cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1493050.v3
title: Cross-cancer profiling of molecular alterations within the human autophagy interaction network

description: Aberrant activation or disruption of autophagy promotes tumorigenesis in various preclinical models of cancer, but whether the autophagy pathway is a target for recurrent molecular alteration in human cancer patient samples is unknown. To address this outstanding question, we surveyed 211 human autophagy-associated genes for tumor-related alterations to DNA sequence and RNA expression levels and examined their association with patient survival outcomes in multiple cancer types with sequence data from The Cancer Genome Atlas consortium. We found 3 (<i>RB1CC1/FIP200, ULK4, WDR45/WIPI4</i>) and one (<i>ATG7</i>) core autophagy genes to be under positive selection for somatic mutations in endometrial carcinoma and clear cell renal carcinoma, respectively, while 29 autophagy regulators and pathway interactors, including previously identified <i>KEAP1, NFE2L2,</i> and <i>MTOR</i>, were significantly mutated in 6 of the 11 cancer types examined. Gene expression analyses revealed that <i>GABARAPL1</i> and <i>MAP1LC3C/LC3C</i> transcripts were less abundant in breast cancer and non-small cell lung cancers than in matched normal tissue controls; <i>ATG4D</i> transcripts were increased in lung squamous cell carcinoma, as were <i>ATG16L2</i> transcripts in kidney cancer. Unsupervised clustering of autophagy-associated mRNA levels in tumors stratified patient overall survival in 3 of 9 cancer types (acute myeloid leukemia, clear cell renal carcinoma, and head and neck cancer). These analyses provide the first comprehensive resource of recurrently altered autophagy-associated genes in human tumors, and highlight cancer types and subtypes where perturbed autophagy may be relevant to patient overall survival.
DOI: 10.6084/m9.figshare.1493046.v2
title: Long-term live imaging reveals cytosolic immune responses of host hepatocytes against <i>Plasmodium</i> infection and parasite escape mechanisms

description: <i>Plasmodium</i> parasites are transmitted by <i>Anopheles</i> mosquitoes to the mammalian host and actively infect hepatocytes after passive transport in the bloodstream to the liver. In their target host hepatocyte, parasites reside within a parasitophorous vacuole (PV). In the present study it was shown that the parasitophorous vacuole membrane (PVM) can be targeted by autophagy marker proteins LC3, ubiquitin, and SQSTM1/p62 as well as by lysosomes in a process resembling selective autophagy. The dynamics of autophagy marker proteins in individual <i>Plasmodium berghei</i>-infected hepatocytes were followed by live imaging throughout the entire development of the parasite in the liver. Although the host cell very efficiently recognized the invading parasite in its vacuole, the majority of parasites survived this initial attack. Successful parasite development correlated with the gradual loss of all analyzed autophagy marker proteins and associated lysosomes from the PVM. However, other autophagic events like nonselective canonical autophagy in the host cell continued. This was indicated as LC3, although not labeling the PVM anymore, still localized to autophagosomes in the infected host cell. It appears that growing parasites even benefit from this form of nonselective host cell autophagy as an additional source of nutrients, as in host cells deficient for autophagy, parasite growth was retarded and could partly be rescued by the supply of additional amino acid in the medium. Importantly, mouse infections with <i>P. berghei</i> sporozoites confirmed LC3 dynamics, the positive effect of autophagy activation on parasite growth, and negative effects upon autophagy inhibition.
DOI: 10.6084/m9.figshare.1493031
title: Profundae diversitas: the uncharted genetic diversity in a newly studied group of fungal root endophytes

description: Endophytes associated with crops have potential as beneficial inoculants in agriculture, but little is known about their genetic diversity and phylogenetic relationships. We carried out the first ever ecological and phylogenetic survey of the culturable fungal root endophytes of a wild barley species. Fungal root endophytes were isolated from 10 populations of wall barley (<i>Hordeum murinum</i>), and 112 taxa of fungi were identified based on internal transcribed spacer sequence similarity. We found representatives from 8 orders, 12 families and 18 genera. Within this group, only 34 isolates (30% of the total) could be confidently assigned to a species, and 23 of the isolates (21% of the total) had no significant match to anything deposited in GenBank (based on &lt;85% sequence similarity). These results suggest a high proportion of novel fungi, with 28% not assigned to a known fungal order. This includes three endophytes that have been shown to significantly improve agronomic traits in cultivated barley. This study has, therefore, revealed a profound diversity of fungal root endophytes in a single wild relative of barley. Extrapolating from this, the study highlights the largely unknown, hugely diverse and potentially useful resource of crop wild relative endophytes.
DOI: 10.6084/m9.figshare.1493046.v3
title: Long-term live imaging reveals cytosolic immune responses of host hepatocytes against <i>Plasmodium</i> infection and parasite escape mechanisms

