cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19778674
title: Data from: Estimates of niche position and breadth vary across spatial scales for native and alien inland fishes

description: Estimates of species’ niche position and breadth is considered fundamental to understanding their ecological and evolutionary responses to natural and anthropogenic environmental change. Methodological challenges arise from the fact that macroecological inference is substantially affected by the selection of a certain geographical extent. This is particularly relevant for understanding alien species introduction success and associated species’ niche characteristics which can be estimated either from their invaded region, their native region, or both. However, surprisingly little is known regarding how the estimation of species niche breadth and position is affected by the geographical extent of investigation, especially for alien species. Here we estimate and compare climatic niche metrics of native and alien Iberian inland fishes using the outlying mean index (OMI) at three different geographical extents spanning from regional to global. Furthermore, we investigate how the introduction date of alien species affects niche characterisation. Our results show that niche metrics differed depending on the geographical extent of the investigation, as well as with respect to species nativity (native vs. alien). Differences in climatic niche position between native and alien species observed at a global scale vanished at a regional scale. The niche breadth of widely distributed alien species was highly underestimated when only considering the invaded region, and further mediated by species’ introduction date into the invaded area. In conclusion, estimating niches of freshwater species, especially of alien invaders should carefully consider the geographical extent of the investigation. We suggest that analyses that jointly consider regional and global scales will improve the estimation of niche characteristics of widely distributed organisms, particularly regarding the climatic niche, and the assessment of the invasive potential of species.
DOI: 10.2908/isoc_eb_ai
title: Artificial intelligence by size class of enterprise
title: Intelligence Artificielle, par classe de taille d’entreprise
title: Künstliche Intelligenz, nach Unternehmensgrößenklassen
DOI: 10.2908/isoc_eb_iot
title: Internet of Things by size class of enterprise
title: Internet des objets, par classe de taille d’entreprise
title: Internet der Dinge, nach Unternehmensgrößenklassen
DOI: 10.2908/isoc_eb_p3d
title: Nutzung von 3D Druckern und Robotern, nach Unternehmensgrößenklassen
title: Utilisation de l'impression 3D et de la robotique, par classe de taille d’entreprise
title: 3D printing and robotics by size class of enterprise
DOI: 10.2908/isoc_ec_esels
title: E-commerce sales of enterprises by size class of enterprise
title: E-Commerce Verkäufe, nach Unternehmensgrößenklassen
title: Ventes électroniques, par classe de taille d’entreprise, par classe de taille d’entreprise
DOI: 10.5281/zenodo.3882572
title: Resonance energy transfer sensitizes and monitors in situ switching of LOV2-based optogenetic actuators

description: Engineered light-dependent switches provide uniquely powerful opportunities to investigate and control cell regulatory mechanisms. Existing tools offer high spatiotemporal resolution, reversibility and repeatability. Yet cellular optogenetics applications remain limited in practice. Validation difficulties constrain most usage to easily verified protein translocation rather than inhibition of diffusible targets. Blue light levels commonly needed for actuation can be cytotoxic, precluding long-term experiments. We describe a simple approach overcoming these obstacles. Resonance energy transfer with an adjacent chromophore modulates actuation sensitivity over a 7-fold range. This simultaneously offers on-line monitoring of light-dependent switching and precise quantification of activation-relaxation properties in intact living cells. Applying this approach to different LOV2-based switches reveals relaxation times up to 11-fold faster than anticipated. <em>In situ</em>–measured parameter values guide the design of target-inhibiting actuation trains with minimal blue-light exposure, and context-based optimisation can increase sensitivity and experimental throughput a further 10-fold without loss of temporal precision.
description: Manuscript post-review cycle, addressing editorial requirements Acknowledgements: This work was supported by the Magnus Ehrnrooths Foundation (MJC), the National Cancer Institute Grant R01CA200417 (MJC and LLL), the European Union Erasmus + programme (FMK), and 7th Framework Programme Initial Training Networks FP7-PEOPLE-2013-ITN Project Number 608346 Project 'Brain Imaging Return To Health' r'Birth (AP, LLG), the Academy of Finland (mobility projects 309736 and 324581 to MJC), the DAAD with funds from the German Federal Ministry of Education and Research (57348387 and 57458932 to FF), and by access to the facilities of the Turku Screening Unit, a member of the Biocentre Finland Drug Discovery and Chemical Biology Network. We thank David Kelly (Beckton Dickinson) for assistance with the Pathway 855 instrument maintenance, Michiyuki Matsuda (University of Kyoto) and Guillaume Jacquemet (Åbo Academy University) for generously providing fluorescent protein templates, Elena Tcarenkova (University of Turku) for helpful discussion and James Conway (University of Turku) for critical reading of the manuscript.
DOI: 10.5281/zenodo.4316597
title: Smartstone probe data of a landslide experiment

