cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3438842
title: Characteristics and survival of adult Swedish PAH and CTEPH patients 2000–2014

description: <b>Objectives:</b> The Swedish Pulmonary Arterial Hypertension Register (SPAHR) is an open continuous register, including pulmonary arterial hypertension (PAH) and chronic thromboembolic pulmonary hypertension (CTEPH) patients from 2000 and onwards. We hereby launch the first data from SPAHR, defining baseline characteristics and survival of Swedish PAH and CTEPH patients. <b>Design:</b> Incident PAH and CTEPH patients 2008–2014 from all seven Swedish PAH-centres were specifically reviewed. <b>Results:</b> There were 457 PAH (median age: 67 years, 64% female) and 183 CTEPH (median age: 70 years, 50% female) patients, whereof 77 and 81%, respectively, were in functional class III–IV at diagnosis. Systemic hypertension, diabetes, ischaemic heart disease and atrial fibrillation were common comorbidities, particularly in those &gt;65 years. One-, 3- and 5-year survival was 85%, 71% and 59% for PAH patients. Corresponding numbers for CTEPH patients with versus without pulmonary endarterectomy were 96%, 89% and 86% versus 91%, 75% and 69%, respectively. In 2014, the incidence of IPAH/HPAH, associated PAH and CTEPH was 5, 3 and 2 per million inhabitants and year, and the prevalence was 25, 24 and 19 per million inhabitants. <b>Conclusion:</b> The majority of the PAH and CTEPH patients were diagnosed at age &gt;65 years, in functional class III–IV, and exhibiting several comorbidities. PAH survival in SPAHR was similar to other registers.
DOI: 10.6084/m9.figshare.3438842.v1
title: Characteristics and survival of adult Swedish PAH and CTEPH patients 2000–2014

description: <b>Objectives:</b> The Swedish Pulmonary Arterial Hypertension Register (SPAHR) is an open continuous register, including pulmonary arterial hypertension (PAH) and chronic thromboembolic pulmonary hypertension (CTEPH) patients from 2000 and onwards. We hereby launch the first data from SPAHR, defining baseline characteristics and survival of Swedish PAH and CTEPH patients. <b>Design:</b> Incident PAH and CTEPH patients 2008–2014 from all seven Swedish PAH-centres were specifically reviewed. <b>Results:</b> There were 457 PAH (median age: 67 years, 64% female) and 183 CTEPH (median age: 70 years, 50% female) patients, whereof 77 and 81%, respectively, were in functional class III–IV at diagnosis. Systemic hypertension, diabetes, ischaemic heart disease and atrial fibrillation were common comorbidities, particularly in those &gt;65 years. One-, 3- and 5-year survival was 85%, 71% and 59% for PAH patients. Corresponding numbers for CTEPH patients with versus without pulmonary endarterectomy were 96%, 89% and 86% versus 91%, 75% and 69%, respectively. In 2014, the incidence of IPAH/HPAH, associated PAH and CTEPH was 5, 3 and 2 per million inhabitants and year, and the prevalence was 25, 24 and 19 per million inhabitants. <b>Conclusion:</b> The majority of the PAH and CTEPH patients were diagnosed at age &gt;65 years, in functional class III–IV, and exhibiting several comorbidities. PAH survival in SPAHR was similar to other registers.
DOI: 10.6084/m9.figshare.3438803
title: Grazing effects on plant diversity in the endemic <i>Erica mackayana</i> heathland community of north-west Spain

description: <b><i>Background</i></b>: Large areas of heathland landscapes in Galicia, north-west Spain, have traditionally been extensively grazed by free-ranging cattle and wild ponies. Recently, a large reduction in the number of these larger herbivores has been observed, with unknown consequences for the habitat. <b><i>Aims</i></b>: To evaluate the effects of grazing and herbivore density on plant diversity, community composition and vegetation structure of the endemic wet heathlands dominated by <i>Erica mackayana</i> in Galicia. <b><i>Methods</i></b>: Field sampling of vascular plants, generalised linear models (GLMs), non-metric multidimensional distance scaling (NMDS). <b><i>Results</i></b>: Grazed sites had significantly higher total and rare species richness and diversity than ungrazed sites. Higher densities of cattle resulted in lower numbers of rare species, while wild pony density had no effect on rare species richness. In grazed sites, vegetation was lower with greater variation in height, resulting in greater heterogeneity of the habitat. Precipitation and summer temperatures were related to plant diversity, mainly beta diversity. Soil organic matter negatively correlated with rare species. <b><i>Discussion</i></b>: Grazing, mostly by wild ponies, was demonstrated to be positively related to plant diversity and vegetation structure. Lack of grazing or high cattle densities resulted in a negative effect on total and rare species richness and diversity. Future climate change may negatively affect heathland plant diversity. Galician wild ponies represent a unique case of sustainable management of a wild species and an invaluable cultural heritage. Moreover, they have a significant role in maintaining the endemic <i>E. mackayana</i> heathlands, what would justify specific conservation actions for these large herbivores.
DOI: 10.6084/m9.figshare.3438803.v1
title: Grazing effects on plant diversity in the endemic <i>Erica mackayana</i> heathland community of north-west Spain