description: <i>Plasmodium</i> parasites are transmitted by <i>Anopheles</i> mosquitoes to the mammalian host and actively infect hepatocytes after passive transport in the bloodstream to the liver. In their target host hepatocyte, parasites reside within a parasitophorous vacuole (PV). In the present study it was shown that the parasitophorous vacuole membrane (PVM) can be targeted by autophagy marker proteins LC3, ubiquitin, and SQSTM1/p62 as well as by lysosomes in a process resembling selective autophagy. The dynamics of autophagy marker proteins in individual <i>Plasmodium berghei</i>-infected hepatocytes were followed by live imaging throughout the entire development of the parasite in the liver. Although the host cell very efficiently recognized the invading parasite in its vacuole, the majority of parasites survived this initial attack. Successful parasite development correlated with the gradual loss of all analyzed autophagy marker proteins and associated lysosomes from the PVM. However, other autophagic events like nonselective canonical autophagy in the host cell continued. This was indicated as LC3, although not labeling the PVM anymore, still localized to autophagosomes in the infected host cell. It appears that growing parasites even benefit from this form of nonselective host cell autophagy as an additional source of nutrients, as in host cells deficient for autophagy, parasite growth was retarded and could partly be rescued by the supply of additional amino acid in the medium. Importantly, mouse infections with <i>P. berghei</i> sporozoites confirmed LC3 dynamics, the positive effect of autophagy activation on parasite growth, and negative effects upon autophagy inhibition.
DOI: 10.6084/m9.figshare.1493031.v1
title: Profundae diversitas: the uncharted genetic diversity in a newly studied group of fungal root endophytes

description: Endophytes associated with crops have potential as beneficial inoculants in agriculture, but little is known about their genetic diversity and phylogenetic relationships. We carried out the first ever ecological and phylogenetic survey of the culturable fungal root endophytes of a wild barley species. Fungal root endophytes were isolated from 10 populations of wall barley (<i>Hordeum murinum</i>), and 112 taxa of fungi were identified based on internal transcribed spacer sequence similarity. We found representatives from 8 orders, 12 families and 18 genera. Within this group, only 34 isolates (30% of the total) could be confidently assigned to a species, and 23 of the isolates (21% of the total) had no significant match to anything deposited in GenBank (based on &lt;85% sequence similarity). These results suggest a high proportion of novel fungi, with 28% not assigned to a known fungal order. This includes three endophytes that have been shown to significantly improve agronomic traits in cultivated barley. This study has, therefore, revealed a profound diversity of fungal root endophytes in a single wild relative of barley. Extrapolating from this, the study highlights the largely unknown, hugely diverse and potentially useful resource of crop wild relative endophytes.
DOI: 10.6084/m9.figshare.1493028
title: GlobWave L2P altimetry: corrected significant wave height for January, 2002

description: This file contains the L2P altimetry data from GlobWave, corresponding to January, 2002.
DOI: 10.6084/m9.figshare.1493028.v1
title: GlobWave L2P altimetry: corrected significant wave height for January, 2002

description: This file contains the L2P altimetry data from GlobWave, corresponding to January, 2002.
DOI: 10.6084/m9.figshare.1493024
title: Risk of bias and methodological appraisal practises in anaesthesiology systematic reviews..xlsx

description: Data abstracted from 207 systematic reviews and meta analyses published in anesthesia concerning methodological quality or risk of bias assessment practices in these reviews. Full search strategy and manuscript published as Risk of bias and methodological appraisal practises in anaesthesiology systematic reviews. in Anaesthesia Journal.
DOI: 10.6084/m9.figshare.1493024.v1
title: Risk of bias and methodological appraisal practises in anaesthesiology systematic reviews..xlsx

description: Data abstracted from 207 systematic reviews and meta analyses published in anesthesia concerning methodological quality or risk of bias assessment practices in these reviews. Full search strategy and manuscript published as Risk of bias and methodological appraisal practises in anaesthesiology systematic reviews. in Anaesthesia Journal.
DOI: 10.6084/m9.figshare.1493014
title: Temporal changes in cranial size in South African vlei rats (<i>Otomys</i>): evidence for the ‘third universal response to warming’

