cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 2: Table S2. of Differences in medical schoolsâ   regional retention of physicians by school type and year of establishment: effect of new schools built under government policy
Creators: name: Kamitani, Satoru
name: Nakamura, Fumiaki
name: Itoh, Mitsuko
name: Sugiyama, Takehiro
name: Toyokawa, Satoshi
name: Kobayashi, Yasuki
Publisher: name: Figshare
Year: 2015
Subjects: subject: Medicine
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Science Policy

description: Numbers of medical schools and student admissions in Japan between 1950 and 2010. (DOCX 17Â kb)
Edit Distance between Merge Trees
Creators: name: Sridharamurthy, Raghavendra
name: Masood, Talha Bin
name: Kamakshidasan, Adhitya
name: Natarajan, Vijay
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computational Geometry (cs.CG)
subject: FOS: Computer and information sciences

description: Topological structures such as the merge tree provide an abstract and succinct representation of scalar fields. They facilitate effective visualization and interactive exploration of feature-rich data. A merge tree captures the topology of sub-level and super-level sets in a scalar field. Estimating the similarity between merge trees is an important problem with applications to feature-directed visualization of time-varying data. We present an approach based on tree edit distance to compare merge trees. The comparison measure satisfies metric properties, it can be computed efficiently, and the cost model for the edit operations is both intuitive and captures well-known properties of merge trees. Experimental results on time-varying scalar fields, 3D cryo electron microscopy data, shape data, and various synthetic datasets show the utility of the edit distance towards a feature-driven analysis of scalar fields.
Photinus parvusater Zaragoza-Caballero 1995
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Photinus
Photinus parvusater

description: Photinus parvusater Zaragoza-Caballero, 1995
MEXICO: MI Endemic
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 303, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
Additional file 2: of Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses
Creators: name: Metzger, Julia
name: Karwath, Matthias
name: Tonda, Raul
name: Beltran, Sergi
name: Águeda, Lídia
name: Gut, Marta
name: Gut, Ivo
name: Distl, Ottmar
Publisher: name: Figshare
Year: 2015
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Inbreeding coefficients (F ROH ) based on runs of homozygosity (ROH). FROH was estimated dividing the total length of ROHs by the length of the genome covered by SNPs (2,242,879,462 bp). (DOCX 15 kb)
Additional file 3: of Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses
Creators: name: Metzger, Julia
name: Karwath, Matthias
name: Tonda, Raul
name: Beltran, Sergi
name: Águeda, Lídia
name: Gut, Marta
name: Gut, Ivo
name: Distl, Ottmar
Publisher: name: Figshare
Year: 2015
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases
subject: Plant Biology
subject: 60506 Virology
subject: Computational Biology

description: Functional annotations in private runs of homozygosity (ROH) of 500-SNP windows. PANTHER gene list analysis ( http://www.pantherdb.org/ ) was performed for genes in private ROH regions which could be exclusively found in one specific horse. The percent of gene hits against total number of process hits involved in specific biological processes are shown. (DOCX 18 kb)
Photinus paulinae Zaragoza-Caballero 2015
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Photinus
Photinus paulinae

description: Photinus paulinae Zaragoza-Caballero, 2015
MEXICO: SO Endemic
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 303, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
Additional file 7: of Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses
Creators: name: Metzger, Julia
name: Karwath, Matthias
name: Tonda, Raul
name: Beltran, Sergi
name: Águeda, Lídia
name: Gut, Marta
name: Gut, Ivo
name: Distl, Ottmar
Publisher: name: Figshare
Year: 2015
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Mutations with high or moderate effects in ROHs (50-SNP windows) of non-breed horses. The ROH position and size (EquCab2.70), the position of SNPs, their mutant allele, potential impact and type are shown. Impact estimations are derived from SNPEff predictions. (DOCX 65 kb)
Additional file 4: of Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses
Creators: name: Metzger, Julia
name: Karwath, Matthias
name: Tonda, Raul
name: Beltran, Sergi
name: Águeda, Lídia
name: Gut, Marta
name: Gut, Ivo
name: Distl, Ottmar
Publisher: name: Figshare
Year: 2015
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Ecology
subject: Developmental Biology
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases
subject: Plant Biology
subject: 60506 Virology
subject: Computational Biology

description: Shared runs of homozygosity (ROHs) in non-breed horses. The consensus private ROH regions and genes of the Dülmen Horse and two Sorraia in 50-SNP and 500-SNP windows are shown. The number of SNPs and size of shared ROH indicate the overlap of homozygous variants. (DOCX 78 kb)
Photinus perezi Zaragoza-Caballero 1995
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Photinus
Photinus perezi

