cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8088605.v1
title: Core alignment of global collection of HSV-1 genomes

description: <i>De novo</i> assembly was performed on the HSV-1 reads using IVA, and contigs were evaluated using the built-in quality tools and with Kraken. to screen for contamination. To analyse our data in a global context, we aligned our <i>de novo</i> assembled contigs along with previously published sequences from around the world to the HSV-1 strain 17 reference genome using parsnp; this restricted the dataset to an alignment of 93,475 common, non-repetitive nucleotide positions including 2,135 parsimony informative sites.
DOI: 10.6084/m9.figshare.8088578.v1
title: Results from a meta-analysis of defence priming by organismal and non-organismal agents in Arabidopsis Thaliana

description: This dataset contains the findings from a meta-analysis of defence priming in <i>Arabidopsis thaliana</i> from 267 experiments across 77 papers. Data are provided as a semicolon delimited CSV file.<br>Plant resistance to biotic stressors can be strengthened by priming the defence response with organismal and non-organismal agents. Stimulation with such agents triggers a minor part of the plant defence response that confers greater speed, strength and/or endurance against subsequent threats. This defence priming of plants could enhance the protection of crops against pests and diseases while reducing the use of agrochemicals.<br>This dataset presents aggregated effect size values resulting from defence priming with numerous agents and subsequent biotic stressors. Responses quantified in the recorded experiments include lesion area, feeding damage, bacterial growth, infection, disease severity, spore production, feeding duration, population increase, herbivore weight, time to pupation and/or reproduction rate. <br>The following data are included in <b>Westman priming rawdata.csv</b> for each experiment:<br><b>First Author</b> - First author of the associated paper<b>Year </b>- Publication year of the associated paper<b>Ecotype </b>- Ecotype of <i>A. thaliana</i> studied<b>Priming agent</b> - Priming agent studied<b>Biotic stress</b> - Biotic stress the response to which was studied<b>Nr of times repeated</b> - Number of times the experiment was repeated in the given study<b>nT </b>- n of treatment group<b>nC </b>- n of control group <b>m1T </b>- Treatment group mean for quantified response<b>m1C </b>- Control group mean for quantified response<b>sd1T </b>- Treatment group standard deviation<b>sd1C </b>- Control group standard deviation<b>g </b>- Effect size, given as Hedge's g<b>var.g </b>- Variance of g<b>Priming_class_Broad</b> - Broad classification of the priming agent<b>Triggering_class_broad </b>- Broad classification of the biotic stressor<br>
DOI: 10.6084/m9.figshare.8088554
title: Table S1 from Differences in stress reactivity between zebrafish with alternative stress coping styles

description: Raw behavioral and cortisol data used in analyses
DOI: 10.6084/m9.figshare.8088554.v1
title: Table S1 from Differences in stress reactivity between zebrafish with alternative stress coping styles

description: Raw behavioral and cortisol data used in analyses
DOI: 10.6084/m9.figshare.8088506
title: GraphEM.nc

description: GraphEM reconstruction netcdf file.<br>
DOI: 10.6084/m9.figshare.8088473
title: CCA.nc

description: CCA reconstruction NetCDF file.
DOI: 10.6084/m9.figshare.8088506.v1
title: GraphEM.nc

description: GraphEM reconstruction netcdf file.<br>
DOI: 10.6084/m9.figshare.8088473.v1
title: CCA.nc

description: CCA reconstruction NetCDF file.
DOI: 10.6084/m9.figshare.8088392
title: fas.zip

description: Observed S-wave FAS used in the study of Source Characteristics, Site Effects, and Path Attenuation from Spectral Analysis of Strong-Motion Recordings in the 2016 Kaikōura Earthquake Sequence
DOI: 10.6084/m9.figshare.8088389
title: A new stem hynobiid salamander (Urodela, Cryptobranchoidea) from the Upper Jurassic (Oxfordian) of Liaoning Province, China

