cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 1: of Oral administration of a select mixture of Bacillus probiotics generates Tr1 cells in weaned F4ab/acRâ   pigs challenged with an F4+ ETEC/VTEC/EPEC strain
Creators: name: Zhou, Dong
name: Zhu, Yao-Hong
name: Zhang, Wei
name: Wang, Meng-Ling
name: Fan, Wen-Yi
name: Song, Dan
name: Yang, Gui-Yan
name: Jensen, Bent
name: Jiu-Feng Wang
Publisher: name: Figshare
Year: 2015
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
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

description: Sequences of oligonucleotide primers used for real-time PCR, length of the respective PCR product and gene accession number. The table shows the sequences of primers used for real-time PCR in this study.
Additional file 2: of Oral administration of a select mixture of Bacillus probiotics generates Tr1 cells in weaned F4ab/acRâ   pigs challenged with an F4+ ETEC/VTEC/EPEC strain
Creators: name: Zhou, Dong
name: Zhu, Yao-Hong
name: Zhang, Wei
name: Wang, Meng-Ling
name: Fan, Wen-Yi
name: Song, Dan
name: Yang, Gui-Yan
name: Jensen, Bent
name: Jiu-Feng Wang
Publisher: name: Figshare
Year: 2015
Subjects: subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical 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

description: Sequences of oligonucleotide primers used for quantitative real-time PCR, length of the respective PCR product and gene accession number. The table shows the sequences of primers used for quantitative real-time PCR in this study.
Experiment-driven atomistic materials modeling: A case study combining X-ray photoelectron spectroscopy and machine learning potentials to infer the structure of oxygen-rich amorphous carbon
Creators: name: Zarrouk, Tigany
name: Ibragimova, Rina
name: Bartók, Albert P.
name: Caro, Miguel A.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: An important yet challenging aspect of atomistic materials modeling is reconciling experimental and computational results. Conventional approaches involve generating numerous configurations through molecular dynamics or Monte Carlo structure optimization and selecting the one with the closest match to experiment. However, this inefficient process is not guaranteed to succeed. We introduce a general method to combine atomistic machine learning (ML) with experimental observables that produces atomistic structures compatible with experiment by design. We use this approach in combination with grand-canonical Monte Carlo within a modified Hamiltonian formalism, to generate configurations that agree with experimental data and are chemically sound (low in energy). We apply our approach to understand the atomistic structure of oxygenated amorphous carbon (a-CO$_{x}$), an intriguing carbon-based material, to answer the question of how much oxygen can be added to carbon before it fully decomposes into CO and CO$_2$. Utilizing an ML-based X-ray photoelectron spectroscopy (XPS) model trained from $GW$ and density functional theory (DFT) data, in conjunction with an ML interatomic potential, we identify a-CO$_{x}$ structures compliant with experimental XPS predictions that are also energetically favorable with respect to DFT. Employing a network analysis, we accurately deconvolve the XPS spectrum into motif contributions, both revealing the inaccuracies inherent to experimental XPS interpretation and granting us atomistic insight into the structure of a-CO$_{x}$. This method generalizes to multiple experimental observables and allows for the elucidation of the atomistic structure of materials directly from experimental data, thereby enabling experiment-driven materials modeling with a degree of realism previously out of reach.
Additional file 1: Table S1. of Single nucleotide polymorphism rs13042395 in the SLC52A3 gene as a biomarker for regional lymph node metastasis and relapse-free survival of esophageal squamous cell carcinoma patients
Creators: name: Hua-Zhen Tan
name: Wu, Zhi-Yong
name: Wu, Jian-Yi
name: Long, Lin
name: Jiao, Ji-Wei
name: Peng, Yu-Hui
name: Xu, Yi-Wei
name: Li, Shan-Shan
name: Wang, Wei
name: Zhang, Jian-Jun
name: Li, En-Min
name: Xu, Li-Yan
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Cell Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Cancer

description: Relapse-free survival for 84 ESCC patients who had radiotherapy after surgery. (DOC 34 kb)
MILLIY TASVIRIY VA MUSIQA SAN'ATI INTYEGRASIYASI VOSITASIDA TALABALARNING IJODIY TAFAKKURINI RIVOJLANTIRISH
Creators: name: Baymetov Botir Boltabayevich
name: Giyasova Nilufar Barotbayevna
Publisher: name: Academic Scientific Research Group
Year: 2024

description: Mazkur maqolada talabalarga tasviriy san’atda milliy musiqa an’analarini aks ettirishga o’rgatish, yosh ijodkorlarda estetik qadiryatlarni tarbiyalash, ohang va ritm orqali insonlarni ruhlantiruvchi, quvvatlantiruvchi tuyg’ularini ikki san’at turi uyg’unligida bir butun ijodiy obrazni hosil qilishni hamda badiiy obraz yaratish sohasi bo‘yicha maxsus qobiliyatlarni rivojlantirish masalalariga qaratilgan.
Pyrgocorypha Stal 1873
Creators: name: Yong, Sheyla
name: Perez-Gelabert, Daniel E.
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Orthoptera
Tettigoniidae
Pyrgocorypha

