cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6916298.v2
title: Sequence alignment for phylogenetic tree construction

description: This alignment was used to build a tree with our MAGs, all taxa previously identified by Burgess et al. (2012) with complete genomes available on NCBI (downloaded 2017-09-06), and all archaeal and bacterial genomes previously used in Hug et al. (2016). The genomes used in this tree and a mapping file can be found on figshare.<br>(genomes in Hug et al.’s tree of life (2016): https://doi.org/10.6084/m9.figshare.6863594.v1, https://doi.org/10.6084/m9.figshare.6863744.v2, https://doi.org/10.6084/m9.figshare.6863813.v1; genomes from Burgess et al. (2012): https://doi.org/10.6084/m9.figshare.6863798.v1).<br> <br>PhyloSift builds an alignment of the concatenated sequences for a set of core markers for each taxon. We used 37 of these single-copy marker genes (ribosomal protein S2 rpsB, S10 rpsJ, L1 rplA, L22, L4/L1e rplD, L2 rplB, S9 rpsl, L3 rplC, L14b/L23e rplN, S5, S19 rpsS, S7, L16/L10E rplP, S13 rpsM, L15, L25/L23, L6 rplF, L11 rplK, L5 rplE, S12/S23, L29, S3 rpsC, S11 rpsK, L10, S8, L18P/L5E, S15P/S13e, S17, S13 rplM, L24; and translation initiation factor IF-2, metalloendopeptidase, phenylalanyl-tRNA synthetase beta subunit, phenylalanyl-tRNA synthetase alpha subunit, tRNA pseudouridine synthase B, Porphobilinogen deaminase, and ribonuclease HII; i.e., PhyloSift markers DNGNGWU00001 - DNGNGWU00040 without DNGNGWU00004, DNGNGWU00008 and DNGNGWU00038). The amino acid alignment of these 37 concatenated genes was trimmed using trimAl v.1.2. Columns with gaps in more than 5% of the sequences were removed, as well as taxa with with less than 75% of the concatenated sequences. MAGs from ARK and ZAV that did not meet this threshold were manually kept in the alignment.
DOI: 10.17632/txwg5n25nc
title: Amplification editing enables efficient and precise duplication of DNA from short sequence to megabase and chromosomal scale

description: This dataset contains the raw data used to generate the Figures in the paper titled "Amplification editing enables efficient and precise duplication of DNA from short sequence to megabase and chromosomal scale".
DOI: 10.6084/m9.figshare.93086.v2
title: ONS Open Melting Point Collection ONSMP029

description: This Dataset ONSMP029 (2706 unique compounds, 7413 measurements) is from a project to collect and curate melting points made available as Open Data. This particular collection was selected from the application of a threshold to favor the likelihood of reliability. Specifically, the entire range of averaged values for a data point was set to 0.01 C to 5 C, with at least two different measurements within this range. Measurements were pooled and processed from the following sources: Alfa Aesar, MDPI, Bergstrom, PhysProp, DrugBank, Bell, Oxford MSDS, Hughes, Griffiths and the Chemical Information Validation Spreadsheet. Links to all the information sources and web services are available from the Open Melting Point Resource page: http://onswebservices.wikispaces.com/meltingpoint
DOI: 10.17632/jgkkh875hc
title: Data for: Remnant vegetation provides genetic connectivity for a critical weight range mammal in a rapidly urbanising landscape

description: Microsatellite genotypes are provided for 681 quenda samples from 42 populations across the greater Perth metropolitan region in GenAlEx format
DOI: 10.17632/vwg6xzmrf9
title: A time- and single-cell-resolved model of murine bone marrow hematopoiesis

description: Data, source code, singularity container, extended figures and tables for the article: "A time- and single-cell-resolved model of murine bone marrow hematopoiesis"