description: Hynobiids are a group of small- to moderate-sized salamanders living primarily in Asia. They are a primitive crown-group clade, with a poor fossil record. Several hynobiid-like taxa have been discovered from the Lower Cretaceous strata of northern China during the last 20 years, with <i>Liaoxitriton zhongjiani</i> and <i>Nuominerpeton aquilonaris</i> identified as the oldest known stem hynobiids. However, the record of pre-Cretaceous hynobiid-like taxa is only known by <i>Liaoxitriton daohugouensis</i>, of which both the morphology and the congeneric status with <i>L</i>. <i>zhongjiani</i> remain problematic. Here, we report on a new hynobiid-like salamander, <i>Linglongtriton daxishanensis</i>, gen. et sp. nov., on the basis of two specimens from the Upper Jurassic Lanqi/Tiaojishan Formation (∼160 Ma) of Liaoning Province, China. <i>Linglongtriton</i> is diagnosed by a unique combination of features revealed by both observation under microscope and micro-computed tomography (μCT) scan of the holotype, including nasals separated from each other at the midline; prootic, opisthotic, and exoccipital retained as discrete elements; dentary with a lateral groove; articular not ossified; metacarpal III enlarged; a single centrale; and distal tarsals 4 and 5 fused into a single element. Phylogenetic analysis identified <i>Linglongtriton</i> and several other hynobiid-like taxa, including <i>Liaoxitriton daohugouensis</i>, as stem hynobiids, thereby extending the temporal range of the stem by at least 40 Ma—from the Early Cretaceous (Aptian–Barremian) to the Middle Jurassic (Bathonian). Comparative study of <i>Linglongtriton</i> with living and fossil hynobiids sheds new lights on the evolution and developmental mechanisms of several characters, including nasal separation and tarsal elements.
DOI: 10.6084/m9.figshare.8088392.v1
title: fas.zip

description: Observed S-wave FAS used in the study of Source Characteristics, Site Effects, and Path Attenuation from Spectral Analysis of Strong-Motion Recordings in the 2016 Kaikōura Earthquake Sequence
DOI: 10.6084/m9.figshare.8088365
title: PCR.nc

description: PCR reconstruction netcdf file.<br>
DOI: 10.6084/m9.figshare.8088377
title: Fees charged by Customs Officers in Plymouth, 1611 & 1638 (transcript)

description: Testimony giving details of fees received by Customers, Controllers, and Searchers in respect of merchant vessels engaged in either coastal or foreign trade. Includes fees for coastal cockets, certificates, bonds, and let-passes.<br>These fees were abolished in 1649 (see https://www.british-history.ac.uk/no-series/acts-ordinances-interregnum/pp1257-1260) but were subsequently reinstated.
DOI: 10.6084/m9.figshare.8088389.v1
title: A new stem hynobiid salamander (Urodela, Cryptobranchoidea) from the Upper Jurassic (Oxfordian) of Liaoning Province, China

description: Hynobiids are a group of small- to moderate-sized salamanders living primarily in Asia. They are a primitive crown-group clade, with a poor fossil record. Several hynobiid-like taxa have been discovered from the Lower Cretaceous strata of northern China during the last 20 years, with <i>Liaoxitriton zhongjiani</i> and <i>Nuominerpeton aquilonaris</i> identified as the oldest known stem hynobiids. However, the record of pre-Cretaceous hynobiid-like taxa is only known by <i>Liaoxitriton daohugouensis</i>, of which both the morphology and the congeneric status with <i>L</i>. <i>zhongjiani</i> remain problematic. Here, we report on a new hynobiid-like salamander, <i>Linglongtriton daxishanensis</i>, gen. et sp. nov., on the basis of two specimens from the Upper Jurassic Lanqi/Tiaojishan Formation (∼160 Ma) of Liaoning Province, China. <i>Linglongtriton</i> is diagnosed by a unique combination of features revealed by both observation under microscope and micro-computed tomography (μCT) scan of the holotype, including nasals separated from each other at the midline; prootic, opisthotic, and exoccipital retained as discrete elements; dentary with a lateral groove; articular not ossified; metacarpal III enlarged; a single centrale; and distal tarsals 4 and 5 fused into a single element. Phylogenetic analysis identified <i>Linglongtriton</i> and several other hynobiid-like taxa, including <i>Liaoxitriton daohugouensis</i>, as stem hynobiids, thereby extending the temporal range of the stem by at least 40 Ma—from the Early Cretaceous (Aptian–Barremian) to the Middle Jurassic (Bathonian). Comparative study of <i>Linglongtriton</i> with living and fossil hynobiids sheds new lights on the evolution and developmental mechanisms of several characters, including nasal separation and tarsal elements.
DOI: 10.6084/m9.figshare.8088323
title: data list.xlsx

