cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5705968
title: Manual nerve tracing files

description: These are the raw manual nerve tracing files corresponding to the subbasal nerve plexus mosaics of the same name. The files are in 'ndf' format, suitable for opening with the NeuronJ plugin to ImageJ. The nerve tracings can be used to generate nerve parameter data from within ImageJ/NeuronJ, or by analyzing with other algorithms.
DOI: 10.6084/m9.figshare.5705812
title: Sex specific data from The relationship between telomere length and mortality risk in non-model vertebrate systems: a meta-analysis

description: Telomere length (TL) has become a biomarker of increasing interest within ecology and evolutionary biology, and has been found to predict subsequent survival in some recent avian studies but not others. Here, we undertake the first formal meta-analysis to test whether there is an overall association between TL and subsequent mortality risk in vertebrates other than humans and model laboratory rodents. We identified 27 suitable studies and obtained standardized estimates of the hazard ratio associated with TL from each. We performed a meta-analysis on these estimates and found an overall significant negative association implying that short telomeres are associated with increased mortality risk, which was robust to evident publication bias. While we found that heterogeneity in the hazard ratios was not explained by sex, follow-up period, maximum lifespan or the age group of the study animals, the TL–mortality risk association was stronger in studies using qPCR compared to terminal restriction fragment methodologies. Our results provide support for a consistent association between short telomeres and increased mortality risk in birds, but also highlight the need for more research into non-avian vertebrates and the reasons why different telomere measurement methods may yield different results.This article is part of the theme issue ‘Understanding diversity in telomere dynamics’.
DOI: 10.6084/m9.figshare.5705812.v1
title: Sex specific data from The relationship between telomere length and mortality risk in non-model vertebrate systems: a meta-analysis

description: Telomere length (TL) has become a biomarker of increasing interest within ecology and evolutionary biology, and has been found to predict subsequent survival in some recent avian studies but not others. Here, we undertake the first formal meta-analysis to test whether there is an overall association between TL and subsequent mortality risk in vertebrates other than humans and model laboratory rodents. We identified 27 suitable studies and obtained standardized estimates of the hazard ratio associated with TL from each. We performed a meta-analysis on these estimates and found an overall significant negative association implying that short telomeres are associated with increased mortality risk, which was robust to evident publication bias. While we found that heterogeneity in the hazard ratios was not explained by sex, follow-up period, maximum lifespan or the age group of the study animals, the TL–mortality risk association was stronger in studies using qPCR compared to terminal restriction fragment methodologies. Our results provide support for a consistent association between short telomeres and increased mortality risk in birds, but also highlight the need for more research into non-avian vertebrates and the reasons why different telomere measurement methods may yield different results.This article is part of the theme issue ‘Understanding diversity in telomere dynamics’.
DOI: 10.6084/m9.figshare.5705809
title: Data from The relationship between telomere length and mortality risk in non-model vertebrate systems: a meta-analysis

description: Telomere length (TL) has become a biomarker of increasing interest within ecology and evolutionary biology, and has been found to predict subsequent survival in some recent avian studies but not others. Here, we undertake the first formal meta-analysis to test whether there is an overall association between TL and subsequent mortality risk in vertebrates other than humans and model laboratory rodents. We identified 27 suitable studies and obtained standardized estimates of the hazard ratio associated with TL from each. We performed a meta-analysis on these estimates and found an overall significant negative association implying that short telomeres are associated with increased mortality risk, which was robust to evident publication bias. While we found that heterogeneity in the hazard ratios was not explained by sex, follow-up period, maximum lifespan or the age group of the study animals, the TL–mortality risk association was stronger in studies using qPCR compared to terminal restriction fragment methodologies. Our results provide support for a consistent association between short telomeres and increased mortality risk in birds, but also highlight the need for more research into non-avian vertebrates and the reasons why different telomere measurement methods may yield different results.This article is part of the theme issue ‘Understanding diversity in telomere dynamics’.
DOI: 10.6084/m9.figshare.5705809.v1
title: Data from The relationship between telomere length and mortality risk in non-model vertebrate systems: a meta-analysis

