhangbu
Publisher: name: arXiv
Year: 2004
Subjects: subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: In this report, I summarize the experimental results on {\bf bulk properties and flow} presented at Quark Matter 2004. It is organized in four sections: 1) Initial condition and stopping; 2) Particle spectra and freeze-outs; 3) Anisotropic flow; 4) Outlook for future measurements.
description: 10 pages, 4 figures, "Rapporteur-Conference Highlights", Quark Matter 2004, Oakland, January 11-17
Literature on applied machine learning in metagenomic classification : A scoping review
Creators: name: Tonkovic, Petar
name: Kalajdziski, Slobodan A.
name: Zdravevski, Eftim
name: Lameski, Petre
name: Corizzo, Roberto
name: Pires, Ivan Miguel
name: Garcia, Nuno M.
name: Lončar-Turukalo, Tatjana
name: Trajkovik, Vladimir
Publisher: name: Biology
Year: 2023
Subjects: classificationCode: 31
subject: Biological sciences
subject: FOS: Biological sciences

description: Applied machine learning in bioinformatics is growing as computer science slowly invades all research spheres. With the arrival of modern next-generation DNA sequencing algorithms, metagenomics is becoming an increasingly interesting research field as it finds countless practical applications exploiting the vast amounts of generated data. This study aims to scope the scientific literature in the field of metagenomic classification in the time interval 2008–2019 and provide an evolutionary timeline of data processing and machine learning in this field. This study follows the scoping review methodology and PRISMA guidelines to identify and process the available literature. Natural Language Processing (NLP) is deployed to ensure efficient and exhaustive search of the literary corpus of three large digital libraries: IEEE, PubMed, and Springer. The search is based on keywords and properties looked up using the digital libraries’ search engines. The scoping review results reveal an increasing number of research papers related to metagenomic classification over the past decade. The research is mainly focused on metagenomic classifiers, identifying scope specific metrics for model evaluation, data set sanitization, and dimensionality reduction. Out of all of these subproblems, data preprocessing is the least researched with considerable potential for improvement.
Additional file 2 of An energy metabolism-based eight-gene signature correlates with the clinical outcome of esophagus carcinoma
Creators: name: Zheng, Weifeng
name: Chaoying Chen
name: Jianghao Yu
name: Chengfeng Jin
name: Tiemei Han
Publisher: name: figshare
Year: 2021
Subjects: subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Cancer
subject: Computational Biology

description: Additional file 2: Supplement Figure S2. The proportions of B cell, CD4+T cell, CD8+T cell, Neutrophil, Macrophage, Dendritic cell (DC), ImmuneScore, StromalScore, and ESTIMATEScore between the two subtypes. The enumeration of six tumor-infiltration immune cells was estimated using the “Tumor Immune Estimation Resource” (TIMER, https://cistrome.shinyapps.io/timer/ ) tool.
Additional file 3 of Mutant Huntingtin affects toll-like receptor 4 intracellular trafficking and cytokine production in mast cells
Creators: name: Pérez-Rodríguez, Marian Jesabel
name: Ibarra-Sánchez, Alfredo
name: Román-Figueroa, Abraham
name: Pérez-Severiano, Francisca
name: González-Espinosa, Claudia
Publisher: name: figshare
Year: 2020
Subjects: subject: Immunology
subject: FOS: Clinical medicine

description: Additional file 3: Figure S3. mHtt expression prevents TLR4-triggered IL-10 and TGF-β mRNA synthesis. a) Time-course of IL-10 mRNA expression in WT and R6/1 cells in response to LPS. b) Time-course of TGF-β mRNA expression in WT and R6/1 cells in response to LPS. Upper panels show an image obtained from a representative experiment, and lower panels show densitometric analysis of different experiments. Data are presented as the mean ± SD from at least three experiments performed with independent cultures. *p
Thünen-Baseline 2017 – 2027: Agrarökonomische Projektionen für Deutschland
Thünen Baseline 2017 – 2027:
Creators: name: Offermann, Frank
name: Banse, Martin
name: Freund, Florian
name: Haß, Marlen
name: Kreins, Peter
name: Laquai, Verena
name: Osterburg, Bernhard
name: Pelikan, Janine
name: Rösemann, Claus
name: Salamon, Petra
name: Offermann, Frank
name: Banse, Martin
name: Freund, Florian
name: Haß, Marlen
name: Kreins, Peter
name: Laquai, Verena
name: Osterburg, Bernhard
name: Pelikan, Janine
name: Rösemann, Claus
name: Salamon, Petra
Publisher: name: Unknown
Year: 2018
Subjects: subject: Agricultural and Food Policy
subject: Environmental Economics and Policy
subject: Farm Management
subject: Land Economics/Use
subject: agricultural policy
subject: impact assessment
subject: model
subject: model network
subject: Agrarpolitik
subject: Politikfolgenabschätzung
subject: Modell
subject: Modellverbund

