cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17608/k6.auckland.14491056.v1
title: HiHi rDNA unit Measuring Spreadsheet

description: Excel spreadsheet used to calculate the rDNA unit size of the HiHi from a BLAST output of nanopore reads. The BLAST output used to generate this spreadsheet was kindly provided by Dr Annabel Whibley of the University of Auckland.
DOI: 10.5281/zenodo.4716113
title: Data set for a fast magnetic bead-based colorimetric immunoassay for the detection of tetrodotoxins in shellfish

description: Data set for the validation of the fast magnetic bead-based colorimetric immunoassay for the detection of tetrodotoxins in shellfish (oyster, mussel and razor clam). Spiked and naturally-contaminated samples.
DOI: 10.5281/zenodo.4716112
title: Data set for a fast magnetic bead-based colorimetric immunoassay for the detection of tetrodotoxins in shellfish

description: Data set for the validation of the fast magnetic bead-based colorimetric immunoassay for the detection of tetrodotoxins in shellfish (oyster, mussel and razor clam). Spiked and naturally-contaminated samples.
DOI: 10.34740/kaggle/dsv/2164872
title: Rice Images
DOI: 10.25442/hku.14481864
title: Minuti&Russell2020_MEPS_ CO2 + Temp effects on HK urchin & gastropod species

description: Future ocean CO2 and temperatures are predicted to increase primary productivity across tropical marine habitats, potentially driving a shift towards algal-dominated systems. However, increased consumption of algae by benthic grazers could potentially counter this shift. Yet, the response of different grazer species to future conditions will be moderated by their physiologies, meaning that they may not be functional equivalents. Here, we experimentally assessed the physiological response of key grazers—the sea urchin <i>Heliocidaris crassispina</i> and 2 gastropod species, <i>Astralium haematragum</i> and <i>Trochus maculatus</i>—to predicted CO2 concentrations (400, 700 and 1000 ppm) and temperature conditions (ambient, +3 and +5°C). In line with metabolic theory, we found that urchin metabolic rate increased at future temperatures regardless of CO2 conditions, with evidence of metabolic acclimation to higher temperatures. The metabolic rate of A. haematragum was depressed only by CO2, whereas <i>T. maculatus</i> initially had elevated metabolic rates at moderate CO2, which were depressed by the combination of the highest CO2 concentration and temperatures. Taxa showed differential survival, with no urchin mortality under any future conditions but substantial mortality of both gastropods under elevated temperatures regardless of CO2 concentration. Importantly, all species had substantially reduced algal consumption in response to elevated CO2, though the urchins only demonstrated an energetic mismatch under combined future CO2 and temperature. Therefore, despite sharing an ecological niche, these key grazers are likely to be differentially affected by future environmental conditions, potentially reducing the strength of eco logical compensatory responses depending on the functional redundancy in this grazing community.
DOI: 10.25442/hku.14481864.v1
title: Minuti&Russell2020_MEPS_ CO2 + Temp effects on HK urchin & gastropod species

description: Future ocean CO2 and temperatures are predicted to increase primary productivity across tropical marine habitats, potentially driving a shift towards algal-dominated systems. However, increased consumption of algae by benthic grazers could potentially counter this shift. Yet, the response of different grazer species to future conditions will be moderated by their physiologies, meaning that they may not be functional equivalents. Here, we experimentally assessed the physiological response of key grazers—the sea urchin <i>Heliocidaris crassispina</i> and 2 gastropod species, <i>Astralium haematragum</i> and <i>Trochus maculatus</i>—to predicted CO2 concentrations (400, 700 and 1000 ppm) and temperature conditions (ambient, +3 and +5°C). In line with metabolic theory, we found that urchin metabolic rate increased at future temperatures regardless of CO2 conditions, with evidence of metabolic acclimation to higher temperatures. The metabolic rate of A. haematragum was depressed only by CO2, whereas <i>T. maculatus</i> initially had elevated metabolic rates at moderate CO2, which were depressed by the combination of the highest CO2 concentration and temperatures. Taxa showed differential survival, with no urchin mortality under any future conditions but substantial mortality of both gastropods under elevated temperatures regardless of CO2 concentration. Importantly, all species had substantially reduced algal consumption in response to elevated CO2, though the urchins only demonstrated an energetic mismatch under combined future CO2 and temperature. Therefore, despite sharing an ecological niche, these key grazers are likely to be differentially affected by future environmental conditions, potentially reducing the strength of eco logical compensatory responses depending on the functional redundancy in this grazing community.
DOI: 10.25442/hku.14481888
title: Minutietal2021_STOT_heatwaves and recovery effects on sea urchin