description: Telomere length (TL) has become a biomarker of increasing interest within ecology and evolutionary biology, and has been found to predict subsequent survival in some recent avian studies but not others. Here, we undertake the first formal meta-analysis to test whether there is an overall association between TL and subsequent mortality risk in vertebrates other than humans and model laboratory rodents. We identified 27 suitable studies and obtained standardized estimates of the hazard ratio associated with TL from each. We performed a meta-analysis on these estimates and found an overall significant negative association implying that short telomeres are associated with increased mortality risk, which was robust to evident publication bias. While we found that heterogeneity in the hazard ratios was not explained by sex, follow-up period, maximum lifespan or the age group of the study animals, the TL–mortality risk association was stronger in studies using qPCR compared to terminal restriction fragment methodologies. Our results provide support for a consistent association between short telomeres and increased mortality risk in birds, but also highlight the need for more research into non-avian vertebrates and the reasons why different telomere measurement methods may yield different results.This article is part of the theme issue ‘Understanding diversity in telomere dynamics’.
DOI: 10.6084/m9.figshare.5705641
title: Cephalopod products

description: Raw sequences of cephalopod products for molecular traceability.<br>
DOI: 10.6084/m9.figshare.5705638
title: Reservoir inflow at Florence Lake and Lake Thomas A. Edison in California, meteorological variables at weather stations KSP, VLC, UBC, TMR and HTT for water year 2010-14 and WRF-Chem Simulations of meteorological variables for two aerosol scenarios at Big Creek Hydroelectric project for water year 2013 and 2014

description: Data set describes daily inflows (cu ft/cc) at Florence Lake and Lake Thomas A. Edison at the Big Creek Hydroelectric System in California for water year 2010-2014.<br><br>Data set contains daily values of temperature (degree Fahrenheit), snow water equivalent (inch) and precipitation (inch) observed at Kaiser Point (KSP), Volcanic knob (VLC), Upper Brunt coral (UBC), Tamarack summit (TMR) and Huntington Lake (HNT) weather stations in California. Data have been provided for water year 2010-14. Meteorological data have been collected from California Data Exchange Center<br> <br>WRF_Chem simulations of the three meteorological variables for two aerosol scenarios- CTRL and CLEAN (with and without aerosol) are provided for a 0.4<sup>o</sup>*0.4<sup>o</sup> grid box with center at (32.37<sup>o</sup>N,-118.97<sup>o</sup>E) for water year 2013 and 2014. The simulations are conducted by Jet Propulsion Laboratory (JPL). <br>
DOI: 10.6084/m9.figshare.5705608
title: Scapular kinematic reconstruction – segmental optimization, multibody optimization with open-loop or closed-loop chains: which one should be preferred?

description: Several numerical approaches have been developed to address the soft tissue artefact, such as the segmental optimization and multibody kinematics optimizations using either open-loop or closed-loop chains. However, it is still not clear which method is the most efficient for scapular kinematics reconstruction. In this study, six kinematic models were compared to a silver standard, i.e. a scapula palpator, during a series of 55 postures with maximal amplitudes of both the arm and scapula performed by 15 subjects. The most accurate approaches were the multibody optimization with a closed-loop chain and the segmental optimization. They provided averaged scapula misorientations of 14.9 ± 6.7° and 16 ± 7.1, respectively. Regarding the closed-loop chain integrating a point-to-ellipsoid scapulothoracic joint, the ellipsoid providing the most accurate results was a thorax-size ellipsoid fitting the area browsed by the scapula. Eventually, considering the high implementation costs of a multibody kinematics optimization, the segmental optimization could be considered as appropriate for scapular kinematics reconstruction.
DOI: 10.6084/m9.figshare.5705557
title: Morphometrics of <i>Leptoplastides marianus</i> (Hoek) (Trilobita, Olenidae) from the Tremadocian of north-western Argentina: taxonomic implications

description: Morphometrics can be an important tool in systematic studies, providing taxonomists with strong elements of quantification and formal hypothesis testing. Here, these tools are tested for the trilobite <i>Leptoplastides marianus</i> (Hoek) which was originally described on the basis of three deformed specimens from west Tarija, Bolivia. Following the conclusions of Harrington & Leanza, a wide range of morphological variation is accepted for this species, and the name was applied to a large number of specimens from north-western Argentina. Based on specimens collected from the quebrada Moya (Huacalera, Jujuy), as well as on material in the Harrington & Leanza collections in the University of Buenos Aires, traditional morphometric and geometric morphometric methods were used to evaluate the variation of the cranidial shape of <i>L. marianus</i> sensu Harrington & Leanza. The results allow discrimination between two clearly different morphotypes. The name <i>L. marianus</i> should be restricted to the type specimens, given the deformation of these materials. In addition, <i>L. argentinensis</i> and <i>L. granulosus</i> are both valid names for the two morphotypes recognized in the present paper.
DOI: 10.6084/m9.figshare.5705557.v1
title: Morphometrics of <i>Leptoplastides marianus</i> (Hoek) (Trilobita, Olenidae) from the Tremadocian of north-western Argentina: taxonomic implications