description: <b><i>Background</i></b>: Large areas of heathland landscapes in Galicia, north-west Spain, have traditionally been extensively grazed by free-ranging cattle and wild ponies. Recently, a large reduction in the number of these larger herbivores has been observed, with unknown consequences for the habitat. <b><i>Aims</i></b>: To evaluate the effects of grazing and herbivore density on plant diversity, community composition and vegetation structure of the endemic wet heathlands dominated by <i>Erica mackayana</i> in Galicia. <b><i>Methods</i></b>: Field sampling of vascular plants, generalised linear models (GLMs), non-metric multidimensional distance scaling (NMDS). <b><i>Results</i></b>: Grazed sites had significantly higher total and rare species richness and diversity than ungrazed sites. Higher densities of cattle resulted in lower numbers of rare species, while wild pony density had no effect on rare species richness. In grazed sites, vegetation was lower with greater variation in height, resulting in greater heterogeneity of the habitat. Precipitation and summer temperatures were related to plant diversity, mainly beta diversity. Soil organic matter negatively correlated with rare species. <b><i>Discussion</i></b>: Grazing, mostly by wild ponies, was demonstrated to be positively related to plant diversity and vegetation structure. Lack of grazing or high cattle densities resulted in a negative effect on total and rare species richness and diversity. Future climate change may negatively affect heathland plant diversity. Galician wild ponies represent a unique case of sustainable management of a wild species and an invaluable cultural heritage. Moreover, they have a significant role in maintaining the endemic <i>E. mackayana</i> heathlands, what would justify specific conservation actions for these large herbivores.
DOI: 10.6084/m9.figshare.3438785
title: Fibrotic gene expression coexists with alveolar proteinosis in early indium lung

description: Occupational inhalation of indium compounds can cause the so-called “indium lung disease”. Most affected individuals show pulmonary alveolar proteinosis (PAP) and fibrotic interstitial lung disease. In animal experiments, inhalation of indium tin oxide or indium oxide has been shown to cause lung damage. However, the mechanisms by which indium compounds lead to indium lung disease remain unknown. In this study, we constructed a mouse model of indium lung disease and analyzed gene expression in response to indium exposure. Indium oxide (In<sub>2</sub>O<sub>3</sub>, 10 mg/kg, primary particle size &lt;100 nm) was administered intratracheally to C57BL/6 mice (male, 8 weeks of age) twice a week for 8 weeks. Four weeks after the final instillation, histopathological analysis exhibited periodic acid-Schiff positive material in the alveoli, characteristic of PAP. Comprehensive gene expression analysis by RNA-Seq, however, revealed expression of fibrosis-related genes, such as surfactant associated protein D, surfactant associated protein A1, mucin 1, and collagen type I and III, was significantly increased, indicating that fibrotic gene expression progresses in early phase of indium lung. These data supported the latest hypothesis that PAP occurs as an acute phase response and is replaced by fibrosis after long-term latency.
DOI: 10.6084/m9.figshare.3438785.v1
title: Fibrotic gene expression coexists with alveolar proteinosis in early indium lung

description: Occupational inhalation of indium compounds can cause the so-called “indium lung disease”. Most affected individuals show pulmonary alveolar proteinosis (PAP) and fibrotic interstitial lung disease. In animal experiments, inhalation of indium tin oxide or indium oxide has been shown to cause lung damage. However, the mechanisms by which indium compounds lead to indium lung disease remain unknown. In this study, we constructed a mouse model of indium lung disease and analyzed gene expression in response to indium exposure. Indium oxide (In<sub>2</sub>O<sub>3</sub>, 10 mg/kg, primary particle size &lt;100 nm) was administered intratracheally to C57BL/6 mice (male, 8 weeks of age) twice a week for 8 weeks. Four weeks after the final instillation, histopathological analysis exhibited periodic acid-Schiff positive material in the alveoli, characteristic of PAP. Comprehensive gene expression analysis by RNA-Seq, however, revealed expression of fibrosis-related genes, such as surfactant associated protein D, surfactant associated protein A1, mucin 1, and collagen type I and III, was significantly increased, indicating that fibrotic gene expression progresses in early phase of indium lung. These data supported the latest hypothesis that PAP occurs as an acute phase response and is replaced by fibrosis after long-term latency.
DOI: 10.6084/m9.figshare.3438779
title: The larval development of the spider crab <i>Rochinia gracilipes</i> (Crustacea: Majoidea: Epialtidae: Pisinae) reared in the laboratory