description: Photinus perezi Zaragoza-Caballero, 1995
MEXICO: VE Endemic
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 303, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
The role of closed timelike curves in particle motion within Van Stockum space-time: A generalization
Creators: name: Dutta, Ayanendu
name: Roy, Dhritimalya
name: Chakraborty, Subenoy
Publisher: name: arXiv
Year: 2022
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The present work analyses the particle motion in the Van Stockum space-time considering the existence of closed timelike curves. Test particles with or without angular momentum are studied in the present geometry. It is found that only non-zero angular momentum test particles exist in the neighborhood of closed timelike curves. The minimum particle energy and the range of backward time jump in closed timelike geodesics are studied within a Cauchy horizon. Finally, a general prescription for CTC and CTG has been presented with appropriate examples.
Linear mixed effects models in functional data analysis
Creators: name: Wang, Wei
Publisher: name: University of British Columbia
Year: 2008

description: Regression models with a scalar response and a functional predictor have been extensively studied. One approach is to approximate the functional predictor using basis function or eigenfunction expansions. In the expansion, the coefficient vector can either be fixed or random. The random coefficient vector is also known as random effects and thus the regression models are in a mixed effects framework. The random effects provide a model for the within individual covariance of the observations. But it also introduces an additional parameter into the model, the covariance matrix of the random effects. This additional parameter complicates the covariance matrix of the observations. Possibly, the covariance parameters of the model are not identifiable. We study identifiability in normal linear mixed effects models. We derive necessary and sufficient conditions of identifiability, particularly, conditions of identifiability for the regression models with a scalar response and a functional predictor using random effects. We study the regression model using the eigenfunction expansion approach with random effects. We assume the random effects have a general covariance matrix and the observed values of the predictor are contaminated with measurement error. We propose methods of inference for the regression model's functional coefficient. As an application of the model, we analyze a biological data set to investigate the dependence of a mouse's wheel running distance on its body mass trajectory.
Additional file 8: of Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses
Creators: name: Metzger, Julia
name: Karwath, Matthias
name: Tonda, Raul
name: Beltran, Sergi
name: Águeda, Lídia
name: Gut, Marta
name: Gut, Ivo
name: Distl, Ottmar
Publisher: name: Figshare
Year: 2015
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Mutations with high or moderate effects in ROHs (500-SNP windows) of non-breed horses. The ROH position and size (EquCab2.70), the position of SNPs, their mutant allele, potential impact and type are shown. Impact estimations are derived from SNPEff predictions. (DOCX 16 kb)
Photinus perotensis Zaragoza-Caballero 1996
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Photinus
Photinus perotensis

description: Photinus perotensis Zaragoza-Caballero, 1996
MEXICO: VE Endemic
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 303, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
Honeycomb lattice iridate on the verge of Mott-collapse
Creators: name: Haraguchi, Yuya
name: Katori, Hiroko Aruga
Publisher: name: arXiv
Year: 2022
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: A new honeycomb lattice iridate (La,Na)IrO$_3$ ($\approx$ LaNaIr$_2$O$_6$) is successfully synthesized from the spin-orbit coupled Mott insulator Na$_2$IrO$_3$ by replacing the interlayer Na$^+$ ions with La$^{3+}$ ions. (La,Na)IrO$_3$ shows a finite Sommerfeld term in heat capacity and a $-\ln T$ dependence of resistivity, indicating a realization of a metallic state driven by a Mott collapse. Furthermore, crystal structure analysis reveals the formation of Ir zig-zag chains with metal-metal bonding, increasing kinetic energy resulting in the Mott collapse. This observation would be due to a Mott collapse induced in a $J_{\mathrm{eff}} = 1/2$ spin-orbit coupling Mott insulator with an Ir honeycomb lattice by topochemical control of the ionic configuration.
description: 7pages, 5 figures, accepted in Journal of Physics: Condensed Matter
Additional file 1: of Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses
Creators: name: Metzger, Julia
name: Karwath, Matthias
name: Tonda, Raul
name: Beltran, Sergi
name: Águeda, Lídia
name: Gut, Marta
name: Gut, Ivo
name: Distl, Ottmar
Publisher: name: Figshare
Year: 2015
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Ecology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Summary of mapping metrics, sequence coverage and number of detected variants in ten horses. (DOCX 174 kb)
Topical Review: Extracting Molecular Frame Photoionization Dynamics from Experimental Data
Creators: name: Hockett, Paul
name: Makhija, Varun
Publisher: name: arXiv
Year: 2022
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Methods for experimental reconstruction of molecular frame (MF) photoionization dynamics, and related properties - specifically MF photoelectron angular distributions (PADs) and continuum density matrices - are outlined and discussed. General concepts are introduced for the non-expert reader, and experimental and theoretical techniques are further outlined in some depth. Particular focus is placed on a detailed example of numerical reconstruction techniques for matrix-element retrieval from time-domain experimental measurements making use of rotational-wavepackets (i.e. aligned frame measurements) - the ``bootstrapping to the MF" methodology - and a matrix-inversion technique for direct MF-PAD recovery. Ongoing resources for interested researchers are also introduced, including sample data, reconstruction codes (the \textit{Photoelectron Metrology Toolkit}, written in python, and associated \textit{Quantum Metrology with Photoelectrons} platform/ecosystem), and literature via online repositories; it is hoped these resources will be of ongoing use to the community.
description: 65 pages, 17 figures. HTML version with interactive figures on Authorea: https://www.authorea.com/users/71114/articles/447808-extracting-molecular-frame-photoionization-dynamics-from-experimental-data Code and data archive on Figshare: http://dx.doi.org/10.6084/m9.figshare.20293782
Photinus phalloentis Zaragoza-Caballero 1996
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Photinus
Photinus phalloentis