description: Data list for 2445 strong motion recordings used in the study of Source Characteristics, Site Effects, and Path Attenuation from Spectral Analysis of Strong-Motion Recordings in the 2016 Kaikōura Earthquake Sequence
DOI: 10.6084/m9.figshare.8088377.v1
title: Fees charged by Customs Officers in Plymouth, 1611 & 1638 (transcript)

description: Testimony giving details of fees received by Customers, Controllers, and Searchers in respect of merchant vessels engaged in either coastal or foreign trade. Includes fees for coastal cockets, certificates, bonds, and let-passes.<br>These fees were abolished in 1649 (see https://www.british-history.ac.uk/no-series/acts-ordinances-interregnum/pp1257-1260) but were subsequently reinstated.
DOI: 10.6084/m9.figshare.8088323.v1
title: data list.xlsx

description: Data list for 2445 strong motion recordings used in the study of Source Characteristics, Site Effects, and Path Attenuation from Spectral Analysis of Strong-Motion Recordings in the 2016 Kaikōura Earthquake Sequence
DOI: 10.6084/m9.figshare.8088302
title: Demographics and Anthropometrics

description: File containing demographic and anthropometric features of 50 subjects
DOI: 10.6084/m9.figshare.8088365.v1
title: PCR.nc

description: PCR reconstruction netcdf file.<br>
DOI: 10.6084/m9.figshare.8088293
title: FBS/BSA media concentration determines CCCP’s ability to depolarize mitochondria and activate PINK1-PRKN mitophagy

description: Mitochondrial quality control is essential for maintaining a healthy population of mitochondria. Two proteins associated with Parkinson disease, the kinase PINK1 and the E3 ubiquitin ligase PRKN, play a central role in the selective degradation of heavily damaged mitochondria (mitophagy), thus avoiding their toxic accumulation. Most of the knowledge on PINK1-PRKN mitophagy comes from <i>in vitro</i> experiments involving the treatment of mammalian cells with high concentrations of mitochondrial uncouplers, such as CCCP. These chemicals have been shown to mediate off target effects, other than mitochondrial depolarization. A matter of controversy between mitochondrial physiologists and cell biologists is the discrepancy between concentrations of CCCP needed to activate mitophagy (usually &gt;10 μM), when compared to the much lower concentrations used to depolarize mitochondria (&lt;1 μM). Thus, there is an urgent need for optimizing the current methods to assess PINK1-PRKN mitophagy <i>in vitro</i>. In this study, we address the utilization of high CCCP concentrations commonly used to activate mitophagy. Combining live fluorescence microscopy and biochemistry, we show that the FBS/BSA in the cell culture medium reduces the ability of CCCP to induce PINK1 accumulation at depolarized mitochondria, subsequent PRKN recruitment and ubiquitin phosphorylation, and ultimately mitochondrial clearance. As a result, high concentrations of CCCP are required to induce mitophagy in FBS/BSA containing media. These data unite mitochondrial physiology and mitophagy studies and are a first step toward a consensus on optimal experimental conditions for PINK1-PRKN mitophagy and mitochondrial physiology investigations to be carried out in parallel. <b>Abbreviations:</b> BSA: bovine serum albumin; CCCP: carbonyl cyanide m-chlorophenylhydrazone; DMEM: dulbecco’s Modified Eagle’s Medium; DNP: 2,4-dinitrophenol; FBS: fetal bovine serum; FCCP: carbonyl cyanide-4-(trifluoromethoxy)phenylhydrazone; GSH: glutathione; HBSS: Hanks‘ balanced salt solution; mtKeima: mitochondria-targeted monomeric keima-red; PBS: phosphate buffered saline; PD: Parkinson disease; PINK1: PTEN induced kinase 1; POE SHSY5Ys: FLAG-PRKN over-expressing SHSY5Y cells; SDS-PAGE: sodium dodecyl sulfate polyacrylamide gel electrophoresis; TMRM: tetramethylrhodamine methyl ester; WB: western blot; WT: wild-type; ΔΨm: mitochondrial membrane potential
DOI: 10.6084/m9.figshare.8088293.v2
title: FBS/BSA media concentration determines CCCP’s ability to depolarize mitochondria and activate PINK1-PRKN mitophagy