description: The files contain data of four Smartstone probes recorded during a landslide experiment. The MATLAB data files are named after the particular pebbles (1 to 4), which were equipped with the probes. The files contain acceleration (acc) and gyroscope (gyr) data as well as a time code (time).
DOI: 10.5281/zenodo.6965859
title: Size spectrum, time series and atom number distribution of macroalgal emission vapors and oxidation products

description: We conducted oxidation and NPF experiments with vapor emissions from real-world coastal macroalgae in a bag reactor. The dataset showed the measurement results of volatile precursors and their oxidation products. The dataset was organized by the order of figures in our submitted manuscript.
DOI: 10.6084/m9.figshare.12004416
title: Genome assemblies and annotations of food-borne Vibrio parahaemolyticus strains

description: <b>Comparative genomic analysis of foodborne Vibrio parahaemolyticus in China.</b><br>
DOI: 10.6084/m9.figshare.21129544
title: Supplementary Material for: Audio Feature Analysis for Acoustic Pain Detection in Term Newborns

description: <b><i>Introduction:</i></b> Crying newborns signal a need or discomfort as part of the innate communication system. Exposure to pain is related to infants’ unfavorable neurodevelopmental outcomes. There is a tremendous need for more objective methods to assess neonatal pain. An audio analysis of acoustic utterances could provide specific information on the patient’s pain level. <b><i>Methods:</i></b> We analyzed 67 videos of 33 term-born newborns recorded during a planned capillary blood sample, including the stimuli, non-noxious thermal stimulus, short noxious stimulus, and prolonged unpleasant stimulus, between December 2020 and March 2021. Two expert raters evaluated the infants’ pain responses using the Neonatal Facial Coding System (NFCS). The mean values of 123 timbre features of the recorded audio data were analyzed by using specific toolboxes and libraries from the following programming environments: MIRtoolbox (MATLAB), MiningSuite (MATLAB), Essentia (Python), AudioCommons timbral models (Python), and Librosa (Python). <b><i>Results:</i></b> The NFCS values were significantly higher during the short noxious stimulus (<i>p</i> &lt; 0.001) and prolonged unpleasant stimulus (<i>p</i> &lt; 0.001) than during the non-noxious thermal stimulus, whereas NFCS values during the short noxious stimulus and prolonged unpleasant stimulus were similar (<i>p</i> = 0.79). Brightness, roughness, percussive energy, and attack times were identified as the features having the highest impact on the NFCS. <b><i>Conclusion:</i></b> This hypothesis-generating study identified several salient acoustic features highly associated with pain responses in term newborns. Our analysis is an encouraging starting point for the targeted analysis of pain-specific acoustic features of neonatal cries and vocalizations from the perspective of real-time acoustic processing.
DOI: 10.6084/m9.figshare.21345978
title: Supplementary Material for: Retinopathy of Prematurity Is a Biomarker for Pathological Processes in the Immature Brain

description: <b><i>Introduction:</i></b> Retinopathy of prematurity (ROP) is considered a neurovascular disease. We investigated whether ROP, mild or severe, is associated with neurodevelopmental impairment (NDI) in extremely preterm children. <b><i>Methods:</i></b> We conducted a multicenter retrospective cohort study in southern Taiwan. A total of 394 children &lt;28 weeks of gestation who survived to discharge from 2011 to 2018 received neurodevelopmental assessment at corrected age of 24 months. Severe ROP was defined as ROP of stages 2 plus or worse, or recipients of retinal therapy, and mild ROP as stage 1 or 2 in at least one eye. NDI was defined as cognitive or motor impairment using the Bayley Scales of Infant and Toddler Development, moderate to severe cerebral palsy, or profound hearing loss. <b><i>Results:</i></b> Among the 374 children validated for analysis, 157 children (42%) had non-ROP, 145 (39%) mild ROP, and 72 (19%) severe ROP. As ROP severity increased progressively from non-ROP, to mild ROP, and to severe ROP, the rates of NDI increased from 25%, to 46%, and to 61%. The multivariable logistic regression showed that the model included three levels of ROP, and neonatal morbidities achieved better overall performance for NDI than the model that included neonatal morbidities alone. Compared with non-ROP, mild ROP and severe ROP had adjusted odds ratios of 1.90 (95% CI: 1.10–3.28) and 2.75 (95% CI: 1.33–5.67) for NDI, respectively. <b><i>Conclusion:</i></b> Mild ROP and severe ROP are independent neonatal morbidities associated with NDI. Neurodevelopmental follow-up of extremely preterm children with any stage of ROP is needed.
DOI: 10.6084/m9.figshare.21346017
title: Supplementary Material for: MRI Characterization of Blood Flow and Oxygen Delivery in the Fetal Sheep whilst Exposed to Sildenafil Citrate