description: Heatwaves are increasing in frequency and intensity, with substantial impacts on ecosystems and species which maintain their function. Whether or not species are harmed by heatwave conditions by being pushed beyond their physiological bounds can depend on whether energy replacement is sufficient to enable recovery from acute stress. We exposed an ecologically important sea urchin, <em>Heliocidaris erythrogramma</em>, to experimental marine heatwave scenarios in context with recent summer heat anomalies in moderate (25 °C), and strong heatwave (26 °C) conditions for 10 days, followed by a 10-day recovery period at normal summer temperature (23 °C). Greater heatwave intensity drove higher metabolic rates which were not matched with a concurrent increase in food consumption or faecal production. However, food consumption increased during the post-heatwave recovery period, likely to replenish an energy deficit. Despite this, mortality increased into the recovery period and seemed to be caused by latent effects, manifesting as a decline in health index as individuals progressed from spine and pedicellariae loss, through to loss of tube foot rigor, bald patch disease, culminating in mortality. We show for the first time that the acute thermal stress of heatwaves can have latent physiological effects that cause mortality even when conditions return to normal. Our results show that the negative effects of heatwaves can manifest after relief from stressful conditions and highlight the importance of understanding the latent effects on physiology and health. This understanding will offer insights into the long-term potential for stress recovery following seemingly sublethal effects and whether the restoration of ambient conditions post-heatwave is sufficient to ensure population stability.
DOI: 10.25442/hku.14481888.v1
title: Minutietal2021_STOT_heatwaves and recovery effects on sea urchin

description: Heatwaves are increasing in frequency and intensity, with substantial impacts on ecosystems and species which maintain their function. Whether or not species are harmed by heatwave conditions by being pushed beyond their physiological bounds can depend on whether energy replacement is sufficient to enable recovery from acute stress. We exposed an ecologically important sea urchin, <em>Heliocidaris erythrogramma</em>, to experimental marine heatwave scenarios in context with recent summer heat anomalies in moderate (25 °C), and strong heatwave (26 °C) conditions for 10 days, followed by a 10-day recovery period at normal summer temperature (23 °C). Greater heatwave intensity drove higher metabolic rates which were not matched with a concurrent increase in food consumption or faecal production. However, food consumption increased during the post-heatwave recovery period, likely to replenish an energy deficit. Despite this, mortality increased into the recovery period and seemed to be caused by latent effects, manifesting as a decline in health index as individuals progressed from spine and pedicellariae loss, through to loss of tube foot rigor, bald patch disease, culminating in mortality. We show for the first time that the acute thermal stress of heatwaves can have latent physiological effects that cause mortality even when conditions return to normal. Our results show that the negative effects of heatwaves can manifest after relief from stressful conditions and highlight the importance of understanding the latent effects on physiology and health. This understanding will offer insights into the long-term potential for stress recovery following seemingly sublethal effects and whether the restoration of ambient conditions post-heatwave is sufficient to ensure population stability.
DOI: 10.5281/zenodo.4534829
title: Making Higher-Order Superposition Work

description: This package contains the raw evaluation data, and the scripts necessary for the reproduction of the results for the paper Making Higher-Order Superposition Work. Problems used for evaluation are available at https://doi.org/10.5281/zenodo.4269591. Zipperposition is available at https://github.com/sneeuwballen/zipperposition. See the README file in the archive below for detailed instructions on how to run it. NOTE: The configuration named fig2_mc_av corresponds to the IC+AV configuration from the paper. The name IC (immediate clausification) was introduces after the submission of the package to Zenodo. Also, Figure 3, which contained the pseudocode, is removed in the camera-ready version of the paper.<br> Thus, all files figD_res(summary).csv with D &gt;= 4 correspond to figures Figure D-1 in the paper. For example,<br> fig7_ressummary.csv corresponds to the figure 6 in the paper. We are sorry for the inconvenience.
DOI: 10.5281/zenodo.4534828
title: Making Higher-Order Superposition Work