description: Photinus phalloentis Zaragoza-Caballero, 1996
MEXICO: VE Endemic
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 303, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
Unsupervised visualization of image datasets using contrastive learning
Creators: name: Böhm, Jan Niklas
name: Berens, Philipp
name: Kobak, Dmitry
Publisher: name: arXiv
Year: 2022
Subjects: subject: Machine Learning (cs.LG)
subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Human-Computer Interaction (cs.HC)
subject: FOS: Computer and information sciences

description: Visualization methods based on the nearest neighbor graph, such as t-SNE or UMAP, are widely used for visualizing high-dimensional data. Yet, these approaches only produce meaningful results if the nearest neighbors themselves are meaningful. For images represented in pixel space this is not the case, as distances in pixel space are often not capturing our sense of similarity and therefore neighbors are not semantically close. This problem can be circumvented by self-supervised approaches based on contrastive learning, such as SimCLR, relying on data augmentation to generate implicit neighbors, but these methods do not produce two-dimensional embeddings suitable for visualization. Here, we present a new method, called t-SimCNE, for unsupervised visualization of image data. T-SimCNE combines ideas from contrastive learning and neighbor embeddings, and trains a parametric mapping from the high-dimensional pixel space into two dimensions. We show that the resulting 2D embeddings achieve classification accuracy comparable to the state-of-the-art high-dimensional SimCLR representations, thus faithfully capturing semantic relationships. Using t-SimCNE, we obtain informative visualizations of the CIFAR-10 and CIFAR-100 datasets, showing rich cluster structure and highlighting artifacts and outliers.
description: ICLR 2023
On Rees algebras of 2-determinantal ideals
Creators: name: Ramkumar, Ritvik
name: Sammartano, Alessio
Publisher: name: arXiv
Year: 2022
Subjects: subject: Commutative Algebra (math.AC)
subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 13A30, 13C40, 05E40, 13D10, 13F55, 13H10, 13P10, 14C05

description: Let I be the ideal of minors of a 2 by n matrix of linear forms with the expected codimension. In this paper we prove that the Rees algebra of I and its special fiber ring are Cohen-Macaulay and Koszul; in particular, they are quadratic algebras. The main novelty in our approach is the analysis of a stratification of the Hilbert scheme of determinantal ideals. We study degenerations of Rees algebras along this stratification, and combine it with certain squarefree Groebner degenerations.
description: Final version. To appear on the Journal of the London Mathematical Society
Additional file 5: of Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses
Creators: name: Metzger, Julia
name: Karwath, Matthias
name: Tonda, Raul
name: Beltran, Sergi
name: Águeda, Lídia
name: Gut, Marta
name: Gut, Ivo
name: Distl, Ottmar
Publisher: name: Figshare
Year: 2015
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Ecology
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Shared runs of homozygosity (ROHs) in breed horses. The consensus private ROH regions and genes of Hanoverian, Arabian, Saxon-Thuringian Heavy Warmblood and Thoroughbred horses in 50-SNP windows are shown. The number of SNPs and size of shared ROH indicate the overlap of homozygous variants. (DOCX 14 kb)
Toktokkus Kaminski & Gearner 2021
Creators: name: Kamiński, Marcin Jan
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Tenebrionidae
Toktokkus