description: <b><i>Introduction:</i></b> Newborns exposed to sildenafil citrate (SC) in utero have increased rates of persistent pulmonary hypertension. The mechanism behind this has not yet been fully elucidated. We aimed to utilize a combination of clinically relevant MRI techniques to comprehensively characterize the haemodynamics of the fetal sheep whilst under the influence of SC. We hypothesized that these MRI techniques would detect SC-induced increases in pulmonary blood flow and oxygen delivery prior to birth. <b><i>Methods:</i></b> At 116–117 days gestational age (term, 150 days), pregnant Merino ewes (<i>n</i> = 9) underwent fetal catheterization surgery. MRI scans were performed during a basal state and then repeated during a constant umbilical vein infusion of SC to measure blood flow and oxygenation within the major vessels of the fetal circulation using phase-contrast-MRI and T<sub>2</sub> oximetry. <b><i>Results:</i></b> Right and left ventricular cardiac outputs were not different between states. Pulmonary blood flow increased during the SC state resulting in elevated pulmonary oxygen delivery. Right to left heart shunting through the foramen ovale was reduced without reducing cerebral oxygen delivery. <b><i>Conclusion:</i></b> SC induces alterations to pulmonary haemodynamics <i>in utero</i>; a characteristic that if maintained may underlie or act as a precursor towards the elevated rates of poor pulmonary outcomes after birth. These MRI techniques are the first to comprehensively characterize sildenafil’s direct impact on the pulmonary vasculature and its indirect detriment to the flow of oxygen-rich blood through the foramen ovale.
DOI: 10.6084/m9.figshare.21493230
title: Supplementary Material for: Recurrent Late-Onset Sepsis in Extremely Low Birth Weight Infants Is Associated with Motor Deficits in Early School Age

description: <b><i>Introduction:</i></b> Sepsis is regarded as a risk factor for brain injury in preterm infants. We herein hypothesize that extremely low birth weight infants (ELBWI, birth weight &lt;1,000 g) having survived recurrent blood culture-proven late-onset sepsis (LOS) episodes are more likely to have an adverse long-term neurologic outcome. <b><i>Methods:</i></b> In a large multicenter observational study of ELBWI ≤28 6/7 weeks, we evaluated the impact of recurrent LOS (blood culture-proven, after day 7 of life) on development at 5–6 years. Neurodevelopment, behavior, and motor qualities were tested by blinded investigators. Univariate and logistic regression analyses were performed. <b><i>Results:</i></b> The cohort consisted of 1343 ELBWI including 1,080 infants without LOS, 186 infants with one LOS, and 77 with recurrent LOS, i.e., 55 infants with two and 22 infants with three LOS episodes. After Bonferroni-Holm correction, multiple logistic regression analysis revealed recurrent sepsis to be significantly associated with adverse motor development (critical MABC-2 testing: 3.3 [1.5–7.3], <i>p</i> = 0.003, <i>p</i><sub>B</sub> = 0.012), whereas no significant impact of recurrent LOS was found on intelligence quotient and behavioral difficulties. Odds of having critical motor testing results for infants with recurrent LOS were 1.7 times (95% confidence interval 1.4–2.3) that of infants with one LOS. <b><i>Conclusion:</i></b> Recurrent sepsis in preterm infants is associated with adverse long-term motor development. However, infants with recurrent infections are also more likely to have preterm-related complications, and reasons for a worse neurodevelopmental outcome remain to be elucidated.
DOI: 10.25829/idiv.1869-11-3082
title: R-code and aggregated data from: The results of biodiversity-ecosystem functioning experiments are realistic

description: R-code and aggregated datasets to run analyses and plot main figures of a 2020 paper in Nature Ecology and Evolution by Jochum et al.
DOI: 10.5281/zenodo.4009497
title: Preprocessed and Harmonised Transcriptomics Datasets for Psoriasis and Atopic Dermatitis

