cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6743276.v1
title: Ribosome profiling in cyanobacteria

description: Supplemental material for "Ribosome profiling of <i>Synechocystis</i> reveals altered ribosome allocation at carbon starvation" by Karlsen <i>et al.</i>, 2018 (DOI: 10.1128/mSystems.00126-18).<br><i>Legends.pdf</i> contains the full legends, while short descriptions are shown below.<br><br><b>Table S1. Grubbs test for outliers in RPF RPKM data at HC and LC.<br><br>Table S2. RNA RPKM, RPF RPKM, and translational efficiencies at HC and LC.<br><br>Table S3. Intragenic PS pattern correlation between samples.<br><br>Figure S1. Puromycin incorporation reveals translation under C<sub>i</sub> starvation.<br><br>Figure S2. Comparison and Pearson correlation of RPF RPKM under the different conditions.<br><br>Figure S3. Transcription level (mRNA) and protein synthesis rate (RPF; ribosome protected footprints) of the slr0373-slr0374-slr0376 operon in HC* (-5 min sample) and LC (24 h sample) conditions.<br><br>Figure S4. Pause score (PS) distribution for every codon in each condition.<br><br>Figure S5. Detailed view of the 5’ UTR pause score (PS) profile in each condition.<br><br>Figure S6. Average ORF pause score (PS) at 5’ and 3’ ends with different filtering of ORFs.<br><br>Figure S7. Pause score (PS) plots for (A) ssl1911 (<i>gifA</i>), (B) slr1834 (<i>psaA</i>) and (C) ssr0390 (<i>psaK1</i>).<br><br>Figure S8. Correlation of 5' UTR, ORF, and 3' UTR RPF RPKM, for each condition, and correlation of 5' UTR, ORF, and 3' UTR fold change (FC) in RPF RPKM from HC* (-5 min) to LC (24 h).<br><br>Figure S9. ORF pause score (PS) patterns are highly correlated between two conditions if the RPF RPKM is high.<br><br>Figure S10. Sucrose density gradient profiles of MNase digested polysomes shows elevated levels of dimerized ribosomes (100S) at LC.</b><b><br></b><b>Figure S11. RPF read length distribution for each sample.</b><b><br></b><b>Figure S12. Total read count per nucleotide at gene 5’ and 3’ ends for each sample.<br></b><b><br>Text S1. Supplemental methods with details of ribosome profiling and RNAseq sample preparation.</b><br><br>
DOI: 10.6084/m9.figshare.25018469.v1
title: Plant Chloroplast and Mitochondrial Genomes

description: Chloroplast and Mitochondrial Genome Database for TIPP_plastid
DOI: 10.6084/m9.figshare.25872640.v1
title: Multi-Agent Reinforcement Learning with Hierarchical Coordination for Emergency Responder Stationing (ICML-2024) (Code and Data)

description: <i>An emergency responder management (ERM) system dispatches responders, such as ambulances, when it receives requests for medical aid. ERM systems can also proactively reposition responders between predesignated waiting locations to cover any gaps that arise due to the prior dispatch of responders or significant changes in the distribution of anticipated requests. Optimal repositioning is computationally challenging due to the exponential number of ways to allocate responders between locations and the uncertainty in future requests. The state-of-the-art approach in proactive repositioning is a hierarchical approach based on spatial decomposition and online Monte Carlo tree search, which may require minutes of computation for each decision in a domain where seconds can save lives. We address the issue of long decision times by introducing a novel reinforcement learning (RL) approach, based on the same hierarchical decomposition, but replacing online search with learning. To address the computational challenges posed by large, variable-dimensional, and discrete state and action spaces, we propose: (1) actor-critic based agents that incorporate transformers to handle variable-dimensional states and actions, (2) projections to fixed-dimensional observations to handle complex states, and (3) combinatorial techniques to map continuous actions to discrete allocations. We evaluate our approach using real-world data from two U.S. cities, Nashville, TN and Seattle, WA. Our experiments show that compared to the state of the art, our approach reduces computation time per decision by three orders of magnitude, while also slightly reducing average ambulance response time by 5 seconds</i>
DOI: 10.6084/m9.figshare.28623644.v1
title: data.zip

description: 456354343442
DOI: 10.6084/m9.figshare.28909766.v1
title: Nutrient availability and seedling growth data from <i>Nothofagus</i> and conifer-broadleaf stands, eastern Wairarapa, New Zealand