description: Mitochondrial quality control is essential for maintaining a healthy population of mitochondria. Two proteins associated with Parkinson disease, the kinase PINK1 and the E3 ubiquitin ligase PRKN, play a central role in the selective degradation of heavily damaged mitochondria (mitophagy), thus avoiding their toxic accumulation. Most of the knowledge on PINK1-PRKN mitophagy comes from <i>in vitro</i> experiments involving the treatment of mammalian cells with high concentrations of mitochondrial uncouplers, such as CCCP. These chemicals have been shown to mediate off target effects, other than mitochondrial depolarization. A matter of controversy between mitochondrial physiologists and cell biologists is the discrepancy between concentrations of CCCP needed to activate mitophagy (usually &gt;10 μM), when compared to the much lower concentrations used to depolarize mitochondria (&lt;1 μM). Thus, there is an urgent need for optimizing the current methods to assess PINK1-PRKN mitophagy <i>in vitro</i>. In this study, we address the utilization of high CCCP concentrations commonly used to activate mitophagy. Combining live fluorescence microscopy and biochemistry, we show that the FBS/BSA in the cell culture medium reduces the ability of CCCP to induce PINK1 accumulation at depolarized mitochondria, subsequent PRKN recruitment and ubiquitin phosphorylation, and ultimately mitochondrial clearance. As a result, high concentrations of CCCP are required to induce mitophagy in FBS/BSA containing media. These data unite mitochondrial physiology and mitophagy studies and are a first step toward a consensus on optimal experimental conditions for PINK1-PRKN mitophagy and mitochondrial physiology investigations to be carried out in parallel. <b>Abbreviations:</b> BSA: bovine serum albumin; CCCP: carbonyl cyanide m-chlorophenylhydrazone; DMEM: dulbecco’s Modified Eagle’s Medium; DNP: 2,4-dinitrophenol; FBS: fetal bovine serum; FCCP: carbonyl cyanide-4-(trifluoromethoxy)phenylhydrazone; GSH: glutathione; HBSS: Hanks‘ balanced salt solution; mtKeima: mitochondria-targeted monomeric keima-red; PBS: phosphate buffered saline; PD: Parkinson disease; PINK1: PTEN induced kinase 1; POE SHSY5Ys: FLAG-PRKN over-expressing SHSY5Y cells; SDS-PAGE: sodium dodecyl sulfate polyacrylamide gel electrophoresis; TMRM: tetramethylrhodamine methyl ester; WB: western blot; WT: wild-type; ΔΨm: mitochondrial membrane potential
DOI: 10.6084/m9.figshare.8088293.v1
title: FBS/BSA media concentration determines CCCP’s ability to depolarize mitochondria and activate PINK1-PRKN mitophagy

