cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9912689.v1
title: Supplementary Material for: Factors Associated with Unsuccessful Recanalization in Mechanical Thrombectomy for Acute Ischemic Stroke

description: <b><i>Introduction:</i></b> Mechanical thrombectomy (MT) for acute ischemic stroke has become a standard therapy, and the recanalization rate has significantly improved. However, some cases of unsuccessful recanalization still occur. We aimed to clarify patient factors associated with unsuccessful recanalization after MT for acute ischemic stroke. <b><i>Methods:</i></b> This was a single-center, retrospective study of 119 consecutive patients with anterior circulation acute ischemic stroke who underwent MT at our hospital between April 2015 and March 2019. Successful recanalization after MT was defined as modified Treatment in Cerebral Ischemia (mTICI) grade 2b or 3, and unsuccessful recanalization was defined as mTICI grades 0–2a. Several factors were analyzed to assess their effect on recanalization rates. <b><i>Results:</i></b> Successful recanalization was achieved in 88 patients (73.9%). The univariate analysis showed that female sex (38.6 vs. 67.7%, <i>p</i> = 0.007), a history of hypertension (53.4 vs. 83.9%, <i>p</i> = 0.003), and a longer time from groin puncture to recanalization (median 75 vs. 124 min, <i>p</i> &lt; 0.001) were significantly associated with unsuccessful recanalization. The multivariate analysis confirmed that female sex (OR 3.18; 95% CI 1.12–9.02, <i>p</i> = 0.030), a history of hypertension (OR 4.84; 95% CI 1.32–17.8, <i>p</i> = 0.018), M2–3 occlusion (OR 4.26; 95% CI 1.36–13.3, <i>p</i> = 0.013), and the time from groin puncture to recanalization (per 10-min increase, OR 1.22; 95% CI 1.09–1.37, <i>p</i> &lt; 0.001) were independently associated with unsuccessful recanalization. <b><i>Conclusion:</i></b> Female sex and a history of hypertension might be predictors of unsuccessful recanalization after MT for anterior circulation acute ischemic stroke. Further studies are needed to fully evaluate predictors of recanalization.
DOI: 10.6084/m9.figshare.9912674
title: Supplementary Material for: Comparison of Neonatal Intubation Practice and Outcomes between the Neonatal Intensive Care Unit and Delivery Room

description: <b><i>Background:</i></b> Characteristics of neonatal tracheal intubations (TI) may vary between the neonatal intensive care unit (NICU) and delivery room (DR). The impact of the setting on TI outcomes is not well characterized. <b><i>Objective:</i></b> The aim of this study was to define variation in neonatal TI practice between settings, and identify the association between setting and TI success and safety outcomes. <b><i>Design:</i></b> This was a retrospective cohort study of TIs in the National Emergency Airway Registry for Neonates from October 2014 to September 2017. The setting (NICU vs. DR) was the exposure of interest. The outcomes were first attempt success, course success, success within 4 attempts, adverse TI-associated events, severe desaturation, and bradycardia. We compared TI characteristics and outcomes between settings in univariable analysis. Factors significant in univariable analysis (<i>p</i> &lt; 0.1) were included in a logistic regression model, with adjustment for clustering by center, to identify the independent impact of the setting on TI outcomes. <b><i>Results:</i></b> There were 3,145 TI encounters (2279 NICU, 866 DR) in 9 centers. Almost all baseline characteristics significantly varied between settings. First attempt success rates were 48% (NICU) and 46% (DR). In multivariable analysis, the setting was not associated with first attempt success. DR was associated with a higher adjusted OR (aOR) of success within 4 attempts (1.48, 95% CI 1.06–2.08) and a lower aOR for bradycardia (0.43, 95% CI 0.26–0.71). <b><i>Conclusion:</i></b> Significant differences in patient, provider, and practice characteristics exist between NICU and DR TIs. There is substantial room for improvement in first attempt success rates. These results suggest interventions to improve safety and success need to be targeted to the distinct setting.
DOI: 10.6084/m9.figshare.9912665
title: Supplementary File 3 from Carotenoid pigmentation in salmon: variation in expression at <i>BCO2-l</i> locus controls a key fitness trait affecting red coloration

description: Supplementary custom python script 3
DOI: 10.6084/m9.figshare.9912668
title: Supplementary File 2 from Carotenoid pigmentation in salmon: variation in expression at <i>BCO2-l</i> locus controls a key fitness trait affecting red coloration

description: Supplementary custom python script 3
DOI: 10.6084/m9.figshare.9912662
title: Supplementary File 1 from Carotenoid pigmentation in salmon: variation in expression at <i>BCO2-l</i> locus controls a key fitness trait affecting red coloration