description: "Rocky Hill PRS all.csv" contains data on nutrient availability beneath Nothofagus and conifer-broadleaf stands in a New Zealand temperate forest, as measured during two 12-week periods with PRS® probes. The six other spreadsheets contain annual relative growth rates of seedlings of six tree species, measured on plots in both forest types over a two-year period. "Hinau" = <i>Elaeocarpus dentatus</i>, "Pigeonwood" = <i>Hedycarya arborea</i>, "Rewarewa" = <i>Knightia excelsa</i>, "Lemonwood" = <i>Pittosporum eugenioides</i>, "Totara" = <i>Podocarpus totara</i>, "Beech" = <i>Nothofagus solandri</i>.
DOI: 10.6084/m9.figshare.23497661.v1
title: Extended data for the manuscript 'Self-Assembled Soft Alloy with Frank-Kasper Phases beyond Metals'

description: Extended data for the manuscript 'Self-Assembled Soft Alloy with Frank-Kasper Phases beyond Metals'
DOI: 10.6084/m9.figshare.29052368.v1
title: Observational study to visualize and confirm Connexin43 localization at the interface between endothelial cells labeled by Flk1:eGFP expression and pericytes labeled by DsRed expression (Ng2:DsRed/+) within murine embryonic stem cell-derived vessels.

description: Observational study to visualize and confirm Connexin43 localization at the interface between endothelial cells labeled by Flk1:eGFP expression and pericytes labeled by DsRed expression (Ng2:DsRed/+) within murine embryonic stem cell-derived vessels from an Flk1:eGFP/+; Ng2/Cspg4:DsRed/+ animal (collection after 14 days in culture). Images acquired on a Zeiss LSM 880 point-scanning confocal microscope to detect Cx43 at the pericyte-endothelial cell interface. Volumetric images taken through the z-axis were acquired at 40x. Images in the figure are compressed z-stacks within a selected range, but the raw image files in .czi format are also included.
DOI: 10.17632/4k763zdwd3
title: Evidence of multiferroic behavior in sintered BaTiO3 obtained from high-energy ball-milled powders

description: Multiferroic BaTiO3 exhibiting ferroelectric and ferromagnetic behavior was synthesized via the high-energy ball milling of pure BaTiO3 (BTO) powders for durations ranging from 15 to 60 min, followed by pressing and sintering at 1200 ◦C X-ray diffraction patterns of all synthesized samples predominantly revealed a BTO phase with a tetragonal structure and a secondary Ba12Fe28Ti15O84 (BFTO) phase. The BFTO phase was formed after milling for more than 30 min because of chemical interactions between the BTO powder and milling media. Vibrating sample magnetometry confirmed the ferromagnetic nature of the sintered pellets. The specific magnetization increased with increasing milling duration, reaching a maximum value of 1.15 emu/g after 60 min of milling. This increase can be attributed to the distortion of the crystal structure and presence of a secondary phase, as confirmed by scanning electron microscopy and energy-dispersive X-ray spectroscopy. Additionally, electrical characterization revealed the dielectric nature of the materials, with relative permittivity ranging from 500 to 1800, maximum spontaneous polarization from 9.77 to 11.31 μC/cm2, coercive field from 3.86 to 11.12 kV/cm,
and AC conductivity from 1 × 10􀀀 6 to 1 × 10􀀀 3 S/cm. The method described in this study is a simple and cost effective approach to produce multiferroic materials with ferroelectric and relaxor ferroelectric behavior at room temperature, broadening their potential for technological applications.
DOI: 10.17632/r6jsy48jjn
title: Real-world experience of bimekizumab for adult patients with plaque psoriasis: A 52-week multicenter retrospective study

description: Our group previously published 16-week real-world evidence supporting the use of bimekizumab, an interleukin (IL)-17A/IL-17F inhibitor, for treatment of plaque psoriasis. However, long-term data remains limited. Herein, we report 1-year real-world evidence results.
DOI: 10.17632/v7bgzx9gmw
title: Experimental data set from a benchmark test of delamination growth with varying crack growth rate and crack front shape under quasi-static and fatigue loading