description: The larval development of the spider crab <i>Rochinia gracilipes</i> Milne-Edwards, 1875 (Crustacea: Decapoda: Brachyura: Majoidea: Epialtidae: Pisinae) is described and illustrated from laboratory-reared larvae. Development consisted of two zoeal stages and one megalopa, following the typical pattern in Majoidea. Zoea I of <i>R. gracilipes, R. debilis</i> and <i>R. carpenteri</i> differed in lengths of the rostral spine of the carapace, in the number of setae and aesthetascs of several head appendages (exopods of antennules, endopods of maxillules, and endopods and scaphognathites of maxillae) and in the length of posterolateral processes of abdominal somites; lateral carapace spines were present only in <i>R. carpenteri</i> and pleopod buds only in <i>R. debilis</i>. Megalopae of <i>Rochinia gracilipes</i> and <i>R. carpenteri</i> differed in several notable characters: a dorsal spine and long rostrum of the carapace, as well as spines in coxa and ischium of pereiopods, appeared only in <i>R. carpenteri</i>, and podobranchiae of the 3rd maxilliped appeared only in <i>R. gracilipes</i>; they also differed in setation of abdomen and pleopods. The comparison of the available information on Pisinae larval development suggested that larval morphology would not help to accurately understand the phylogenetic relationships of this subfamily of spider crabs.
DOI: 10.6084/m9.figshare.3438779.v1
title: The larval development of the spider crab <i>Rochinia gracilipes</i> (Crustacea: Majoidea: Epialtidae: Pisinae) reared in the laboratory

description: The larval development of the spider crab <i>Rochinia gracilipes</i> Milne-Edwards, 1875 (Crustacea: Decapoda: Brachyura: Majoidea: Epialtidae: Pisinae) is described and illustrated from laboratory-reared larvae. Development consisted of two zoeal stages and one megalopa, following the typical pattern in Majoidea. Zoea I of <i>R. gracilipes, R. debilis</i> and <i>R. carpenteri</i> differed in lengths of the rostral spine of the carapace, in the number of setae and aesthetascs of several head appendages (exopods of antennules, endopods of maxillules, and endopods and scaphognathites of maxillae) and in the length of posterolateral processes of abdominal somites; lateral carapace spines were present only in <i>R. carpenteri</i> and pleopod buds only in <i>R. debilis</i>. Megalopae of <i>Rochinia gracilipes</i> and <i>R. carpenteri</i> differed in several notable characters: a dorsal spine and long rostrum of the carapace, as well as spines in coxa and ischium of pereiopods, appeared only in <i>R. carpenteri</i>, and podobranchiae of the 3rd maxilliped appeared only in <i>R. gracilipes</i>; they also differed in setation of abdomen and pleopods. The comparison of the available information on Pisinae larval development suggested that larval morphology would not help to accurately understand the phylogenetic relationships of this subfamily of spider crabs.
DOI: 10.6084/m9.figshare.3438743
title: hypocotyl3.czi

description: ---Experiment Date: 28 Jan 2016Experiment Commentary: Confocal microscopy image of hypocotyl. Cell walls stained using FM4-64 [5ug/ml]. Nucelus marked using 35s::GFP:eIF3a (see reference for more detail).Device: Zeiss LSM780Species: Arabidopsis thaliana (Thale cress)Organ/tissue type: HypocotylImaging probes: FM4-64 + GFP-nucleusObjective Lens: x40/1.2 water
DOI: 10.6084/m9.figshare.3438743.v1
title: hypocotyl3.czi

description: ---Experiment Date: 28 Jan 2016Experiment Commentary: Confocal microscopy image of hypocotyl. Cell walls stained using FM4-64 [5ug/ml]. Nucelus marked using 35s::GFP:eIF3a (see reference for more detail).Device: Zeiss LSM780Species: Arabidopsis thaliana (Thale cress)Organ/tissue type: HypocotylImaging probes: FM4-64 + GFP-nucleusObjective Lens: x40/1.2 water
DOI: 10.6084/m9.figshare.3438662
title: A Bayesian model for single cell transcript expression analysis on MERFISH data