description: This package contains the raw evaluation data, and the scripts necessary for the reproduction of the results for the paper Making Higher-Order Superposition Work. Problems used for evaluation are available at https://doi.org/10.5281/zenodo.4269591. Zipperposition is available at https://github.com/sneeuwballen/zipperposition. See the README file in the archive below for detailed instructions on how to run it. NOTE: The configuration named fig2_mc_av corresponds to the IC+AV configuration from the paper. The name IC (immediate clausification) was introduces after the submission of the package to Zenodo. Also, Figure 3, which contained the pseudocode, is removed in the camera-ready version of the paper.<br> Thus, all files figD_res(summary).csv with D &gt;= 4 correspond to figures Figure D-1 in the paper. For example,<br> fig7_ressummary.csv corresponds to the figure 6 in the paper. We are sorry for the inconvenience.
DOI: 10.25919/xbqb-px51
title: PacBio HiFi DNA sequencing reads of the leaf rust fungus Puccinia triticina

description: PacBio HiFi DNA sequencing reads of the leaf rust fungus Puccinia triticina for fully-phased, chromosome-scale genome assembly. High molecular DNA from urediniospores was extracted and PacBio HiFi reads were sequenced.
DOI: 10.5281/zenodo.4722698
title: Plumed files for 'Molecular simulations capture the transient exposure of a buried phosphorylation site in the autoinhibited state of a protein'

description: Plumed files and hills files employed in 'Molecular simulations capture the transient exposure of a buried phosphorylation site in the autoinhibited state of a protein'.
DOI: 10.6084/m9.figshare.14494263.v1
title: Modified IEEE 39 & 20-node integrated electricity and gas system

description: a test system
DOI: 10.6084/m9.figshare.14494263
title: Modified IEEE 39 & 20-node integrated electricity and gas system

description: a test system
DOI: 10.6084/m9.figshare.14494005
title: Supplementary Material for: Trends in Peritoneal Dialysis Technique Survival, Death, and Transfer to Hemodialysis: A Decade of Data from the RDPLF

description: <b><i>Introduction:</i></b> There is limited information on the trends of peritoneal dialysis (PD) technique survival over time. This study aimed to estimate the effect of calendar time on technique survival, transfer to hemodialysis (HD) (and the individual causes of transfer), and patient survival. <b><i>Methods:</i></b> This retrospective, multicenter study, based on data from the French Language Peritoneal Dialysis Registry, analyzed 14,673 patients who initiated PD in France between January 1, 2005, and December 31, 2016. Adjusted Cox regressions with robust variance were used to examine the probability of a composite end point of either death or transfer to HD, death, and transfer to HD, accounting for the nonlinear impact of PD start time. <b><i>Results:</i></b> There were 10,201 (69.5%) cases of PD cessation over the study period: 5,495 (37.4%) deaths and 4,706 (32.1%) transfers to HD. The rate of PD cessation due to death or transfer to HD decreased over time (PR 0.96, 95% CI: 0.95–0.97). Compared to 2009–2010, starting PD between 2005 and 2008 or 2011 and 2016 was strongly associated with a lower rate of transfer to HD (PR 0.88, 95% CI: 0.81–0.96, and PR 0.91, 95% CI: 0.84–0.99, respectively), mostly due to a decline in the rate of infection-related transfers to HD (PR 0.96, 95% CI: 0.94–0.98). <b><i>Conclusions:</i></b> Rates of the composite end point of either death or transfer to HD, death, and transfer to HD have decreased in recent decades. The decline in transfers to HD rates, observed since 2011, is mainly the result of a significant decline in infection-related transfers.
DOI: 10.6084/m9.figshare.14493948
title: Supplementary Material for: Epidemiology and Outcomes of Acute Kidney Diseases: A Comparative Analysis

