cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1536260.v13
title: Supplementary Data 3 - Study sites: location, population wing length, monitoring method, tide

description: ------------------------------------------------------------------------------------------------------<br>Description of the dataset "Supplementary Data 3 - Study sites.csv"<br>--------------------------------------------------------------------------------------------------------<br> The dataset <br> - is used in the paper "Defying the 24-h day: Unexpected diversity in socially synchronized rhythms of shorebirds - Supplementary Actograms" by Bulla et al 2016<br> - contains estimates of mean female and male wing length for each population of biparental shorebirds from a specific study site, plus the locations of the study site, whether the locations had tide, and whether the tide was used by the population for foraging, and how the incubation was monitored.<br>--------------------------------------------------------------------------------------------------------<br> Questions can be directed to: Martin Bulla (bulla.mar@gmail.com)<br>--------------------------------------------------------------------------------------------------------<br> Values are separated by comma. <br>--------------------------------------------------------------------------------------------------------<br> 1. scinam : scientific name of the species<br> 2. sp : four letter abbreviation of the species's English name<br> 3. study_site : name of the study site<br> 4. site_abbreviation : four letter abbreviation of the study site<br> 5. type : was the study site at the breeding ground (breeding) or not (wintering)<br> 6. lat : latitude of the study site (decimal)<br> 7. lon : longitude of the study site (decimal)<br> 8. tidal_habitat : is the study site at primarily tidal habitat (y=yes, n=no)<br> 9. tidal_used : if the study site is at primarily tidal habitat, do the birds use it for foraging (y=yes, n=no)<br>10. incubation_monitoring : method used to monitor incubation (for details see the paper's Extended Data Table 4)<br>11. sexing_method : identifies the method used to sex individuals to estimate the mean female and male wing length<br>12. pop_wing_f : mean female wing length for the population<br>13. f_wing_N : sample size used for the female mean estimate<br>14. pop_wing_m : mean male wing length for the population<br>15. m_wing_N : sample size used for the male mean estimate<br>16. data_source : is the mean wing estimate based on the primary data ("our primary data") or literature (citation))<br><br>--------------------------------------------------------------------------------------------------------<br><br>WHEN USING THIS DATA, PLEASE CITE:<br><br>Bulla et al (2016). Supplementary Data 3 - Study sites: location, population wing length, monitoring method, tide. <br> figshare. https://dx.doi.org/10.6084/m9.figshare.1536260. Retrieved ADD DATETIME.<br><br>--------------------------------------------------------------------------------------------------------
DOI: 10.6084/m9.figshare.1535338.v1
title: Multiscale modelling of epithelial tissue homeostasis and repair

description: Poster contribution for the CNRS - Jacques Monod Conference "Building, repairing and evolving biological tissues" held in Roscoff, France on September 13-17, 2015 (http://www.cnrs.fr/insb/cjm/2015/Vincent_e.html). This poster is based on joint work with Jochen Kursawe, Fergus Cooper and Ruth Baker at the University of Oxford and Jeremy Zartman, Cody Narciso and Pavel Brodskiy at the University of Notre Dame. Poster title: Multiscale modelling of epithelial tissue homeostasis and repair Poster abstract: The movement and organization of epithelial tissues plays a central role during development, growth, disease and wound healing. These processes occur as a result of cell adhesion, migration, division, differentiation and death, and involve multiple processes acting at the cellular and molecular level. Alongside experimental approaches, mathematical and computational modelling can help us understand what factors are involved in regulating cell- and tissue-level behaviour, and how this can go wrong. I describe our work to develop and apply multiscale modelling approaches to understand aspects of epithelial dynamics in several settings, including tissue size control in the Drosophila embryonic epidermis and tissue self-renewal and response to perturbation in the mammalian gut. I highlight the biological insights gained through this work, as well as ongoing challenges associated with such multiscale modelling approaches. Here are full details of the references listed in the poster: 1. J. Kursawe, P. Brodskiy, J. Zartman, R. Baker, A. Fletcher. Capabilities and limitations of tissue size control through passive mechanical forces. bioRxiv doi: http://dx.doi.org/10.1101/023184 2. A. Fletcher, M. Osterfield, R. Baker and S. Shvartsman (2014). Vertex models of epithelial morphogenesis. Biophys. J. 106:2291-2304.<br>3. A. Fletcher, J. Osborne, P. Maini and D. Gavaghan (2013). Implementing vertex dynamics models of cell populations in biology within a consistent computational framework. Prog. Biophys. Mol. Biol. 113(2):299-326.<br>4. C. Narciso, P. Brodskiy, G. Garston, R. Baker, A. Fletcher, J. Zartman (2015). Patterning of wound-induced intercellular Ca2+ flashes in a developing epithelium. Phys. Biol. 12(5):056005.<br>5. G. Mirams, C. Arthurs, M. Bernabeu, R. Bordas, J. Cooper, A. Corrias, Y. Davit, S-J. Dunn, A. Fletcher, D. Harvey, M. Marsh, J. Osborne, P. Pathmanathan, J. Pitt-Francis, J. Southern, N. Zemzemi and D. Gavaghan (2013). Chaste: an open source C++ library for computational physiology and biology. PLoS Comput. Biol. 9:e1002970.<br>6. J. Osborne, M. Bernabeu, M. Bruna, B. Calderhead, J. Cooper, N. Dalchau, S.-J. Dunn, A. Fletcher, R. Freeman, D. Groen, B. Knapp, G.J. McInerny, G. Mirams, J. Pitt-Francis, B. Sengupta, D. Wright, C. Yates, D.JGavaghan, S. Emmott and C. Deane (2014). Ten simple rules for effective computational research. PLOS Comput. Biol. 10(3):e1003506.
DOI: 10.6084/m9.figshare.1534721
title: protective role of surfactant protein D in ocular Staphylococcus aureus infection

