cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5977651
title: Drosophila melanogaster wing images from genetic manipulations of planar cell polarity and tissue growth genes (UAS-genex.RNAi and NP6333-GAL4)

description: These are images of <i>Drosophila melanogaster </i>wings from RNAi knockdowns (using VDRC RNAi lines) crossed to the NP6333-GAL4 line (also known as the <i>Pen</i>-GAL4 line). These crosses (and images) were done just to test the lines. The UAS-<i>narrow</i>.RNAi did not seem to work, but all the other ones did.<br>Crosses were performed by Runyang Yin in the Dworkin lab at McMaster University.<br>All crosses were done at 24°C in a Percival Growth Chamber (12:12 light cycle). Adult flies were stored in 70% ethanol prior to dissection in 70% glycerol/PBS (with a drop of phenol as a bacterio-static agent).<br><br>All images were taken on an Olympus BX-43 microscope with a 4X objective (40X total magnification). The objective is UPlanSApo (NA 0.16. FN26.5). Images were captured on an Olympus DP80 digital camera using Olympus cellSenStandard software (v1.14). <br><br>Image resolution pixels: 4080 x 3072Image size actual: 2.2 mm x 1.7 mm537.5 nm/pixel<br>24bit RGB (8 bit/channel)<br>genes manipulated<i>fat</i><i><br></i><i>narrow</i> (not really PCP or growth, but has an effect on morphogenesis). Note this construct did not seem to do much, so these pictures may not really be a manipulation of <i>narrow</i>. We re-ordered it and the new strain had much clearer effects.<br><i>starry night</i> (<i>stan</i>)<i>Van Gogh</i> (<i>vang</i>)<br><br>
DOI: 10.6084/m9.figshare.5977651.v2
title: Drosophila melanogaster wing images from genetic manipulations of planar cell polarity and tissue growth genes (UAS-genex.RNAi and NP6333-GAL4)

description: These are images of <i>Drosophila melanogaster </i>wings from RNAi knockdowns (using VDRC RNAi lines) crossed to the NP6333-GAL4 line (also known as the <i>Pen</i>-GAL4 line). These crosses (and images) were done just to test the lines. The UAS-<i>narrow</i>.RNAi did not seem to work, but all the other ones did.<br>Crosses were performed by Runyang Yin in the Dworkin lab at McMaster University.<br>All crosses were done at 24°C in a Percival Growth Chamber (12:12 light cycle). Adult flies were stored in 70% ethanol prior to dissection in 70% glycerol/PBS (with a drop of phenol as a bacterio-static agent).<br><br>All images were taken on an Olympus BX-43 microscope with a 4X objective (40X total magnification). The objective is UPlanSApo (NA 0.16. FN26.5). Images were captured on an Olympus DP80 digital camera using Olympus cellSenStandard software (v1.14). <br><br>Image resolution pixels: 4080 x 3072Image size actual: 2.2 mm x 1.7 mm537.5 nm/pixel<br>24bit RGB (8 bit/channel)<br>genes manipulated<i>fat</i><i><br></i><i>narrow</i> (not really PCP or growth, but has an effect on morphogenesis). Note this construct did not seem to do much, so these pictures may not really be a manipulation of <i>narrow</i>. We re-ordered it and the new strain had much clearer effects.<br><i>starry night</i> (<i>stan</i>)<i>Van Gogh</i> (<i>vang</i>)<br><br>
DOI: 10.6084/m9.figshare.5977651.v1
title: Drosophila melanogaster wing images from genetic manipulations of planar cell polarity and tissue growth genes (UAS-genex.RNAi and NP6333-GAL4)

description: These are images of <i>Drosophila melanogaster </i>wings from RNAi knockdowns (using VDRC RNAi lines) crossed to the NP6333-GAL4 line (also known as the Pen-GAL4 line).<br>Crosses were performed by Ronyoung in the Dworkin lab at McMaster University.<br>All crosses were done at 24°C in a Percival Growth Chamber (12:12 light cycle). Adult flies were stored in 70% ethanol prior to dissection in 70% glycerol/PBS (with a drop of phenol as a bacterio-static agent).<br><br>All images were taken on an Olympus BX-43 microscope with a 4X objective (40X total magnification). The objective is UPlanSApo (NA 0.16. FN26.5). Images were captured on an Olympus DP80 digital camera using Olympus cellSenStandard software (vXX). <br>More info to come.Image resolution:
DOI: 10.6084/m9.figshare.5977558
title: Supplementary Material for: The Effect of Improved Dysphagia Care on Outcome in Patients with Acute Stroke: Trends from 8-Year Data of a Large Stroke Register