description: <b><i>Introduction:</i></b> Acute kidney diseases and disorders (AKD) encompass acute kidney injury (AKI) and subacute or persistent alterations in kidney function that occur after an initiating event. Unlike AKI, accurate estimates of the incidence and prognosis of AKD are not available and its clinical significance is uncertain. <b><i>Methods:</i></b> We studied the epidemiology and long-term outcome of AKD (as defined by the KDIGO criteria), with or without AKI, in a retrospective cohort of adults hospitalized at a single centre for &gt;24 h between 2012 and 2016 who had a baseline eGFR ≥60 mL/min/1.73 m<sup>2</sup> and were alive at 30 days. In patients for whom follow-up data were available, the risks of major adverse kidney events (MAKEs), CKD, kidney failure, and death were examined by Cox and competing risk regression analyses. <b><i>Results:</i></b> Among 62,977 patients, 906 (1%) had AKD with AKI and 485 (1%) had AKD without AKI. Follow-up data were available for 36,118 patients. In this cohort, compared to no kidney disease, AKD with AKI was associated with a higher risk of MAKEs (40.25 per 100 person-years; hazard ratio [HR] 2.51, 95% confidence interval [CI] 2.16–2.91), CKD (27.84 per 100 person-years); subhazard ratio [SHR] 3.18, 95% CI 2.60–3.89), kidney failure (0.56 per 100 person-years; SHR 24.84, 95% CI 5.93–104.03), and death (14.86 per 100 person-years; HR 1.52, 95% CI 1.20–1.92). Patients who had AKD without AKI also had a higher risk of MAKEs (36.21 per 100 person-years; HR 2.26, 95% CI 1.89–2.70), CKD (22.94 per 100 person-years; SHR 2.69, 95% CI 2.11–3.43), kidney failure (0.28 per 100 person-years; SHR 12.63, 95% CI 1.48–107.64), and death (14.86 per 100 person-years; HR 1.57, 95% CI 1.19–2.07). MAKEs after AKD were driven by CKD, especially in the first 3 months. <b><i>Conclusions:</i></b> These findings establish the burden and poor prognosis of AKD and support prioritisation of clinical initiatives and research strategies to mitigate such risk.
DOI: 10.6084/m9.figshare.14493708
title: Supplementary Material for: Pembrolizumab as Second-Line Therapy for Advanced Hepatocellular Carcinoma: A Subgroup Analysis of Asian Patients in the Phase 3 KEYNOTE-240 Trial

description: <b><i>Introduction:</i></b> KEYNOTE-240 investigated the efficacy and safety of pembrolizumab plus best supportive care (BSC) in sorafenib-treated patients with advanced hepatocellular carcinoma (HCC). Results for the subgroup of patients from Asia are described. <b><i>Methods:</i></b> Adults with advanced HCC previously treated with sorafenib were randomized 2:1 to pembrolizumab or placebo plus BSC. Here, the Asian subgroup comprised patients enrolled in Hong Kong, Japan, Korea, the Philippines, Taiwan, and Thailand. Primary endpoints were progression-free survival (PFS) per blinded central imaging review and overall survival (OS). Secondary endpoints included objective response rate (ORR) per blinded central imaging review, duration of response (DOR), and safety. <b><i>Results:</i></b> The Asian subgroup included 157 patients. As of January 2, 2019, the median follow-up in this subgroup was 13.8 months for pembrolizumab and 8.3 months for placebo. The median PFS was 2.8 months for pembrolizumab (95% confidence interval [CI] 2.6–4.1) versus 1.4 months (95% CI 1.4–2.4) for placebo (hazard ratio [HR] 0.48; 95% CI 0.32–0.70). The median OS was 13.8 months (95% CI 10.1–16.9) for pembrolizumab versus 8.3 months (95% CI 6.3–11.8) for placebo (HR 0.55; 95% CI 0.37–0.80). ORR was 20.6% (95% CI 13.4–29.5) for pembrolizumab versus 2.0% (95% CI 0.1–10.6) for placebo (difference: 18.5%; 95% CI 8.3–27.6). The median DOR was 8.6 and 2.8 months for pembrolizumab and placebo, respectively. Any grade treatment-related adverse events (TRAEs) occurred in 63 patients (58.9%) receiving pembrolizumab and 24 patients (48.0%) receiving placebo; 14 (13.1%) and 2 (4.0%) patients experienced grade 3–5 TRAEs, respectively. No treatment-related deaths occurred. <b><i>Conclusion:</i></b> Pembrolizumab demonstrated antitumor activity and was well tolerated in the Asian subgroup of KEYNOTE-240. A trend toward greater benefit with pembrolizumab in the Asian subgroup was observed compared with the overall cohort, supporting further evaluation of pembrolizumab treatment in this population.
DOI: 10.5281/zenodo.4722761
title: condition_A/B.sam_chr4_hg38

description: Illumina Nextera Tn5 adaptor was removed by <strong>Trimmomatic;</strong> align to hg38 by <strong>bowtie2</strong> with param <code>--very-sensitive --no-unal --no-mixed --no-discordant -X2000</code>; <code><strong>samtools</strong> convert .sam to .bam with chrM|chrUn|random|RANDOM removed;</code>
DOI: 10.5281/zenodo.4722760
title: condition_A/B.sam_chr4_hg38

