cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28225550.v1
title: <b>SNP calling</b><b> </b><b>counts</b><b> </b><b>from individual and pool sequencing data.</b>

description: <i>Bromus auleticus</i>, a valuable forage grass native to the Pampa biome, is currently suffering genetic erosion. Therefore, it is central to assess the appropriate methodologies for developing population genomic studies and contributing to the conservation of this plant genetic resource. This study evaluated five accessions using two genotyping strategies: individual sequencing (ind-seq) and pooled sequencing (pool-seq). To compare their efficacy, was investigated the correlation between allele frequencies calculated using each approach. Geneticdiversity and population structure were also analyzed using both methods. These comparisons explicitly accounted for the potential effects of one or more of the following parameters: sample size, missing data, sequencing depth, and minor allele frequencies. Notably, the highest concordance and percentage of common SNPs between ind-seq and pool-seq was achieved using 30 to 60 plants per accession, with a maximum missing data threshold of 10% and a more tolerant minimum allele frequency threshold for pool-seq (0.01) compared to ind-seq (0.05). Reaching maximum similarity in allele frequencies also required a higher sequencing depth for pool-seq (4.8 million reads-Mr) than for ind-seq (0.9 Mr). Pools of 50 individuals yielded the highest number of polymorphic sites, averaging over 9,000 across all accessions at a sequencing depth of 4.8 Mr. Under these conditions, pool-seq consistently yielded a means across all accessions of 0.09 higher expected heterozygosity and 0.24 lower allelic richness compared to ind-seq across all accessions. The population structure detected with both methodologies showed agreement, aligning with the outcrossing nature of <i>B. auleticus</i> and the geographical origin of each accession. The average inbreeding coefficient of 0.2 indicates signs of inbreeding, highlighting the importance of conservation efforts of this valuable plant genetic resource. Based on these findings, two workflows were proposed to carry out population genomics studies of <i>Bromus auleticus</i>.
DOI: 10.17632/bth7g6cvw5
title: Supplementary file for Multi-tool Drilling Path Optimization by Multi-Agent Reinforcement Learning Approach

description: The details of workpieces can be checked in this file.
DOI: 10.6084/m9.figshare.17072759.v3
title: Code and data to reproduce "Landscape structure and species life history effects on abundance-occupancy relationships"

description: <pre>## Landscape structure and species life history effects on abundance-occupancy relationships<br><br>### Citation<br><br>Code and data to reproduce the analyses from<br><br>&gt; Dallas, TA, LA Holian, and C Ten Caten 2024. Landscape structure and species life history affect abundance-occupancy relationships. <br><br><br><br><br><br>## Compiling the project<br><br>To compile the R markdown, the following terminal command can be issued from the directory where the files are all located.<br><br>Note: this is not really recommended to compile it this way, as it will have to run for quite a long time. <br><br>```<br>Rscript -e 'install.packages(c("plyr", "dplyr", "igraph", "viridis"))'<br><br>Rscript -e 'rmarkdown::render("DallasNeonRicker.Rmd", output_format="pdf_document")'<br><br>```<br><br><br><br>```{r}<br><br>sessionInfo()<br><br>```<br><br>R version 4.1.0 (2021-05-18)<br>Platform: x86_64-pc-linux-gnu (64-bit)<br>Running under: Ubuntu 20.04.2 LTS<br><br>Matrix products: default<br>BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3<br>LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3<br><br>locale:<br> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C <br> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 <br> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 <br> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C <br> [9] LC_ADDRESS=C LC_TELEPHONE=C <br>[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C <br><br>attached base packages:<br>[1] stats graphics grDevices utils datasets methods base <br><br>other attached packages:<br>[1] dplyr_1.0.7 plyr_1.8.6 igraph_1.2.8<br><br>loaded via a namespace (and not attached):<br> [1] Rcpp_1.0.7 fansi_0.5.0 crayon_1.4.1 utf8_1.2.2 <br> [5] R6_2.5.1 lifecycle_1.0.0 magrittr_2.0.1 pillar_1.6.2 <br> [9] rlang_0.4.11 vctrs_0.3.8 generics_0.1.0 ellipsis_0.3.2 <br>[13] tools_4.1.0 glue_1.4.2 purrr_0.3.4 compiler_4.1.0 <br>[17] pkgconfig_2.0.3 tidyselect_1.1.1 tibble_3.1.4 <br><br><br><br></pre>
DOI: 10.6084/m9.figshare.19419335.v2
title: CLIMIFUN fungi

description: CLIMIFUN ITS dataset
DOI: 10.6084/m9.figshare.27610683.v2
title: Time-series China urban land use mapping (2016–2022): An approach for achieving spatial-consistency and semantic-transition rationality in temporal domain