description: Supplementary custom python script 1
DOI: 10.6084/m9.figshare.9912659
title: Supplementary Scripts read me from Carotenoid pigmentation in salmon: variation in expression at <i>BCO2-l</i> locus controls a key fitness trait affecting red coloration

description: Information regarding supplementary custom python scripts
DOI: 10.6084/m9.figshare.9912665.v1
title: Supplementary File 3 from Carotenoid pigmentation in salmon: variation in expression at <i>BCO2-l</i> locus controls a key fitness trait affecting red coloration

description: Supplementary custom python script 3
DOI: 10.6084/m9.figshare.9912668.v1
title: Supplementary File 2 from Carotenoid pigmentation in salmon: variation in expression at <i>BCO2-l</i> locus controls a key fitness trait affecting red coloration

description: Supplementary custom python script 3
DOI: 10.6084/m9.figshare.9912674.v1
title: Supplementary Material for: Comparison of Neonatal Intubation Practice and Outcomes between the Neonatal Intensive Care Unit and Delivery Room

description: <b><i>Background:</i></b> Characteristics of neonatal tracheal intubations (TI) may vary between the neonatal intensive care unit (NICU) and delivery room (DR). The impact of the setting on TI outcomes is not well characterized. <b><i>Objective:</i></b> The aim of this study was to define variation in neonatal TI practice between settings, and identify the association between setting and TI success and safety outcomes. <b><i>Design:</i></b> This was a retrospective cohort study of TIs in the National Emergency Airway Registry for Neonates from October 2014 to September 2017. The setting (NICU vs. DR) was the exposure of interest. The outcomes were first attempt success, course success, success within 4 attempts, adverse TI-associated events, severe desaturation, and bradycardia. We compared TI characteristics and outcomes between settings in univariable analysis. Factors significant in univariable analysis (<i>p</i> &lt; 0.1) were included in a logistic regression model, with adjustment for clustering by center, to identify the independent impact of the setting on TI outcomes. <b><i>Results:</i></b> There were 3,145 TI encounters (2279 NICU, 866 DR) in 9 centers. Almost all baseline characteristics significantly varied between settings. First attempt success rates were 48% (NICU) and 46% (DR). In multivariable analysis, the setting was not associated with first attempt success. DR was associated with a higher adjusted OR (aOR) of success within 4 attempts (1.48, 95% CI 1.06–2.08) and a lower aOR for bradycardia (0.43, 95% CI 0.26–0.71). <b><i>Conclusion:</i></b> Significant differences in patient, provider, and practice characteristics exist between NICU and DR TIs. There is substantial room for improvement in first attempt success rates. These results suggest interventions to improve safety and success need to be targeted to the distinct setting.
DOI: 10.6084/m9.figshare.9912659.v1
title: Supplementary Scripts read me from Carotenoid pigmentation in salmon: variation in expression at <i>BCO2-l</i> locus controls a key fitness trait affecting red coloration

description: Information regarding supplementary custom python scripts
DOI: 10.6084/m9.figshare.9912662.v1
title: Supplementary File 1 from Carotenoid pigmentation in salmon: variation in expression at <i>BCO2-l</i> locus controls a key fitness trait affecting red coloration

description: Supplementary custom python script 1
DOI: 10.6084/m9.figshare.9912623
title: Mapping trends in insecticide resistance phenotypes in African malaria vectors

description: The mean predictions for the prevalence of resistance (susceptibility test mortality) were produced by a model that used susceptibility test data from field populations and a large number of potential explanatory variables. Full details are given in the linked PLoS Biology article.<br>A zip folder is provided for each year from 2005 to 2017. Each zip folder contains a raster comprising of a GRD and GRI file. Each raster has five bands: <br>- band 1 is mortality after alpha-cypermethrin exposure;- band 2 is mortality after DDT exposure;- band 3 is mortality after deltametrin exposure;- band 4 is mortality after lambda-cyhalothrin exposure;- band 5 is mortality after permethrin exposure.<br>The rasters are at a 2.5 arcminute (approx. 5 km) resolution. Each grid cell has a value for the predicted mean prevalence of resistance (susceptibility test mortality) on a scale 0.0 to 1.0.<br><br>The above data can be visualised and processed in a range of geographical information system packages (e.g. ArcGIS and QGIS) or spatial data packages in R (http://cran.r-project.org/web/views/Spatial.html). <br><br>In addition, files containing the numerical values behind each figure in the linked article are provided in files S1 to S8.
DOI: 10.6084/m9.figshare.9912650
title: Bimodal regulation of the PRC2 complex by USP7 underlies tumorigenesis