description: This report presents selected results of the Thünen Baseline 2017 – 2027 as well as the assumptions upon which these results are based. The Thünen Baseline is established using and combining several models of the Thünen model network. The baseline assumes a continuation of the current policy framework and the implementation of already decided policy changes. This report describes the outcome of model projections of agricultural trade, prices, production, income and environmental impacts. The presentation focuses on the development of the German agricultural sector compared to the base period 2014 - 2016. In the Thünen Baseline 2017 - 2027, sluggish demand on world agricultural markets in combination with a stronger Euro implies that the real prices of most agricultural commodities will decline. One exception is dairy products, where strong export demand supports the producer price for milk in Germany. As a consequence, the income of many farms is projected to be lower than in the base period 2014-2016. However, a sensitivity analysis based on a scenario which assumes a depreciation of the Euro highlights the extent to which export-oriented sectors depend on macroeconomic developments.
Additional file 3 of An energy metabolism-based eight-gene signature correlates with the clinical outcome of esophagus carcinoma
Creators: name: Zheng, Weifeng
name: Chaoying Chen
name: Jianghao Yu
name: Chengfeng Jin
name: Tiemei Han
Publisher: name: figshare
Year: 2021
Subjects: subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Cancer
subject: Computational Biology

description: Additional file 3: Supplement Figure S3. Kaplan-Meier analysis on the eight genes using the optimal cut-off value of the expression level of each gene.
Betriebs- und Unternehmensstrukturen in der deutschen Landwirtschaft: Workshop zu vorläufigen Ergebnissen und methodischen Ansätzen
Creators: name: Forstner, Bernd
name: Zavyalova, Ekaterina
name: Forstner, Bernd
name: Zavyalova, Ekaterina
Publisher: name: Unknown
Year: 2017
Subjects: subject: Agricultural Finance
subject: Farm Management
subject: Production Economics
subject: Agricultural structure
subject: Farm structure
subject: Agricultural Structure Survey
subject: Agrarstruktur,
subject: Betriebsstruktur
subject: Unternehmensstruktur
subject: Agrarstatistik

description: Many of the farm enterprises in Germany comprise several legally independent farms. These enterprises in the agricultural and the agriculture-related sectors are often split between several members of one family. Especially due to professionalization and growth in agricultural diversification and production commercial farms emerge beside the original farm. This trend and the statistical coverage of such structures can cause difficulties for policy analyses. For this reason the Thünen-Institute started a research project on farm and enterprise structures in the German agriculture. The main goal of the project is to find out how prevalent are complex structures in German agriculture and how are these covered by the official agricultural statistics. Within the project there was a regional empirical study on the basis of expert interviews carried out so far in order to estimate the prevalence of complex farm structures. Moreover the available data sources about agriculture and agriculture-related sectors as well as applied survey methodologies were analyzed with the help of literature and data research and numerous expert interviews. As part of the project workshop, the preliminary results of the research project on the topic “Farm and enterprise structures in German agriculture” were presented and discussed. The results so far show that the current methodology of official agricultural statistics in Germany can cover only a part of the units relevant to policy analysis and consulting in terms of company and company structures. Furthermore it was found out that neither of the currently available information sources on agriculture or the agriculture-related sector can provide further insights regarding complex farm and enterprise structures as far as these sources are not combined with each other. Therefore the next work steps are to estimate the overall extent of individual farm and enterprise “unites” (for example, biogas plants). These results will be completed with an empirical study. After that the influence of complex structures on the income situation of agricultural households should be estimated. In the context of the workshop, four keynote presentations were held on the following topics: (1) dealing with complex companies in the German Statistical Business Register; (2) the consequence of missing information regarding complex structures in policy analysis; (3) managing complex farms in German official agricultural statistics; as well as (4) the agricultural statistics system in Austria.
description: DOI:10.3220/WP1510569554000
Additional file 1 of Elevated levels of interleukin-12/23p40 may serve as a potential indicator of dysfunctional heart rate variability in type 2 diabetes
Creators: name: Wegeberg, A. M.
name: Okdahl, T.
name: Riahi, S.
name: Ejskjaer, N.
name: Pociot, F.
name: Størling, J.
name: Brock, B.
name: Brock, C.
Publisher: name: figshare
Year: 2022
Subjects: subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 1: Table S1a. Cardiovascular parameters. Table S1b. Neuroinflammatory parameters. Table S2. Associations between neuroinflammatory markers and neurocardiac function.
TOWARD AN INSTITUTIONAL ANALYSIS OF FARM INCOME STABILIZATION
INSTITUCIONALNA ANALYZA STABILIZACIE VYNOSOV POL'NOHOSPODARSKEHO PODNIKU
Creators: name: VALENTINOV, Vladislav
name: HEIDELBACH, Olaf
name: VALENTINOV, Vladislav
name: HEIDELBACH, Olaf
Publisher: name: Unknown
Year: 2006
Subjects: subject: Agricultural and Food Policy
subject: Farm Management
subject: institutional mechanisms
subject: farm income stabilization
subject: insurance activity
subject: incentive attributes
subject: transaction costs