description: The global urbanization trend is geographically manifested through city expansion and the renewal of internal urban structures and functions. Time-series urban land use (ULU) maps are vital for capturing dynamic land changes in the urbanization process, giving valuable insights into urban development and its environmental consequences. Recent studies have mapped ULU in some cities with a unified model, but ignored the regional differences among cities; and they generated ULU maps year by year, but ignored temporal correlations between years; thus, they could be weak in large-scale and long time-series ULU monitoring. Accordingly, we introduce an temporal-spatial-semantic collaborative (TSS) mapping framework to generating accurate ULU maps with considering regional differences and temporal correlations. Firstly, to support model training, a large-scale ULU sample dataset based on OpenStreetMap (OSM) and Sentinel-2 imagery is automatically constructed, providing a total number of 56,412 samples with a size of 512 × 512 which are divided into six sub-regions in China and used for training different classification models. Then, an urban land use mapping network (ULUNet) is proposed to recognize ULU. This model utilizes a primary and an auxiliary encoder to process noisy OSM samples and can enhance the model's robustness under noisy labels. Finally, taking the temporal correlations of ULU into consideration, the recognized ULU are optimized, whose boundaries are unified by a time-series co-segmentation, and whose categories are modified by a knowledge-data driven method. To verify the effectiveness of the proposed method, we consider all urban areas in China (254,566 km2), and produce a time-series China urban land use dataset (CULU) at a 10-m resolution, spanning from 2016 to 2022, with an overall accuracy of CULU is 82.42%. Through comparison, it can be found that CULU outperforms existing datasets such as EULUC-China and UFZ-31cities in data accuracies, spatial boundaries consistencies and land use transitions logicality. The results indicate that the proposed method and generated dataset can play important roles in land use change monitoring, ecological-environmental evolution analysis, and also sustainable city development.
DOI: 10.17632/3jy68skzrv
title: Data for: Structural and Operational Factors as Determinant of Meaningful Community Participation in Sustainable Disaster Recovery Programs: The Case of Bangladesh

description: Primary data collected through 230 sampled survey.
DOI: 10.17632/fykvyxt9w5
title: LINF_180010700

description: PapD-like protein; Leishmania infantum (strain JPCM5)
DOI: 10.17632/jvw7f27cch
title: Nivolumab/relatlimab-associated cutaneous immune-related adverse events in patients treated for advanced melanoma: Supplemental file

description: Supplementary tables I (multivariable analysis of patient characteristics associated with developing cirAEs on nivolumab-relatlimab) and II (choice of therapy for the management of first, second, and third cirAEs)
DOI: 10.6084/m9.figshare.1252073.v1
title: A juvenile specimen of a new coelurosaur (Dinosauria: Theropoda) from the Middle–Late Jurassic Shishugou Formation of Xinjiang, People's Republic of China

description: We describe the anatomy of a new coelurosaurian theropod <i>Aorun zhaoi</i> gen. et sp. nov., from the Middle–Late Jurassic of Xinjiang, China. Histological analysis of the holotype and only known specimen shows that the new taxon is represented by the skeleton of a juvenile individual aged no more than one year. A phylogenetic analysis of theropod relationships places <i>Aorun</i> as a basal member of the Coelurosauria. Although the sole use of a sub-adult ontogenetic exemplar is potentially problematic for phylogenetic reconstruction, we show that the phylogenetic position of <i>Aorun</i> as a member of Coelurosauria is robust to the exclusion of characters known to change during theropod ontogeny. <i>Aorun</i> is the seventh theropod taxon, and temporally oldest coelurosaur, known from the Shishugou Formation, which has one of the most taxonomically diverse Jurassic coelurosaurian theropod faunas in the world.http://zoobank.org/urn:lsid:zoobank.org:pub:5CC73577-9EB3-47AB-9983-1677B278EFFD
DOI: 10.17632/4tsrs9k8z5
title: Survey Questionnaire: Street Vendors Informal Borrowing Practices and Implications on Business

description: Since the instrument was researcher-made, experts were consulted to validate its content. A panel of three expert evaluators, well-versed in the discipline, structure, and logic of research, validated the content of the research instrument. The panel of expert validators consisted of individuals with diverse qualifications. These included (1)a dean of the College of Business Administration of a prestigious and accredited private higher education institution, who is well versed in the finance and entrepreneurial dynamics, (2) an academic director of a business administration program who has a profound understanding of entrepreneurship, (3) and chairperson of trade, commerce, industry, investment and entrepreneurship, and a provincial board member of the 2nd district of Misamis Oriental. These expert validators comprehensively understand research methods and have experience in finance and entrepreneurial domains. 
Further, a pilot test was conducted on at least 30 street vendors who were non-respondents of the study to evaluate the internal consistency of the parameters. The pilot test was done at the Carmen public market, a setting that mirrored the main locale of the study in terms of informal financing and economic activity. The researcher employed a convenient sampling procedure for the pilot testing. After pilot testing, the data were arrayed and treated using Cronbach's alpha. 