description: Genus Pyrgocorypha Stål, 1873
Stål, 1873: 50.
Type species: Conocephalus subulatus Thunberg, 1815 (= Pyrgocorypha subulata); by original designation.
description: Published as part of Yong, Sheyla & Perez-Gelabert, Daniel E., 2014, Grasshoppers, Crickets and Katydids (Insecta: Orthoptera) of Cuba: an annotated checklist, pp. 401-438 in Zootaxa 3827 (4) on page 430, DOI: 10.11646/zootaxa.3827.4.1, http://zenodo.org/record/228581
3D-2D Neural Nets for Phase Retrieval in Noisy Interferometric Imaging
Creators: name: Proppe, Andrew H.
name: Thekkadath, Guillaume
name: England, Duncan
name: Bustard, Philip J.
name: Bouchard, Frédéric
name: Lundeen, Jeff S.
name: Sussman, Benjamin J.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Optics (physics.optics)
subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Machine Learning (cs.LG)
subject: Image and Video Processing (eess.IV)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: In recent years, neural networks have been used to solve phase retrieval problems in imaging with superior accuracy and speed than traditional techniques, especially in the presence of noise. However, in the context of interferometric imaging, phase noise has been largely unaddressed by existing neural network architectures. Such noise arises naturally in an interferometer due to mechanical instabilities or atmospheric turbulence, limiting measurement acquisition times and posing a challenge in scenarios with limited light intensity, such as remote sensing. Here, we introduce a 3D-2D Phase Retrieval U-Net (PRUNe) that takes noisy and randomly phase-shifted interferograms as inputs, and outputs a single 2D phase image. A 3D downsampling convolutional encoder captures correlations within and between frames to produce a 2D latent space, which is upsampled by a 2D decoder into a phase image. We test our model against a state-of-the-art singular value decomposition algorithm and find PRUNe reconstructions consistently show more accurate and smooth reconstructions, with a x2.5 - 4 lower mean squared error at multiple signal-to-noise ratios for interferograms with low (< 1 photon/pixel) and high (~100 photons/pixel) signal intensity. Our model presents a faster and more accurate approach to perform phase retrieval in extremely low light intensity interferometry in presence of phase noise, and will find application in other multi-frame noisy imaging techniques.
Decentralized Proactive Model Offloading and Resource Allocation for Split and Federated Learning
Creators: name: Huang, Binbin
name: Zhao, Hailiang
name: Wang, Lingbin
name: Qian, Wenzhuo
name: Yin, Yuyu
name: Deng, Shuiguang
Publisher: name: arXiv
Year: 2024
Subjects: subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: FOS: Computer and information sciences

description: In the resource-constrained IoT-edge computing environment, Split Federated (SplitFed) learning is implemented to enhance training efficiency. This method involves each terminal device dividing its full DNN model at a designated layer into a device-side model and a server-side model, then offloading the latter to the edge server. However, existing research overlooks four critical issues as follows: (1) the heterogeneity of end devices' resource capacities and the sizes of their local data samples impact training efficiency; (2) the influence of the edge server's computation and network resource allocation on training efficiency; (3) the data leakage risk associated with the offloaded server-side sub-model; (4) the privacy drawbacks of current centralized algorithms. Consequently, proactively identifying the optimal cut layer and server resource requirements for each end device to minimize training latency while adhering to data leakage risk rate constraint remains a challenging issue. To address these problems, this paper first formulates the latency and data leakage risk of training DNN models using Split Federated learning. Next, we frame the Split Federated learning problem as a mixed-integer nonlinear programming challenge. To tackle this, we propose a decentralized Proactive Model Offloading and Resource Allocation (DP-MORA) scheme, empowering each end device to determine its cut layer and resource requirements based on its local multidimensional training configuration, without knowledge of other devices' configurations. Extensive experiments on two real-world datasets demonstrate that the DP-MORA scheme effectively reduces DNN model training latency, enhances training efficiency, and complies with data leakage risk constraints compared to several baseline algorithms across various experimental settings.
Polana (Angusana) DeLong & Freytag 1972
Creators: name: Domahovski, Alexandre Cruz
name: Cavichioli, Rodney Ramiro
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hemiptera
Cicadellidae
Polana

description: Polana (Angusana) DeLong & Freytag, 1972
Type-species Gypona exornata Fowler, 1903: 315.
Diagnosis. Coloration (Figs 1–4, 31–38) forming patterns of yellow, orange, red and black maculae; forewing (Figs 4, 31–38) with two wide white or yellowish area near costal margin, one at basal third and one at apical third, alar appendix developed, wider than first apical cell width; head (Fig. 1) distinctly narrower than pronotum, transocular width about seven-tenths of humeral width of pronotum; sternite VII of male (Fig. 5) as long as wide or longer than wide, almost fully hiding the subgenital plates; male pygofer (Figs 7, 8) without basodorsal process; subgenital plate (Fig. 9) narrow, with hair-like setae on external margin; connective (Fig. 10) Y-shaped; aedeagus (Figs 13, 14) with apodemal processes.
Species of Polana (Angusana)
P. exornata (Fowler, 1903): 315. (Gypona). Costa Rica (new record) and Panama.
P. pilosa Gonçalves, Takiya and Mejdalani, 2018: 144. Peru.
P. eliasi sp. nov. Brazil: Rondônia.
description: Published as part of Domahovski, Alexandre Cruz & Cavichioli, Rodney Ramiro, 2022, A new species of Polana (Angusana) (Hemiptera: Cicadellidae: Gyponini): new record, key to males and description of the female terminalia of Polana exornata, pp. 275-282 in Zootaxa 5104 (2) on page 276, DOI: 10.11646/zootaxa.5104.2.6, http://zenodo.org/record/6280931
Pyrgocorypha uncinata Harris 1841
Creators: name: Yong, Sheyla
name: Perez-Gelabert, Daniel E.
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Orthoptera
Tettigoniidae
Pyrgocorypha
Pyrgocorypha uncinata