description: <b><i>Background:</i></b> Early dysphagia screening and appropriate management are recommended by current guidelines to reduce complications and case fatality in acute stroke. However, data on the potential benefit of changes in dysphagia care on patient outcome are limited. Our objective was to assess the degree of implementation of dysphagia guidelines and determine the impact of modifications in dysphagia screening and treatment practices on disease complications and outcome in stroke patients over time. <b><i>Methods:</i></b> In this prospective register-based study (“Stroke Register of Northwestern Germany”), all adult stroke patients admitted to 157 participating hospitals between January, 2008 and December, 2015 were included (<i>n</i> = 674,423). Dysphagia incidence upon admission, the proportion of patients receiving a standardized swallowing screening, and the percentage of dysphagic patients being referred to a speech language therapist (SLT) for treatment were obtained per year. Pneumonia rate, modified Rankin Scale (mRS) at discharge, and in-hospital mortality were compared between groups of dysphagic vs. non-dysphagic patients over time. <b><i>Results:</i></b> Screening proportions continuously increased from 47.2% in 2008 to 86.6% in 2015. But the proportion diagnosed with dysphagia remained stable with about 19%. The number of dysphagic patients receiving SLT treatment grew from 81.6 up to 87.0%. Pneumonia incidence was higher in dysphagic stroke cases (adjusted OR 5.4 [5.2–5.5], <i>p</i> &lt; 0.001), accompanied by a worse mRS at discharge (adjusted OR for mRS ≥3: 3.1 [3.0–3.1], <i>p</i> &lt; 0.001) and higher mortality (adjusted OR 3.1 [3.0–3.2], <i>p</i> &lt; 0.001). The order of magnitude of these end points did not change over time. <b><i>Conclusion:</i></b> Although advances have been made in dysphagia care, prevalent screening and treatment practices remain insufficient to reduce pneumonia rate, improve functional outcome, and decrease case fatality in dysphagic stroke patients. More research is urgently needed to develop more effective swallowing therapies.
DOI: 10.6084/m9.figshare.5977552
title: Extracellular vesicles mediate low dose ionizing radiation-induced immune and inflammatory responses in the blood

description: <b>Purpose:</b> Radiation-induced bystander effects (RIBE) imply the involvement of complex signaling mechanisms, which can be mediated by extracellular vesicles (EVs). Using an in vivo model, we investigated EV-transmitted RIBE in blood plasma and radiation effects on plasma EV miRNA profiles. <b>Materials and methods:</b> C57Bl/6 mice were total-body irradiated with 0.1 and 2 Gy, bone marrow-derived EVs were isolated, and injected systemically into naive, ‘bystander’ animals. Proteome profiler antibody array membranes were used to detect alterations in plasma, both in directly irradiated and bystander mice. MiRNA profile of plasma EVs was determined by PCR array. <b>Results:</b> M-CSF and pentraxin-3 levels were increased in the blood of directly irradiated and bystander mice both after low and high dose irradiations, CXCL16 and lipocalin-2 increased after 2 Gy in directly irradiated and bystander mice, CCL5 and CCL11 changed in bystander mice only. Substantial overlap was found in the cellular pathways regulated by those miRNAs whose level were altered in EVs isolated from the plasma of mice irradiated with 0.1 and 2 Gy. Several of these pathways have already been associated with bystander responses. <b>Conclusion:</b> Low and high dose effects overlapped both in EV-mediated alterations in signaling pathways leading to RIBE and in their systemic manifestations.
DOI: 10.6084/m9.figshare.5977549
title: Supplementary Material for: Apparent Diffusion Coefficient Signal Intensity Ratio Predicts the Effect of Revascularization on Ischemic Cerebral Edema