Reliability Statistics
Scale N Items Cronbach’s α Interpretation
Price 30 5 .80 Good reliability
Inventory 30 5 .91 Great reliability
Net Income 30 5 .88 Good reliability
Gross Sales 30 5 .81 Good reliability
Selling Strategies 30 5 .87 Good reliability
Business Outcome 30 5 .94 Great reliability
Overall 30 30 .70 Acceptable Reliability
DOI: 10.17632/68b3sh76rd
title: Taguchi Mixes- Compressive strength

description: 28-day Compressive strength
DOI: 10.17632/pwbvcbdszx
title: Rawmat_eyetrack_data

description: Eyetracking data from the paper "Novel Techniques for Anticipating the Focus of Visual Atten-tion across different Mining Landscapes"
DOI: 10.17632/sp2bvhmmj6
title: Investigating the prevalence of tobacco or other substance use (TOSU) and factors associated among the medical students: a nationwide cross-sectional survey from Bangladesh

description: Investigating the prevalence of tobacco or other substance use (TOSU) and factors associated among the medical students: a nationwide cross-sectional survey from Bangladesh
DOI: 10.17632/vvn5bnngxm
title: Assessment of Climate Change Impact on Ambient Air Quality of Industrial, Urban and Rural Belts in and around Ahmedabad Metro City, Gujarat, India

description: Intergovernmental Panel on Climate Change (IPCC) stated that climate change could attribute directly by natural processes or indirectly through anthropogenic changes in the composition of the atmosphere. The impacts of climate change due to deforestation, industrialization, urbanization and agricultural practices on air quality and human health and ecosystem are vulnerable. The aim of this study was to correlate impacts of climate change on ambient air quality (AAQ: NOx, SOx, NH3, PM2.5, PM10 - µg/m3), meteorological parameters (MET: Temperature (°C), Surface Temp. (°C), Light Intensity (Lux), Wind Speed (kmh), Relative Humidity (%), greenhouse gases (GHG: CO2, N2O, CH4 - ppmv) and air quality index (AQI) of industrial (IN), urban (UR) and rural (RU) belts in and around Ahmedabad Metro City (AMC), Gujarat, India during Phase-I (P-I, January), Phase-II (P-II, February) and Phase-III (P-III, March) in 2021. Gradients of AAQ in studied zones was NOx (IN: 35.21, UR: 26.85, RU: 15.41), SOx (IN: 76.48, UR: 34.41, RU: 12.59), NH3 (UR: 49.33, IN: 42.36, RU: 11.17), PM2.5 (UR: 5.50, IN: 3.06, RU: 2.28) and PM10 (IN: 7.12, UR: 5.38, RU: 2.19); MET (Temperature: UR: 40.40, RU: 31.70, IN: 27.60; Surface Temp.: UR: 43.17, RU: 35.20, IN: 31.97; Light Intensity: UR: 1446.00, RU: 10294.00, IN: 6360.70; Wind Speed: IN: 4.67, RU: 3.73, UR: 2.40; Relative Humidity: IN: 41.77, UR: 35.93, RU: 32.97); AQI (P-I: IN: 77.40, UR: 54.76, RU: 16.71; P-II: IN: 102.42, UR: 68.45, RU: 25.64; P-III: IN: 123.04, UR: 84.79, RU: 41.87; IN: 100.95- Unhealthy for Sensitive People, UR: 69.33, RU: 28.07-Good; AMC: 66.12-Moderate); GHG (CO2: RU: 1359.14, IN: 1002.71, UR: 884.05; N2O: IN: 154.39, UR: 138.86, RU: 128.11; CH4: RU: 0.78, UR: 0.73, IN: 0.64). Overall, NOx & SOx were more in IN, NH3 & PM2.5 in UR, PM10 in RU; Temperature, Surface Temp. & Light Intensity in UR, Wind Speed & Relative Humidity in IN; AQI in IN was Unhealthy for Sensitive People, Moderate in UR, Good in RU and Moderate in AMC; CO2 in IN, N2O in UR, CH4 in RU. The study concludes that the air quality of Ahmedabad Metro City is on ‘Good (Rural) to Moderate (Urban)’ scale for normal living, and ‘Unhealthy for Sensitive People’ for population residing in or near industrial zone. The findings of the present study warrant the implicative measures of climate change policies to promote public transportation in lower pollution levels for lesser greenhouse emissions on crossroads. Garbage burning and linked toxic emissions need an immediate management solutions in fringe areas of the city. The dust re-suspension on the roads due to the vehicular movement is the low-hanging fruit for immediate improvements in city’s air quality. The brick oven sector, although outside the town body limits, has a significant role in reducing pollution and providing the co-benefits attributable to the combination of fuels (including biomass), alternative pollutants like Black Carbon has a significant role to play within the climate policy.
DOI: 10.17632/zmycy7t9h9
title: ontonotes-conll2012

description: ** Please cite the original paper and distribution but not this distribution. **