description: Multiplexed error-robust fluorescence in-situ hybridization (MERFISH) is a new technology to obtain spatially resolved gene or transcript expression profiles in single cells for hundreds to thousands of genes in parallel. We present a Bayesian model for expression analysis on MERFISH data. We show that the model successfully captures the uncertainty in MERFISH data and eliminates systematic biases that can occur in raw RNA molecule counts obtained with MERFISH. Our model accurately estimates transcript expression, fold-change and coefficient of variation along with credible intervals and control of the expected false discovery rate.This enables MERFISH to scale towards the whole genome while being able to control the uncertainty in the obtained results.
DOI: 10.6084/m9.figshare.3438662.v2
title: A Bayesian model for single cell transcript expression analysis on MERFISH data

description: Multiplexed error-robust fluorescence in-situ hybridization (MERFISH) is a new technology to obtain spatially resolved gene or transcript expression profiles in single cells for hundreds to thousands of genes in parallel. We present a Bayesian model for expression analysis on MERFISH data. We show that the model successfully rescues systematic biases occurring in raw RNA molecule counts obtained with MERFISH. Our model accurately estimates transcript expression, fold-change and coefficient of variation along with credible intervals and control of the expected false discovery rate.
DOI: 10.6084/m9.figshare.3438662.v3
title: A Bayesian model for single cell transcript expression analysis on MERFISH data

description: Multiplexed error-robust fluorescence in-situ hybridization (MERFISH) is a new technology to obtain spatially resolved gene or transcript expression profiles in single cells for hundreds to thousands of genes in parallel. We present a Bayesian model for expression analysis on MERFISH data. We show that the model successfully rescues systematic biases occurring in raw RNA molecule counts obtained with MERFISH. Our model accurately estimates transcript expression, fold-change and coefficient of variation along with credible intervals and control of the expected false discovery rate.
DOI: 10.6084/m9.figshare.3438662.v4
title: A Bayesian model for single cell transcript expression analysis on MERFISH data

description: Multiplexed error-robust fluorescence in-situ hybridization (MERFISH) is a new technology to obtain spatially resolved gene or transcript expression profiles in single cells for hundreds to thousands of genes in parallel. We present a Bayesian model for expression analysis on MERFISH data. We show that the model successfully captures the uncertainty in MERFISH data and eliminates systematic biases that can occur in raw RNA molecule counts obtained with MERFISH. Our model accurately estimates transcript expression, fold-change and coefficient of variation along with credible intervals and control of the expected false discovery rate.This enables MERFISH to scale towards the whole genome while being able to control the uncertainty in the obtained results.
DOI: 10.6084/m9.figshare.3438662.v5
title: A Bayesian model for single cell transcript expression analysis on MERFISH data

description: Multiplexed error-robust fluorescence in-situ hybridization (MERFISH) is a new technology to obtain spatially resolved gene or transcript expression profiles in single cells for hundreds to thousands of genes in parallel. We present a Bayesian model for expression analysis on MERFISH data. We show that the model successfully captures the uncertainty in MERFISH data and eliminates systematic biases that can occur in raw RNA molecule counts obtained with MERFISH. Our model accurately estimates transcript expression, fold-change and coefficient of variation along with credible intervals and control of the expected false discovery rate.This enables MERFISH to scale towards the whole genome while being able to control the uncertainty in the obtained results.
DOI: 10.6084/m9.figshare.3438656
title: Longitudinal data from MRET study

description: Prosaccade and antisaccade latency and directional error rate data for cerebral malaria survivors and controls.
DOI: 10.6084/m9.figshare.3438647
title: Autophagy activation by novel inducers prevents BECN2-mediated drug tolerance to cannabinoids