description: Staphylococcus aureus is one of the most common pathogens causing keratitis. Surfactant protein D (SP-D) plays a critical role in host defense and innate immunity. In order to investigate the role of SP-D in ocular S. aureus infection, the eyes of wild-type (WT) and SP-D knockout (SP-D KO) C57BL/6 mice were infected with S. aureus (107 CFU/eye) in the presence and absence of cysteine protease inhibitor (E64). Bacterial counts in the ocular surface were examined 3, 6, 12, 24 hrs after infection. Bacterial phagocytosis by neutrophils and bacterial invasion in ocular epithelial cells were evaluated quantitatively. S. aureus-induced ocular injury was determined with corneal fluorescein staining. The results demonstrated that SP-D is expressed in ocular surface epithelium and the lacrimal gland; WT mice had increased clearance of S. aureus from the ocular surface (p&lt;0.05) and reduced ocular injury compared with SP-D KO mice. The protective effects of SP-D include increased bacterial phagocytosis by neutrophils (p&lt;0.05) and decreased bacterial invasion into epithelial cells (p&lt;0.05) in WT mice compared to in SP-D KO mice. In the presence of inhibitor (E64), WT mice showed enhanced bacterial clearance (p&lt;0.05) and reduced ocular injury compared to absent E64 while SP-D KO mice did not. Collectively, we concluded that SP-D protects the ocular surface from S. aureus infection but cysteine protease impairs SP-D function in this murine model, and that cysteine protease inhibitor may be a potential therapeutic agent in S. aureus keratitis.
DOI: 10.6084/m9.figshare.1535359.v2
title: The Explorer Islamabad Issue 8

description: The Explorer Islamabad August issue
DOI: 10.6084/m9.figshare.1536260.v14
title: Supplementary Data 3 - Study sites: location, population wing length, monitoring method, tide