description: This data repository provides the processed data to reproduce the findings presented in the article entitled "A benchmark test for validating 3D simulation methods for delamination growth under quasi-static and fatigue loading" by the same authors. In this work, a comprehensive benchmark case consisting of a double cantilever beam (DCB)-like specimen with partially reinforced arms is presented. The benchmark case is both simple in terms of geometry (easily introduced in a simulation model) and complex in terms of the phenomenology of the crack advance, with varying crack growth rate and front shape. The test configuration, the methodology and the data processing are addressed in the related article. A total number of seven specimens are tested: four under quasi-static and three under fatigue loading conditions. Load-displacement curves and crack front geometries processed from X-ray radiography are provided for all the tests performed. In addition, a complete set of elastic, fracture and fatigue properties for the material are provided in the article. This data set, in conjunction with the associated article, constitutes a comprehensive benchmark test against which existing or future delamination growth models can be evaluated.
DOI: 10.6084/m9.figshare.12951359.v3
title: Response of subtropical forests to warming are modulated by nutrient stoichiometry

description: We performed a field warming experiment in <i>Cunninghamia lanceolata </i>plantations in southern China. Foliar and soil elements, non-structural carbohydrates, stable isotopes, and potential nutritional limitations were investigated.
DOI: 10.6084/m9.figshare.24287731.v3
title: Database for ChatMOF

description: ChatMOF is an autonomous Artificial Intelligence (AI) system that is built to predict and generate of metal-organic frameworks (MOFs). By leveraging a large-scale language model (gpt-3.5-turbo), ChatMOF extracts key details from textual inputs and delivers appropriate responses, thus eliminating the necessity for rigid structured queries. The system is comprised of three core components (i.e. an agent, a toolkit, and an evaluator) and it forms a robust pipeline that manages a variety of tasks, including data retrieval, property prediction, and structure generation. The study further explores the merits and constraints of using large language models (LLMs) AI system in material sciences using and showcases its transformative potential for future advancements.
DOI: 10.6084/m9.figshare.26970568.v2
title: Cryptotis.parvus.SNP.vcf

description: Dataset containing 22,786 Single Nucleotide Polymorphisms (SNPs) obtained through double-digest restriction site associated DNA sequencing. The dataset contains 76 shrews from the <i>Cryptotis</i> genus, including samples from across New Mexico, Colorado, Texas, Kansas, Louisiana, and Florida. Dataset was used to perfom a rangewide taxonomic assessment of <i>Cryptotis parvus</i> and a conservation assessment of peripheral <i>C. parvus</i> populations in New Mexico.
DOI: 10.6084/m9.figshare.27650430.v1
title: Supplementary Tables (1-13)

description: Supplementary Tables are part of the project THOR (Targeting smooth muscle cells in atherosclerosis therapy) of the Open Discovery Innovation Network (ODIN) initiative.
DOI: 10.17632/f7r3stvcts
title: Data set on selected groundwater sources in Omuaran, Nigeria

description: The main focus of this data presentation is to describe the quality of drinking water in Omu-Aran, Kwara State. The water quality index was also employed as an important informational tool and was evaluated using Weighted Average Water Quality Index (WAWQI) to represent the groundwater quality in the study area using ten parameters namely pH, Turbidity, DO, Nitrite, Electrical Conductivity, Total Dissolved Solids, Total hardness, Chloride, Fluoride and Total Coliform. The drinking water quality index values range from 19.5 - 97.8 and from 31.7 – 201.7 for both dry and wet seasons respectively. WQI distribution of water samples throughout sampling period suggest that 64 % of water samples were of good quality, 20% of ground water samples were considered as excellent, 4 % fall under poor category while 12 % are classified as unsuitable for drinking.
DOI: 10.17632/rth2wcgrc3
title: LINF_180013800

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.6084/m9.figshare.21428184.v1
title: DVS Gesture pre-processed

description: A pre-processed version of the original dataset from IBM with reduced time step precision of ms instead of us
DOI: 10.6084/m9.figshare.23605521.v3
title: Replicating and Extending Hemispheric Asymmetries in Auditory Distraction: No Metacognitive Awareness for the Left-Ear Disadvantage for Changing-State Sounds