description: Toktokkus Kamiński & Gearner, 2021
Notes. The most recent taxonomic contributions concerning Toktokkus were published by Kamiński et al. (2021), Gearner et al. (2022), and Kamiński (2022).
Species and subspecies included (16). T. barclayi Kamiński & Gearner, 2021, T. congolensis Kamiński & Gearner, 2021, T. herero Gearner, 2021, T. makuya Gearner, 2021, T. mariae Kamiński, 2022, T. mashunus (Péringuey, 1896), T. mulleri (Péringuey, 1899), T. o-serraferrus Gearner, Lumen, Kamiński, 2022, T. schultzei (Péringuey, 1908), T. tschinkeli Kamiński & Gearner, 2021, T. tuberculipennis (Haag-Rutenberg, 1871), T. vialis vialis (Burchell, 1822), T. vialis sellatus (Haag-Rutenberg, 1875), T. vialis tuberculifer (Haag-Rutenberg, 1871), T. waclawae Kamiński, 2021, T. zofiae sp. nov.
description: Published as part of Kamiński, Marcin Jan, 2024, New taxa of Afrotropical Toktokkies (Coleoptera: Tenebrionidae: Molurina) from the Natural History Museum of Basel, pp. 77-87 in Zootaxa 5446 (1) on page 83, DOI: 10.11646/zootaxa.5446.1.4, http://zenodo.org/record/11084604
Additional file 1: Table S1. of Comparison of treatment response, remission rate and drug adherence in polyarticular juvenile idiopathic arthritis patients treated with etanercept, adalimumab or tocilizumab
Creators: name: Horneff, Gerd
name: Klein, Ariane
name: Klotsche, Jens
name: Minden, Kirsten
name: Hans-Iko Huppertz
name: Weller-Heinemann, Frank
name: Kuemmerle-Deschner, Jasmin
name: Johannes-Peter Haas
name: Hospach, Anton
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Pharmacology
subject: Ecology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Patient characteristics (unweighted as reported in BIKER). (DOCX 17 kb)
Photinus platyphallos Zaragoza-Caballero 1995
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Photinus
Photinus platyphallos

description: Photinus platyphallos Zaragoza-Caballero, 1995
MEXICO: OA Endemic
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 303, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
Adaptive Analytical Ray Tracing of Black Hole Photon Rings
Creators: name: Cárdenas-Avendaño, Alejandro
name: Lupsasca, Alexandru
name: Zhu, Hengrui
Publisher: name: arXiv
Year: 2022
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Recent interferometric observations by the Event Horizon Telescope have resolved the horizon-scale emission from sources in the vicinity of nearby supermassive black holes. Future space-based interferometers promise to measure the "photon ring"--a narrow, ring-shaped, lensed feature predicted by general relativity, but not yet observed--and thereby open a new window into strong gravity. Here we present AART: an Adaptive Analytical Ray-Tracing code that exploits the integrability of light propagation in the Kerr spacetime to rapidly compute high-resolution simulated black hole images, together with the corresponding radio visibility accessible on very long space-ground baselines. The code samples images on a nonuniform adaptive grid that is specially tailored to the lensing behavior of the Kerr geometry and is therefore particularly well-suited to studying photon rings. This numerical approach guarantees that interferometric signatures are correctly computed on long baselines, and the modularity of the code allows for detailed studies of equatorial sources with complex emission profiles and time variability. To demonstrate its capabilities, we use AART to simulate a black hole movie of a stochastic, non-stationary, non-axisymmetric equatorial source; by time-averaging the visibility amplitude of each snapshot, we are able to extract the projected diameter of the photon ring and recover the shape predicted by general relativity.
description: 39 pages, 16 figures. Updated to match published version. V4: corrected two very minor typos (in Eqs. 50 and 70)
The cost of longevity: loss of sexual function in natural clones of Populus tremuloides
Creators: name: Ally, Dilara
Publisher: name: University of British Columbia
Year: 2008

