cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5394631.v1
title: Electronic_supplementary_data_cytb_sequence from Into the dark: patterns of middle ear adaptations in subterranean eulipotyphlan mammals

description: Evolution of the middle ear ossicles was a key innovation for mammals, enhancing the transmission of airborne sound. Radiation into various habitats from a terrestrial environment resulted in diversification of the auditory mechanisms among mammals. However, due to the paucity of phylogenetically controlled investigations, how middle ear traits have diversified with functional specialization remains unclear. In order to identify the respective patterns for various lifestyles and to gain insights into fossil forms, we employed a high-resolution tomography technique and compared the middle ear morphology of eulipotyphlan species (moles, shrews and hedgehogs), a group that has radiated into various environments, such as terrestrial, aquatic and subterranean habitats. Three-dimensional geometric morphometric analysis was conducted within a phylogenetically controlled framework. Quantitative shapes were found to strongly reflect the degree of subterranean lifestyle and weakly involve phylogeny. Our analyses demonstrate that subterranean adaptation should include a relatively shorter anterior process of the malleus, an enlarged incus, an enlarged stapes footplate and a reduction of the orbicular apophysis. These traits arguably allow improving low-frequency sound transmission at low frequencies and inhibiting the low-frequency noise which disturbs the subterranean animals to hear airborne sounds.
DOI: 10.6084/m9.figshare.5394619
title: Raw larval abundance and environmental data for Thompson et al. from Larval abundances of rockfishes that were historically targeted by fishing increased over 16 years in association with a large marine protected area

description: Abundance of each rockfish species (column X-BK adjusted by SHF (column F)) and environmental conditions (column H-T)
DOI: 10.6084/m9.figshare.5394604
title: Barramundi MO2max (fed vs. unfed fish) data from Fish face a trade-off between ‘eating big’ for growth efficiency and ‘eating small’ to retain aerobic capacity

description: Feeding provides the necessary energy to fuel all fitness-related processes including activity, growth and reproduction. Nevertheless, prey consumption and digestive processes can have physical and physiological trade-offs with other critical functions, many of which are not clearly understood. Using an ambush predator, barramundi (<i>Lates calcarifer</i>), fed meals ranging 0.6–3.4% of body mass, we examined interrelations between meal size, growth efficiency and surplus aerobic metabolic capacity (aerobic scope, AS). Large meals required a greater absolute investment of energy to process (a larger so-called specific dynamic action, SDA), but the percentage of digestible meal energy required in the SDA response (SDA coefficient) decreased with increasing meal size. Combined with the findings that growth rate and growth efficiency also increased with food intake, our results demonstrate that it is energetically advantageous for fish to select large prey. However, following a large meal, SDA processes occupied up to 77% of the available AS, indicating that other oxygen-demanding activities like swimming may be compromised while large meals are processed. This trade-off between meal size and AS suggests that fishes like barramundi would benefit from regulating prey size based on imminent requirements and threats.
DOI: 10.6084/m9.figshare.5394619.v1
title: Raw larval abundance and environmental data for Thompson et al. from Larval abundances of rockfishes that were historically targeted by fishing increased over 16 years in association with a large marine protected area

description: Abundance of each rockfish species (column X-BK adjusted by SHF (column F)) and environmental conditions (column H-T)
DOI: 10.6084/m9.figshare.5394610
title: Main mode code from Quantifying the dominant growth mechanisms of dimorphic yeast using a lattice-based model

description: The core MATLAB code used to generate the simulations in this study.
DOI: 10.6084/m9.figshare.5394604.v1
title: Barramundi MO2max (fed vs. unfed fish) data from Fish face a trade-off between ‘eating big’ for growth efficiency and ‘eating small’ to retain aerobic capacity