description: <b><i>Background:</i></b> Apparent diffusion coefficient (ADC) imaging is a biomarker of cytotoxic injury that predicts edema formation and outcome after ischemic stroke. It therefore has the potential to serve as a “tissue clock” to describe the extent of ischemic injury and potentially predict response to therapy. The goal of this study was to determine the relationship between baseline ADC signal intensity, revascularization, and edema formation. <b><i>Methods:</i></b> We examined the ADC signal intensity ratio (ADCr) of the stroke lesion (defined as the baseline DWI hyperintense region) compared to the contralateral normal hemisphere in 65 subjects from the Mechanical Retrieval and Recanalization of Stroke Clots Using Embolectomy trial. The associations between ADCr, neurologic outcome, and cerebral edema were examined. Finally, we explored the interaction between baseline ADCr and vessel recanalization at day 7 on post-stroke edema. <b><i>Results:</i></b> We found that lower initial ADCr was associated with a worse outcome on the modified Rankin Scale (mRS) at 90 days (52.2% of those with ADCr &lt;64% were mRS 5–6 vs. 19.1% with ADCr ≥64%, <i>p =</i> 0.006). Those subjects with reconstitution of flow distal to the initial vessel occlusion showed greater normalization of ADCr on follow-up scan (increase in ADCr of 16.4 ± 2.07 vs. 1.99 ± 4.33%, <i>p =</i> 0.0039). In those patients with low baseline ADCr, successful revascularization was associated with reduced edema (median swelling volume 164 mL [interquartile range (IQR) 53.3–190 mL] vs. 20.7 mL [IQR 3.20–55.1 mL], <i>p =</i> 0.024). <b><i>Conclusions:</i></b> This study reaffirms the association of ADCr with outcome after stroke, supports the idea that reperfusion may attenuate rather than enhance post-stroke edema, and indicates that the degree of edema with and without revascularization may be predicted by ADCr.
DOI: 10.6084/m9.figshare.5977534
title: Supplementary Material for: High-Concentrate Diet-Induced Change of Cellular Metabolism Leads to Decreases of Immunity and Imbalance of Cellular Activities in Rumen Epithelium

description: <b><i>Background/Aims:</i></b> In animals, the immune and cellular processes of tissue largely depend on the status of local metabolism. However, in the rumen epithelium, how the cellular metabolism affects epithelial immunity, and cellular processes, when the diet is switched from energy-rich to energy-excess status, with regard to animal production and health, have not as yet been reported. <b><i>Methods:</i></b> RNA-seq was applied to compare the biological processes altered by an increase of dietary concentration from 10% to 35% with those altered by an increase of dietary concentration from 35% to 65% (dietary concentrate: the non-grass component in diet, including corn, soya bean meal and additive. High concentrate diet composed of 35% grass, 55% corn, 8% soya bean meal and 2% additive). In addition to the functional analysis of enriched genes in terms of metabolism, the immune system, and cellular process, the highly correlated genes to the enriched metabolism genes were identified, and the function and signaling pathways related to the differentially expressed neighbors were compared among the groups. <b><i>Results:</i></b> The variation trends of molar proportions of ruminal SCFAs and those of enriched pathways belonging to metabolism, immune system, and cellular process were altered with the change of diets. With regard to metabolism, lipid metabolism and amino acid metabolism were most affected. According to the correlation analysis, both innate and adaptive immune responses were promoted by the metabolism genes enriched under the 65% concentrate diet. However, the majority of immune responses were suppressed under the 35% concentrate diet. Moreover, the exclusive upregulation of cell growth and dysfunction of cellular transport and catabolism were induced by the metabolism genes enriched under the 65% concentrate diet. On the contrary, a balanced regulation of cellular processes was detected under the 35% concentrate diet. <b><i>Conclusions:</i></b> These results indicated that the alterations of cellular metabolism promote the alterations in cellular immunity, repair, and homeostasis in the rumen epithelium, thereby leading to the switch of concentrate effects from positive to negative with regard to animal production and health.
DOI: 10.6084/m9.figshare.5977534.v1
title: Supplementary Material for: High-Concentrate Diet-Induced Change of Cellular Metabolism Leads to Decreases of Immunity and Imbalance of Cellular Activities in Rumen Epithelium