description: ------------------------------------------------------------------------------------------------------<br>Description of the dataset "Supplementary Data 3 - Study sites.csv"<br>--------------------------------------------------------------------------------------------------------<br> The dataset <br> - is used in the paper "Defying the 24-h day: Unexpected diversity in socially synchronized rhythms of shorebirds - Supplementary Actograms" by Bulla et al 2016<br> - contains estimates of mean female and male wing length for each population of biparental shorebirds from a specific study site, plus the locations of the study site, whether the locations had tide, and whether the tide was used by the population for foraging, and how the incubation was monitored.<br>--------------------------------------------------------------------------------------------------------<br> Questions can be directed to: Martin Bulla (bulla.mar@gmail.com)<br>--------------------------------------------------------------------------------------------------------<br> Values are separated by comma. <br>--------------------------------------------------------------------------------------------------------<br> 1. scinam : scientific name of the species<br> 2. sp : four letter abbreviation of the species's English name<br> 3. study_site : name of the study site<br> 4. site_abbreviation : four letter abbreviation of the study site<br> 5. type : was the study site at the breeding ground (breeding) or not (wintering)<br> 6. lat : latitude of the study site (decimal)<br> 7. lon : longitude of the study site (decimal)<br> 8. tidal_habitat : is the study site at primarily tidal habitat (y=yes, n=no)<br> 9. tidal_used : if the study site is at primarily tidal habitat, do the birds use it for foraging (y=yes, n=no)<br>10. incubation_monitoring : method used to monitor incubation (for details see the paper's Extended Data Table 4)<br>11. sexing_method : identifies the method used to sex individuals to estimate the mean female and male wing length<br>12. pop_wing_f : mean female wing length for the population<br>13. f_wing_N : sample size used for the female mean estimate<br>14. pop_wing_m : mean male wing length for the population<br>15. m_wing_N : sample size used for the male mean estimate<br>16. data_source : is the mean wing estimate based on the primary data ("our primary data") or literature (citation))<br><br>--------------------------------------------------------------------------------------------------------<br><br>WHEN USING THIS DATA, PLEASE CITE:<br><br>Bulla et al (2016). Supplementary Data 3 - Study sites: location, population wing length, monitoring method, tide. <br> figshare. https://dx.doi.org/10.6084/m9.figshare.1536260. Retrieved ADD DATETIME.<br><br>--------------------------------------------------------------------------------------------------------
DOI: 10.6084/m9.figshare.1534714
title: 3-D histology volume reconstructions of axonal tract tracing data

description: 3-D histology reconstructions supporting the study Three-dimensional histology volume reconstruction of axonal tract tracing data: exploring topographical organization in subcortical projections from rat barrel cortex (Zakiewicz et al., 2015, PLoS One). We share volumetric reconstructions of histological images from 4 tract-tracing experiments derived from the Rodent Brain Workbench (www.rbwb.org), see Whole Brain Connectivity Atlas; 2-D image repository. The original experimental material is described in Zakiewicz et al. (2011, PLoS One, 6(8):e22669), while technical details are provided in Zakiewicz et al. (2015, PLoS One). The image volumes are in Neuroimaging Informatics Technology Initiative (NIfTI) format. RE-USE OF THESE DATA is allowed provided that reference is given to the following publication: Zakiewicz IM, Majka P, Wójcik DK, Bjaalie JG, Leergaard TB. Three-dimensional histology volume reconstruction of axonal tract tracing data: exploring topographical organization in subcortical projections from rat barrel cortex. PLoS ONE, 2015.
DOI: 10.6084/m9.figshare.1534714.v1
title: 3-D histology volume reconstructions of axonal tract tracing data

description: 3-D histology reconstructions supporting the study Three-dimensional histology volume reconstruction of axonal tract tracing data: exploring topographical organization in subcortical projections from rat barrel cortex (Zakiewicz et al., 2015, PLoS One). We share volumetric reconstructions of histological images from 4 tract-tracing experiments derived from the Rodent Brain Workbench (www.rbwb.org), see Whole Brain Connectivity Atlas; 2-D image repository. The original experimental material is described in Zakiewicz et al. (2011, PLoS One, 6(8):e22669), while technical details are provided in Zakiewicz et al. (2015, PLoS One). The image volumes are in Neuroimaging Informatics Technology Initiative (NIfTI) format. RE-USE OF THESE DATA is allowed provided that reference is given to the following publication: Zakiewicz IM, Majka P, Wójcik DK, Bjaalie JG, Leergaard TB. Three-dimensional histology volume reconstruction of axonal tract tracing data: exploring topographical organization in subcortical projections from rat barrel cortex. PLoS ONE, 2015.
DOI: 10.6084/m9.figshare.1534717
title: Impacts of Droplet Activation on Fast and Slow Responses in a Coupled Aerosol-Climate Model

description: Several “activation parameterizations” are available for researchers to use when coupling aerosol models to cloud microphysical schemes in global models. While these schemes often perform adequately in offline simulations, the input parameters supplied by a coupled global model may yield a biased sample of aerosol properties and meteorological conditions. In some situations, this could grossly skew the resulting cloud microphysical properties simulated by the global model. By applying a suite of activation parameterizations to a new coupled aerosol- climate model (including a novel statistical emulation of a detailed parcel model), we assess the model’s sensitivity to the base state cloud droplet number distributions in the context of present day vs pre-industrial aerosol and precursor emissions scenarios by analyzing fast responses. Equilibrium simulations are currently in progress.
DOI: 10.6084/m9.figshare.1535359.v1
title: The Explorer Islamabad

description: The Explorer Islamabad August issue
DOI: 10.6084/m9.figshare.1534695
title: Bulk leaf carbon and nitrogen stable isotope composition in eight conifer species in the Priest River Experimental Forest