description: Mitochondrial quality control is essential for maintaining a healthy population of mitochondria. Two proteins associated with Parkinson disease, the kinase PINK1 and the E3 ubiquitin ligase PRKN, play a central role in the selective degradation of heavily damaged mitochondria (mitophagy), thus avoiding their toxic accumulation. Most of the knowledge on PINK1-PRKN mitophagy comes from <i>in vitro</i> experiments involving the treatment of mammalian cells with high concentrations of mitochondrial uncouplers, such as CCCP. These chemicals have been shown to mediate off target effects, other than mitochondrial depolarization. A matter of controversy between mitochondrial physiologists and cell biologists is the discrepancy between concentrations of CCCP needed to activate mitophagy (usually &gt;10 μM), when compared to the much lower concentrations used to depolarize mitochondria (&lt;1 μM). Thus, there is an urgent need for optimizing the current methods to assess PINK1-PRKN mitophagy <i>in vitro</i>. In this study, we address the utilization of high CCCP concentrations commonly used to activate mitophagy. Combining live fluorescence microscopy and biochemistry, we show that the FBS/BSA in the cell culture medium reduces the ability of CCCP to induce PINK1 accumulation at depolarized mitochondria, subsequent PRKN recruitment and ubiquitin phosphorylation, and ultimately mitochondrial clearance. As a result, high concentrations of CCCP are required to induce mitophagy in FBS/BSA containing media. These data unite mitochondrial physiology and mitophagy studies and are a first step toward a consensus on optimal experimental conditions for PINK1-PRKN mitophagy and mitochondrial physiology investigations to be carried out in parallel. <b>Abbreviations:</b> BSA: bovine serum albumin; CCCP: carbonyl cyanide m-chlorophenylhydrazone; DMEM: dulbecco’s Modified Eagle’s Medium; DNP: 2,4-dinitrophenol; FBS: fetal bovine serum; FCCP: carbonyl cyanide-4-(trifluoromethoxy)phenylhydrazone; GSH: glutathione; HBSS: Hanks‘ balanced salt solution; mtKeima: mitochondria-targeted monomeric keima-red; PBS: phosphate buffered saline; PD: Parkinson disease; PINK1: PTEN induced kinase 1; POE SHSY5Ys: FLAG-PRKN over-expressing SHSY5Y cells; SDS-PAGE: sodium dodecyl sulfate polyacrylamide gel electrophoresis; TMRM: tetramethylrhodamine methyl ester; WB: western blot; WT: wild-type; ΔΨm: mitochondrial membrane potential
DOI: 10.6084/m9.figshare.8088263
title: Raster connectivity – an important tool for landscape planning and conservation. A case study on butterflies and burnet moths

description: Species data from Šardice surroundings - butterflies and burnet moths. Data were used for evaluation of raster connectivity.
DOI: 10.6084/m9.figshare.8088227
title: Magnesium sulphate can prolong pregnancy in patients with severe early-onset preeclampsia

description: <i>Objective</i>: To assess whether long-term use of magnesium sulphate prolongs pregnancy in patients with severe early-onset preeclampsia. <i>Methods</i>: Retrospective cohort study included all singleton pregnancies with severe early-onset preeclampsia, expectantly managed in our institution between 2005 and 2013. Obstetric and perinatal outcomes were compared between patients managed using a current protocol that tolerates long-term (over 48 h) use of magnesium sulphate (long-term group, <i>n</i> = 26) and a historical control group (control group, <i>n</i> = 15) that underwent conventional treatment (up to 48 h use of magnesium sulphate). <i>Results</i>: Long-term group showed significant prolongation of pregnancy compared with the control group (9.2 ± 7.9 versus 16.6 ± 9.3 d, log-rank test, <i>p</i> = 0.021), which was also observed in patients with severe preeclampsia occurring before 28 weeks’ gestation (<i>n</i> = 11, 4.5 ± 5.2 versus 13.2 ± 6.8 d, log-rank test, <i>p</i> = 0.035). In contrast to a progressive decrease of platelet count in patients managed without magnesium sulphate, administration of magnesium sulphate for 7 d prevented the decrease of platelet count (<i>p</i> = 0.001). Thirty two percent of patients (13/41) experienced a major complication irrespective of duration of magnesium sulphate use. <i>Conclusions</i>: Long-term use of magnesium sulphate prolonged pregnancy in patients with severe early-onset preeclampsia and can help alleviate progression of preeclampsia.
DOI: 10.6084/m9.figshare.8088227.v1
title: Magnesium sulphate can prolong pregnancy in patients with severe early-onset preeclampsia