description: bigwig files
DOI: 10.6084/m9.figshare.9912650.v2
title: Bimodal regulation of the PRC2 complex by USP7 underlies tumorigenesis

description: bigwig files
DOI: 10.6084/m9.figshare.9912650.v1
title: Bimodal regulation of the PRC2 complex by USP7 underlies tumorigenesi

description: bigwig files
DOI: 10.6084/m9.figshare.9912587
title: Table S4 from Escaping the evolutionary trap? Sex chromosome turnover in basilisks and related lizards (Corytophanidae: Squamata)

description: List of genes, primers and relative gene dose ratios (r) between males and females for autosomal control and X-specific genes in six iguanian species (r = 1 corresponds to autosomal or pseudoautosomal position, while r = 0.5 corresponds to X-specificity). The Cp for the gene eef1a1 was used for normalization from the same run. The symbol "x" means that qPCR test was not successful (e.g. lack of amplification or presence of a secondary product).
DOI: 10.6084/m9.figshare.9912590
title: Table S3 from Escaping the evolutionary trap? Sex chromosome turnover in basilisks and related lizards (Corytophanidae: Squamata)

description: PCR and qPCR primers used.
DOI: 10.6084/m9.figshare.9912587.v1
title: Table S4 from Escaping the evolutionary trap? Sex chromosome turnover in basilisks and related lizards (Corytophanidae: Squamata)

description: List of genes, primers and relative gene dose ratios (r) between males and females for autosomal control and X-specific genes in six iguanian species (r = 1 corresponds to autosomal or pseudoautosomal position, while r = 0.5 corresponds to X-specificity). The Cp for the gene eef1a1 was used for normalization from the same run. The symbol "x" means that qPCR test was not successful (e.g. lack of amplification or presence of a secondary product).
DOI: 10.6084/m9.figshare.9912584
title: Table S1 from Escaping the evolutionary trap? Sex chromosome turnover in basilisks and related lizards (Corytophanidae: Squamata)

description: List of specimens used in study.
DOI: 10.6084/m9.figshare.9912590.v1
title: Table S3 from Escaping the evolutionary trap? Sex chromosome turnover in basilisks and related lizards (Corytophanidae: Squamata)

description: PCR and qPCR primers used.
DOI: 10.6084/m9.figshare.9912581
title: Table S5 from Escaping the evolutionary trap? Sex chromosome turnover in basilisks and related lizards (Corytophanidae: Squamata)

description: List of genes expressed in eye tissue, their homology in the green anole Anolis carolinensis and chicken Gallus gallus genomes and the FPKM expression values.
DOI: 10.6084/m9.figshare.9912581.v1
title: Table S5 from Escaping the evolutionary trap? Sex chromosome turnover in basilisks and related lizards (Corytophanidae: Squamata)

description: List of genes expressed in eye tissue, their homology in the green anole Anolis carolinensis and chicken Gallus gallus genomes and the FPKM expression values.
DOI: 10.6084/m9.figshare.9912569
title: Table S2 from Escaping the evolutionary trap? Sex chromosome turnover in basilisks and related lizards (Corytophanidae: Squamata)

description: BLAST results of male-specific RAD markers.
DOI: 10.6084/m9.figshare.9912569.v1
title: Table S2 from Escaping the evolutionary trap? Sex chromosome turnover in basilisks and related lizards (Corytophanidae: Squamata)

description: BLAST results of male-specific RAD markers.
DOI: 10.6084/m9.figshare.9912551
title: Mt. Field data from Roberts Ecology (2020)

description: Vegetation and site data from Mt. Field, Tasmania (Minchin 1983 Dissertation; Minchin 1989 Vegetatio 83:97-100.) <br><br>424 sample units, 209 species from original 438 sample units and 221 species; four environmental variables. Collected by Peter Minchin in Mt. Field, Tasmania. Used by permission.<br><br>Taxonomic treatment as recorded in 1983. Abundances recorded in six cover classes, midpoints = 0.05, 0.55, 5.5, 20, 50, 85]<br><br>
DOI: 10.6084/m9.figshare.9912551.v1
title: Mt. Field data from Roberts Ecology (2020)

description: Vegetation and site data from Mt. Field, Tasmania (Minchin 1983 Dissertation; Minchin 1989 Vegetatio 83:97-100.) <br><br>424 sample units, 209 species from original 438 sample units and 221 species; four environmental variables. Collected by Peter Minchin in Mt. Field, Tasmania. Used by permission.<br><br>Taxonomic treatment as recorded in 1983. Abundances recorded in six cover classes, midpoints = 0.05, 0.55, 5.5, 20, 50, 85]<br><br>
DOI: 10.6084/m9.figshare.9912482
title: Supplementary Material for: MicroRNA-296-5p Promotes Cell Invasion and Drug Resistance by Targeting Bcl2-Related Ovarian Killer, Leading to a Poor Prognosis in Pancreatic Cancer