description: <b><i>Background/Aims:</i></b> In animals, the immune and cellular processes of tissue largely depend on the status of local metabolism. However, in the rumen epithelium, how the cellular metabolism affects epithelial immunity, and cellular processes, when the diet is switched from energy-rich to energy-excess status, with regard to animal production and health, have not as yet been reported. <b><i>Methods:</i></b> RNA-seq was applied to compare the biological processes altered by an increase of dietary concentration from 10% to 35% with those altered by an increase of dietary concentration from 35% to 65% (dietary concentrate: the non-grass component in diet, including corn, soya bean meal and additive. High concentrate diet composed of 35% grass, 55% corn, 8% soya bean meal and 2% additive). In addition to the functional analysis of enriched genes in terms of metabolism, the immune system, and cellular process, the highly correlated genes to the enriched metabolism genes were identified, and the function and signaling pathways related to the differentially expressed neighbors were compared among the groups. <b><i>Results:</i></b> The variation trends of molar proportions of ruminal SCFAs and those of enriched pathways belonging to metabolism, immune system, and cellular process were altered with the change of diets. With regard to metabolism, lipid metabolism and amino acid metabolism were most affected. According to the correlation analysis, both innate and adaptive immune responses were promoted by the metabolism genes enriched under the 65% concentrate diet. However, the majority of immune responses were suppressed under the 35% concentrate diet. Moreover, the exclusive upregulation of cell growth and dysfunction of cellular transport and catabolism were induced by the metabolism genes enriched under the 65% concentrate diet. On the contrary, a balanced regulation of cellular processes was detected under the 35% concentrate diet. <b><i>Conclusions:</i></b> These results indicated that the alterations of cellular metabolism promote the alterations in cellular immunity, repair, and homeostasis in the rumen epithelium, thereby leading to the switch of concentrate effects from positive to negative with regard to animal production and health.
DOI: 10.6084/m9.figshare.5977471
title: Long term in situ permafrost thaw effects on bacterial communities and potential aerobic respiration

description: These data and script accompany the article "Long term in situ permafrost thaw effects on bacterial communities and potential aerobic respiration" (doi:10.1038/s41396-018-0176-z) and was used to create the figures and tables found in the article.<br><br>The file <i>Monteux_Deepthaw_figs_and_tabs.R</i> is the main script, and the different data files are described in the first section of that script.<br><br>The up-stream bioinformatics script used to obtain the data files here are found at <b>https://bitbucket.org/smonteux/monteux_deep_thaw/</b> and the raw sequence files are deposited in the Sequence Read Archive (BioProject <b>RJNA396994</b>)
DOI: 10.21227/fv4j-d022
title: OCTA-500

description: Optical coherence tomography angiography (OCTA) is a novel imaging modality that allows a micron-level resolution to present the three-dimensional structure of the retinal vascular.We propose a new multi-modality dataset, dubbed OCTA-500. It contains 500 subjects with two field of view (FOV) types, including OCT and OCTA volumes, six types of projections, four types of text labels and two types of pixel-level labels. The dataset contains more than 360K images with a size of about 80GB. We will upload the encrypted dataset first, and the password will be released later in this article.
DOI: 10.6084/m9.figshare.5977375.v1
title: Hoover and Berbesque-raw data.xlsx

description: These are length width ratio data for a group of Early Archaic period North American hunter-gatherers. There are two tables--one for length-width ratios and one for a smaller subset used for directional asymmetry analysis (for assessing sidedness). The DA set is smaller due to the need for right/left sides.
DOI: 10.6084/m9.figshare.5977375.v2
title: Hoover and Berbesque-raw data.xlsx

description: These are length width ratio data for a group of Early Archaic period North American hunter-gatherers. There are three tables--one values, one for length-width ratios, and one for a smaller subset used for directional asymmetry analysis (for assessing sidedness). The DA set is smaller due to the need for paired (right and left) sides.
DOI: 10.6084/m9.figshare.5977345
title: segmentation.rar

description: 20m,10Hz nocturnal boundary layer turbulence data,(2200-0400),<br>by CSAT3 3D Sonic Anemometer,<br>at the edge of the Tengger Desert,China(103.92E, 37.75N),<br>from Aug. 2014 to Oct. 2015.<br>Data are .mat<br>
DOI: 10.6084/m9.figshare.5977345.v2
title: segmentation.rar