description: Pyrgocorypha uncinata (Harris, 1841)
Conocephalus uncinatus Harris, 1841: 132; Bolívar, 1888: 116 –164. Pyrgocorypha uncinata: Rehn, 1909: 211; Zayas, 1976: 63, fig. 52.
Unspecified primary type, from Alabama, Southeastern U. S. A. Type lost? Its deposition has been cited as “H. collection (Alabama)”.
Distribution. Cuba, Hispaniola, Central America, Mexico and southern United States.
description: Published as part of Yong, Sheyla & Perez-Gelabert, Daniel E., 2014, Grasshoppers, Crickets and Katydids (Insecta: Orthoptera) of Cuba: an annotated checklist, pp. 401-438 in Zootaxa 3827 (4) on page 430, DOI: 10.11646/zootaxa.3827.4.1, http://zenodo.org/record/228581
Parametrically long lifetime of superdiffusion in non-integrable spin chains
Creators: name: McRoberts, Adam J.
name: Moessner, Roderich
Publisher: name: arXiv
Year: 2024
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: Superdiffusion is surprisingly easily observed even in systems without the integrability underpinning this phenomenon. Indeed, the classical Heisenberg chain -- one of the simplest many-body systems, and firmly believed to be non-integrable -- evinces a long-lived regime of anomalous, superdiffusive spin dynamics at finite temperature. Similarly, superdiffusion persists for long timescales, even at high temperature, for small perturbations around a related integrable model. Eventually, however, ordinary diffusion is believed to be asymptotically restored. We examine the timescales governing the lifetime of the superdiffusive regime, and argue that it diverges algebraically fast -- both in deviation from the integrable limit, and at low temperature, where we find $t^* \sim T^{-ζ}$ with an exponent possibly as large as $ζ= 8$. This can render the crossover to ordinary diffusion practically inaccessible.
description: 4 pages
Additional file 2 Figure S1. of Decreased expression levels of Ifi genes is associated to the increased resistance to spontaneous arthritis disease in mice deficiency of IL-1RA
Creators: name: Xiaoyun Liu
name: Jiao, Yan
name: Yanhong Cao
name: Deng, Nan
name: Yonghui Ma
name: Hasty, Karen
name: Kang, Andrew
name: Chen, Hong
name: Stuart, John
name: Weikuan Gu
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Physiology
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: Plant Biology

description: Network of known arthritis relevant up and down regulated genes when congenics vs DBA/1 wild type. The 138 nodes in the graph below show the selected traits. Only nodes with edges are displayed. The 167 edges between the nodes, filtered from the 9453 total edges and drawn as lines, show Pearson correlation coefficients greater than 0.75 or less than -0.75. The graph’s canvas is 40.0 by 40.0 cm, and the node labels are drawn with a 16.0 point font, and the edge labels are drawn with a 16.0 point font. Figure S2 Network of known arthritis relevant up and down regulated genes when congenics vs DBA-/-. The 101 nodes in the graph below show the selected traits. Only nodes with edges are displayed. The 38 edges between the nodes, filtered from the 5050 total edges and drawn as lines, show Pearson correlation coefficients greater than 0.75 or less than -0.75. The graph’s canvas is 40.0 by 40.0 cm, and the node labels are drawn with a 16.0 point font, and the edge labels are drawn with a 16.0 point font. Figure S3 Network of known arthritis relevant up and down regulated genes when congenics are compared to BALB/c wild type. The 92 nodes in the graph below show the selected traits. Only nodes with edges are displayed. The 40 edges between the nodes, filtered from the 4186 total edges and drawn as lines, show Pearson correlation coefficients greater than 0.75 or less than -0.75. The graph’s canvas is 40.0 by 40.0 cm, and the node labels are drawn with a 16.0 point font, and the edge labels are drawn with a 16.0 point font. (DOCX 71 kb)
Additional file 2: of P311 induces the transdifferentiation of epidermal stem cells to myofibroblast-like cells by stimulating transforming growth factor β1 expression
Creators: name: Haisheng Li
name: Zhihui Yao
name: Weifeng He
name: Hongyan Gao
name: Bai, Yang
name: Sisi Yang
name: Zhang, Lu
name: Rixing Zhan
name: Jianglin Tan
name: Junyi Zhou
name: Takata, Masao
name: Wu, Jun
name: Gaoxing Luo
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Evolutionary Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Developmental Biology
subject: Cancer
subject: Hematology