description: Bulk leaf carbon and nitrogen stable isotope composition, specific leaf area, nitrogen and carbon concentration for eight conifer species in the Priest River Experimental Forest, Idaho, USA. These data were used in the paper: Duursma, R.A., Marshall, J.D., 2006. Vertical canopy gradients in δ13C correspond with leaf nitrogen content in a mixed-species conifer forest. Trees 20, 496–506. Variables: species - abgr (Abies grandis), abla (Abies lasiocarpa), laoc (Larix occidentalis), pico (Pinus contorta), pimo (Pinus monticola), pipo (Pinus ponderosa), psme (Pseudotsuga menziesii), thpl (Thuja plicata), tshe (Tsuga heterophylla)<br>plot - one of 22 90x90m plots in the Priest River Experimental Forest<br>subplot - one of (up to) five subplots in the plot.<br>elev90 - Altitude (m asl) from a 90m DEM.<br>treenr - unique tree number<br>loc - sampling location (either low, mid or top of the crown)<br>year - 2001 or 2002<br>DOY - day of year of sampling<br>totheight - total tree height (m)<br>hcb - height to crown base (m)<br>dbh - diameter at breast height (cm)<br>height - height of the leaf sample (m)<br>delta15 - nitrogen stable isotope composition (permil)<br>nperc - nitrogen percent by dry mass (%)<br>delta13 - carbon stable isotope composition (permil)<br>cperc - carbon percent by dry mass (%)<br>SLA - specific leaf area (cm g-1)<br>narea - nitrogen per unit area (g m-2)
DOI: 10.6084/m9.figshare.1534721.v1
title: protective role of surfactant protein D in ocular Staphylococcus aureus infection

description: Staphylococcus aureus is one of the most common pathogens causing keratitis. Surfactant protein D (SP-D) plays a critical role in host defense and innate immunity. In order to investigate the role of SP-D in ocular S. aureus infection, the eyes of wild-type (WT) and SP-D knockout (SP-D KO) C57BL/6 mice were infected with S. aureus (107 CFU/eye) in the presence and absence of cysteine protease inhibitor (E64). Bacterial counts in the ocular surface were examined 3, 6, 12, 24 hrs after infection. Bacterial phagocytosis by neutrophils and bacterial invasion in ocular epithelial cells were evaluated quantitatively. S. aureus-induced ocular injury was determined with corneal fluorescein staining. The results demonstrated that SP-D is expressed in ocular surface epithelium and the lacrimal gland; WT mice had increased clearance of S. aureus from the ocular surface (p&lt;0.05) and reduced ocular injury compared with SP-D KO mice. The protective effects of SP-D include increased bacterial phagocytosis by neutrophils (p&lt;0.05) and decreased bacterial invasion into epithelial cells (p&lt;0.05) in WT mice compared to in SP-D KO mice. In the presence of inhibitor (E64), WT mice showed enhanced bacterial clearance (p&lt;0.05) and reduced ocular injury compared to absent E64 while SP-D KO mice did not. Collectively, we concluded that SP-D protects the ocular surface from S. aureus infection but cysteine protease impairs SP-D function in this murine model, and that cysteine protease inhibitor may be a potential therapeutic agent in S. aureus keratitis.
DOI: 10.6084/m9.figshare.1536260.v16
title: Supplementary Data 3 - Study sites: location, population wing length, monitoring method, tide