description: Morphometrics can be an important tool in systematic studies, providing taxonomists with strong elements of quantification and formal hypothesis testing. Here, these tools are tested for the trilobite <i>Leptoplastides marianus</i> (Hoek) which was originally described on the basis of three deformed specimens from west Tarija, Bolivia. Following the conclusions of Harrington & Leanza, a wide range of morphological variation is accepted for this species, and the name was applied to a large number of specimens from north-western Argentina. Based on specimens collected from the quebrada Moya (Huacalera, Jujuy), as well as on material in the Harrington & Leanza collections in the University of Buenos Aires, traditional morphometric and geometric morphometric methods were used to evaluate the variation of the cranidial shape of <i>L. marianus</i> sensu Harrington & Leanza. The results allow discrimination between two clearly different morphotypes. The name <i>L. marianus</i> should be restricted to the type specimens, given the deformation of these materials. In addition, <i>L. argentinensis</i> and <i>L. granulosus</i> are both valid names for the two morphotypes recognized in the present paper.
DOI: 10.6084/m9.figshare.5705554
title: Species of <i>Hollinella</i> (Palaeocopida: Ostracoda: Crustacea) as stratigraphical indices of the Late Permian–Early Triassic post-extinction interval

description: Members of the ostracod order Palaeocopida, except three very rare genera (Puncia, Manawa and Promanawa), disappeared from the stratigraphical record close to the Permian–Triassic boundary (PTB) event. Species of the genus <i>Hollinella</i> are often present just after the end-Palaeozoic mass extinction event, in latest Permian and earliest Triassic beds. They are among the last representatives of Palaeocopida, the typical Palaeozoic straight dorsal border ostracods. The Early Triassic species have been assigned by most authors to <i>Hollinella tingi</i> (Patte, 1935), but this assignment is incorrect. This species is present in the latest Permian and the earliest Triassic, and therefore is considered a biostratigraphical index fossil of the post-mass extinction interval. A revision of <i>Hollinella</i> species from this interval is presented here. Three <i>Hollinella</i> species occur in the earliest Triassic: <i>H. panxiensis</i> Wang, 1978; <i>H. magninoda</i> Wang, 1978; and <i>Hollinella</i> (<i>Hollinella</i>) <i>lungcamensis</i> Crasquin sp. nov. The new species of the post-PTB event is present in strata exposed in the northern part of Vietnam. All three species of <i>Hollinella</i> cross the PTB and <i>H.</i> (<i>H.</i>) <i>lungcamensis</i> is characteristic of the post-extinction period (latest Changhsingian–earliest Induan). http://zoobank.org/urn:lsid:zoobank.org:pub:C8BA4418-B7FE-4B28-ADA0-28BE317687A4
DOI: 10.6084/m9.figshare.5705554.v1
title: Species of <i>Hollinella</i> (Palaeocopida: Ostracoda: Crustacea) as stratigraphical indices of the Late Permian–Early Triassic post-extinction interval

description: Members of the ostracod order Palaeocopida, except three very rare genera (Puncia, Manawa and Promanawa), disappeared from the stratigraphical record close to the Permian–Triassic boundary (PTB) event. Species of the genus <i>Hollinella</i> are often present just after the end-Palaeozoic mass extinction event, in latest Permian and earliest Triassic beds. They are among the last representatives of Palaeocopida, the typical Palaeozoic straight dorsal border ostracods. The Early Triassic species have been assigned by most authors to <i>Hollinella tingi</i> (Patte, 1935), but this assignment is incorrect. This species is present in the latest Permian and the earliest Triassic, and therefore is considered a biostratigraphical index fossil of the post-mass extinction interval. A revision of <i>Hollinella</i> species from this interval is presented here. Three <i>Hollinella</i> species occur in the earliest Triassic: <i>H. panxiensis</i> Wang, 1978; <i>H. magninoda</i> Wang, 1978; and <i>Hollinella</i> (<i>Hollinella</i>) <i>lungcamensis</i> Crasquin sp. nov. The new species of the post-PTB event is present in strata exposed in the northern part of Vietnam. All three species of <i>Hollinella</i> cross the PTB and <i>H.</i> (<i>H.</i>) <i>lungcamensis</i> is characteristic of the post-extinction period (latest Changhsingian–earliest Induan). http://zoobank.org/urn:lsid:zoobank.org:pub:C8BA4418-B7FE-4B28-ADA0-28BE317687A4
DOI: 10.6084/m9.figshare.5705548
title: Supplementary Material for: Differential Kinetics of Aspergillus nidulans and Aspergillus fumigatus Phagocytosis