description: Most clonal plants exhibit a modular structure at multiple levels. At the level of the organs, they are characterized by functional modules, such as, internodes, leaves, branches. At the level of the genetic individual (clone or genet), they possess independent evolutionary and physiological units (ramets). These evolutionary units arise through the widespread phenomenon of clonal reproduction, achieved in a variety of ways including rhizomes, stolons, bulbils, or lateral roots. The focus of this study was Populus tremuloides, trembling aspen, a dioecious tree that reproduces sexually by seed and asexually through lateral roots. Local forest patches in western populations of Populus tremuloides consisted largely of multiple genotypes. Multi-clonal patches were dominated by a single genotype, and in one population (Riske Creek) we found several patches (five out of 17) consisting of a single genotype. A second consequence of modularity is that during the repeated cycle of ramet birth, development and death, somatic mutations have the opportunity to occur. Eventually, the clone becomes a mosaic of mutant and non-mutant cell lineages. We found that neutral somatic mutations accumulated across 14 microsatellite loci at a rate of between 10^-6 and 10^-5 per locus per year. We suggest that neutral genetic divergence, under a star phylogeny model of clonal growth, is an alternative way to estimate clone age. Previous estimates of clone age couple the mean growth rate per year of shoots with the area covered by the clone. This assumes a positive linear relationship between clone age and clone size. We found, however, no repeatable pattern across our populations in terms of the relationship of either shape or size to the number of somatic changes. A final consequence of modularity is that during clonal growth, natural selection is relaxed for traits involving sexual function. This means that mutations deleterious to sexual function can accumulate, reducing the overall sexual fitness of a clone. We coupled neutral genetic divergence within clones with pollen fitness data to infer the rate and effect of mildly deleterious mutations. Mutations reduced relative sexual fitness in clonal aspen populations by about 0.12x10^-3 to 1.01x10^-3 per year. Furthermore, the decline in sexual function with clone age is evidence that clonal organisms are vulnerable to the effects of senescence.
Transverse momentum dependent distribution functions in the threshold limit
Creators: name: Kang, Zhong-Bo
name: Samanta, Kajal
name: Shao, Ding Yu
name: Zeng, Yang-Li
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: Nuclear Experiment (nucl-ex)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We apply the joint threshold and transverse momentum dependent (TMD) factorization theorem to introduce new threshold-TMD distribution functions, including threshold-TMD parton distribution functions (PDFs) and fragmentation functions (FFs). We apply Soft-Collinear Effective Theory and renormalization group methods to carry out QCD evolution for both threshold-TMD PDFs and FFs. We show the universality of threshold-TMD functions among three standard processes, i.e. the Drell-Yan production in $pp$ collisions, semi-inclusive deep-inelastic scattering and back-to-back two hadron production in $e^+e^-$ collisions. In the end, we present the numerical predictions for different threshold-TMD functions and also transverse momentum distributions at $pp$, $ep$, and $e^+e^-$ collisions.
description: 28 pages, 6 figures. Major update: A three-loop perturbative analysis has been added. Matches published version in JHEP
Additional file 1 of A distinct dimer configuration of a diatom Get3 forming a tetrameric complex with its tail-anchored membrane cargo
Creators: name: Chen, Chi-Chih
name: Huang, Yu-Ru
name: Chan, Yuen Ting
name: Lin, Hung-Yun
name: Lin, Han-Jia
name: Hsiao, Chwan-Deng
name: Ko, Tzu-Ping
name: Lin, Tai-Wen
name: Lan, Ya-Hsuan
name: Lin, Hsuan-Ya
name: Chang, Hsin-Yang
Publisher: name: figshare
Year: 2024
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: FOS: Biological sciences
subject: Computational Biology