description: Supplementary information containing Supplementary Materials and Methods presenting methods of Gel contraction assay and in-vitro scratch wound assay, Figure S1. showing the α-SMA expression in the epidermis of mouse burn wounds, Figure S2. showing characterization of primary mouse and human EpSCs, Figure S3. showing successful transfection of the P311 adenovirus into mouse EpSCs, Figure S4. showing that P311 induced a myofibroblast-like phenotype in primary human EpSCs, Figure S5. showing the effect of P311 on the mesenchymal function of EpSCs, Figure S6. showing the quantification of the total Smad2 and Smad3 protein, and Figure S7. showing the effect of P311 on TGFβ1 promoter activity. (DOC 14540 kb)
Self-interacting quantum particles
Creators: name: Giardino, Sergio
Publisher: name: arXiv
Year: 2024
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The real Hilbert space formalism developed within the quaternionic quantum mechanics ($\mathbb H$QM) is fully applied to the simple model of the autonomous particle. This framework permits novel insights within the usual description of the complex autonomous particle, particulaly concening the energy of a non-stationary motion. Through the appraisal of the physical role played by a fully quaternionic scalar potential, a original self-interaction within the quaternionic autonomous particle has been determined as well. Scattering processes are considered to illustrate these novel features.
description: Accept by Int. J. Geom. Meth. Mod. Phys
Orchelimum Serville 1838
Creators: name: Yong, Sheyla
name: Perez-Gelabert, Daniel E.
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Orthoptera
Tettigoniidae
Orchelimum

description: Genus Orchelimum Serville, 1838
Orchelimum Serville, 1838 [1839]: 522.
Type species: Orchelimum cuticulare Serville, 1838
description: Published as part of Yong, Sheyla & Perez-Gelabert, Daniel E., 2014, Grasshoppers, Crickets and Katydids (Insecta: Orthoptera) of Cuba: an annotated checklist, pp. 401-438 in Zootaxa 3827 (4) on page 430, DOI: 10.11646/zootaxa.3827.4.1, http://zenodo.org/record/228581
A dormant, overmassive black hole in the early Universe
Creators: name: Juodžbalis, Ignas
name: Maiolino, Roberto
name: Baker, William M.
name: Tacchella, Sandro
name: Scholtz, Jan
name: D'Eugenio, Francesco
name: Schneider, Raffaella
name: Trinca, Alessandro
name: Valiante, Rosa
name: DeCoursey, Christa
name: Curti, Mirko
name: Carniani, Stefano
name: Chevallard, Jacopo
name: de Graaff, Anna
name: Arribas, Santiago
name: Bennett, Jake S.
name: Bourne, Martin A.
name: Bunker, Andrew J.
name: Charlot, Stéphane
name: Jiang, Brian
name: Koudmani, Sophie
name: Perna, Michele
name: Robertson, Brant
name: Sijacki, Debora
name: Übler, Hannah
name: Williams, Christina C.
name: Willott, Chris
name: Witstok, Joris
Publisher: name: arXiv
Year: 2024
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Recent observations have found a large number of supermassive black holes already in place in the first few hundred million years after Big Bang. The channels of formation and growth of these early, massive black holes are not clear, with scenarios ranging from heavy seeds to light seeds experiencing bursts of high accretion rate. Here we present the detection, from the JADES survey, of broad Halpha emission in a galaxy at z=6.68, which traces a black hole with mass of ~ 4 * 10^8 Msun and accreting at a rate of only 0.02 times the Eddington limit. The host galaxy has low star formation rate (~ 1 Msun/yr, a factor of 3 below the star forming main sequence). The black hole to stellar mass ratio is ~ 0.4, i.e. about 1,000 times above the local relation, while the system is closer to the local relations in terms of dynamical mass and velocity dispersion of the host galaxy. This object is most likely the tip of the iceberg of a much larger population of dormant black holes around the epoch of reionisation. Its properties are consistent with scenarios in which short bursts of super-Eddington accretion have resulted in black hole overgrowth and massive gas expulsion from the accretion disk; in between bursts, black holes spend most of their life in a dormant state.
description: 43 pages, 19 figures. Updated to accepted version
MOESM1 of PDL regeneration via cell homing in delayed replantation of avulsed teeth
Creators: name: Wenting Zhu
name: Zhang, Qian
name: Zhang, Yang
name: Cen, Lian
name: Wang, Jun
Publisher: name: Figshare
Year: 2015
Subjects: subject: Cell Biology
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology
subject: Computational Biology

description: Additional file 1: Table S1. Comparison of periodontal healing pattern for two groups.
Dynamics of quantum cellular automata electron transition in triple quantum dots
Creators: name: Aizawa, Takumi
name: Shinozaki, Motoya
name: Fujiwara, Yoshihiro
name: Kumasaka, Takeshi
name: Izumida, Wataru
name: Ludwig, Arne
name: Wieck, Andreas D.
name: Otsuka, Tomohiro
Publisher: name: arXiv
Year: 2024
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: The quantum cellular automata (QCA) effect is a transition in which multiple electron move coordinately by Coulomb interactions and observed in multiple quantum dots. This effect will be useful for realizing and improving quantum cellular automata and information transfer using multiple electron transfer. In this paper, we investigate the real-time dynamics of the QCA charge transitions in a triple quantum dot by using fast charge-state readout realized by rf reflectometry. We observe real-time charge transitions and analyze the tunneling rate comparing with the first-order tunneling processes. We also measure the gate voltage dependence of the QCA transition and show that it can be controlled by the voltage.
description: 11pages, 4 figures
Orchelimum (Orchelimum) concinnum Scudder 1862
Creators: name: Yong, Sheyla
name: Perez-Gelabert, Daniel E.
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Orthoptera
Tettigoniidae
Orchelimum
Orchelimum concinnum