description: The objective of the paper is to compare the major institutional mechanisms of farm income stabilization (market, government, civil society) in order to find out how the mutual substitution of the mechanisms can serve to overcome their limitations. The major identified limitations include: for the market mechanism - opportunism and poor insurability of systemic risks; for the government mechanism - opportunistic behavior of recipients of farm income stabilization services, agency problems in the implementation of public programs, high potential for bureaucratization and excessive complexity of insurance programs. The incentive problems of the civil society mechanism do not include mainly those that are characteristic of both markets and governments. However, this mechanism possesses problems specific to cooperative organizations. These problems have been shown to originate from high social capital-dependence of the civil society mechanism, which means that while these problems are able to significantly increase transaction costs of civil society mechanism, the actual size of these transaction costs depends on the availability of social capital in the respective communities. The economic context of transition to market has been shown to create additional constraints on market and government mechanisms and opportunities for the civil society mechanism. Therefore, the optimal role of the government is to invest in social capital in order to reduce the transaction costs of the civil society mechanism.
Modeling the Optical Afterglow of GRB 030329
Creators: name: Huang, Y. F.
name: Cheng, K. S.
name: Gao, T. T.
Publisher: name: arXiv
Year: 2005
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: The best-sampled afterglow light curves are available for GRB 030329. A distinguishing feature of this event is the obvious rebrightening at around 1.6 days after the burst. Proposed explanations for the rebrightening mainly include the two-component jet model and the refreshed shock model, although a sudden density-jump in the circumburst environment is also a potential choice. Here we re-examine the optical afterglow of GRB 030329 numerically in light of the three models. In the density-jump model, no obvious rebrightening can be produced at the jump moment. Additionally, after the density jump, the predicted flux density decreases rapidly to a level that is significantly below observations. A simple density-jump model thus can be excluded. In the two-component jet model, although the observed late afterglow (after 1.6 days) can potentially be explained as emission from the wide-component, the emergence of this emission actually is too slow and it does not manifest as a rebrightening as previously expected. The energy-injection model seems to be the most preferred choice. By engaging a sequence of energy-injection events, it provides an acceptable fit to the rebrightening at $\sim 1.6$ d, as well as the whole observed light curve that extends to $\sim 80$ d. Further studies on these multiple energy-injection processes may provide a valuable insight into the nature of the central engines of gamma-ray bursts.
description: 18 pages, 3 figures; a few references added and minor word changes; now accepted for publication in ApJ
What's the temperature in tropical caves?
Creators: name: Mejía-Ortíz, Luis Manuel
name: Christman, Mary C.
name: Pipan, Tanja
name: Culver, David C.
Publisher: name: American University
Year: 2023