description: Cannabinoids and related drugs generate profound behavioral effects (such as analgesic effects) through activating CNR1 (cannabinoid receptor 1 [brain]). However, repeated cannabinoid administration triggers lysosomal degradation of the receptor and rapid development of drug tolerance, limiting the medical use of marijuana in chronic diseases. The pathogenic mechanisms of cannabinoid tolerance are not fully understood, and little is known about its prevention. Here we show that a protein involved in macroautophagy/autophagy (a conserved lysosomal degradation pathway), BECN2 (beclin 2), mediates cannabinoid tolerance by preventing CNR1 recycling and resensitization after prolonged agonist exposure, and deletion of Becn2 rescues CNR1 activity in mouse brain and conveys resistance to analgesic tolerance to chronic cannabinoids. To target BECN2 therapeutically, we established a competitive recruitment model of BECN2 and identified novel synthetic, natural or physiological stimuli of autophagy that sequester BECN2 from its binding with GPRASP1, a receptor protein for CNR1 degradation. Co-administration of these autophagy inducers effectively restores the level and signaling of brain CNR1 and protects mice from developing tolerance to repeated cannabinoid usage. Overall, our findings demonstrate the functional link among autophagy, receptor signaling and animal behavior regulated by psychoactive drugs, and develop a new strategy to prevent tolerance and improve medical efficacy of cannabinoids by modulating the BECN2 interactome and autophagy activity.
DOI: 10.6084/m9.figshare.3438647.v1
title: Autophagy activation by novel inducers prevents BECN2-mediated drug tolerance to cannabinoids

description: Cannabinoids and related drugs generate profound behavioral effects (such as analgesic effects) through activating CNR1 (cannabinoid receptor 1 [brain]). However, repeated cannabinoid administration triggers lysosomal degradation of the receptor and rapid development of drug tolerance, limiting the medical use of marijuana in chronic diseases. The pathogenic mechanisms of cannabinoid tolerance are not fully understood, and little is known about its prevention. Here we show that a protein involved in macroautophagy/autophagy (a conserved lysosomal degradation pathway), BECN2 (beclin 2), mediates cannabinoid tolerance by preventing CNR1 recycling and resensitization after prolonged agonist exposure, and deletion of Becn2 rescues CNR1 activity in mouse brain and conveys resistance to analgesic tolerance to chronic cannabinoids. To target BECN2 therapeutically, we established a competitive recruitment model of BECN2 and identified novel synthetic, natural or physiological stimuli of autophagy that sequester BECN2 from its binding with GPRASP1, a receptor protein for CNR1 degradation. Co-administration of these autophagy inducers effectively restores the level and signaling of brain CNR1 and protects mice from developing tolerance to repeated cannabinoid usage. Overall, our findings demonstrate the functional link among autophagy, receptor signaling and animal behavior regulated by psychoactive drugs, and develop a new strategy to prevent tolerance and improve medical efficacy of cannabinoids by modulating the BECN2 interactome and autophagy activity.
DOI: 10.6084/m9.figshare.3438641
title: Supplementary Material for: Safety and Efficacy of a Novel Double-Stapling Technique for Distal Esophageal Resection and Esophago-Jejunal Anastomosis

description: <i>Background:</i> The purpose of this study was to evaluate safety and efficacy of a new esophagojejunal anastomosis (EJA) technique allowing the insertion of the anvil of a common circular stapler without hand-sewn securing. <i>Methods:</i> From August 2014 to May 2015, 20 consecutive patients with esophagogastric junction adenocarcinoma underwent surgery. EJA was performed using a new technique; the free margins of the esophageal stump were suspended and the anvil of a circular stapler on a new dedicated and registered support bar (characterized by a push-rod making possible to hook-unhook the anvil of the circular stapler) was inserted into the lumen. Subsequently, the linear suturing stapler was closed over the bar and fired to suture the distal stump of the esophagus; the bar was retracted and the push-rod of the anvil was pulled out through the linear suture. Finally, the anastomosis was performed using a circular stapler. <i>Results:</i> There were no intraoperative complications, and R0 resection was achieved in all cases. Postoperative course has been uneventful for 18 patients (90%). Only 1 patient (5%) developed fistula, conservatively treated. <i>Conclusions:</i> Our preliminary clinical experience suggested that this technique was safe and efficient (for all online suppl. material, see www.karger.com/doi/10.1159/000446856).
DOI: 10.6084/m9.figshare.3438596
title: S. pimpinellifolium_GBS_data_Celik et al. (2016)

description: <em>A SAM (Sequence Alignment/Map) file contained all the merged tags of the GBS and sample key</em>
DOI: 10.6084/m9.figshare.3438596.v1
title: S. pimpinellifolium_GBS_data_Celik et al. (2016)

description: <em>A SAM (Sequence Alignment/Map) file contained all the merged tags of the GBS and sample key</em>
DOI: 10.6084/m9.figshare.3438590
title: RATHER Invasive Lobular Breast Cancer Cohort Subtype Assignments

description: Subtype assignment of invasibe lobular cancer (ILC) samples of RATHER, METABRIC and TCGA. RATHER subtype IR is similar to subtype 1 in METABRIC and TCGA. RATHER subtype HR is similar to subtype 2 in METABRIC and TCGA.