description: 20m,10Hz nocturnal boundary layer turbulence data,(2200-0400),<br>by CSAT3 3D Sonic Anemometer,<br>at the edge of the Tengger Desert,China(103.92E, 37.75N),<br>from Aug. 2014 to Oct. 2015.<br>Data are .mat<br>
DOI: 10.6084/m9.figshare.5977345.v1
title: segmentation.rar

description: 20m,10Hz nocturnal boundary layer turbulence data,(2200-0400),<br>by CSAT3 3D Sonic Anemometer,<br>at the edge of the Tengger Desert,China(103.92E, 37.75N),<br>from Aug. 2014 to Oct. 2015.<br>Data are .mat<br>
DOI: 10.6084/m9.figshare.5977303
title: Supplementary Material for: Identification of in vivo Sulci on the External Surface of Eight Adult Chimpanzee Brains: Implications for Interpreting Early Hominin Endocasts

description: The only direct source of information about hominin brain evolution comes from the fossil record of endocranial casts (endocasts) that reproduce details of the external morphology of the brain imprinted on the walls of the braincase during life. Surface traces of sulci that separate the brain’s convolutions (gyri) are reproduced sporadically on early hominin endocasts. Paleoneurologists rely heavily on published descriptions of sulci on brains of great apes, especially chimpanzees (humans’ phylogenetically closest living relatives), to guide their identifications of sulci on ape-sized hominin endocasts. However, the few comprehensive descriptions of cortical sulci published for chimpanzees usually relied on post mortem brains, (now) antiquated terminology for some sulci, and photographs or line drawings from limited perspectives (typically right or left lateral views). The shortage of adequate descriptions of chimpanzee sulcal patterns partly explains why the identities of certain sulci on australopithecine endocasts (e.g., the inferior frontal and middle frontal sulci) have been controversial. Here, we provide images of lateral and dorsal surfaces of 16 hemispheres from 4 male and 4 female adult chimpanzee brains that were obtained using in vivo magnetic resonance imaging. Sulci on the exposed surfaces of the frontal, parietal, temporal, and occipital lobes are identified on the images based on their locations, positions relative to each other, and homologies known from comparative studies of cytoarchitecture in primates. These images and sulcal identifications exceed the quantity and quality of previously published illustrations of chimpanzee brains with comprehensively labeled sulci and, thus, provide a larger number of examples for identifying sulci on hominin endocasts than hitherto available. Our findings, even in a small sample like the present one, overturn published claims that australopithecine endocasts reproduce derived configurations of certain sulci in their frontal lobes that never appear on chimpanzee brains. The sulcal patterns in these new images also suggest that changes in two gyri that bridge between the parietal and occipital lobes may have contributed to cortical reorganization in early hominins. It is our hope that these labeled in vivo chimpanzee brains will assist future researchers in identifying sulci on hominin endocasts, which is a necessary first step in the quest to learn how and when the external morphology of the human cerebral cortex evolved from apelike precursors.
DOI: 10.6084/m9.figshare.5977153
title: Pearson Correlations. Influence of dominant wind patterns in a distal region of the NW Iberian Margin during the last glaciation

description: Pearson Correlations between the analysed data.
DOI: 10.6084/m9.figshare.12894590
title: Data and Source MSMEs.xlsx

description: The data provided in this repository is the datasets of the article “Micro, Small, and Medium Enterprises (MSMEs) and Poverty Reduction: Empirical Evidence from Indonesia”. The raw data are gathered from The Ministry of Cooperatives and SMEs in Indonesia and the Central Bureau of Statistic Indonesia. In addition, this article uses secondary data from the period of 1997-2018 to estimate the effect of MSMEs on poverty reduction in Indonesia both directly and indirectly.
DOI: 10.6084/m9.figshare.5977153.v1
title: Pearson Correlations. Influence of dominant wind patterns in a distal region of the NW Iberian Margin during the last glaciation

description: Pearson Correlations between the analysed data.
DOI: 10.6084/m9.figshare.5977150
title: Geochemical and foraminiferal data. Influence of dominant wind patterns in a distal region of the NW Iberian Margin during the last glaciation

description: Geochemical and foraminiferal data.
DOI: 10.6084/m9.figshare.5977150.v1
title: Geochemical and foraminiferal data. Influence of dominant wind patterns in a distal region of the NW Iberian Margin during the last glaciation

description: Geochemical and foraminiferal data.