description: Hourly temperature was measured for approximately one year at 17 stations in three caves in Quintana Roo, Mexico. Thirteen of these stations were in the extensive twilight zones of all three caves. All seventeen stations showed seasonality in temperature with a 3C drop during the Nortes season. Two of the caves, Muévelo Sabrosito and Muévelo Rico, showed greater variability during the winter months while in Río Secreto (Tuch) variability was greatest during the rainy season. Río Secreto is less open to the surface than the other two. All sites also showed a daily temperature cycle, although it was very faint in some Río Secreto (Tuch) sites. While temperature variability is diminished relative to surface variation, its temporal pattern is worthy of further study.
Effects of Substituting Calcium for Yttrium on the Superconducting Properties of YBa2Cu3Oz Bulk Samples
Creators: name: Nazarova, E. K.
name: Zaleski, A. J.
name: Zahariev, A. L.
name: Stoyanova-Ivanova, A. K.
name: Zalamova, K. N.
Publisher: name: arXiv
Year: 2004
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We report systematic studies of AC magnetic susceptibility and transport properties of Y(1-x)Ca(x)Ba2Cu3Oz bulk samples with 0\leq x\leq 0.4. Single phase materials, reduction of carrier concentration and decrease of Tc to 85 K were obtained at doping levels up to 20%. For Y0.7Ca0.3Ba2Cu3Oz sample the improvement of grains boundary transport and screening capabilities has been observed as a result of the optimal ratio between carrier concentration and impurity phase BaCuO2 presence. The appearence of bulk pinning and nonlinear effects starting at the highest temperature were detected also.
description: 12 pages, 8 figures, accepted in Physica C
Gravitational waves and mass ejecta from binary neutron star mergers: Effect of the spin orientation
Creators: name: Chaurasia, Swami Vivekanandji
name: Dietrich, Tim
name: Ujevic, Maximiliano
name: Hendriks, Kai
name: Dudi, Reetika
name: Fabbri, Francesco Maria
name: Tichy, Wolfgang
name: Brügmann, Bernd
Publisher: name: arXiv
Year: 2020
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We continue our study of the binary neutron star parameter space by investigating the effect of the spin orientation on the dynamics, gravitational wave emission, and mass ejection during the binary neutron star coalescence. We simulate seven different configurations using multiple resolutions to allow a reasonable error assessment. Due to the particular choice of the setups, five configurations show precession effects, from which two show a precession ("wobbling") of the orbital plane, while three show a "bobbing" motion, i.e., the orbital angular momentum does not precess, while the orbital plane moves along the orbital angular momentum axis. Considering the ejection of mass, we find that precessing systems can have an anisotropic mass ejection, which could lead to a final remnant kick of $\sim 40 \rm km/s$ for the studied systems. Furthermore, for the chosen configurations, antialigned spins lead to larger mass ejecta than aligned spins, so that brighter electromagnetic counterparts could be expected for these configurations. Finally, we compare our simulations with the precessing, tidal waveform approximant IMRPhenomPv2_NRTidalv2 and find good agreement between the approximant and our numerical relativity waveforms with phase differences below 1.2 rad accumulated over the last $\sim$ 16 gravitational wave cycles.
description: 18 pages, 16 figures
The assembly of massive galaxies from NIR observations of the Hubble Deep Field South
Creators: name: Fontana, A.
name: Donnarumma, I.
name: Vanzella, E.
name: Giallongo, E.
name: Menci, N.
name: Nonino, M.
name: Saracco, P.
name: Cristiani, S.
name: D'Odorico, S.
name: Poli, F.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We use a deep K(AB)<25 galaxy sample in the Hubble Deep Field South to trace the evolution of the cosmological stellar mass density from z~ 0.5 to z~3. We find clear evidence for a decrease of the average stellar mass density at high redshift, 22 is 20^{+20}_{-5} % of the local value. In the mass--limited subsample at z>2, the fraction of passively fading galaxies is at most 25%, although they can contribute up to about 40% of the stellar mass density. On the other hand, star--forming galaxies at z>2 form stars with an average specific rate at least ~4 x10^{-10} yr$^{-1}$, 3 times higher than the z2.
description: Accepted for publication on ApJLetters
What's the temperature in tropical caves?
Creators: name: Mejía-Ortíz, Luis Manuel
name: Christman, Mary C.
name: Pipan, Tanja
name: Culver, David C.
Publisher: name: Public Library of Science
Year: 2023
Subjects: classificationCode: 31
subject: Biological sciences
subject: FOS: Biological sciences

description: Hourly temperature was measured for approximately one year at 17 stations in three caves in Quintana Roo, Mexico. Thirteen of these stations were in the extensive twilight zones of all three caves. All seventeen stations showed seasonality in temperature with a 3C drop during the Nortes season. Two of the caves, Muévelo Sabrosito and Muévelo Rico, showed greater variability during the winter months while in Río Secreto (Tuch) variability was greatest during the rainy season. Río Secreto is less open to the surface than the other two. All sites also showed a daily temperature cycle, although it was very faint in some Río Secreto (Tuch) sites. While temperature variability is diminished relative to surface variation, its temporal pattern is worthy of further study.
[Halle (Saale), Universitäts- und Landesbibliothek Sachsen-Anhalt, Morbio 7 (7)]
Creators: name: Nikolaus, V.
Publisher: name: Universitäts- und Landesbibliothek Sachsen-Anhalt
Year: 1451
Subjects: subject: Papsturkunde
subject: Urkunde
subject: 090

description: Papst Nikolaus V. befreit den Generalprior und die Brüder vom Augustiner-Eremitenorden vom jährlichen Census, nachdem diese Befreiung zeitweise ausgesetzt war.
Interpreting social accounting matrix (SAM) as an information channel
Creators: name: Sbert, Mateu
name: Chen, Shuning
name: Feixas, Miquel
name: Vila, Marius
name: Golan, Amos
Publisher: name: American University
Year: 2023