description: <i>Objective</i>: To assess whether long-term use of magnesium sulphate prolongs pregnancy in patients with severe early-onset preeclampsia. <i>Methods</i>: Retrospective cohort study included all singleton pregnancies with severe early-onset preeclampsia, expectantly managed in our institution between 2005 and 2013. Obstetric and perinatal outcomes were compared between patients managed using a current protocol that tolerates long-term (over 48 h) use of magnesium sulphate (long-term group, <i>n</i> = 26) and a historical control group (control group, <i>n</i> = 15) that underwent conventional treatment (up to 48 h use of magnesium sulphate). <i>Results</i>: Long-term group showed significant prolongation of pregnancy compared with the control group (9.2 ± 7.9 versus 16.6 ± 9.3 d, log-rank test, <i>p</i> = 0.021), which was also observed in patients with severe preeclampsia occurring before 28 weeks’ gestation (<i>n</i> = 11, 4.5 ± 5.2 versus 13.2 ± 6.8 d, log-rank test, <i>p</i> = 0.035). In contrast to a progressive decrease of platelet count in patients managed without magnesium sulphate, administration of magnesium sulphate for 7 d prevented the decrease of platelet count (<i>p</i> = 0.001). Thirty two percent of patients (13/41) experienced a major complication irrespective of duration of magnesium sulphate use. <i>Conclusions</i>: Long-term use of magnesium sulphate prolonged pregnancy in patients with severe early-onset preeclampsia and can help alleviate progression of preeclampsia.
DOI: 10.6084/m9.figshare.8088200
title: Supplementary Material for: Direct Admission versus Secondary Transfer for Acute Stroke Patients Treated with Intravenous Thrombolysis and Thrombectomy: Insights from the Endovascular Treatment in Ischemic Stroke Registry

description: <b><i>Background:</i></b> To date, thrombectomy for large vessel occlusion (LVO) strokes can be performed only in comprehensive stroke centers with thrombectomy capacity. We compared the clinical outcome of patients first referred to a primary stroke center to those admitted directly to a comprehensive stroke center and treated on site in the multicentric observational Endovascular Treatment in Ischemic Stroke (ETIS) registry. <b><i>Methods:</i></b> From our perspective, multicenter, observational ETIS registry, we analyzed anterior circulation stroke patients, treated within 8 h, who underwent thrombectomy after thrombolysis and were admitted to a comprehensive stroke center either with drip and ship or mothership. Clinical and safety outcomes were compared between 2 groups. <b><i>Results:</i></b> A total of 971 patients were analyzed: 298 were treated with the mothership approach and 673 with drip and ship. Significantly more functional independence (90-day modified Rankin Scale [mRS] 0–2) was achieved in mothership (60.1%) than in drip and ship patients (52.6%; adjusted relative risk [RR] 0.87, 95% CI 0.77–0.98, <i>p</i> = 0.018). Excellent outcome (90-day mRS 0–1) was achieved in 45.3% of the mothership group, compared to 37.9% of the drip and ship group (RR 0.84, 95% CI 0.71–0.98; <i>p</i> = 0.026). According to the distance between the primary stroke center and the comprehensive stroke center, greater functional independence was achieved in mothership than in drip and ship &gt;12.5 miles patients (adjusted RR 0.82; 95% CI 0.71–0.94). Results in the drip-ship group stratified according to time between cerebral imaging and groin puncture (categorized according to the median cut-off: 140 min) were similar. Symptomatic intracerebral hemorrhage rate and mortality within 90 days was similar in both groups (7.5 vs. 5.9%, <i>p</i> = 0.40; 17.4 vs. 16.1%, <i>p</i> = 0.63). <b><i>Conclusions:</i></b> Our study suggests that LVO stroke patients directly admitted to a comprehensive stroke center present a higher chance of functional independence, especially when the distance between the primary stroke center and comprehensive stroke center is &gt;12.5 miles or when the time between cerebral imaging and groin puncture is ≥140 min.