description: Invasive aspergillosis mainly occurs in immunocompromised patients and is commonly caused by <i>Aspergillus fumigatus</i>, while <i>A.</i><i>nidulans</i> is rarely the causative agent. However, in chronic granulomatous disease (CGD) patients, <i>A. nidulans</i> is a frequent cause of invasive aspergillosis and is associated with higher mortality. Immune recognition of <i>A. nidulans </i>was compared to <i>A. fumigatus </i>to offer an insight into why <i>A. nidulans</i> infections are prevalent in CGD. Live cell imaging with J774A.1 macrophage-like cells and LC3-GFP-mCherry bone marrow-derived macrophages (BMDMs) revealed that phagocytosis of <i>A. nidulans </i>was slower compared to <i>A. fumigatus</i>. This difference could be attributed to slower migration of J774A.1 cells and a lower percentage of migrating BMDMs. In addition, delayed phagosome acidification and LC3-associated phagocytosis was observed with <i>A. nidulans</i>. Cytokine and oxidative burst measurements in human peripheral blood mononuclear cells revealed a lower oxidative burst upon challenge with <i>A. nidulans</i>. In contrast, <i>A. nidulans</i> induced significantly higher concentrations of cytokines. Collectively, our data demonstrate that <i>A. nidulans </i>is phagocytosed and processed at a slower rate compared to <i>A. fumigatus,</i> resulting in reduced fungal killing and increased germination of conidia. This slower rate of <i>A. nidulans</i> clearance may be permissive for overgrowth within certain immune settings.
DOI: 10.6084/m9.figshare.5705548.v1
title: Supplementary Material for: Differential Kinetics of Aspergillus nidulans and Aspergillus fumigatus Phagocytosis

description: Invasive aspergillosis mainly occurs in immunocompromised patients and is commonly caused by <i>Aspergillus fumigatus</i>, while <i>A.</i><i>nidulans</i> is rarely the causative agent. However, in chronic granulomatous disease (CGD) patients, <i>A. nidulans</i> is a frequent cause of invasive aspergillosis and is associated with higher mortality. Immune recognition of <i>A. nidulans </i>was compared to <i>A. fumigatus </i>to offer an insight into why <i>A. nidulans</i> infections are prevalent in CGD. Live cell imaging with J774A.1 macrophage-like cells and LC3-GFP-mCherry bone marrow-derived macrophages (BMDMs) revealed that phagocytosis of <i>A. nidulans </i>was slower compared to <i>A. fumigatus</i>. This difference could be attributed to slower migration of J774A.1 cells and a lower percentage of migrating BMDMs. In addition, delayed phagosome acidification and LC3-associated phagocytosis was observed with <i>A. nidulans</i>. Cytokine and oxidative burst measurements in human peripheral blood mononuclear cells revealed a lower oxidative burst upon challenge with <i>A. nidulans</i>. In contrast, <i>A. nidulans</i> induced significantly higher concentrations of cytokines. Collectively, our data demonstrate that <i>A. nidulans </i>is phagocytosed and processed at a slower rate compared to <i>A. fumigatus,</i> resulting in reduced fungal killing and increased germination of conidia. This slower rate of <i>A. nidulans</i> clearance may be permissive for overgrowth within certain immune settings.
DOI: 10.6084/m9.figshare.5705479
title: Upper Quarter Y Balance Test

description: Normative data and reliability of the Upper Quarter Y Balance Test
DOI: 10.6084/m9.figshare.5705479.v1
title: Upper Quarter Y Balance Test

description: Normative data and reliability of the Upper Quarter Y Balance Test
DOI: 10.6084/m9.figshare.5705476
title: Supplementary Material for: Optical Coherence Tomography: Clinicopathologic Correlations - The 2016 Gordon K. Klintworth Lecture