description: Information theory, and the concept of information channel, allows us to calculate the mutual information between the source (input) and the receiver (output), both represented by probability distributions over their possible states. In this paper, we use the theory behind the information channel to provide an enhanced interpretation to a Social Accounting Matrix (SAM), a square matrix whose columns and rows present the expenditure and receipt accounts of economic actors. Under our interpretation, the SAM’s coefficients, which, conceptually, can be viewed as a Markov chain, can be interpreted as an information channel, allowing us to optimize the desired level of aggregation within the SAM. In addition, the developed information measures can describe accurately the evolution of a SAM over time. Interpreting the SAM matrix as an ergodic chain could show the effect of a shock on the economy after several periods or economic cycles. Under our new framework, finding the power limit of the matrix allows one to check (and confirm) whether the matrix is well-constructed (irreducible and aperiodic), and obtain new optimization functions to balance the SAM matrix. In addition to the theory, we also provide two empirical examples that support our channel concept and help to understand the associated measures.
Recalibrating 3D ConvNets with Project & Excite
Creators: name: Rickmann, Anne-Marie
name: Roy, Abhijit Guha
name: Sarasua, Ignacio
name: Wachinger, Christian
Publisher: name: arXiv
Year: 2020
Subjects: subject: Image and Video Processing (eess.IV)
subject: Machine Learning (cs.LG)
subject: Machine Learning (stat.ML)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Computer and information sciences

description: Fully Convolutional Neural Networks (F-CNNs) achieve state-of-the-art performance for segmentation tasks in computer vision and medical imaging. Recently, computational blocks termed squeeze and excitation (SE) have been introduced to recalibrate F-CNN feature maps both channel- and spatial-wise, boosting segmentation performance while only minimally increasing the model complexity. So far, the development of SE blocks has focused on 2D architectures. For volumetric medical images, however, 3D F-CNNs are a natural choice. In this article, we extend existing 2D recalibration methods to 3D and propose a generic compress-process-recalibrate pipeline for easy comparison of such blocks. We further introduce Project & Excite (PE) modules, customized for 3D networks. In contrast to existing modules, Project \& Excite does not perform global average pooling but compresses feature maps along different spatial dimensions of the tensor separately to retain more spatial information that is subsequently used in the excitation step. We evaluate the modules on two challenging tasks, whole-brain segmentation of MRI scans and whole-body segmentation of CT scans. We demonstrate that PE modules can be easily integrated into 3D F-CNNs, boosting performance up to 0.3 in Dice Score and outperforming 3D extensions of other recalibration blocks, while only marginally increasing the model complexity. Our code is publicly available on https://github.com/ai-med/squeeze_and_excitation .
description: Accepted for publication at IEEE Transactions on Medical Imaging
Additional file 4 of An energy metabolism-based eight-gene signature correlates with the clinical outcome of esophagus carcinoma
Creators: name: Zheng, Weifeng
name: Chaoying Chen
name: Jianghao Yu
name: Chengfeng Jin
name: Tiemei Han
Publisher: name: figshare
Year: 2021
Subjects: subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Cancer
subject: Computational Biology

description: Additional file 4: Supplement Figure S4. A. the differences on the expression level of these 8 gene between the two groups; B. single sample GSEA analysis results of pathways significantly associated with the 8-gene signature.
Was ordinary matter synthesised from mirror matter? An attempt to explain why $Ω_{Baryon} \approx 0.2Ω_{Dark}$
Creators: name: Foot, R.
name: Volkas, R. R.
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: The cosmological dust has begun to settle. A likely picture is a universe comprised (predominantly) of three components: ordinary baryons ($Ω_B \approx 0.05$), non-baryonic dark matter ($Ω_{Dark} \approx 0.22$) and dark energy ($Ω_Λ \approx 0.7$). We suggest that the observed similarity of the abundances of ordinary baryons and non-baryonic dark matter ($Ω_{B}/Ω_{Dark} \approx 0.20$) hints at an underlying similarity between the fundamental properties of ordinary and dark matter particles. This is necessarily the case if dark matter is identified with mirror matter. We examine a specific mirror matter scenario where $Ω_B/Ω_{Dark} \approx 0.20$ is naturally obtained.
description: 6 pages, RevTeX; minor changes and additional explanations; version accepted by Phys Rev D Rapid Communications
QCD Hard Scattering and the Sign of the Spin Asymmetry A_LL^pi
Creators: name: Jager, Barbara
name: Kretzer, Stefan
name: Stratmann, Marco
name: Vogelsang, Werner
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Recent preliminary PHENIX data are consistent with a negative and sizable longitudinal double-spin asymmetry A_LL^pi for pi^0 production at moderate transverse momentum p_perp \simeq 1 - 4 GeV and central rapidity. By means of a systematic investigation of the relevant degrees of freedom we show that the perturbative QCD framework at leading power in p_perp produces at best a very small negative asymmetry in this kinematic range.
description: 4 pages, 3 figures, final version published in PRL (only minor changes; note: title changed in published version)
Interpreting social accounting matrix (SAM) as an information channel
Creators: name: Sbert, Mateu
name: Chen, Shuning
name: Feixas, Miquel
name: Vila, Marius
name: Golan, Amos
Publisher: name: Entropy
Year: 2023
Subjects: classificationCode: 46
subject: Information and computing sciences