description: Two experiments explored hemispheric asymmetries in auditory distraction by manipulating the spatial location of presentation of to-be-ignored sound. Previous research revealed a left-ear disadvantage for the presentation of changing-state sequences during short-term serial recall (Hadlington et al., 2004; 2006), but did not provide a direct measure of the changing-state effect as no steady-state condition was incorporated. Experiment 1 addressed this by comparing changing-state with steady-state sequences in a visual-verbal serial recall task, and confirmed that the additional disruption produced via left-ear presentation stemmed from the acoustically varying nature of the sound. This left-ear disadvantage for the changing-state effect highlights right hemisphere dominance for processing acoustic variation within unattended sound. Using the same stimuli, Experiment 2 replicated these results and gained insight into participant’s metacognitive monitoring of the disruptive potential of auditory distractors. Participants prospectively rated the extent to which they would be distracted by steady-state and changing-state sequences presented to the left ear, right ear, or both ears, and judged whether the sounds had a beneficial or detrimental effect on their performance after each trial. Participants showed both prospective and retrospective awareness that changing-state sequences were more disruptive than steady-state sequences (cf. Bell et al., 2021). However, participants did not expect disruption to vary by auditory location and were unaware that changing-state sequences were more disruptive when presented to the left ear, relative to the right ear or both ears. Therefore, individuals have metacognitive awareness of the greater disruptive impact of changing- over steady-state sound, but not the accompanying left-ear disadvantage. Implications of these findings are considered in the context of theoretical accounts of auditory distraction.
DOI: 10.6084/m9.figshare.28590416.v1
title: Data of "Are lichens biocompasses? Revisiting an old prediction using new techniques"

description: These are the original data files used in the study: "Are lichens biocompasses? Revisiting an old prediction using new techniques"
DOI: 10.6084/m9.figshare.19982108.v1
title: 中华草龟和中华花龟的群体遗传学研究与微卫星标记开发

description: 4个群体80个样本的CO1和CYTB基因序列
DOI: 10.6084/m9.figshare.26367139.v3
title: Closing the Gap: A User Study on the Real-world Usefulness of AI-powered Vulnerability Detection & Repair in the IDE

description: Updated with camera-ready paper and artifact for evaluation. Added reviewer comments from ICSE 2025 - Artifact Evaluation.
DOI: 10.6084/m9.figshare.26952070.v2
title: Greenhouse gas fluxes and water physicochemical indices of urban rivers in China

description: The greenhouse gas fluxes and water physicochemical indexes of urban rivers in China were collected and classified by city
DOI: 10.6084/m9.figshare.28358573.v1
title: Data sources list for Occurrence records of tropical Asian butterflies (1970-2024)

description: Data sources list for Occurrence records of tropical Asian butterflies (1970-2024)
DOI: 10.17632/yzd96xjfsx
title: Th2 response drives itch in dystrophic epidermolysis bullosa pruriginosa: a case-control study_supplemental

description: Supplemental methods, results and figures for paper entitled 'Th2 response drives itch in dystrophic epidermolysis bullosa pruriginosa: a case-control study'
DOI: 10.6084/m9.figshare.17099912.v1
title: NDC-SDG Linkages

description: The NDC-SDG linkage analysis is a comprehensive study, which examines the degree of alignment between the (I)NDCs and the 169 targets of the 2030 Sustainable Development Agenda. Climate action texts were extracted from the NDCs and aligned with relevant targets. The study was carried by WRI to support joint implementation of both the Paris Agreement and the 2030 Agenda.<br><br>https://www.climatewatchdata.org/data-explorer/emission-pathways?emission-pathways-categories=All Selected&emission-pathways-indicators=All Selected&emission-pathways-locations=All Selected&emission-pathways-models=All Selected&emission-pathways-scenarios=All Selected&emission-pathways-subcategories=All Selected&page=1<br>
DOI: 10.6084/m9.figshare.28248038.v3
title: GloGCI-World Ghost Cities Index Ranking

description: Due to rapid urbanization over the past 20 years, many newly developed areas have lagged in socio-economic maturity, creating an imbalance with older cities and leading to the rise of "ghost cities". However, the complexity of socio-economic factors has hindered global studies from measuring this phenomenon. To address this gap, a unified framework based on urban vitality theory and multi-source data is proposed to measure the Ghost City Index (GCI), which has been validated using various data sources. The study encompasses 8,841 natural cities worldwide with areas exceeding 5 km², categorizing each into new urban areas (developed after 2005) and old urban areas (developed before 2005). Urban vitality was gauged using the density of road networks, points of interest (POIs), and population density with 1 km resolution across morphological, functional, and social dimensions. By comparing urban vitality in new and old urban areas, we quantify the GCI globally using the theory of urban vitality for the first time. The results reveal that the vitality of new urban areas is 7.69% that of old ones. The top 5% (442) of cities were designated as ghost cities, a finding mirrored by news media and other research. This study sheds light on strategies for sustainable global urbanization, crucial for the United Nations' Sustainable Development Goals.The code file gives the calculation process of data respectively, and the excel file gives the obtained data. For the explanation of the fields in “citypoint.shp”, please refer to the Supplementary Information of the paper (https://doi.org/10.1016/j.habitatint.2025.103350).Ref: Zhang, Y., Tu, T., & Long, Y. (2025). Inferring ghost cities on the globe in newly developed urban areas based on urban vitality with multi-source data. Habitat International, 158, 103350. https://doi.org/10.1016/j.habitatint.2025.103350<br><br>
DOI: 10.6084/m9.figshare.5125936.v1
title: Supplementary Material for: Semantic Features of ‘Stepped' versus ‘Continuous' Contours in German Intonation