description: Feeding provides the necessary energy to fuel all fitness-related processes including activity, growth and reproduction. Nevertheless, prey consumption and digestive processes can have physical and physiological trade-offs with other critical functions, many of which are not clearly understood. Using an ambush predator, barramundi (<i>Lates calcarifer</i>), fed meals ranging 0.6–3.4% of body mass, we examined interrelations between meal size, growth efficiency and surplus aerobic metabolic capacity (aerobic scope, AS). Large meals required a greater absolute investment of energy to process (a larger so-called specific dynamic action, SDA), but the percentage of digestible meal energy required in the SDA response (SDA coefficient) decreased with increasing meal size. Combined with the findings that growth rate and growth efficiency also increased with food intake, our results demonstrate that it is energetically advantageous for fish to select large prey. However, following a large meal, SDA processes occupied up to 77% of the available AS, indicating that other oxygen-demanding activities like swimming may be compromised while large meals are processed. This trade-off between meal size and AS suggests that fishes like barramundi would benefit from regulating prey size based on imminent requirements and threats.
DOI: 10.6084/m9.figshare.5394610.v1
title: Main mode code from Quantifying the dominant growth mechanisms of dimorphic yeast using a lattice-based model

description: The core MATLAB code used to generate the simulations in this study.
DOI: 10.6084/m9.figshare.5394595
title: Driving script from Quantifying the dominant growth mechanisms of dimorphic yeast using a lattice-based model

description: MATLAB code that calls the model code to run the different scenarios considered in this study.
DOI: 10.6084/m9.figshare.5394595.v1
title: Driving script from Quantifying the dominant growth mechanisms of dimorphic yeast using a lattice-based model

description: MATLAB code that calls the model code to run the different scenarios considered in this study.
DOI: 10.6084/m9.figshare.5394568
title: Data from Paternal arbuscular mycorrhizal fungal status affects DNA methylation in seeds

description: Data file
DOI: 10.6084/m9.figshare.5394568.v1
title: Data from Paternal arbuscular mycorrhizal fungal status affects DNA methylation in seeds

description: Data file
DOI: 10.6084/m9.figshare.5394553
title: count_table.gz

description: Count table for the final model for the paper:Bertl, J.; Guo, Q.; Rasmussen, M. J.; Besenbacher, S; Nielsen, M. M.; Hornshøj, H.; Pedersen, J. S. & Hobolth, A. A Site Specific Model And Analysis Of The Neutral Somatic Mutation Rate In Whole-Genome Cancer Data.
DOI: 10.6084/m9.figshare.5394553.v2
title: count_table.gz

description: Count table for the final model for the paper:Bertl, J.; Guo, Q.; Rasmussen, M. J.; Besenbacher, S; Nielsen, M. M.; Hornshøj, H.; Pedersen, J. S. & Hobolth, A. A Site Specific Model And Analysis Of The Neutral Somatic Mutation Rate In Whole-Genome Cancer Data.
DOI: 10.6084/m9.figshare.5394538
title: The postcranial skeleton of <i>Ennatosaurus tecton</i> (Synapsida, Caseidae)

description: The postcranial material referable to the Russian caseid <i>Ennatosaurus tecton</i> from the middle Permian is described. Although the cranium has been recently restudied in detail, the descriptions currently available for the postcranial skeleton are essentially limited to the original short account on the holotype provided by Efremov in 1956. The postcranium of <i>Ennatosaurus</i> is informative with respect to both taxonomy and phylogeny, with autapomorphic characters present particularly in the vertebral column. In addition to the anatomical description of the elements presented here, eight principal component analyses were conducted to investigate the position of the various osteological elements of <i>Ennatosaurus</i> within caseid morphospace. The inclusion of members of all major groups of ‘pelycosaurs’ and selected outgroup taxa allowed us to make more extensive preliminary inferences regarding postcranial morphospace occupation of these basal synapsids for each individually considered bone. The analysis revealed a major decoupling among the morphospaces of stylopodial and zeugopodial elements, with femora and humeri showing a shared common pattern, and a wider overlap in their respective morphospace. Conversely, the ulnae, radii, tibiae and fibulae show well-separated regions of morphospace in the different clades, indicating their potential importance, not only for functional and biomechanical studies, but also for taxonomic differentiation. Finally, a 3D photogrammetric model of the mounted specimen at the Paleontological Institute in Moscow forms the basis for the first <i>in vivo</i> reconstruction of <i>Ennatosaurus tecton</i>, providing a potentially realistic picture of the Russian caseid in life.
DOI: 10.6084/m9.figshare.5394538.v1
title: The postcranial skeleton of <i>Ennatosaurus tecton</i> (Synapsida, Caseidae)