description: Information theory, and the concept of information channel, allows us to calculate the mutual information between the source (input) and the receiver (output), both represented by probability distributions over their possible states. In this paper, we use the theory behind the information channel to provide an enhanced interpretation to a Social Accounting Matrix (SAM), a square matrix whose columns and rows present the expenditure and receipt accounts of economic actors. Under our interpretation, the SAM’s coefficients, which, conceptually, can be viewed as a Markov chain, can be interpreted as an information channel, allowing us to optimize the desired level of aggregation within the SAM. In addition, the developed information measures can describe accurately the evolution of a SAM over time. Interpreting the SAM matrix as an ergodic chain could show the effect of a shock on the economy after several periods or economic cycles. Under our new framework, finding the power limit of the matrix allows one to check (and confirm) whether the matrix is well-constructed (irreducible and aperiodic), and obtain new optimization functions to balance the SAM matrix. In addition to the theory, we also provide two empirical examples that support our channel concept and help to understand the associated measures.
Using neural networks for efficient evaluation of high multiplicity scattering amplitudes
Creators: name: Badger, Simon
name: Bullock, Joseph
Publisher: name: arXiv
Year: 2020
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Precision theoretical predictions for high multiplicity scattering rely on the evaluation of increasingly complicated scattering amplitudes which come with an extremely high CPU cost. For state-of-the-art processes this can cause technical bottlenecks in the production of fully differential distributions. In this article we explore the possibility of using neural networks to approximate multi-variable scattering amplitudes and provide efficient inputs for Monte Carlo integration. We focus on QCD corrections to $e^+e^-\to$ jets up to one-loop and up to five jets. We demonstrate reliable interpolation when a series of networks are trained to amplitudes that have been divided into sectors defined by their infrared singularity structure. Complete simulations for one-loop distributions show speed improvements of at least an order of magnitude over a standard approach.
description: 26 pages
Isogenous components of Jacobian surfaces
Creators: name: Beshaj, Lubjana
name: Elezi, Artur
name: Shaska, Tony
Publisher: name: American University
Year: 2023

description: Let be a genus 2 curve defined over a field K, charK=p⩾0, and its Jacobian, where ι is the principal polarization of attached to . Assume that is (n, n)-geometrically reducible with E1 and E2 its elliptic components. We prove that there are only finitely many curves (up to isomorphism) defined over K such that E1 and E2 are N-isogenous for n=2 and N=2,3,5,7 with or n=2, N=3,5,7 with . The same holds if n=3 and N=5. Furthermore, we determine the Kummer and Shioda–Inose surfaces for the above and show how such results in positive characteristic p>2 suggest nice applications in cryptography.
Additional file 5 of An energy metabolism-based eight-gene signature correlates with the clinical outcome of esophagus carcinoma
Creators: name: Zheng, Weifeng
name: Chaoying Chen
name: Jianghao Yu
name: Chengfeng Jin
name: Tiemei Han
Publisher: name: figshare
Year: 2021
Subjects: subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Cancer
subject: Computational Biology

description: Additional file 5: Supplement Figure S5. A. ROC curve of the 8-gene signature for 1-year, 3-year and 5-year DFS; B. Kaplan-Meier survival curve of DFS based on the 8-gene signature. ROC, receiver operating characteristic; AUC, area under the curve; HR, hazard ratio; CI, confidence interval.
Isogenous components of Jacobian surfaces
Creators: name: Beshaj, Lubjana
name: Elezi, Artur
name: Shaska, Tony
Publisher: name: European Journal of Mathematics
Year: 2023
Subjects: classificationCode: 49
subject: Mathematical sciences

description: Let be a genus 2 curve defined over a field K, charK=p⩾0, and its Jacobian, where ι is the principal polarization of attached to . Assume that is (n, n)-geometrically reducible with E1 and E2 its elliptic components. We prove that there are only finitely many curves (up to isomorphism) defined over K such that E1 and E2 are N-isogenous for n=2 and N=2,3,5,7 with or n=2, N=3,5,7 with . The same holds if n=3 and N=5. Furthermore, we determine the Kummer and Shioda–Inose surfaces for the above and show how such results in positive characteristic p>2 suggest nice applications in cryptography.
Negative accounting earnings and gross domestic product
Creators: name: Gaertner, Fabio B.
name: Kausar, Asad
name: Steele, Logan B.
Publisher: name: American University
Year: 2023