description: Additional file1: Figure S1 Purification and characterization of Pt-Get3a protein. Figure S2 Omit maps of bound nucleotides. Figure S3 SDS-PAGE analysis of pulldown assay. Figure S4 Multiple sequence alignment of Get3 homologs. Figure S5 Structure of the helix bundle motif. Figure S6 SAXS solution structural analysis of Pt-Get3a dimer. Figure S7 Conserved residues in yeast ScGet3 involved in Get1, Get2, and Get4 binding are highlighted in dark blue. Figure S8 Conformation of introduced fragments in transgenic diatom strains. Figure S9 SEC analysis of the Pt-Get3a/TA complex in the presence of approximately 100 mM NaCl. Figure S10 SEC and SDS-PAGE analysis of Get3/TA complex. Figure S11 SDS PAGE analysis of coexpression of Pt-Get3a and Sec61γ substrate. Figure S12 TA-bound Pt-Get3a complex in the tetrameric state. Figure S13 SAXS solution structural analysis of the Pt-Get3a/TA tetramer complex. Figure S14 The α-helical subdomain of the open Pt-Get3a tetramer and closed MjGet3 tetramer. Figure S15 Structural comparison. Table S1 ATPase activity assay. Table S2 Parameters of multipulse electroporation. Table S3 Sequences, properties, and functions of TA substrates examined in this study. Table S4 PCR primers used in this study.
Additional file 1: Table S1. of Systematic review of structural interventions for intimate partner violence in low- and middle-income countries: organizing evidence for prevention
Creators: name: Bourey, Christine
name: Williams, Whitney
name: Bernstein, Erin
name: Stephenson, Rob
Publisher: name: Figshare
Year: 2015
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: PRISMA checklist. (PDF 87Â kb)
Additional file 2: Figure S2. of Shared and divergent pathways for flower abscission are triggered by gibberellic acid and carbon starvation in seedless Vitis vinifera L
Creators: name: Domingos, Sara
name: Fino, Joana
name: Vânia Cardoso
name: Sánchez, Claudia
name: Ramalho, José
name: Larcher, Roberto
name: Paulo, Octávio
name: Oliveira, Cristina
name: Goulao, Luis
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Quantitative rtPCR validation of the RNA-seq. NCBI reference, gene identification (GID), fold change quantification by q-rtPCR and RNA seq, primers and amplicon length (bp) for abscission related-genes (A). NCBI reference, primers and amplicon length are also given for references genes (B). Data are means of 3 replicates. The pearson correlation coefficient between qRT-PCR and RNA-Seq obtained fold-changes (R = 0.84) is significant at p-value ≤ 0.001 (C). (PDF 176 kb)
Photinus plumbeus Gorham 1880
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Photinus
Photinus plumbeus

description: Photinus plumbeus Gorham, 1880
MEXICO: VE; Guatemala
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 303, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
Characterization of BphD, a C-C bond hydrolase involved in the degradation of polychlorinated biphenyls
Creators: name: Horsman, Geoffrey
Publisher: name: University of British Columbia
Year: 2008

description: Microbial aromatic compound degradation often involves carbon-carbon bond hydrolysis of a meta-cleavage product (MCP). BphDLB400 (EC 3.7.1.8), the MCP hydrolase from the biphenyl degradation pathway of Burkholderia xenovorans LB400, hydrolyzes 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate (HOPDA) to 2-hydroxypenta-2,4-dienoate (HPD) and benzoate. Although MCP hydrolases contain the catalytic triad (Ser112-His265-Asp237) and structural fold of the α/β-hydrolase superfamily, previous studies suggest they deviate from the classical hydrolytic mechanism in two respects: (1) enol-keto tautomerization precedes hydrolysis and (2) hydrolysis involves a gem-diol intermediate. Stopped-flow kinetic studies revealed rapid accumulation of a transient intermediate possessing a red-shifted absorption spectrum (λmax = 492 nm) versus HOPDA (λmax = 434 nm), consistent with an enzyme-bound, strained enolate (E:Sse). In studies with BphDLB400 variants, S112A trapped the E:Sse intermediate, implying that Ser112 is required for subsequent tautomerization and hydrolysis. His265 is required for E:Sse formation, as H265A variants instead generated a species assigned to a non-strained HOPDA enolate, which was not spectroscopically observed in the WT enzyme. The proposed importance of double bond strain in the reaction was supported by crystallographic observation of a non-planar, strained substrate in the S112A:HOPDA complex. Inhibition of BphDLB400 by 3-Cl HOPDA was investigated to understand a block in the degradation of polychlorinated biphenyls. BphDLB400 preferentially hydrolyzed 3-substituted HOPDAs in the order H > F > Cl > Me, indicating that steric bulk impairs catalysis. Kinetic analyses further indicated that large 3-substituents impede formation of the strained enolate by binding in an alternate conformation, as observed in the S112A:3-Cl HOPDA crystal structure. Finally, rate-determining hydrolysis of a benzoyl-enzyme was suggested from the observations that: (i) HOPDA and p-nitrophenyl benzoate were transformed with similar kcat values and (ii) yielded a common product ratio in the presence of methanol. Overall, the studies demonstrate the importance of an intermediate possessing significant double bond strain in an MCP hydrolase, establish the role of the catalytic His in forming this intermediate, indicate a mechanism of inhibition, and suggest the possibility that hydrolysis may proceed via an acyl-enzyme.
Additional file 2: Table S2. of Systematic review of structural interventions for intimate partner violence in low- and middle-income countries: organizing evidence for prevention
Creators: name: Bourey, Christine
name: Williams, Whitney
name: Bernstein, Erin
name: Stephenson, Rob
Publisher: name: Figshare
Year: 2015
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Characteristics of interventions and studies. (PDF 191Â kb)
Additional file 4: Table S2. of Shared and divergent pathways for flower abscission are triggered by gibberellic acid and carbon starvation in seedless Vitis vinifera L
Creators: name: Domingos, Sara
name: Fino, Joana
name: Vânia Cardoso
name: Sánchez, Claudia
name: Ramalho, José
name: Larcher, Roberto
name: Paulo, Octávio
name: Oliveira, Cristina
name: Goulao, Luis
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology

description: Parameters for hormone identification in Mass Spectrometry. Cone voltage potential, collision energy (CE) and other performance characteristics. (PDF 67 kb)
Additional file 4: Figure S2. of Promoter-based identification of novel non-coding RNAs reveals the presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana
Creators: name: Qu, Ge
name: Kruszka, Katarzyna
name: Plewka, Patrycja
name: Yang, Shu-Yi
name: Tzyy-Jen Chiou
name: Jarmolowski, Artur
name: Szweykowska-Kulinska, Zofia
name: Echeverria, Manuel
name: Karlowski, Wojciech
Publisher: name: Figshare
Year: 2015
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Developmental Biology
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases
subject: Plant Biology
subject: 60506 Virology
subject: Computational Biology

description: 5’ and 3’ RACE mapping of the TSS and TTS in the sno-miR775 gene. Single major signals in 5’ nested RACE PCR (left) and 3’ nested RACE PCR (right) indicate the transcription start site (TSS) and transcription termination site (TTS), respectively, of the sno-miR775 gene. (PDF 50 kb)
Perfect kagome-lattice antiferromagnets with J$_{eff}$ = 1/2: The Co$^{2+}$-analogs of copper minerals volborthite and vesignieite
Creators: name: Haraguchi, Yuya
name: Ohnoda, Takehiro
name: Matsuo, Akira
name: Kindo, Koichi
name: Katori, Hiroko Aruga
Publisher: name: arXiv
Year: 2022
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We report the synthesis, crystal structure, and magnetic properties of Co$^{2+}$ kagome magnets Co$_3$V$_2$O$_7$(OH)$_2$$\cdot$2H$_2$O and BaCo$_3$(VO$_4$)$_2$(OH)$_2$, which can be recognized as Co-analogues of the intensively researched quantum kagome magnet volborthite Cu$_3$V$_2$O$_7$(OH)$_2$$\cdot$2H$_2$O and vesignieite BaCu$_3$(VO$_4$)$_2$(OH)$_2$. For each compound, the ground state is seemingly A-type antiferromagnetic order. At low temperatures, applying a magnetic field causes a metamagnetic-like transition described by the transition in which antiferromagnetically-aligned canted moments change to ferromagnetically-aligned ones. These ground and field-induced states include a canted ferromagnetic component perpendicular to the kagome planes favored by Dzyaloshinskii-Moriya interactions. These magnetic properties are well characterized by the J$_{eff}$ = 1/2 physics. Our findings will be the first step toward clarifying the J$_{eff}$ = 1/2 kagome physics, which has been little studied experimentally or theoretically.
description: 9 pages, 7+1 figures, accepted for publication in Physical Review B
Additional file 13: Figure S7. of Shared and divergent pathways for flower abscission are triggered by gibberellic acid and carbon starvation in seedless Vitis vinifera L
Creators: name: Domingos, Sara
name: Fino, Joana
name: Vânia Cardoso
name: Sánchez, Claudia
name: Ramalho, José
name: Larcher, Roberto
name: Paulo, Octávio
name: Oliveira, Cristina
name: Goulao, Luis
Publisher: name: Figshare
Year: 2016
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology
subject: Computational Biology

description: Acyclic graphs with the mostly enriched GO categories in differentially expressed genes. The top 5 and top 5-related biological processes, molecular function and cellular component at GAc 7d (A), SH5d (B) and SH7d(C) are shown. The color scale presented is related with the p-value, where the redder the node, lower the p-value. The nodes with black outline are the top 5 enriched categories. (PDF 440 kb)
Additional file 5: Figure S3. of Promoter-based identification of novel non-coding RNAs reveals the presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana
Creators: name: Qu, Ge
name: Kruszka, Katarzyna
name: Plewka, Patrycja
name: Yang, Shu-Yi
name: Tzyy-Jen Chiou
name: Jarmolowski, Artur
name: Szweykowska-Kulinska, Zofia
name: Echeverria, Manuel
name: Karlowski, Wojciech
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology
subject: Computational Biology