The paradigmatic hematopoietic tree model is increasingly recognized to be limited as it is based on heterogeneous populations and largely inferred from non-homeostatic cell fate assays. Here, we combine persistent labeling with time-series single-cell RNA-Seq to build a real-time, quantitative model of in vivo tissue dynamics for murine bone marrow hematopoiesis. We couple cascading single-cell expression patterns with dynamic changes in differentiation and growth speeds. The resulting explicit linkage between molecular states and cellular behavior reveals widely varying self-renewal and differentiation properties across distinct lineages. Transplanted stem cells show strong acceleration of differentiation at specific stages of erythroid and neutrophil production, illustrating how the new model can quantify the impact of perturbations. Our reconstruction of dynamic behavior from snapshot measurements is akin to how a kinetoscope allows sequential images to merge into a movie. We posit that this approach is generally applicable to understanding tissue scale dynamics at high resolution.
DOI: 10.6084/m9.figshare.1037485.v1
title: <i>Azadinium caudatum</i> var. <i>margalefii</i>, a poorly known member of the toxigenic genus <i>Azadinium</i> (Dinophyceae)

description: <i>Azadinium caudatum</i> is a poorly known planktonic dinoflagellate, which mainly attracts attention due to the occurrence of many toxigenic species in the genus <i>Azadinium</i>. The availability of two Scottish isolates of <i>A. caudatum</i> var. <i>margalefii</i> allowed for the first time a detailed analysis of biological and physiological traits of the species, specifically on the potential presence of azaspiracid toxins (AZAs). With a mean overall swimming speed of 85 µm s<sup>−1</sup> and regularly interspersed high-speed jumps, <i>A. caudatum</i> var. <i>margalefii</i> exhibited a similar swimming behaviour to other species of the genus. Cells had a single, large, highly reticulated chloroplast with a typical pigment composition for peridinin-containing dinoflagellates. No pyrenoids were visible under light microscopy. A round to ovoid nucleus was centrally located. Cell division was by desmoschisis, i.e. the parent theca was shared by the daughter cells. Growth rate <i>µ</i> ranged from 0.07 to 0.32 day<sup>−1</sup> and was reduced at lower temperatures. With growth rate becoming light saturated at intensities of about 40 µE m<sup>−2</sup> s<sup>−1</sup> and a half-saturation light intensity of about 13 µE m<sup>−2</sup> s<sup>−1</sup>, <i>A. caudatum</i> var. <i>margalefii</i> appears to be relatively low-light adapted. Neither strain produced any known AZAs in measureable amounts.
DOI: 10.6084/m9.figshare.13359365.v1
title: Supplementary Material for: Incidence of Stroke and Ischemic Stroke Subtypes: A Community-Based Study in Brno, Czech Republic

description: <b><i>Background:</i></b> There are few contemporary epidemiological data on stroke for Central Europe. We performed a population-based study evaluating the incidence of stroke, stroke types, and ischemic stroke (IS) subtypes in Brno, the second biggest city in the Czech Republic (CR). <b><i>Methods:</i></b> Using the National Registry of Hospitalized Patients, and hospital databases, we identified all patients hospitalized with a stroke diagnosis in Brno hospitals in 2011. For Brno residents with validated stroke diagnosis, we calculated (a) the overall incidence of hospitalized stroke, (b) incidence rates for IS, subarachnoid hemorrhage (SAH) and intracerebral hemorrhage (ICH), and (c) incidence rates for IS subtypes. We calculated the average annual age- and sex-standardized incidence (European Standard Population and World Health Organization), to compare our results with other studies. <b><i>Results:</i></b> The overall crude incidence of stroke in Brno was 213/100,000 population. The incidence of stroke for stroke types were as follows: SAH, 6.9; ICH, 26.4; and IS, 180 cases per 100,000 population, respectively. The WHO-standardized annual stroke incidence was 107 for all strokes and 88 for IS, 14.4 for ICH, and 5 for SAH. For IS subtypes, the WHO-standardized incidence was large artery atherosclerosis 25.8, cardioembolism 27.8, lacunar 21.6, other determined etiology 6.2, and undetermined etiology 6.5 cases per 100,000 population. <b><i>Conclusions:</i></b> The stroke incidence is lower than that previously reported for the CR and Eastern Europe probably reflecting socioeconomic changes in post-communistic countries in the region. These findings could contribute to stroke prevention strategies and influence health policies.
DOI: 10.6084/m9.figshare.21632537.v1
title: Table S3

description: Reagents table
DOI: 10.6084/m9.figshare.23675388.v1
title: Supplementary files for one-gene mutation induces lizard color divergence

description: This folder contains:(1) The input files to run FastSimCoal26 analyses, including the joint minor allele frequency spectrum (.obs file) and .tpl and .est in subfolders files for each model that we fit in FSC26. For each analysis, the filename of the .obs file will have to be changed to match the .tpl file before running FSC26. 'SC_maxL.par' is file with model specification and maximum likelihood parameters of the model with highest likelihood among four models, and 'seed.txt' is the seed for the run.(2) The aminoacid sequences of <i>Tyrp1 </i>for <i>P. putjatai</i> from dune and meadow population, and two lizard species (<i>Sceloporus undulatus, Anolis carolinensis</i>) have light color.(3) The ab1 file of <i>Tyrp1 </i>sequences from 30 dark lizards from meadow population, and 30 light lizards from dune population.
DOI: 10.6084/m9.figshare.24444937.v2
title: An exhaustive dataset of Diptera Wing Interferential Patterns (WIPs).