description: <b><i>Background/Aims:</i></b> Pancreatic ductal adenocarcinoma (PDAC) is characterized by aggressive invasion, early metastasis, and resistance to chemotherapy, leading to a poor prognosis. To clarify the molecular mechanism of these malignant characteristics, we performed a genome-wide microRNA (miRNA) array analysis utilizing micro-cancer tissues from patients with unresectable PDAC (stage IV), obtained by endoscopic ultrasound-fine needle aspiration (EUS-FNA). <b><i>Methods:</i></b> The expression profiles of 2,042 miRNAs were determined using micro-cancer tissues from 13 patients with unresectable PDAC obtained by EUS-FNA. The relationship between individual miRNA levels and overall survival (OS) was analyzed. Possible target genes for miRNAs were bioinformatically analyzed using the online database miRDB. Pancreatic cancer cell lines PANC-1, MIA PaCa-2, and PK-8 were transfected with miRNA mimic or small interfering RNA, and cell invasion, epithelial-mesenchymal transition (EMT), and apoptosis markers were examined. miRNA and mRNA expressions were examined by quantitative polymerase chain reaction. <b><i>Results:</i></b> Of 2,042 miRNAs, the 10 that exhibited the lowest correlation coefficient (<i>p</i> ≤ 0.005) between miRNA expression level and OS among the patients were identified. The miRDB and expression analysis in cancer cell lines for the 10 miRNAs identified miR-296-5p and miR-1207-5p as biomarkers predictive of shorter survival (<i>p</i> &lt; 0.0005). Bioinformative target gene analysis and transfection experiments with miRNA mimics showed that <i>Bcl2-related</i> <i>ovarian</i> <i>killer</i> (<i>BOK</i>), a pro-apoptotic gene, is a target for miR296-5p in pancreatic cancer cells; transfection of miR-296-5p mimic into PANC-1, MIA PaCa-2, and PK-8 cells resulted in significant suppression of <i>BOK</i> mRNA and protein expression. These transfectants showed significantly higher invasion capability compared with control cells, and knock down of <i>BOK</i> in pancreatic cancer cells similarly enhanced invasion capability. Transfectants of miR-296-5p mimic also exhibited aberrant expression of EMT markers, including vimentin and N-cadherin. Moreover, these transfectants showed a significantly lower apoptosis rate in response to 5-fluorouracil and gemcitabine with a decrease of <i>BOK</i> expression, suggesting a role of miR-296-5p in drug resistance. <b><i>Conclusion:</i></b> These results suggest that miR-296-5p is a useful biomarker for a poor prognosis in patients with PDAC, and that the miR-296-5p/BOK signaling axis plays an important role in cell invasion, drug resistance, and EMT in PDACs.
DOI: 10.6084/m9.figshare.9911936
title: <i>In situ</i> characterisation of biofilms formed by psychrotrophic meat spoilage pseudomonads

description: Psychrotrophic <i>Pseudomonas</i> species form biofilms on meat during refrigerated and temperature abuse conditions. Biofilm growth leads to slime formation on meat which is a key organoleptic degradation characteristic. Limited research has been undertaken characterising biofilms grown on meat during chilled aerobic storage. In this work, biofilms formed by two key meat spoilage organisms, <i>Pseudomonas fragi</i> and <i>Pseudomonas lundensis</i> were studied <i>in situ</i> using five strains from each species. Biofilm structures were studied using confocal microscope images, cellular arrangement, cell counts and biomass quantifications. This work demonstrated that highly dense, compact biofilms are a characteristic of <i>P. fragi</i> strains. <i>P. lundensis</i> formed biofilms with loosely arranged cells. The cells in <i>P. fragi</i> biofilm appear to be vertically oriented whereas this characteristic was absent in <i>P. lundensis</i> biofilms formed under identical conditions. Despite the continued access to nutrients, biofilms formed on meat by proteolytic <i>Pseudomonas</i> species dispersed after a population maximum was reached.
DOI: 10.6084/m9.figshare.9911918
title: Analysis of spatiotemporal specificity of small RNAs regulating hPSC differentiation and beyond