description: Illumina Nextera Tn5 adaptor was removed by <strong>Trimmomatic;</strong> align to hg38 by <strong>bowtie2</strong> with param <code>--very-sensitive --no-unal --no-mixed --no-discordant -X2000</code>; <code><strong>samtools</strong> convert .sam to .bam with chrM|chrUn|random|RANDOM removed;</code>
DOI: 10.5281/zenodo.4646699
title: HGI-30 DATA Set

description: Household garbage data set is made up of 30 kinds of garbage.
DOI: 10.5281/zenodo.4646698
title: HGI-30 DATA Set

description: Household garbage data set is made up of 30 kinds of garbage.
DOI: 10.5281/zenodo.4720751
title: MEDDOPROF corpus: training set

description: The MEDDOPROF Shared Task tackles the detection of occupations and employment statuses in clinical cases in Spanish from different specialties. Systems capable of automatically processing clinical texts are of interest to the medical community, social workers, researchers, the pharmaceutical industry, computer engineers, AI developers, policy makers, citizen’s associations and patients. Additionally, other NLP tasks (such as anonymization) can also benefit from this type of data. MEDDOPROF has three different sub-tasks: <strong>1) MEDDOPROF-NER</strong>: Participants must find the beginning and end of occupation mentions and classify them as PROFESION (PROFESSION), SITUACION_LABORAL (WORKING_STATUS) or ACTIVIDAD (ACTIVIDAD). <strong>2) MEDDOPROF-CLASS: </strong>Participants must find the beginning and end of occupation mentions and classify them according to their referent (PACIENTE [patient], FAMILIAR [family member], SANITARIO [health professional] or OTRO [other]). <strong>3) MEDDOPROF-NORM</strong>: Participants must find the beginning and end of occupation mentions and normalize them according to a reference codes list. MEDDOPROF is part of the IberLEF 2021 workshop, which is co-located with the SEPLN 2021 conference. For further information, please visit https://temu.bsc.es/meddoprof/ or email us at encargo-pln-life@bsc.es MEDDOPROF is promoted by the Plan de Impulso de las Tecnologías del Lenguaje de la Agenda Digital (Plan TL). <strong>UPDATE 26/04/21</strong>: A new version of the training data has been uploaded after detecting some minor errors in some of the annotations. Training data for Task 3 (MEDDOPROF-NORM) has also been added. Please make sure to download the latest version! <strong>Resources:</strong> - Web - Codes Reference List (for MEDDOPROF-NORM) - Annotation Guidelines
DOI: 10.5519/qd.foa4a7jc
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (4 records)
DOI: 10.5281/zenodo.4722747
title: Detection of Sub-Micro- and Nanoplastic Particles on Gold Nanoparticle-Based Substrates by Surface-Enhanced Raman Scattering (SERS) Spectroscopy

description: These datasets are used to produce the figures/tables published in our Nanomaterials article entitled: Detection of Sub-Micro- and Nanoplastic Particles on Gold Nanoparticle-Based Substrates by Surface-Enhanced Raman Scattering (SERS) Spectroscopy by Jessica Caldwell, Patricia Taladriz-Blanco, Barbara Rothen-Rutishauser, and Alke Petri-Fink <br> <strong>Abstract: </strong>Small plastic particles such as micro- (&lt;5 mm), sub-micro- (1 µm–100 nm) and nanoplastics (&lt;100 nm) are known to be ubiquitous within our surrounding environment. However, to date relatively few methods exist for the reliable detection of nanoplastic particles in relevant sample matrices such as foods or environmental samples. This lack of relevant data is likely a result of key limitations (e.g., resolution and/or scattering efficiency) for common analytical techniques such as Fourier transform infrared or Raman spectroscopy. This study aims to address this knowledge gap in the field through the creation of surface enhanced Raman scattering spectroscopy substrates utilizing spherical gold nanoparticles with 14 nm and 46 nm diameters to improve the scattering signal obtained during Raman spectroscopy measurements. The substrates are then used to analyze polystyrene particles with sizes of 161 nm or 33 nm and poly(ethylene terephthalate) particles with an average size of 62 nm. Through this technique, plastic particles could be detected at concentrations as low as 10 µg/mL, and analytical enhancement factors of up to 446 were achieved.