description: The datasets uploaded within this record contain transcriptomics data of psoriasis and atopic dermatitis patients retrieved from the NCBI Gene Expression Omnibus and EBI ArrayExpress repositories. Overall, we retrieved 39 transcriptomics datasets, produced through both DNA microarrays and RNA-Sequencing technologies, along with relative meta-data tables. After data collection, each dataset was quality checked and preprocessed in order to obtain a harmonised source of data, ready-to-use for the research community. Beside, a thorough quality check was carried out on the retrieved meta-data, and data dictionaries were created (both for DNA microarry and RNA-Seq datasets) in order to homogenise the phenotypic data, enabling the comparability across the datasets.
description: {"references": ["Federico, A., Hautanen, V., Christian, N. et al. Manually curated and harmonised transcriptomics datasets of psoriasis and atopic dermatitis patients. Sci Data 7, 343 (2020). https://doi.org/10.1038/s41597-020-00696-8"]}
DOI: 10.5281/zenodo.6418163
title: ICE-LAPSE image dataset

description: ######################################################## Image dataset acquired within the project "ICE-LAPSE: Analysis of Antarctic benthos dynamics by using non-destructive monitoring devices and permanent stations'', PNRA 2013/AZ1.16, funded by the Italian National Antarctic Program. The dataset is in support of the publication entitled: Long-term Automated Visual Monitoring of Antarctic Benthic Fauna Simone Marini 1,2∗ , Federico Bonofiglio 1 , Lorenzo P. Corgnati 1 ,<br> Andrea Bordone 3, Stefano Schiaparelli 4 , Andrea Peirano 3 1 National Research Council of Italy (CNR), Institute of Marine Sciences, La Spezia, 19132, Italy,<br> 2 Stazione Zoologica Anton Dohrn, Naples, 80121, Italy<br> 3 ENEA-Marine Environment Research Centre, La Spezia, 19132, Italy<br> 4 DISTAV, Università di Genova, Genova, 16132, Italy ∗E-mail: simone.marini@sp.ismar.cnr.it. Related Scientific Publications: Marini, S., Bonofiglio, F., Corgnati, L. P., Bordone, A., Schiaparelli, S., & Peirano, A. (2022). Long-term automated visual monitoring of Antarctic benthic fauna. <em>Methods in Ecology and Evolution</em>, 00, 1– 19. https://doi.org/10.1111/2041-210X.13898 ######################################################## The dataset consists of the following files: - Raw_Images.tgz contains the images in CR2 format<br> - JPG_Images.tgz contains the images in JPG format<br> - 640x427_Images.tgz contains the images in JPG format, with resolution 640x427 Pixels<br> - ICE-LAPSE_Tags.tgz contains<br> - the textual_Tags folder,<br> - the Tagged_Images folder,<br> - the SpeciesColorLabel image representing the legend for the tagged images contained in the Tagged_Images folder<br> - the SpeciesDistribution.csv spreadsheet listing the species for each image - iFDO_Dataset.tgz contains the images renamed according to the iFDO standard - Deployment in Tethys bay - Mario Zucchelli Station- 2015_GUARD1-PNRA-2015_iFDO.yaml contains the iFDO metadata information.
DOI: 10.5281/zenodo.6577187
title: WRF model configuration and data used for the NHESS manuscript "Droughts in Germany: Performance of Regional Climate Models in reproducing observed characteristics"

description: The file contains: the namelist.input document with the description of the WRF model configuration used in Warscher et al. (2019) WRF simulation outputs from the reanalysis run: monthly values for the time period 1980-2009 of precipitation, maximum and minimum temperature (needed for the SPEI calculation) from the innermost (5 km grid resolution) and second innermost (15 km) domain; from both domains the same section, relevant for the study, was taken; the data was bilineraily interpolated to 12.5 km horizontal grid resolution to match the EUR-11 CORDEX format
description: {"references": ["Warscher, M., Wagner, S., Marke, T., Laux, P., Smiatek, G., Strasser, U., & Kunstmann, H. (2019). A 5 km resolution regional climate simulation for central europe: performance in high mountain areas and seasonal, regional and elevation-dependent variations. Atmosphere, 10(11), 682."]}
DOI: 10.6084/m9.figshare.20065652
title: Supplementary Material for: Clinical usefulness of blenderized food for selenium deficiency in pediatric patients with severe motor and intellectual disabilities