description: Using museum collections and recently collected specimens we studied geographical and temporal (from 1906 to 2013) changes in skull size of two sibling species of rodents, <i>Otomys auratus</i> and <i>O. angoniensis</i>, in northern South Africa occupying distinct temperate grassland (<i>O. auratus</i>) and subtropical savanna (<i>O. angoniensis</i>) biomes. We hypothesised that cranial size should vary in space and time within species according to Bergmann's Rule, which predicts an inverse relationship between body size and temperature. We used the greatest length of the skull (GLS) as a robust indicator of body size. Cranial size of both <i>O. auratus</i> and <i>O. angoniensis</i> decreased significantly over the past 100 years, as expected given historical evidence of warming across northern South Africa since the 1950s. In terms of geographical patterns, GLS was inversely correlated with both latitude and longitude in <i>O. auratus</i> but these trends were correlated with annual rainfall rather than mean annual temperature. Conversely, cranial size of <i>O. angoniensis</i> was weakly positively correlated with longitude but with no climatic variables. Our results demonstrate rapid morphological changes in two herbivorous South African rodents over the past 100 years. Whilst the general decline in size with time in relation to increased temperature is consistent with Bergmann's Rule, multiple drivers may underlie geographical trends in the two species.
DOI: 10.6084/m9.figshare.1493014.v3
title: Temporal changes in cranial size in South African vlei rats (<i>Otomys</i>): evidence for the ‘third universal response to warming’

description: Using museum collections and recently collected specimens we studied geographical and temporal (from 1906 to 2013) changes in skull size of two sibling species of rodents, <i>Otomys auratus</i> and <i>O. angoniensis</i>, in northern South Africa occupying distinct temperate grassland (<i>O. auratus</i>) and subtropical savanna (<i>O. angoniensis</i>) biomes. We hypothesised that cranial size should vary in space and time within species according to Bergmann's Rule, which predicts an inverse relationship between body size and temperature. We used the greatest length of the skull (GLS) as a robust indicator of body size. Cranial size of both <i>O. auratus</i> and <i>O. angoniensis</i> decreased significantly over the past 100 years, as expected given historical evidence of warming across northern South Africa since the 1950s. In terms of geographical patterns, GLS was inversely correlated with both latitude and longitude in <i>O. auratus</i> but these trends were correlated with annual rainfall rather than mean annual temperature. Conversely, cranial size of <i>O. angoniensis</i> was weakly positively correlated with longitude but with no climatic variables. Our results demonstrate rapid morphological changes in two herbivorous South African rodents over the past 100 years. Whilst the general decline in size with time in relation to increased temperature is consistent with Bergmann's Rule, multiple drivers may underlie geographical trends in the two species.
DOI: 10.6084/m9.figshare.1493014.v2
title: Temporal changes in cranial size in South African vlei rats (<i>Otomys</i>): evidence for the ‘third universal response to warming’

description: Using museum collections and recently collected specimens we studied geographical and temporal (from 1906 to 2013) changes in skull size of two sibling species of rodents, <i>Otomys auratus</i> and <i>O. angoniensis</i>, in northern South Africa occupying distinct temperate grassland (<i>O. auratus</i>) and subtropical savanna (<i>O. angoniensis</i>) biomes. We hypothesised that cranial size should vary in space and time within species according to Bergmann's Rule, which predicts an inverse relationship between body size and temperature. We used the greatest length of the skull (GLS) as a robust indicator of body size. Cranial size of both <i>O. auratus</i> and <i>O. angoniensis</i> decreased significantly over the past 100 years, as expected given historical evidence of warming across northern South Africa since the 1950s. In terms of geographical patterns, GLS was inversely correlated with both latitude and longitude in <i>O. auratus</i> but these trends were correlated with annual rainfall rather than mean annual temperature. Conversely, cranial size of <i>O. angoniensis</i> was weakly positively correlated with longitude but with no climatic variables. Our results demonstrate rapid morphological changes in two herbivorous South African rodents over the past 100 years. Whilst the general decline in size with time in relation to increased temperature is consistent with Bergmann's Rule, multiple drivers may underlie geographical trends in the two species.
DOI: 10.6084/m9.figshare.1493010.v1
title: Deubiquitinase inhibition by WP1130 leads to ULK1 aggregation and blockade of autophagy