description: The postcranial material referable to the Russian caseid <i>Ennatosaurus tecton</i> from the middle Permian is described. Although the cranium has been recently restudied in detail, the descriptions currently available for the postcranial skeleton are essentially limited to the original short account on the holotype provided by Efremov in 1956. The postcranium of <i>Ennatosaurus</i> is informative with respect to both taxonomy and phylogeny, with autapomorphic characters present particularly in the vertebral column. In addition to the anatomical description of the elements presented here, eight principal component analyses were conducted to investigate the position of the various osteological elements of <i>Ennatosaurus</i> within caseid morphospace. The inclusion of members of all major groups of ‘pelycosaurs’ and selected outgroup taxa allowed us to make more extensive preliminary inferences regarding postcranial morphospace occupation of these basal synapsids for each individually considered bone. The analysis revealed a major decoupling among the morphospaces of stylopodial and zeugopodial elements, with femora and humeri showing a shared common pattern, and a wider overlap in their respective morphospace. Conversely, the ulnae, radii, tibiae and fibulae show well-separated regions of morphospace in the different clades, indicating their potential importance, not only for functional and biomechanical studies, but also for taxonomic differentiation. Finally, a 3D photogrammetric model of the mounted specimen at the Paleontological Institute in Moscow forms the basis for the first <i>in vivo</i> reconstruction of <i>Ennatosaurus tecton</i>, providing a potentially realistic picture of the Russian caseid in life.
DOI: 10.6084/m9.figshare.5394472.v1
title: Introducción a GeoGebra

description: Presentación sobre "Introducción a GeoGebra", realizado para la primera sesión del Workshop del Instituto GeoGebra de Santiago, realizado el miércoles 20 de agosto de 2014.
DOI: 10.6084/m9.figshare.5394388
title: Protein NMR spectroscopy: folded vs. unfolded protein

description: Figure showing the relationship between the 2D 1H-15N HSQC spectra of folded and unfolded proteins. The signal dispersion in the proton dimension is significantly diminished for unfolded proteins. Note that alpha-helix-rich proteins also exhibit low signal dispersion in the proton dimension; however, the example protein here contains mosts beta-strands, and therefore shows many signals &gt; 8.5 ppm.<br>The NMR spectra are of the same protein with the amino acid sequence indicated on the top. In the middle, left, the 2D 1H-15N HSQC spectrum of a folded 2x10 kDa dimer. On the right, the HSQC spectrum of the unfolded monomer. In both cases, the resonance from S156 is circled, with its position in the amino acid sequence indicated. On the bottom is the PDB file 4mjh depicting the structure of the folded dimer. On the bottom right is a structural model of an intrinsically disordered protein shown as an example. This was taken from the Protein Ensemble Database PED1AAD, with the number of residues trimmed to equal that of the folded structure (PDB 4mjh).
DOI: 10.6084/m9.figshare.5394394
title: Protein dynamics probed by methyl NMR

description: A figure depicting the timescales of biomolecular motion accessible to methyl-based nuclear spin relaxation experiments.
DOI: 10.6084/m9.figshare.5394421
title: Principal Components Analysis Results

description: res_pca_rotation is the rotation matrix that arose from a principal components analysis on our publication data from 2012-2017; it contains information about the correlation structure of each variable and each principal component. res_pca_summary contains information about the std. dev and cumulative variance for each component. This is the information we used to threshold our choice of components to 4.
DOI: 10.6084/m9.figshare.5394394.v1
title: Protein dynamics probed by methyl NMR

description: A figure depicting the timescales of biomolecular motion accessible to methyl-based nuclear spin relaxation experiments.
DOI: 10.6084/m9.figshare.5394337
title: The being of the past in the present: memory and information

description: Information as the way of the past to be availble in the present
DOI: 10.6084/m9.figshare.5394325
title: Zero or nothing Data.xlsx

description: Four experiments regarding the perception of empty frames as zeros.as described in Zero or nothing? Perceiving empty frames as null numerosity
DOI: 10.6084/m9.figshare.5394325.v1
title: Zero or nothing Data.xlsx

description: Four experiments regarding the perception of empty frames as zeros.as described in Zero or nothing? Perceiving empty frames as null numerosity
DOI: 10.6084/m9.figshare.5394337.v2
title: The being of the past in the present: memory and information