description: The distribution of small RNAs on the sno-miR775 and (b) sno-miR779. Small RNA sequences were adopted from following samples: GSM575246 (WT), GSM154361 (dcl1-7), GSM1533542 (dcl3) GSM154364 (dcl4-2), GSM893124 (rdr2) and GSM575247 (rdr6). The visualization of reads mapping was carried out by Golden Helix GenomeBrowseÂŽ visualization tool v2.1.0. (PDF 179 kb)
Additional file 1: of Genital tract lesions in sexually mature Göttingen minipigs during the initial stages of experimental vaginal infection with Chlamydia trachomatis serovar D
Creators: name: Erneholm, Karin
name: Lorenzen, Emma
name: Bøje, Sarah
name: Olsen, Anja
name: Andersen, Peter
name: Cassidy, Joseph
name: Follmann, Frank
name: Jensen, Henrik
name: Agerholm, Jørgen
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Body temperatures (oC). Data show mean rectal temperatures and whiskers represent 95 % confidence intervals. At day 0, the mean temperature was significantly increased compared to all other time points. (PDF 47 kb)
Probability package for Macaulay2
Creators: name: Torrance, Douglas A.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Algebraic Geometry (math.AG)
subject: Probability (math.PR)
subject: FOS: Mathematics
subject: 60-04, 14-04

description: We introduce the Probability package for Macaulay2, which provides an interface for users to compute probabilities and generate random variates from a wide variety of univariate probability distributions.
description: Various improvements based on referee comments
Physically demanding occupations among females and sex-related differences to develop osteoarthritis of the hip : a systematic review and meta-analysis
Creators: name: Unverzagt, Susanne
name: Bergmann, Annekatrin
name: Denny, Kathleen
name: Frese, Thomas
name: Hirpa, Selamawit
name: Weyer, Johannes
Publisher: name: Universitäts- und Landesbibliothek Sachsen-Anhalt
Year: 2024
Subjects: subject: 610

description: Background: Hip osteoarthritis (HOA) is a leading cause of disability increasing with age and is more prevalent in women and in various physically demanding occupations. This systematic review identifies and summarises occupational exposures for women in physically demanding occupations and discusses sex differences and consequences. Methods: In this systematic review, we searched various electronic databases for reports published between date of database inception and October 2022. We included cohort studies and case-control studies that assessed the association between exposure to physically demanding occupations and the development of HOA. We then assessed the methodological quality of selected studies, extracted relative effects, compared the risk for women and men and meta-analytically reviewed the effects of physically demanding occupations. All steps were based on a study protocol published in PROSPERO (CRD42015016894). Results: We included six cohort studies and two case-control studies in this systematic review. These studies showed a considerably increased risk of developing HOA in both sexes. Women working in traditionally female-dominated occupations such as cleaning, sales, catering, childcare and hairdressing that are physically demanding, have a higher risk of developing HOA than men in similarly physically demanding occupations. Conversely, in traditionally male-dominated occupations with a high heterogeneity of work activities, such as agriculture, crafts, construction, as well as in low-skilled occupations, the risk was higher for men. One exception are health occupations, which are grouped together with a wide range of other technical occupations, making it difficult to draw conclusions. Conclusions: Existing studies indicate an association between various occupations with a high physical workload and an increased risk of developing HOA. Occupational prevention and individual health promotion strategies should focus on reducing the effects of heavy physical workloads at work. The aforementioned as well as early detection should be specifically offered to women in female-dominated occupations and to people working in elementary occupations.
Additional file 2: of Genital tract lesions in sexually mature Göttingen minipigs during the initial stages of experimental vaginal infection with Chlamydia trachomatis serovar D
Creators: name: Erneholm, Karin
name: Lorenzen, Emma
name: Bøje, Sarah
name: Olsen, Anja
name: Andersen, Peter
name: Cassidy, Joseph
name: Follmann, Frank
name: Jensen, Henrik
name: Agerholm, Jørgen
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Serum antibodies. Detection of serum antibodies against C. trachomatis, measured as the difference in OD values day (x) and day 0. (PDF 57 kb)