description: We present a quantitative analysis of small RNA dynamics during the transition from hPSCs to the three germ layer lineages to identify spatiotemporal-specific small RNAs that may be involved in hPSC differentiation. To determine the degree of spatiotemporal specificity, we utilized two algorithms, namely normalized maximum timepoint specificity index (NMTSI) and across-tissue specificity index (ASI). NMTSI could identify spatiotemporal-specific small RNAs that go up or down at just one timepoint in a specific lineage. ASI could identify spatiotemporal-specific small RNAs that maintain high expression from intermediate timepoints to the terminal timepoint in a specific lineage. Beyond analyzing single small RNAs, we also quantified the spatiotemporal-specificity of microRNA families and observed their differential expression patterns in certain lineages. To clarify the regulatory effects of group miRNAs on cellular events during lineage differentiation, we performed a gene ontology (GO) analysis on the downstream targets of synergistically up- and downregulated microRNAs. To provide an integrated interface for researchers to access and browse our analysis results, we designed a web-based tool at https://keyminer.pythonanywhere.com/km/.
DOI: 10.6084/m9.figshare.9911927
title: Shuanggou peridotite (JGR-2019JB017552R).xlsx

description: The table includes whole-rock major, trace, PGE, and Re-Os isotope data of mantle peridotites (harzburgites and lherzolites) in the Shuanggou ophiolite, and clinopyroxene compositions in the lherzolites. Whole-rock major elements were analyzed using X-ray fluorescence (XRF) with &lt;5% at the Australian Laboratory Services P/L. Trace element compositions were measured using an inductively coupled plasma mass spectrometry (ICP-MS) at the State Key Laboratory of Ore Deposit Geochemistry, Chinese Academy of Sciences (SKLODG), following the procedure of Qi et al. (2000). In-situ analysis of clinopyroxenes in the lherzolites was analyzed by an Agilent 7900× ICP-MS (LA-ICP-MS) coupled with Coherent GeoLasPro 193-nm Laser Ablation system at the SKLODG following the experimental conditions and procedures from Liu et al. (2008). Whole-rock PGE data are measured an isotope dilution (ID)–ICP–MS at the SKLODG following the procedure of Qi et al. (2011). Whole-rock Re-Os isotope data are measured by a Isoprobe-T Mass Spectrometer and a Neptune multicollector (MC)-ICP-MS at the State Key Laboratory of Lithospheric Evolution, Institute of Geology and Geophysics, Chinese Academy of Sciences, following the method of Chu et al (2009). ReferenceChu, Z.Y., Wu, F.Y., Walker, R.J., Rudnick, R.L., Pitcher, L., Puchtel, I.S., Yang, Y.H., & Wilde, S.A. (2009). Temporal evolution of the lithospheric mantle beneath the eastern North China Craton. Journal of Petrology, 50, 1857-1898.Liu, Y., Hu, Z., Gao, S., Günther, D., Xu, J., Gao, C., & Chen, H. (2008). In situ analysis of major and trace elements of anhydrous minerals by LA-ICP-MS without applying an internal standard. Chemical Geology, 257(1-2), 34-43.Qi, L., Gao, J., Huang, X., Hu, J., Zhou, M. F., & Zhong, H. (2011). An improved digestion technique for determination of platinum group elements in geological samples. Journal of Analytical Atomic Spectrometry, 26(9), 1900-1904.Qi, L., Hu, J., & Gregoire, D. C. (2000). Determination of trace elements in granites by inductively coupled plasma mass spectrometry. Talanta, 51(3), 507-513.
DOI: 10.6084/m9.figshare.9911936.v1
title: <i>In situ</i> characterisation of biofilms formed by psychrotrophic meat spoilage pseudomonads

description: Psychrotrophic <i>Pseudomonas</i> species form biofilms on meat during refrigerated and temperature abuse conditions. Biofilm growth leads to slime formation on meat which is a key organoleptic degradation characteristic. Limited research has been undertaken characterising biofilms grown on meat during chilled aerobic storage. In this work, biofilms formed by two key meat spoilage organisms, <i>Pseudomonas fragi</i> and <i>Pseudomonas lundensis</i> were studied <i>in situ</i> using five strains from each species. Biofilm structures were studied using confocal microscope images, cellular arrangement, cell counts and biomass quantifications. This work demonstrated that highly dense, compact biofilms are a characteristic of <i>P. fragi</i> strains. <i>P. lundensis</i> formed biofilms with loosely arranged cells. The cells in <i>P. fragi</i> biofilm appear to be vertically oriented whereas this characteristic was absent in <i>P. lundensis</i> biofilms formed under identical conditions. Despite the continued access to nutrients, biofilms formed on meat by proteolytic <i>Pseudomonas</i> species dispersed after a population maximum was reached.