description: Introduction: This study aimed to assess the preventive or therapeutic effects of blenderized food (BF) on selenium deficiency in pediatric patients with severe motor and intellectual disabilities (SMID). Methods: The medical records of all 40 consecutive pediatric patients with SMID who underwent nutritional assessment were retrospectively reviewed and compared between two groups: the enteral formula (EF) group and the BF group fed with BF providing more than 10% of total caloric intake. Next, for the selenium-deficient patients who were newly started on blenderized tube feeds after the first nutritional assessment, improvement of selenium deficiency and change of dietary contents were assessed. Results: The BF group patients had a significantly lower prevalence of selenium deficiency and higher serum selenium levels than the EF group patients. In all 7 selenium-deficient patients who started blenderized tube feeds after the first nutritional assessment, serum selenium levels were significantly increased at the second nutritional assessment, even though total selenium intake, selenium intake by EF, and total caloric intake did not differ significantly, and, in fact, caloric intake was significantly decreased by EF. Conclusion: Combined feeding of BFs can be useful for prevention and therapy of selenium deficiency in pediatric SMID patients.
DOI: 10.6084/m9.figshare.20254683
title: Supplementary Material for: Serum Creatinine Patterns in Neonates Treated with Therapeutic Hypothermia for Neonatal Encephalopathy

description: <b><i>Introduction:</i></b> There is large variability in kidney function and injury in neonates with neonatal encephalopathy (NE) treated with therapeutic hypothermia (TH). Acute kidney injury (AKI) definitions that apply categorical approaches may lose valuable information about kidney function in individual patients. Centile serum creatinine (SCr) over postnatal age (PNA) may provide more valuable information in TH neonates. <b><i>Methods:</i></b> Data from seven TH neonates and one non-TH-treated, non-NE control cohorts were pooled in a retrospective study. SCr centiles over PNA, and AKI incidence (definition: SCr ↑≥0.3 mg/dL within 48 h, or ↑ ≥1.5 fold vs. the lowest prior SCr within 7 days) and mortality were calculated. Repeated measurement linear models were applied to SCr trends, modeling SCr on PNA, birth weight or gestational age (GA), using heterogeneous autoregressive residual covariance structure and maximum likelihood methods. Findings were compared to patterns in the control cohort. <b><i>Results:</i></b> Among 1,136 TH neonates, representing 4,724 SCr observations, SCr (10th–25th–50th–75th–90th–95th) PNA centiles (day 1–10) were generated. In TH neonates, the AKI incidence was 132/1,136 (11.6%), mortality 193/1,136 (17%). AKI neonates had a higher mortality (37.2–14.3%, <i>p</i> &lt; 0.001). Median SCr patterns over PNA were significantly higher in nonsurvivors (<i>p</i> &lt; 0.01) or AKI neonates (<i>p</i> &lt; 0.001). In TH-treated neonates, PNA and GA or birth weight explained SCr variability. Patterns over PNA were significantly higher in TH neonates to controls (801 neonates, 2,779 SCr). <b><i>Conclusions:</i></b> SCr patterns in TH-treated NE neonates are specific. Knowing PNA-related patterns enable clinicians to better assess kidney function and tailor pharmacotherapy, fluids, or kidney supportive therapies.
DOI: 10.6084/m9.figshare.20583558
title: China Urban Lake Dataset (CULD)

description: A high-resolution circa-2020 map of urban lakes ( ≥0.001 km<sup>2</sup>) in China. The 10-m-resoultion Sentinel-2 imagery as well as a simple but robust water extraction method were used to generate waterbodies in China on Google Earth Engine. After initially filtering out urban water bodies based on the spatial relationships with urban area boundary, we combined high-resolution historical imagery to manually remove non-lake waters such as rivers and paddy fields, and to edit and supplement the missing urban lakes separately. The accuracy of our dataset was evaluated in terms of both area and count of lakes by comparing with manually vectorizing results in randomly sampled urban units. The results showed that our dataset is highly accurate and trustworthy, with the averaged accuracy of 81.85% in area and 93.35% in count.
DOI: 10.6084/m9.figshare.21431649.v1
title: Phthorimaea operculella genome repeat sequences annotation

description: Phthorimaea operculella genome repeat sequences annotation information. chr1-15, repetitive sequence annotated from chromosomal 1 to 15; chr16-29, repetitive sequence annotated from chromosomal 16 to 29.
DOI: 10.6084/m9.figshare.21510693.v1
title: Contig orders and orientations on Phthorimaea operculella chromosomes

description: Contig orders and orientations on Phthorimaea operculella chromosomes.