description: Orchelimum (Orchelimum) concinnum Scudder, 1862
Scudder, 1862: 452; Zayas, 1976: 67, fig. 61.
Lectotype male, from Cape Cod, Massachusetts, Northeastern U. S. A. [ANSP].
Distribution. Caribbean and North America.
Notes. Two specimens in the Zayas collection from ”Península de Zapata, Las Villas prov., V-1960 ”.
description: Published as part of Yong, Sheyla & Perez-Gelabert, Daniel E., 2014, Grasshoppers, Crickets and Katydids (Insecta: Orthoptera) of Cuba: an annotated checklist, pp. 401-438 in Zootaxa 3827 (4) on page 430, DOI: 10.11646/zootaxa.3827.4.1, http://zenodo.org/record/228581
SonoTraceLab -- A Raytracing-Based Acoustic Modelling System for Simulating Echolocation Behavior of Bats
Creators: name: Jansen, Wouter
name: Steckel, Jan
Publisher: name: arXiv
Year: 2024
Subjects: subject: Audio and Speech Processing (eess.AS)
subject: Sound (cs.SD)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Computer and information sciences

description: Echolocation is the prime sensing modality for many species of bats, who show the intricate ability to perform a plethora of tasks in complex and unstructured environments. Understanding this exceptional feat of sensorimotor interaction is a key aspect into building more robust and performant man-made sonar sensors. In order to better understand the underlying perception mechanisms it is important to get a good insight into the nature of the reflected signals that the bat perceives. While ensonification experiments are in important way to better understand the nature of these signals, they are as time-consuming to perform as they are informative. In this paper we present SonoTraceLab, an open-source software package for simulating both technical as well as biological sonar systems in complex scenes. Using simulation approaches can drastically increase insights into the nature of biological echolocation systems, while reducing the time- and material complexity of performing them.
Singular solutions for complex second order elliptic equations and their application to time-harmonic diffuse optical tomography
Creators: name: Curran, Jason
name: GABURRO, ROMINA
name: Nolan, Clifford
Publisher: name: University of Limerick
Year: 2024
Subjects: classificationCode: 49
subject: Mathematical sciences

description: We construct singular solutions of a complex elliptic equation of second order, having an isolated singularity of any order. In particular, we extend results obtained for the real partial differential equation in divergence form by Alessandrini in 1990. Our solutions can be applied to the determination of the optical properties of an anisotropic medium in time-harmonic Diffuse Optical Tomography (DOT)
Additional file 1: of P311 induces the transdifferentiation of epidermal stem cells to myofibroblast-like cells by stimulating transforming growth factor Î˛1 expression
Creators: name: Haisheng Li
name: Zhihui Yao
name: Weifeng He
name: Hongyan Gao
name: Bai, Yang
name: Sisi Yang
name: Zhang, Lu
name: Rixing Zhan
name: Jianglin Tan
name: Junyi Zhou
name: Takata, Masao
name: Wu, Jun
name: Gaoxing Luo
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Space Science
subject: Cell Biology
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: FOS: Biological sciences

description: Supplementary information containing Table S1. presenting primer sequences used for real-time PCR, and Table S2. presenting the characterization of epithelial to myofibroblast/ myofibroblast-like cell transdifferentiation in 36 articles. (PDF 487 kb)
Measurements and modelling of induced flow in collective vertical migration
Creators: name: Mohebbi, Nina
name: Hwang, Joonha
name: Fu, Matthew K.
name: Dabiri, John O.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: Hydrodynamic interactions between swimming or flying organisms can lead to complex flows on the scale of the group. These emergent fluid dynamics are often more complex than a linear superposition of individual organism flows, especially at intermediate Reynolds numbers. This paper presents an approach to estimate the flow induced by multiple swimmer wakes in proximity using a semianalytical model that conserves mass and momentum in the aggregation. The key equations are derived analytically, while the implementation and solution of these equations are carried out numerically. This model was informed by and compared with empirical measurements of induced vertical migrations of brine shrimp, Artemia salina. The response of individual swimmers to ambient background flow and light intensity was evaluated. In addition, the time-resolved three-dimensional spatial configuration of the swimmers was measured using a recently developed laser scanning system. Numerical results using the model found that the induced flow at the front of the aggregation was insensitive to the presence of downstream swimmers, with the induced flow tending towards asymptotic beyond a threshold aggregation length. Closer swimmer spacing led to higher induced flow speeds, in some cases leading to model predictions of induced flow exceeding swimmer speeds required to maintain a stable spatial configuration. This result was reconciled by comparing two different models for the near-wake of each swimmer. The results demonstrate that aggregation-scale flows result from a complex, yet predictable interplay between individual organism wake structure and aggregation configuration and size.
Additional file 1: Figure S1. of Metabolomic biosignature differentiates melancholic depressive patients from healthy controls
Creators: name: Yashu Liu
name: Yieh, Lynn
name: Yang, Tao
name: Drinkenburg, Wilhelmus
name: Peeters, Pieter
name: Steckler, Thomas
name: Vaibhav Narayan
name: Wittenberg, Gayle
name: Jieping Ye
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences

description: Effect of storage time correction. Figure S2. The distributions of original and imputed metabolite features: Glyoxylate ratio, Caffeine ratio, Elaidicacid ratio and Indole 3 propionic acid ratio. Figure S3. QQ plots of the p-values of the two-sample t-tests on raw features, k-means and hierarchical clustering representatives. Table S1. Classification performance obtained by Random Forest on metabolite data using the standard undersampling technique. Table S2. Classification performance obtained by Support Vector Machines on metabolite data using the standard undersampling technique. Table S3. Top 30 individual metabolic features selected by different feature selection methods. Table S4. Top 30 individual metabolic features selected by different feature selection methods. Table S5. Top cluster-representatives (K-means) selected by different feature selection methods. Table S6. Top cluster-representatives (hierarchical clustering) selected by different feature selection methods. Table S7. Top cluster-representatives (hierarchical clustering) selected by different feature selection methods. (DOCX 812Â kb)
Anaxipha exigua Chopard 1968
Creators: name: Yong, Sheyla
name: Perez-Gelabert, Daniel E.
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Orthoptera
Haglotettigoniidae
Anaxipha
Anaxipha exigua

description: Anaxipha exigua Chopard, 1968
[= Anaxipha insularis (F. Walker, 1869)]
Rehn, 1909: 223; Otte & Perez-Gelabert, 2009: 139.
Distribution. Jamaica.
Notes. There is one specimen identified with this name in the CZACC collection. Its presence in Cuba needs to be confirmed.
Antillicharis similis (F. Walker, 1869)
[= Orocharis similis (F. Walker, 1869) = Orocharis canotus Saussure, 1878] Otte & Perez-Gelabert, 2009: 248.
Distribution. Dominican Republic.
Notes. In the most recent revision of the family for the Caribbean (Otte & Perez-Gelabert, 2009) the distribution of this species is restricted to Hispaniola. Gundlach (1891) and Rehn (1909) previously recorded it from Cuba, and there are several specimens identified with this name in the CZACC and Zayas collections. A more detailed examination of those Cuban specimens should clarify whether they belong to this species.
description: Published as part of Yong, Sheyla & Perez-Gelabert, Daniel E., 2014, Grasshoppers, Crickets and Katydids (Insecta: Orthoptera) of Cuba: an annotated checklist, pp. 401-438 in Zootaxa 3827 (4) on page 430, DOI: 10.11646/zootaxa.3827.4.1, http://zenodo.org/record/228581
Polana (Angusana) DeLong & Freytag 1972
Creators: name: Domahovski, Alexandre Cruz
name: Cavichioli, Rodney Ramiro
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hemiptera
Cicadellidae
Polana

description: Key to males of Angusana
1. Pygofer (Fig. 8) with acute process near mid-length of dorsal margin, directed inward. Aedeagus (Figs 13, 14) with shaft bearing conspicuous ventral process near base, bifid apically................................... P. eliasi sp. nov. (Brazil)
- Pygofer (Gonçalves, Takiya and Mejdalani, 2018: 146, fig. 4) without processes. Aedeagal shaft (Gonçalves, Takiya and Mejdalani, 2018: 146, figs 8, 9) without ventral process near base................................................. 2
2. Style (Gonçalves, Takiya and Mejdalani, 2018: 146, figs 6, 7) with apex subacute, bearing small dorsal denticles. Aedeagus (Gonçalves, Takiya and Mejdalani, 2018: 146, figs 8, 9) with apex tapered bearing single pair of apical processes................................................................................................ P. pilosa (Peru)
- Style (DeLong & Freytag, 1972: 255, fig. 81) with apex acute, without denticles.Aedeagus (DeLong & Freytag, 1972: 255, figs 79, 80) with apex expanded laterary, bearing two pairs of subapical processes........ P. exornata (Costa Rica and Panama)
description: Published as part of Domahovski, Alexandre Cruz & Cavichioli, Rodney Ramiro, 2022, A new species of Polana (Angusana) (Hemiptera: Cicadellidae: Gyponini): new record, key to males and description of the female terminalia of Polana exornata, pp. 275-282 in Zootaxa 5104 (2) on pages 281-282, DOI: 10.11646/zootaxa.5104.2.6, http://zenodo.org/record/6280931
Stitching for Neuroevolution: Recombining Deep Neural Networks without Breaking Them
Creators: name: Guijt, Arthur
name: Thierens, Dirk
name: Alderliesten, Tanja
name: Bosman, Peter A. N.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Neural and Evolutionary Computing (cs.NE)
subject: FOS: Computer and information sciences