description: Information as the way of the past to be availble in the present
DOI: 10.6084/m9.figshare.5394223
title: Quantum Computing - Key Words for Orientation (2017) English and German

description: This work can only be an actual and general overview which contains possibly staying facts in Quantum Computing. A detailed, deep research is for the author not possible but treasury Search Items and Key Words besides significant topics are interesting results by their writing down. Details can be found by every reader for himself by using Search Machines. Besides the value of scientifically Orientation is important.
DOI: 10.6084/m9.figshare.5393977
title: Perspectives on invasive amphibians in Brazil

description: Two files containing spreadsheets with:1. Calculations and data about projections on distributional range (reduction or expansion) of invasive amphibians in Brazil.2. Acoustic correlation data.<br><br>
DOI: 10.6084/m9.figshare.5394223.v2
title: Quantum Computing - Key Words for Orientation (2017) English and German

description: This work can only be an actual and general overview which contains possibly staying facts in Quantum Computing. A detailed, deep research is for the author not possible but treasury Search Items and Key Words besides significant topics are interesting results by their writing down. Details can be found by every reader for himself by using Search Machines. Besides the value of scientifically Orientation is important.
DOI: 10.6084/m9.figshare.5393977.v1
title: Perspectives on invasive amphibians in Brazil

description: Two files containing spreadsheets with:1. Calculations and data about projections on distributional range (reduction or expansion) of invasive amphibians in Brazil.2. Acoustic correlation data.<br><br>
DOI: 10.6084/m9.figshare.5394223.v1
title: Quantum Computing - Key Words for Orientation (2017) English and German

description: This work can only be an actual and general overview which contains possibly staying facts in Quantum Computing. A detailed, deep research is for the author not possible but treasury Search Items and Key Words besides significant topics are interesting results by their writing down. Details can be found by every reader for himself by using Search Machines. Besides the value of scientifically Orientation is important.
DOI: 10.6084/m9.figshare.5393932
title: The interplay between selective and nonselective inhibition during single word production

description: Includes the following four folders: (1) raw data obtained from the PWI-SST, (2) R (and SPSS files) used for the statistical analyses, (3) script for the PWI-SST experiment in Presentation software, and (4) stimuli used in the PWI-SST.
DOI: 10.6084/m9.figshare.5393932.v1
title: The interaction between selective and nonselective inhibition during single word production (Vromans & Jongman)

description: Includes the following four folders: (1) raw data obtained from the PWI-SST, (2) SPSS files used for the statistical analyses, (3) script for the PWI-SST experiment in Presentation software, and (4) stimuli used in the PWI-SST.
DOI: 10.6084/m9.figshare.5393884.v2
title: PubCaseFinder: A diagnosis assistant system for rare diseases using published case reports

description: Lightning talk slides for BioHackathon17
DOI: 10.6084/m9.figshare.5393878.v1
title: BH17 LT by yamamoto

description: Slides used for my lightning talk at the BioHackathon 2017 Symposium.
DOI: 10.6084/m9.figshare.5393338
title: EEG Data

description: EEG Data
DOI: 10.6084/m9.figshare.5393323
title: Estimating Age at a Specified Length from the von Bertalanffy Growth Function

description: Estimating the time required (i.e., age) for fish in a population to reach a specific length (e.g., legal harvest length) is useful for understanding population dynamics and simulating the potential effects of length-based harvest regulations. The age at which a population reaches a specific mean length is typically estimated by fitting a von Bertalanffy growth function to length-at-age data and then rearranging the best-fit equation to solve for age at the specified length. This process precludes the use of standard frequentist methods to compute confidence intervals and compare estimates of age at the specified length among populations. We provide a parameterization of the von Bertalanffy growth function that has age at a specified length as a parameter. With this parameterization, age at a specified length is directly estimated, and standard methods can be used to construct confidence intervals and make among-group comparisons for this parameter. We demonstrate use of the new parameterization with two data sets. Received March 30, 2017; accepted June 9, 2017 Published online September 8, 2017
DOI: 10.6084/m9.figshare.5393317
title: Implanted hair-follicle-associated pluripotent (HAP) stem cells encapsulated in polyvinylidene fluoride membrane cylinders promote effective recovery of peripheral nerve injury