description: Pictures of Wing interferential patterns (WIPs) from various Dipteran insects. The dataset 2399 pictures of 6 families (Culicidae, Calliphoridae, Muscidae, Tabanidae, Ceratopogonidae Psychodidae) and 18 genera. Each genus is documented by a variable number of species (class), with 1 to more than 300 samples covering, in most cases, species variation. The dataset complet the dataset https://doi.org/10.6084/m9.figshare.22083050.v4.
DOI: 10.6084/m9.figshare.26323711.v1
title: CICMalDroid2020

description: Zero shot learning based research project. Model was trained on 3 families of CICMalDroid2020 and was tested on all of its 5 families.
DOI: 10.6084/m9.figshare.27601056.v1
title: Carbon orignal research Data.xlsx

description: <b>Impact of biochar C:N ratios on dynamics of soil organic carbon fractions and greenhouse gas emissions in two soil types</b>
DOI: 10.6084/m9.figshare.27988478.v1
title: Combined data and code package.

description: Geospatial analyses of human-environment interactions are challenged by the multi-scale, multi-dimensional nature of human-environment systems. Research in such contexts must often rely on integrating multiple, independently produced data sources, which presents heterogenous data qualities and interoperability challenges. Understanding data quality and transparency becomes increasingly important in these contexts, and multi‐granularity and context specific spatial data quality indicators are needed. We develop a data pedigree system that accounts for multiple data quality aspects, geospatial ambiguities that may hinder interoperability, and the fitness-for-use of each data source for indicating causal linkages between human activities and environmental change. We demonstrate its application to a particularly challenging and data sparse case study of identifying the location and timing of transnational cocaine trafficking, or ‘narco-trafficking’, in Central America with five spatial and temporal data quality indicators: geographic clarity, geographic interpretation, provenance, temporal specificity, and narco-trafficking certainty. The proposed data pedigree system provides a systematic and coherent analytical framework for interoperability, comparison, and corroboration of fragmented and incomplete data, which are needed to support advanced geospatial analyses, such as causal inference techniques. The study demonstrates the transferability and operationalization of the data pedigree system for examining complex human-environment interactions, especially those influenced by illicit economies.
DOI: 10.6084/m9.figshare.28179977.v1
title: Navigation for Festival Maps on Mobile Devices

description: This repository contains the transcriptions of the needs assessment interviews conducted with six young event-goers, as well as the transcriptions of the expert-based think-aloud user testing of the prototype developed for the study.
DOI: 10.6084/m9.figshare.28399916.v1
title: Flow Pattern Identification and Detection in T-Junction Microchannels for Shear Thinning Non-Newtonian Fluids : Comsol files

description: Simulation setups for the simulations which were done for the manuscripts.
DOI: 10.6084/m9.figshare.5129581.v1
title: Supplementary Material for: Concordant Patterns of Brain Structure in Mothers with Recurrent Depression and Their Never-Depressed Daughters

description: <b><i>Background:</i></b> A growing body of research has demonstrated that having a mother with a history of major depressive disorder (MDD) is one of the strongest predictors of depression in adolescent offspring. Few studies, however, have assessed neural markers of this increased risk for depression, or examined whether risk-related anomalies in adolescents at maternal risk for depression are related to neural abnormalities in their depressed mothers. We addressed these questions by examining concordance in brain structure in two groups of participants: mothers with a history of depression and their never-depressed daughters, and never-depressed mothers and their never-depressed daughters. <b><i>Method:</i></b> We scanned mothers with (remitted; RMD) and without (control; CTL) a history of recurrent episodes of depression and their never-depressed daughters, computed cortical gray matter thickness, and tested whether mothers' thickness predicted daughters' thickness. <b><i>Results:</i></b> Both RMD mothers and their high-risk daughters exhibited focal areas of thinner cortical gray matter compared with their CTL/low-risk counterparts. Importantly, the extent of thickness anomalies in RMD mothers predicted analogous abnormalities in their daughters; this pattern was not present in CTL/low-risk dyads. <b><i>Conclusions:</i></b> We identified neuroanatomical risk factors that may underlie the intergenerational transmission of risk for MDD. Our findings suggest that there is concordance in brain structure in dyads that is affected by maternal depression, and that the location, direction, and extent of neural anomalies in high-risk offspring mirror those of their recurrent depressed mothers.
DOI: 10.6084/m9.figshare.8323670.v1
title: Raw data for NVDI calculation