description: Traditional approaches to neuroevolution often start from scratch. This becomes prohibitively expensive in terms of computational and data requirements when targeting modern, deep neural networks. Using a warm start could be highly advantageous, e.g., using previously trained networks, potentially from different sources. This moreover enables leveraging the benefits of transfer learning (in particular vastly reduced training effort). However, recombining trained networks is non-trivial because architectures and feature representations typically differ. Consequently, a straightforward exchange of layers tends to lead to a performance breakdown. We overcome this by matching the layers of parent networks based on their connectivity, identifying potential crossover points. To correct for differing feature representations between these layers we employ stitching, which merges the networks by introducing new layers at crossover points. To train the merged network, only stitching layers need to be considered. New networks can then be created by selecting a subnetwork by choosing which stitching layers to (not) use. Assessing their performance is efficient as only their evaluation on data is required. We experimentally show that our approach enables finding networks that represent novel trade-offs between performance and computational cost, with some even dominating the original networks.
description: 10 pages, submitted to GECCO 2024
Effects of Dark Matter on $f$-mode oscillations of Neutron Stars
Creators: name: Shirke, Swarnim
name: Pradhan, Bikram Keshari
name: Chatterjee, Debarati
name: Sagunski, Laura
name: Schaffner-Bielich, Jürgen
Publisher: name: arXiv
Year: 2024
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: The effect of dark matter (DM) on $f$-mode oscillations in DM admixed neutron stars (NSs) is investigated in a comprehensive analysis with particular attention to the role of the nuclear equation of state. Hadronic matter is modeled by the relativistic mean field model and the DM model is based on the neutron decay anomaly. The non-radial $f$-mode oscillations for such DM admixed NS are studied in a full general relativistic framework. We investigate the impact of DM, DM self-interaction, and DM fraction on the $f$-mode characteristics. We derive relations encoding the effect of DM on $f$-mode parameters. We then perform a systematic study by varying all the model parameters within their known uncertainty range and obtain a universal relation for the DM fraction based on the total mass of the star and DM self-interaction strength. We also perform a correlation study among model parameters, NS observables, in particular, $f$-mode parameters. Finally, we check the $f$-mode universal relations (URs) for the case of DM admixed NSs and demonstrate the existence of a degeneracy between purely hadronic NSs and DM admixed NSs.
description: 27 pages, 22 figures, 5 tables. Published in PRD. Accepted version of the manuscript
Falcicula hebardi Rehn 1903
Creators: name: Yong, Sheyla
name: Perez-Gelabert, Daniel E.
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Orthoptera
Haglotettigoniidae
Falcicula
Falcicula hebardi

description: Falcicula hebardi Rehn, 1903
Rehn, 1909: 224.
Distribution. From Maryland and Texas to northern Florida, U. S. A.
Notes. Rehn (1909) annotates: “This species, which has previously been recorded only from Georgia and Florida, is known as a Cuban insect on the basis of three females from Cabañas… ”. The presence of this North American species in Cuba should be confirmed with new collections.
description: Published as part of Yong, Sheyla & Perez-Gelabert, Daniel E., 2014, Grasshoppers, Crickets and Katydids (Insecta: Orthoptera) of Cuba: an annotated checklist, pp. 401-438 in Zootaxa 3827 (4) on page 430, DOI: 10.11646/zootaxa.3827.4.1, http://zenodo.org/record/228581
Additional file 3: of Feedback activation of neurofibromin terminates growth factor-induced Ras activation
Creators: name: Hennig, Anne
name: Markwart, Robby
name: Wolff, Katharina
name: Schubert, Katja
name: Cui, Yan
name: Prior, Ian
name: Esparza-Franco, Manuel
name: Ladds, Graham
name: Rubio, Ignacio
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Molecular Biology
subject: Physiology
subject: Developmental Biology
subject: Cancer
subject: Science Policy
subject: Plant Biology
subject: Computational Biology

description: Combined knockdown of MEK1 and MEK2 causes prolonged Ras activation. EGF-induced Ras activation was assessed biochemically after single or combined siRNA-mediated knockdown of MEK1 and MEK2. RBD designates the coomassie-stained Ras binding domain used to collect Ras-GTP from cell lysates. Note that single knockdown of MEK1 or MEK2 leads to opposite effects on Ras-GTP levels, pointing to different roles of both kinases in Ras activity control. The same effect was previously reported by Kamioka et al. [13]. (PDF 28364Â kb)
Additional file 1: of Feedback activation of neurofibromin terminates growth factor-induced Ras activation
Creators: name: Hennig, Anne
name: Markwart, Robby
name: Wolff, Katharina
name: Schubert, Katja
name: Cui, Yan
name: Prior, Ian
name: Esparza-Franco, Manuel
name: Ladds, Graham
name: Rubio, Ignacio
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Molecular Biology
subject: Physiology
subject: Pharmacology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Developmental Biology

description: EGF-induced electrophoretic mobility shift of Sos is sensitive to MEK (10 μM UO126) and Erk (50 μM FR180204) but not Rsk (10 μM BI-D1870) or PI3K (100nM Wortmannin) inhibition. HeLa cells pre-treated with the indicated inhibitors or subjected to siRNA-mediated knockdown of neurofibromin (siNF1) were deprived of serum overnight and challenged 30 min with EGF. Lysates were processed for immunodetection of Sos, Rsk1/2/3 and Erk. (PDF 598 kb)
Neoconocephalus fuscinervis Redtenbacher 1891
Creators: name: Yong, Sheyla
name: Perez-Gelabert, Daniel E.
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Orthoptera
Tettigoniidae
Neoconocephalus
Neoconocephalus fuscinervis