description: This study analyses the meaning spaces of German pitch contours using two modes of melodic movement: continuous or in steps of sustained pitch. Both the continuous and stepped movements are represented by a set of five basic patterns, the latter being derived from the former. Thirty-six German native speakers judged the pattern sets on a 12-scale semantic differential. The semantic profiles confirm that stepped contours can be conceived of as stylized intonation, in a formal as well as in a functional sense. On the one hand, continuous (non-stylized) and stepped (stylized) contours are assigned different overall meanings (especially on the scales astonished - commonplace and interested - not interested). On the other hand, listeners organize the two contour sets in a similar fashion, which speaks in favour of parallel pattern inventories of continuous and stepped movement, respectively. However, the meaning space of the stylized patterns is affected by formal restrictions, for instance in the step transformation of continuous rises.
DOI: 10.6084/m9.figshare.7710932.v1
title: Performance and egg quality of laying hens fed with mineral sources and rosemary oil

description: Abstract In order to evaluate the effect of rosemary oil and micro mineral sources on the performance and egg quality of laying hens, 288 hens were used and distributed in a completely randomized design using a 2x3 factorial (mineral sources x rosemary oil) with six different diets and six replications. Diets were formulated containing inorganic or organic minerals, with or without added rosemary oil (100 and 200 mg kg-1). The treatments showed interaction for average egg weight, yolk color, albumen and yolk percentage, with significant results from the use of organic minerals compared to inorganic minerals. The addition of 200 mg kg-1 rosemary oil in diets improved laying rate, egg mass, specific gravity, number of pores on the shell when compared to other treatments. In conclusion, the use of 200 mg kg-1 of rosemary oil improves the performance of red laying hen eggs. The association between organic minerals and 100 mg kg-1 rosemary oil in laying hen diets increases yolk color and percentage of albumen. The use of organic minerals is superior to inorganic minerals as to improve the quality of eggs, increasing average egg weight, yolk color and percentage of albumen.
DOI: 10.6084/m9.figshare.97395.v4
title: Thirty Nine Minoan Sites

description: These are the 39 sites and distance between them used in a series of papers by T.S.Evans, C.Knappett and R.J.Rivers. They represent major centres in the Middle Bronze age of the Aegean (era of Minoan civilisation). Information on these excel files and on some of the papers using this data is contained in a pdf or can be found following the links provided. I also provide figures shwoing the location of these sites along with a QGIS project file used to create the figures.
DOI: 10.6084/m9.figshare.12568625.v1
title: data.zip

description: Data and code are under review and subject to change. For issues contact the lead author: kirstin.holsman@noaa.gov<br><br>Corresponding citation:K Holsman A. Haynie, A. Hollowed, J. Reum, K. Aydin, A. Hermann,W. Cheng, A Faig, J. Ianelli, K. Kearney, A. Punt. Ecosystem-based fisheriesmanagement forestalls climate-driven collapse. Nature Communications.DOI: 10.1038/s41467-020-18300-3<br><br>Citation for the data:Holsman, K. K., A. Haynie, A. Hollowed, J. C. P. Reum, K. Aydin, A. J. Hermann, W. Cheng, A. Faig, J. N. Ianelli, K. Kearney, and A. E. Punt. 2020. The Alaska Climate Integrated Modeling study Multispecies Ecosystem Based Fisheries Management and climate change simulation and results. doi: 10.6084/m9.figshare.12568625<br><br>Supporting code available at:https://github.com/kholsman/EBM_Holsman_NatCommand http://doi.org/10.5281/zenodo.3965248 (archived location)<br><br>____________________________________________data.zip includes:<br>"data/in" intermediate data files from the ACLIM project used to generate paper results and figures<br>"data/out" final data from analyses as reported in the paper.<br>
DOI: 10.6084/m9.figshare.21276192.v1
title: Tan et al. (2022) Fungal Planet description sheets: 1436–1477 - Persoonia 49: 261-350

description: Alignments and phylogenetic trees processed through Mesquite and belonging to new species described in this Fungal Planet set contributed by the Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands. See the figure legends associated with each file in the original publication for more details.