description: Konchitchki and Patatoukas Journal of Accounting and Economics 57 (1-2), 76–88, (2014a) show that aggregate accounting earnings growth predicts future nominal gross domestic product (GDP) growth and that professional macro forecasters do not fully incorporate the information contained in aggregate accounting earnings. Based on results from prior literature, which find that accounting earnings reflect bad economic news in a timelier manner than good news, we condition Konchitchki and Patatoukas’s GDP growth forecast model on the sign of earnings changes. We show that negative changes in aggregate earnings predict future GDP growth while positive changes in earnings do not. Furthermore, we show that professional macro forecasters underreact to the information contained in negative changes in aggregate earnings about future GDP growth. Additional tests suggest our findings are a result of conservative accruals in earnings.
Mechanisms of pattern formation during T cell adhesion
Creators: name: Weikl, Thomas R.
name: Lipowsky, Reinhard
Publisher: name: arXiv
Year: 2004
Subjects: subject: Subcellular Processes (q-bio.SC)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Cell Behavior (q-bio.CB)
subject: FOS: Biological sciences
subject: FOS: Physical sciences

description: T cells form intriguing patterns during adhesion to antigen-presenting cells. The patterns at the cell-cell contact zone are composed of two types of domains, which either contain short TCR/MHCp receptor-ligand complexes or the longer LFA-1/ICAM-1 complexes. The final pattern consists of a central TCR/MHCp domain surrounded by a ring-shaped LFA-1/ICAM-1 domain, while the characteristic pattern formed at intermediate times is inverted with TCR/MHCp complexes at the periphery of the contact zone and LFA-1/ICAM-1 complexes in the center. In this article, we present a statistical-mechanical model of cell adhesion and propose a novel mechanism for the T cell pattern formation. Our mechanism for the formation of the intermediate inverted pattern is based (i) on the initial nucleation of numerous TCR/MHCp microdomains, and (ii) on the diffusion of free receptors and ligands into the contact zone. Due to this inward diffusion, TCR/MHCp microdomains at the rim of the contact zone grow faster and form an intermediate peripheral ring for sufficiently large TCR/MHCp concentrations. In agreement with experiments, we find that the formation of the final pattern with a central TCR/MHCp domain requires active cytoskeletal transport processes. Without active transport, the intermediate inverted pattern seems to be metastable in our model, which might explain patterns observed during natural killer (NK) cell adhesion. At smaller TCR/MHCp complex concentrations, we observe a different regime of pattern formation with intermediate multifocal TCR/MHCp patterns which resemble experimental patterns found during thymozyte adhesion.
description: 12 pages, 8 figures
Negative accounting earnings and gross domestic product
Creators: name: Gaertner, Fabio B.
name: Kausar, Asad
name: Steele, Logan B.
Publisher: name: Review of Accounting Studies
Year: 2023
Subjects: classificationCode: 3501
subject: Accounting, auditing and accountability

description: Konchitchki and Patatoukas Journal of Accounting and Economics 57 (1-2), 76–88, (2014a) show that aggregate accounting earnings growth predicts future nominal gross domestic product (GDP) growth and that professional macro forecasters do not fully incorporate the information contained in aggregate accounting earnings. Based on results from prior literature, which find that accounting earnings reflect bad economic news in a timelier manner than good news, we condition Konchitchki and Patatoukas’s GDP growth forecast model on the sign of earnings changes. We show that negative changes in aggregate earnings predict future GDP growth while positive changes in earnings do not. Furthermore, we show that professional macro forecasters underreact to the information contained in negative changes in aggregate earnings about future GDP growth. Additional tests suggest our findings are a result of conservative accruals in earnings.
DEMOGRAPHIC AGEING AND THE DEVELOPMENT OF BURDEN CARRIED BY THE PRODUCTIVE POPULATION IN NUTS II - SOUTH-EAST
DEMOGRAFICKE STARNUTI OBYVATELSTVA A VYVOJ ZATIZENI PRODUKTIVNI POPULACE V PODMINKACH VYSSIHO UZEMNE SPRAVNIHO CELKU JIHOVYCHOD
Creators: name: VOSTA, Lubomir
name: MINARIK, Bohumil
name: VOSTA, Lubomir
name: MINARIK, Bohumil
Publisher: name: Unknown
Year: 2007
Subjects: subject: Agricultural and Food Policy
subject: Public Economics
subject: population
subject: demographic ageing
subject: productive population
subject: burden coefficients
subject: NUTS II
subject: NUTS III