description: Autophagy represents an intracellular degradation process which is involved in both regular cell homeostasis and disease settings. In recent years, the molecular machinery governing this process has been elucidated. The ULK1 kinase complex consisting of the serine/threonine protein kinase ULK1 and the adapter proteins ATG13, RB1CC1 and ATG101, is centrally involved in the regulation of autophagy initiation. This complex is in turn regulated by the activity of different nutrient- or energy-sensing kinases, including MTOR, AMPK, and AKT. However, next to phosphorylation processes it has been suggested that ubiquitination of ULK1 positively influences ULK1 function. Here we report that the inhibition of deubiquitinases by the compound WP1130 leads to increased ULK1 ubiquitination, the transfer of ULK1 to aggresomes, and the inhibition of ULK1 activity. Additionally, WP1130 can block the autophagic flux. Thus, treatment with WP1130 might represent an efficient tool to inhibit the autophagy-initiating ULK1 complex and autophagy.
DOI: 10.6084/m9.figshare.1493010.v2
title: Deubiquitinase inhibition by WP1130 leads to ULK1 aggregation and blockade of autophagy

description: Autophagy represents an intracellular degradation process which is involved in both regular cell homeostasis and disease settings. In recent years, the molecular machinery governing this process has been elucidated. The ULK1 kinase complex consisting of the serine/threonine protein kinase ULK1 and the adapter proteins ATG13, RB1CC1, and ATG101, is centrally involved in the regulation of autophagy initiation. This complex is in turn regulated by the activity of different nutrient- or energy-sensing kinases, including MTOR, AMPK, and AKT. However, next to phosphorylation processes it has been suggested that ubiquitination of ULK1 positively influences ULK1 function. Here we report that the inhibition of deubiquitinases by the compound WP1130 leads to increased ULK1 ubiquitination, the transfer of ULK1 to aggresomes, and the inhibition of ULK1 activity. Additionally, WP1130 can block the autophagic flux. Thus, treatment with WP1130 might represent an efficient tool to inhibit the autophagy-initiating ULK1 complex and autophagy.
DOI: 10.6084/m9.figshare.1493010.v3
title: Deubiquitinase inhibition by WP1130 leads to ULK1 aggregation and blockade of autophagy

description: Autophagy represents an intracellular degradation process which is involved in both regular cell homeostasis and disease settings. In recent years, the molecular machinery governing this process has been elucidated. The ULK1 kinase complex consisting of the serine/threonine protein kinase ULK1 and the adapter proteins ATG13, RB1CC1, and ATG101, is centrally involved in the regulation of autophagy initiation. This complex is in turn regulated by the activity of different nutrient- or energy-sensing kinases, including MTOR, AMPK, and AKT. However, next to phosphorylation processes it has been suggested that ubiquitination of ULK1 positively influences ULK1 function. Here we report that the inhibition of deubiquitinases by the compound WP1130 leads to increased ULK1 ubiquitination, the transfer of ULK1 to aggresomes, and the inhibition of ULK1 activity. Additionally, WP1130 can block the autophagic flux. Thus, treatment with WP1130 might represent an efficient tool to inhibit the autophagy-initiating ULK1 complex and autophagy.
DOI: 10.6084/m9.figshare.1492991
title: Cyclopiazonic acid biosynthesis gene cluster gene <i>cpaM</i> is required for speradine A biosynthesis

description: Speradine A is a derivative of cyclopiazonic acid (CPA) found in culture of an <i>Aspergillus tamarii</i> isolate. Heterologous expression of a predicted methyltransferase gene, <i>cpaM,</i> in the <i>cpa</i> biosynthesis gene cluster of <i>A. tamarii</i> resulted in the speradine A production in a 2-oxoCPA producing <i>A. oryzae</i> strain, indicating <i>cpaM</i> is involved in the speradine A biosynthesis.
DOI: 10.6084/m9.figshare.1492990
title: Cushion-open HOBO logger climate data from Pink Mountain, BC 2014

description: Environmental data was recorded on and off Silene acaulis cushion plants in order to measure the potential abiotic stree amelioration provided by these cushions at peak growing season. This study took place in Pink Mountain, British Columbia, Canada which is an alpine/tundra ecosystem. A total of 4 HOBO loggers were uses (2 within cushions, 2 in the open) in two locations on the mountain (one pair on a ridge facing west and one pair in a swail)
DOI: 10.6084/m9.figshare.1492989
title: Left Atrial Segmentation Challenge 2013: MRI testing