description: Hair follicle-associated-pluripotent (HAP) stem cells are located in the bulge area of the hair follicle, express the stem-cell marker, nestin, and have been shown to differentiate to nerve cells, glial cells, keratinocytes, smooth muscle cells, cardiac muscle cells, and melanocytes. Transplanted HAP stem cells promote the recovery of peripheral nerve and spinal cord injuries and have the potential for heart regeneration as well. In the present study, we implanted mouse green fluorescent protein (GFP)-expressing HAP stem-cell spheres encapsulated in polyvinylidene fluoride (PVDF)-membrane cylinders into the severed sciatic nerve of immunocompetent and immunocompromised (nude) mice. Eight weeks after implantation, immunofluorescence staining showed that the HAP stem cells differentiated into neurons and glial cells. Fluorescence microscopy showed that the HAP stem cell hair spheres promoted rejoining of the sciatic nerve of both immunocompetent and immunodeficient mice. Hematoxylin and eosin (H&E) staining showed that the severed scatic nerves had regenerated. Quantitative walking analysis showed that the transplanted mice recovered the ability to walk normally. HAP stem cells are readily accessible from everyone, do not form tumors, and can be cryopreserved without loss of differentiation potential. These results suggest that HAP stem cells may have greater potential than iPS or ES cells for regenerative medicine.
DOI: 10.6084/m9.figshare.5393317.v1
title: Implanted hair-follicle-associated pluripotent (HAP) stem cells encapsulated in polyvinylidene fluoride membrane cylinders promote effective recovery of peripheral nerve injury

description: Hair follicle-associated-pluripotent (HAP) stem cells are located in the bulge area of the hair follicle, express the stem-cell marker, nestin, and have been shown to differentiate to nerve cells, glial cells, keratinocytes, smooth muscle cells, cardiac muscle cells, and melanocytes. Transplanted HAP stem cells promote the recovery of peripheral nerve and spinal cord injuries and have the potential for heart regeneration as well. In the present study, we implanted mouse green fluorescent protein (GFP)-expressing HAP stem-cell spheres encapsulated in polyvinylidene fluoride (PVDF)-membrane cylinders into the severed sciatic nerve of immunocompetent and immunocompromised (nude) mice. Eight weeks after implantation, immunofluorescence staining showed that the HAP stem cells differentiated into neurons and glial cells. Fluorescence microscopy showed that the HAP stem cell hair spheres promoted rejoining of the sciatic nerve of both immunocompetent and immunodeficient mice. Hematoxylin and eosin (H&E) staining showed that the severed scatic nerves had regenerated. Quantitative walking analysis showed that the transplanted mice recovered the ability to walk normally. HAP stem cells are readily accessible from everyone, do not form tumors, and can be cryopreserved without loss of differentiation potential. These results suggest that HAP stem cells may have greater potential than iPS or ES cells for regenerative medicine.
DOI: 10.6084/m9.figshare.5393323.v1
title: Estimating Age at a Specified Length from the von Bertalanffy Growth Function

description: Estimating the time required (i.e., age) for fish in a population to reach a specific length (e.g., legal harvest length) is useful for understanding population dynamics and simulating the potential effects of length-based harvest regulations. The age at which a population reaches a specific mean length is typically estimated by fitting a von Bertalanffy growth function to length-at-age data and then rearranging the best-fit equation to solve for age at the specified length. This process precludes the use of standard frequentist methods to compute confidence intervals and compare estimates of age at the specified length among populations. We provide a parameterization of the von Bertalanffy growth function that has age at a specified length as a parameter. With this parameterization, age at a specified length is directly estimated, and standard methods can be used to construct confidence intervals and make among-group comparisons for this parameter. We demonstrate use of the new parameterization with two data sets. Received March 30, 2017; accepted June 9, 2017 Published online September 8, 2017
DOI: 10.6084/m9.figshare.5393203
title: Appendix_S2.biom

description: Operational Taxonomic Unit (OTU) table in the Biological Observation Matrix (BIOM) format associated with the following publication in the American Journal of Botany: "Fungal endophyte communities in the temperate fern <i>Polystichum munitum</i> show early colonization and extensive temporal turnover"
DOI: 10.6084/m9.figshare.5393164
title: Fonseca_etal_Ecological_Applications

description: Results of Fonseca et al. (In Press) Ecological Applications<br>