description: Neoconocephalus fuscinervis (Redtenbacher, 1891)
[= Conocephaloides fuscinervis Redtenbacher, 1891] T. Walker & Greenfield, 1983: 379.
Notes. The validity of name is unresolved (T. Walker & Greenfield, 1983). Eades et al. (2011) mention a syntype from Cuba. Its presence in Cuba needs confirmation.
description: Published as part of Yong, Sheyla & Perez-Gelabert, Daniel E., 2014, Grasshoppers, Crickets and Katydids (Insecta: Orthoptera) of Cuba: an annotated checklist, pp. 401-438 in Zootaxa 3827 (4) on page 431, DOI: 10.11646/zootaxa.3827.4.1, http://zenodo.org/record/228581
Additional file 2: of Feedback activation of neurofibromin terminates growth factor-induced Ras activation
Creators: name: Hennig, Anne
name: Markwart, Robby
name: Wolff, Katharina
name: Schubert, Katja
name: Cui, Yan
name: Prior, Ian
name: Esparza-Franco, Manuel
name: Ladds, Graham
name: Rubio, Ignacio
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Computational Biology

description: Details of the “GEF only” and “GAP only” model. (PDF 174 kb)
An efficient algorithm for identifying rainbow ortho-convex 4-sets in k-colored point sets
Creators: name: Flores-Peñaloza, David
name: Lopez, Mario A.
name: Marín, Nestaly
name: Orden, David
Publisher: name: arXiv
Year: 2024
Subjects: subject: Computational Geometry (cs.CG)
subject: Combinatorics (math.CO)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics
subject: G.2.1; F.2.2
subject: 68U05 (Primary), 68R05 (Secondary)

description: Let $P$ be a $k$-colored set of $n$ points in the plane, $4 \leq k \leq n$. We study the problem of deciding if $P$ contains a subset of four points of different colors such that its Rectilinear Convex Hull has positive area. We show this problem to be equivalent to deciding if there exists a point $c$ in the plane such that each of the open quadrants defined by $c$ contains a point of $P$, each of them having a different color. We provide an $O(n \log n)$-time algorithm for this problem, where the hidden constant does not depend on $k$; then, we prove that this problem has time complexity $Ω(n \log n)$ in the algebraic computation tree model. No general position assumptions for $P$ are required.
description: 17 pages, 4 figures, accepted version
Quantum transport in randomized quantum graphs
Creators: name: Silva, Alison A.
name: Bazeia, D.
name: Andrade, Fabiano M.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Quantum Physics (quant-ph)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: This work deals with quantum transport in open quantum graphs. We consider the case of complete graphs on $n$ vertices with an edge removed and attached to two leads, to represent the entrance and exit channels, from where we calculate the transmission coefficient. We include the possibility of several vertices being connected or not and associate it with a randomization parameter $p$. To implement the calculation, we had to introduce the transmission coefficient of randomized quantum graphs (RQG), and we also proposed a procedure to obtain the exact and approximate but reliable results for such transmission coefficients. The main results show that the transport is importantly affected by the removal of connections between pairs of vertices, but they also indicate the presence of a region where the transmission is fully suppressed, even when the number of edge removal is not too small.
description: 9 pages, 10 figures
Convergence of reputations under indirect reciprocity
Creators: name: Morsky, Bryce
name: Plotkin, Joshua B.
name: Akçay, Erol
Publisher: name: arXiv
Year: 2024
Subjects: subject: Populations and Evolution (q-bio.PE)
subject: FOS: Biological sciences
subject: 92B05, 91D99

description: Previous research has shown how indirect reciprocity can promote cooperation through evolutionary game theoretic models. Most work in this field assumes a separation of time-scales: individuals' reputations equilibrate at a fast time scale for given frequencies of strategies while the strategies change slowly according to the replicator dynamics. Much of the previous research has focused on the behaviour and stability of equilibria for the replicator dynamics. Here we focus on the underlying reputational dynamics that occur on a fast time scale. We describe reputational dynamics as systems of differential equations and conduct stability analyses on their equilibria. We prove that reputations converge to a unique equilibrium for each of the five standard norms whether assessments are public or private. These results confirm a crucial but previously unconfirmed assumption underlying the theory of indirect reciprocity for the most studied set of norms.
MOESM3 of In silico profiling for secondary metabolites from Lepidium meyenii (maca) by the pharmacophore and ligand-shape-based joint approach
Creators: name: Yi, Fan
name: Tan, Xiao-Lei
name: Yan, Xin
name: Liu, Hai-Bo
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Molecular Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer

description: Additional file 3. Total GeneMANIA report of maca.
MOESM2 of Robust succinic acid production from crude glycerol using engineered Yarrowia lipolytica
Creators: name: Cuijuan Gao
name: Xiaofeng Yang
name: Huaimin Wang
name: Rivero, Cristina
name: Li, Chong
name: Zhiyong Cui
name: Qingsheng Qi
name: Lin, Carol
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Additional file 2: Figure S2. Time profiles of glycerol consumption rate, SA productivity and SA yield in fed-batch fermentation. Arrows showed the feeding points.