description: Raw data for NVDI calculation
DOI: 10.6084/m9.figshare.11984259.v2
title: Security Compliance in Agile Development: A Systematic Mapping Study

description: Companies adopting agile development tend to face challenges in complying with security norms. Existing research either focuses on how to integrate security into agile methods or on discussing compliance issues of agile methods but independently of the regulation type, in particular of security standards. A comprehensive overview of this scattered field is still missing. To close this gap, we report on a systematic mapping study.Starting with a set of 2,383 papers, this work distills 11 relevant publications addressing security compliance in agile software development. With this study, we contribute by providing a description of the maturity of the field, as well as domains where security compliant agile software engineering was investigated.
DOI: 10.6084/m9.figshare.13606529.v1
title: Transcripts in-depth patient interviews

description: Ten transcripts of ten individual in-depth patient interviews. Patients diagnosed with diabetes mellitus type two and receiving diabetes care from both a general practitioner and a practice nurse.
DOI: 10.6084/m9.figshare.22285027.v1
title: Realwave for IGBT Current.mat

description: Matlab data file; It's a IGBT resonance current data set of a real power supply. Under normal circumstances, the resonant current was a series of sine signals, and its amplitude was related to the load real-time condition. When the spark flashover occurred in the electric field of the ESP, the current in the IGBT increased rapidly from the 503rd sample point.
DOI: 10.6084/m9.figshare.28180361.v1
title: Results of enrichment analysis for 77 transcripts with intraspecific variants in NMR.

description: Results of enrichment analysis for 77 transcripts with intraspecific variants in NMR.
DOI: 10.6084/m9.figshare.5120968.v1
title: Supplementary Material for: Tötungsdelikte an Kindern – erste Eindrücke aus einem kriminologischen Forschungsprojekt

description: <i>Hintergrund: </i>TÖtungsdelikte an Kindern in Deutschland sind trotz des großen medialen und politischen Interesses bisher nicht ausreichend erforscht. Das hier vorgestellte kriminologische Forschungsprojekt strebt an, verlÄssliche Daten zu Erscheinungsbild, HintergrÜnden und strafrechtlicher Aufarbeitung zu erlangen. <i>Methoden und Ergebnisse: </i>Empirische Grundlage ist die Analyse der Strafakten aller vorsÄtzlichen, vollendeten TÖtungsdelikte an Kindern &lt;6 Jahren im Zeitraum 1997–2006 in Deutschland. Im ersten Teil des Beitrags werden einige Ergebnisse zur PhÄnomenologie skizziert. Erste vorlÄufige Auswertungen auf der Basis etwa der HÄlfte der FÄlle lassen erkennen, dass eine Differenzierung nach Fallgruppen unerlÄsslich ist, um sinnvolle Analysen durchzufÜhren. Vorgeschlagen wird folgende Unterscheidung: Neonatizide, MisshandlungstÖtungen, TÖtungen durch VernachlÄssigung, TÖtungen im Zusammenhang mit einer akuten, schweren psychischen Erkrankung, erweiterte Suizide, gezielte TÖtungen und sonstige TÖtungen. Diese Fallgruppen sind in sich durchaus heterogen und nicht Überschneidungsfrei. <i>Diskussion: </i>Im zweiten Teil des Beitrags werden einige Probleme der strafrechtlichen Bewertung der FÄlle dargestellt, die sich daraus ergeben, dass es einerseits nicht selten schwierig ist, die Tat vollstÄndig aufzuklÄren, andererseits immer auch wertende AbwÄgungen zu treffen sind.
DOI: 10.6084/m9.figshare.5539810.v1
title: Dataset of generated and evaluated residential buildings of two storeys with random U-values for opaque and transparent exterior elements