description: The paper reports on the development of characteristics of the burden carried by the productive population in consequence of the demographic ageing of population in the conditions of the higher territorial administrative unit South-East (consisting of two NUTS Ill units — the South Moravian and Vysocina regions) in the past 12 years. Population was divided into age groups and the burden on the productive population was analysed using burden coefficients, age index and coefficients describing the dynamics of burden changes, specifically the inflow, outflow and substitution coefficients. It is stated in the work that there is a gradual deterioration of all coefficient values in accordance with the current trend, which more and more resembles the situation in developed European countries. Both the initial and current situation of most indicators are a bit better in the Vysocina region. However, this region is inhabited by a smaller portion of the unit's population so that indicators of NUTS II correspond more significantly with the situation in the South Moravian region. Over next years there is nothing else to expect than further deterioration of the situation, in which an increase in the burden on the productive population will be (as a result of the expected decrease in the proportion of the pre-productive population) more and more imposed by the post-productive component of the population.
Natural gas infrastructure development in North America under integrated markets
Creators: name: Avraam, Charalampos
name: Chu, Daniel
name: Siddiqui, Sauleh
Publisher: name: American University
Year: 2023

description: The exploitation of low-cost shale gas in the Marcellus Formation, the deregulation initiatives in the U.S. and Mexico, and the emergence of natural gas as a bridging fuel to a low-carbon economy has fueled the growth of North American natural gas production, which is projected to keep growing in the mid-term to support the increasing LNG exports. Greater introduction of renewables and deeper electrification suppress both supply and demand for natural gas in the long-term. The long lead times of pipeline operation and field exploitation render the timing of natural gas abatement critical to natural gas infrastructure stakeholders. Full integration of the U.S., Canadian, and Mexican natural gas markets implies that the abatement trajectories of the three countries are tightly linked. This paper studies the development of the integrated North American natural gas markets and infrastructure under different assumptions on resource availability, technological progress, and global crude oil prices. We quantify the impact of each scenario by using the North American Natural Gas Model. Our analysis shows that cross-border U.S.-Mexico trade is more resilient under all three shocks compared to U.S.-Canada trade. Increasing Mexican production could drive the growth of the domestic Mexican market instead of reducing U.S.-Mexico trade.
Additional file 1 of Mutant Huntingtin affects toll-like receptor 4 intracellular trafficking and cytokine production in mast cells
Creators: name: Pérez-Rodríguez, Marian Jesabel
name: Ibarra-Sánchez, Alfredo
name: Román-Figueroa, Abraham
name: Pérez-Severiano, Francisca
name: González-Espinosa, Claudia
Publisher: name: figshare
Year: 2020
Subjects: subject: Immunology
subject: FOS: Clinical medicine

description: Additional file 1: FigureS1. Growth of bone marrow cultures and cell viability of WT and R6/1 BMMCs. a) Total bone marrow from tibias and femurs from WT and R6/1 mice was seeded in a T75 flask with RPMI medium, supplemented with IL-3 and cultured as described in the Methods section. Cells in culture supernatants were counted. Data are presented as the mean ± SD from at least 20 cultures obtained from the same number of mice. b) One million BMMCs of each genotype were re-suspended in 1 mL of supplemented RPMI, mixed with the Muse™ Count Viability Kit reagent (Millipore) and analyzed for viability with the Muse™ Cell Analyzer. ***p
Local density of states induced by anisotropic impurity scattering in a d-wave superconductor
Creators: name: Pisarski, P.
name: Haran, G.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: We study a single impurity effect on the local density of states in a d-wave superconductor accounting for the momentum-dependent impurity potential. We show that the anisotropy of the scattering potential can alter significantly the spatial dependence of the quasiparticle density of states in the vicinity of the impurity.
description: 8 pages, revtex4, 14 figures
Additional file 2 of Mutant Huntingtin affects toll-like receptor 4 intracellular trafficking and cytokine production in mast cells
Creators: name: Pérez-Rodríguez, Marian Jesabel
name: Ibarra-Sánchez, Alfredo
name: Román-Figueroa, Abraham
name: Pérez-Severiano, Francisca
name: González-Espinosa, Claudia
Publisher: name: figshare
Year: 2020
Subjects: subject: Immunology
subject: FOS: Clinical medicine

description: Additional file 2: Figure S2. Effect of inhibition of IKK or ERK1/2 on LPS-induced TNF mRNA synthesis. WT BMMCs were pre-incubated for 15 min at 37 °C with a) BAY117085 (10 μM) or b) FR180204 (10 μM) and then stimulated with LPS (500 ng/mL). The cells were collected at different times post-stimulus and total RNA was extracted to detect TNF mRNA by RT-PCR. The upper part of each panel shows a representative image from at least three independent experiments, while TNF mRNA accumulation is shown in the lower panel. Data are presented as the mean ± SD from at least three independent experiments performed with different cell cultures. &p