description: This fileset is associated with the Left Atrial Segmentation Challenge 2013 (LASC'13). LASC'13 was part of the STACOM'13 workshop, held in conjunction with MICCAI'13. Seven international research groups, comprising 11 algorithms, participated in the challenge. For a detailed report, please refer to: Tobon-Gomez C, Geers AJ, Peters, J, Weese J, Pinto K, Karim R, Ammar M, Daoudi A, Margeta J, Sandoval Z, Stender B, Zheng Y, Zuluaga, MA, Betancur J, Ayache N, Chikh MA, Dillenseger J-L, Kelm BM, Mahmoudi S, Ourselin S, Schlaefer A, Schaeffter T, Razavi R, Rhode KS. Benchmark for Algorithms Segmenting the Left Atrium From 3D CT and MRI Datasets. IEEE Transactions on Medical Imaging, 34(7):1460–1473, 2015.The challenge is also featured on http://www.cardiacatlas.org/challenges/left-atrium-segmentation-challenge/ The data and code of the challenge have been made publicly available to serve as a benchmark for left atrial segmentation algorithms. Code is hosted on https://github.com/catactg/lasc Feel free to contact us with any questions. This fileset consists of 20 MRI datasets for testing segmentation algorithms. Included are the ground truth segmentation and helper files for standardisation. clippointid1.csv: PointID of clvein1.vtp at which to clip PV1 clippointid2.csv: PointID of clvein2.vtp at which to clip PV2 clippointid3.csv: PointID of clvein3.vtp at which to clip PV3 clippointid4.csv: PointID of clvein4.vtp at which to clip PV4 clvein1.vtp: Centerline of PV1 clvein2.vtp: Centerline of PV2 clvein3.vtp: Centerline of PV3 clvein4.vtp: Centerline of PV4 gt_noclip_mesh.vtp: Surface mesh extracted from gt_noclip.mhd gt_noclip.mhd + gt_noclip.zraw: Labeled image representation of GT gt_std_mesh.vtp: Surface mesh after standardisation gt_std.mhd + gt_std.zraw: Image representation of GT with labels copied from gt_std_mesh.vtp image.mhd + image.raw: Image to segment mitralplane.csv: Point, normal, and insideout flag describing mitral plane location
DOI: 10.6084/m9.figshare.1492990.v1
title: Cushion-open HOBO logger climate data from Pink Mountain, BC 2014

description: Environmental data was recorded on and off Silene acaulis cushion plants in order to measure the potential abiotic stree amelioration provided by these cushions at peak growing season. This study took place in Pink Mountain, British Columbia, Canada which is an alpine/tundra ecosystem. A total of 4 HOBO loggers were uses (2 within cushions, 2 in the open) in two locations on the mountain (one pair on a ridge facing west and one pair in a swail)
DOI: 10.6084/m9.figshare.1492991.v1
title: Cyclopiazonic acid biosynthesis gene cluster gene <i>cpaM</i> is required for speradine A biosynthesis

description: Speradine A is a derivative of cyclopiazonic acid (CPA) found in culture of an <i>Aspergillus tamarii</i> isolate. Heterologous expression of a predicted methyltransferase gene, <i>cpaM,</i> in the <i>cpa</i> biosynthesis gene cluster of <i>A. tamarii</i> resulted in the speradine A production in a 2-oxoCPA producing <i>A. oryzae</i> strain, indicating <i>cpaM</i> is involved in the speradine A biosynthesis.
DOI: 10.6084/m9.figshare.1492981
title: The pedestrian data set

description: The pedestrian data set
DOI: 10.6084/m9.figshare.1492991.v3
title: Cyclopiazonic acid biosynthesis gene cluster gene <i>cpaM</i> is required for speradine A biosynthesis

description: Speradine A is a derivative of cyclopiazonic acid (CPA) found in culture of an <i>Aspergillus tamarii</i> isolate. Heterologous expression of a predicted methyltransferase gene, <i>cpaM,</i> in the <i>cpa</i> biosynthesis gene cluster of <i>A. tamarii</i> resulted in the speradine A production in a 2-oxoCPA producing <i>A. oryzae</i> strain, indicating <i>cpaM</i> is involved in the speradine A biosynthesis.
DOI: 10.15468/dl.gjjxcw
title: Occurrence Download

description: A dataset containing 587 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Conwentzia psociformis (Curtis, 1834)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 587 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0094823-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.