description: The geometric data was generated using the EPSAP algorithm; the construction elements physical properties were saved from the EPSAP algorithm database; and, the performance data was obtained using the FPOP algorithm coupled to the simulation engine EnergyPlus v8.8.0. The weather files used in the simulations were the PRT_Lisboa, PRT_Porto, ESP_Toledo, ITA_Milan, ROU_Bucharest, SWE_Kiruna, SWE_Stockholm data available at the Department of Energy (URL https://energyplus.net/weather).<br>
DOI: 10.6084/m9.figshare.7970135.v1
title: Hotspots of mammal defaunation

description: Percentage of mammal species per grid cell with DI &gt; 0.7 or abundance reductions of at least 70% due to hunting.
DOI: 10.17632/7hwtk2pxj5
title: Coperate Governance

description: This Dataset is about corporate governance
DOI: 10.17632/s5v4zz7yj5
title: Remote sensing satellite images dataset for objects detection 

description: The dataset comprises of 92 satellite images containing 61 training set, 21 validation set and 10 testing set, together with the annotation files. Sample images from testing dataset are presented in Fig. 3. The images in the dataset were annotated using the roboflow application. The dataset contains 5 categories of objects: residence, roads, shoreline, swimming pool and vegetation. The dataset can be used to train, validate and test variants of YOLO models [2] for object detection from remote sensing satellite images.
DOI: 10.6084/m9.figshare.28522109.v1
title: Supplementary Material for: Inhaled nitric oxide for bronchopulmonary dysplasia–associated pulmonary hypertension: A systematic review and narrative synthesis

description: Introduction: Inhaled nitric oxide (iNO) is a selective pulmonary vasodilator. However, its effectiveness in the treatment of bronchopulmonary dysplasia–associated pulmonary hypertension (BPD-PH) and severe BPD remains uncertain. Here we systematically reviewed whether iNO treatment increased or decreased mortality and morbidity among preterm infants with severe BPD or BPD-PH. 
Methods: We systematically searched the Ovid MEDLINE, Embase, Cumulative Index to Nursing and Allied Health Literature, Cochrane CENTRAL, and ICHUSHI databases for randomized and non-randomized studies that compared the effects of iNO in patients with severe BPD or BPD-PH. The primary outcome was mortality. Two authors independently screened the articles and extracted the data. A meta-analysis and certainty of evidence assessment using the Cochrane Grading of Recommendations Assessment, Development, and Evaluation criteria were planned.
Results: Among the 1710 articles, none had a relevant control group and no studies met the eligibility criteria. Using a post hoc analysis, we summarized the ineligible studies that evaluated patients with severe BPD or BPD-PH who received iNO therapy. Although some studies included in the narrative review indicated a decreased pulmonary arterial pressure in patients with severe BPD or BPD-PH at the initiation of iNO therapy, none included a comparator group.
Conclusions: Despite the use of iNO in patients with severe BPD and BPD-PH, no published studies compared the outcomes between patients with BPD treated with versus without iNO. Although some studies without comparator groups reported the effectiveness of iNO in patients with severe BPD and BPD-PH, our results suggest that iNO therapy should be initiated with caution and careful consideration of the target population.
DOI: 10.17632/whb6rychpx
title: Nigeria's 2023 Presidential Election Dataset

description: This dataset contains tweets mined from August, 2022 to February, 2023 about Nigeria's 2023 presidential election. The data is based on the three major presidential aspirants in the 2023 presidential election. These aspirants are Atiku Abubakar, Bola Ahmed Tinubu and Peter Obi. The data was mined using the Twitter API and Tweepy Python library using the following hastags: #obi, #atiku, #bat, #ObiDatti, #Atikulate and #batified.
DOI: 10.6084/m9.figshare.23804319.v1
title: Data for "Reconstruction of Violent Tornado Environments in Europe: High-Resolution Dynamical Downscaling of ERA5"

description: Raw ERA5 data on hybrid-sigma levels (files starting with 'N_') and post-processed convective parameters using thundeR v1.0 R language package (files with phrase "<i>parameters"). Each date denote a separate violent tornado event that was evaluated in "Reconstruction of Violent Tornado Environments in Europe: High-Resolution Dynamical Downscaling of ERA5"</i> (https://doi.org/10.1029/2022GL098242).
DOI: 10.6084/m9.figshare.24587364.v1
title: PTB dataset

description: A processed dataset of Myocardial infarction.