description: <b><i>Background/Aims:</i></b> Spectral domain optical coherence tomography (SD-OCT) has become a mainstay of ophthalmic practice that has revolutionized the assessment and treatment of a variety of ocular disorders. Studies that directly correlate SD-OCT and histopathology are necessary to demonstrate the actual nature of the retinal pathology responsible for the images that resemble histologic sections, but are generated by mathematical algorithms. <b><i>Methods:</i></b> Careful correlative light microscopy was performed on a small number of eyes undergoing enucleation for intraocular tumors that had pertinent findings imaged by SD-OCT. Expeditious processing and a fixation technique that prevented retinal detachment minimized tissue distortion and sectioning artifact. <b><i>Results:</i></b> The retinal layers disclosed by SD-OCT images do not correspond directly to light microscopy. Photoreceptor ellipsoids can persist in foveal detachments without a distinct ellipsoid band in corresponding SD-OCT images. Lipidized histiocytes can appear as bright hyperreflective spots, and clumps of subretinal macrophages as “shaggy photoreceptors” overlying choroidal tumors. <b><i>Conclusion:</i></b> The meaningful interpretation of SD-OCT's striking visual imagery requires a firm foundation in ocular histology and pathology. The accuracy of interpretation can be improved by correlative studies that directly compare OCT and histopathology.
DOI: 10.6084/m9.figshare.5705476.v1
title: Supplementary Material for: Optical Coherence Tomography: Clinicopathologic Correlations - The 2016 Gordon K. Klintworth Lecture

description: <b><i>Background/Aims:</i></b> Spectral domain optical coherence tomography (SD-OCT) has become a mainstay of ophthalmic practice that has revolutionized the assessment and treatment of a variety of ocular disorders. Studies that directly correlate SD-OCT and histopathology are necessary to demonstrate the actual nature of the retinal pathology responsible for the images that resemble histologic sections, but are generated by mathematical algorithms. <b><i>Methods:</i></b> Careful correlative light microscopy was performed on a small number of eyes undergoing enucleation for intraocular tumors that had pertinent findings imaged by SD-OCT. Expeditious processing and a fixation technique that prevented retinal detachment minimized tissue distortion and sectioning artifact. <b><i>Results:</i></b> The retinal layers disclosed by SD-OCT images do not correspond directly to light microscopy. Photoreceptor ellipsoids can persist in foveal detachments without a distinct ellipsoid band in corresponding SD-OCT images. Lipidized histiocytes can appear as bright hyperreflective spots, and clumps of subretinal macrophages as “shaggy photoreceptors” overlying choroidal tumors. <b><i>Conclusion:</i></b> The meaningful interpretation of SD-OCT's striking visual imagery requires a firm foundation in ocular histology and pathology. The accuracy of interpretation can be improved by correlative studies that directly compare OCT and histopathology.
DOI: 10.6084/m9.figshare.5705467
title: Readme

description: Descriptive overview of the files contained in this collection.
DOI: 10.6084/m9.figshare.5705467.v1
title: Readme

description: Descriptive overview of the files contained in this collection.
DOI: 10.6084/m9.figshare.5705458
title: Supplementary Material for: Relationship Between Short-Term Blood Pressure Variability and Incidence of Acute Kidney Injury in Critically Ill Patients

description: <b><i>Background/Aims:</i></b> Blood pressure (BP) variability is associated with cardiovascular events, and cerebral and renal damage. The aim of this study was to investigate any potential relationship between short-term BP variability and incidence of acute onset conditions, such as acute kidney injury (AKI), in critically ill patients. <b><i>Methods:</i></b> BP was monitored to analyze its variability in critically ill patients in present study. Short-term BP variability was assessed as average real variability (ARV), standard deviation (SD) and coefficient of variation (CV) of 24-hour BP. <b><i>Results:</i></b> A total of 565 patients were included, 41.2% (n=233) of which presented with AKI after admission (AKI stage I, n = 94; stage II, n = 37; stage III, n = 102). The mean APACHE II score was 21.5 for all patients. ARV of 24 h systolic BP was significantly higher in patients with AKI (p&lt;0.001). This association remained (p=0.006) after adjustment for potential confounders. The incidence of AKI increased with the ARV from 14.0% (ARV ≤6 mmHg) to 73.9% (ARV &gt;14 mmHg). A weak association was also found between BP variability and hospital mortality in critically ill patients. <b><i>Conclusion:</i></b> BP variability is correlated with the incidence of AKI in critically ill patients.