description: ------------------------------------------------------------------------------------------------------<br>Description of the dataset "Supplementary Data 3 - Study sites.csv"<br>--------------------------------------------------------------------------------------------------------<br> The dataset <br> - is used in the paper "Unexpected diversity in socially synchronized rhythms of shorebirds" Nature 2016 by M. Bulla et al<br> - contains estimates of mean female and male wing length for each population of biparental shorebirds from a specific study site, plus the locations of the study site, whether the locations had tide, and whether the tide was used by the population for foraging, and how the incubation was monitored.<br>--------------------------------------------------------------------------------------------------------<br> Questions can be directed to: Martin Bulla (bulla.mar@gmail.com)<br>--------------------------------------------------------------------------------------------------------<br> Values are separated by comma. <br>--------------------------------------------------------------------------------------------------------<br> 1. scinam : scientific name of the species<br> 2. sp : four letter abbreviation of the species's English name<br> 3. study_site : name of the study site<br> 4. site_abbreviation : four letter abbreviation of the study site<br> 5. type : was the study site at the breeding ground (breeding) or not (wintering)<br> 6. lat : latitude of the study site (decimal)<br> 7. lon : longitude of the study site (decimal)<br> 8. tidal_habitat : is the study site at primarily tidal habitat (y=yes, n=no)<br> 9. tidal_used : if the study site is at primarily tidal habitat, do the birds use it for foraging (y=yes, n=no)<br>10. incubation_monitoring : method used to monitor incubation (for details see the paper's Extended Data Table 4)<br>11. sexing_method : identifies the method used to sex individuals to estimate the mean female and male wing length<br>12. pop_wing_f : mean female wing length for the population<br>13. f_wing_N : sample size used for the female mean estimate<br>14. pop_wing_m : mean male wing length for the population<br>15. m_wing_N : sample size used for the male mean estimate<br>16. data_source : is the mean wing estimate based on the primary data ("our primary data") or literature (citation))<br><br>--------------------------------------------------------------------------------------------------------<br><br>WHEN USING THIS DATA, PLEASE CITE:<br><br>Bulla et al (2016). Supplementary Data 3 - Study sites: location, population wing length, monitoring method, tide. <br> figshare. https://doi.org/10.6084/m9.figshare.1536260. Retrieved ADD DATETIME.<br><br>--------------------------------------------------------------------------------------------------------
DOI: 10.6084/m9.figshare.1534694
title: Supplemental files: "Food for thought: Mathematical approaches for the conversion of high-resolution sclerochronological oxygen isotope records into sub-annually resolved time series"

description: Supplement R code and Excel worksheets demonstrating the fitting of various models to sclerochronological records and interpretation of isotope-derived water temperature time series. Accompanies manuscript by Müller et al. (submitted) Food for thought: Mathematical approaches for the conversion of high-resolution sclerochronological oxygen isotope records into sub-annually resolved time series. Palaeogeography, Palaeoclimatology, Palaeoecology
DOI: 10.6084/m9.figshare.1534717.v1
title: Impacts of Droplet Activation on Fast and Slow Responses in a Coupled Aerosol-Climate Model

description: Several “activation parameterizations” are available for researchers to use when coupling aerosol models to cloud microphysical schemes in global models. While these schemes often perform adequately in offline simulations, the input parameters supplied by a coupled global model may yield a biased sample of aerosol properties and meteorological conditions. In some situations, this could grossly skew the resulting cloud microphysical properties simulated by the global model. By applying a suite of activation parameterizations to a new coupled aerosol- climate model (including a novel statistical emulation of a detailed parcel model), we assess the model’s sensitivity to the base state cloud droplet number distributions in the context of present day vs pre-industrial aerosol and precursor emissions scenarios by analyzing fast responses. Equilibrium simulations are currently in progress.
DOI: 10.6084/m9.figshare.1534695.v1
title: Bulk leaf carbon and nitrogen stable isotope composition in eight conifer species in the Priest River Experimental Forest

description: Bulk leaf carbon and nitrogen stable isotope composition, specific leaf area, nitrogen and carbon concentration for eight conifer species in the Priest River Experimental Forest, Idaho, USA. These data were used in the paper: Duursma, R.A., Marshall, J.D., 2006. Vertical canopy gradients in δ13C correspond with leaf nitrogen content in a mixed-species conifer forest. Trees 20, 496–506. Variables: species - abgr (Abies grandis), abla (Abies lasiocarpa), laoc (Larix occidentalis), pico (Pinus contorta), pimo (Pinus monticola), pipo (Pinus ponderosa), psme (Pseudotsuga menziesii), thpl (Thuja plicata), tshe (Tsuga heterophylla)<br>plot - one of 22 90x90m plots in the Priest River Experimental Forest<br>subplot - one of (up to) five subplots in the plot.<br>elev90 - Altitude (m asl) from a 90m DEM.<br>treenr - unique tree number<br>loc - sampling location (either low, mid or top of the crown)<br>year - 2001 or 2002<br>DOY - day of year of sampling<br>totheight - total tree height (m)<br>hcb - height to crown base (m)<br>dbh - diameter at breast height (cm)<br>height - height of the leaf sample (m)<br>delta15 - nitrogen stable isotope composition (permil)<br>nperc - nitrogen percent by dry mass (%)<br>delta13 - carbon stable isotope composition (permil)<br>cperc - carbon percent by dry mass (%)<br>SLA - specific leaf area (cm g-1)<br>narea - nitrogen per unit area (g m-2)