Extended version of OntoNotesV5.0 used in CoNLL2012,
includes extension version of v4 English, Arabic, Chinese (test data of 3 langs are v9), and v12 English 

This data is processed based on the official script
(v4) https://conll.cemantix.org/2012/data.html
(v12) https://cemantix.org/data/ontonotes.html
(v12 script) https://github.com/yuchenlin/OntoNotes-5.0-NER-BIO

directory structure (only top level directories showed here, refer to https://conll.cemantix.org/2012/data.html for the lower-level ones)
conll-2012
├── v12
│   └── data
│       ├── conll-2012-test
│       │   └── data
│       │       └── english
│       ├── development
│       │   └── data
│       │       └── english
│       ├── test
│       │   └── data
│       │       └── english
│       └── train
│           └── data
│               └── english
└── v4
    └── data
        ├── development
        │   └── data
        │       ├── arabic
        │       ├── chinese
        │       └── english
        ├── test
        │   └── data
        │       ├── arabic
        │       ├── chinese
        │       └── english
        └── train
            └── data
                ├── arabic
                ├── chinese
                └── english
DOI: 10.6084/m9.figshare.11542470.v1
title: Year of Loss - Continent

description: Hansen, M.C., Potapov, P.V., Moore, R., Hancher, M., Turubanova, S.A., Tyukavina, A., Thau, D., Stehman, S.V., Goetz, S.J., Loveland, T.R., Kommareddy, A., Egorov, A., Chini, L., Justice, C.O., Townshend, J.R.G., 2013. High-Resolution Global Maps of 21st-Century Forest Cover Change. Science 342, 850–853. https://doi.org/10.1126/science.1244693
DOI: 10.6084/m9.figshare.5241721.v1
title: Erratum: Changes in Perinatal Care and Outcomes in Newborns at the Limit of Viability in Spain: The EPI-SEN Study

description: <b><i>Background:</i></b> Advances in perinatal care can influence morbidity and mortality in newborns at the limit of viability. Knowledge of these changes over time may help improve clinical decision making, optimize resource allocation and increase quality of care. <b><i>Objectives:</i></b> To evaluate the influence on morbidity and mortality of changes introduced in the perinatal care of preterm infants (22-26 weeks' gestational age, GA) in Spain between two consecutive periods (2002-2006 and 2007-2011). <b><i>Methods:</i></b> An analysis of prospectively collected data in a national database network (SEN1500) was performed. All live newborn infants of 22-26 weeks' GA born in or transferred to referral centers of the SEN1500 network in the first 28 days of life were included. Perinatal interventions, clinical management, neonatal morbidity, and survival until hospital discharge were retrieved. <b><i>Results:</i></b> A total of 5,470 newborns were included (2,533 and 2,937 in each period, respectively). The major changes introduced during the second period were as follows: (1) lower proportion of extramural births (11.0 vs. 8.9%, p = 0.01), (2) increase in antenatal steroids (69.5 vs. 80.8%, p &lt; 0.001), (3) delivery by C-section (41.8 vs. 48.3%, p &lt; 0.001) and (4) use of CPAP during resuscitation (7.8 vs. 20.7%, p &lt; 0.001). Death in the delivery room decreased from 5.1 to 3.2% (p &lt; 0.001). Survival increased from 49.9 to 57.9% (p &lt; 0.001), and survival without major morbidity increased from 18.1 to 21.2% (p = 0.006). <b><i>Conclusions:</i></b> During the second period, a greater attachment to practices proven to have a beneficial impact on survival and reduction of morbidity in the extremely preterm infant was noted, and survival and survival without major morbidity increased. A more conservative approach was detected for newborns of 22 weeks' GA.
DOI: 10.6084/m9.figshare.19038605.v1
title: Processed DepMap CCLE 21Q3 expression data

description: CCLE 21Q3 processed expression data
DOI: 10.6084/m9.figshare.28428899.v1
title: Supplementary Material for: Iron Mettle- Unveiling an Unusual Incidental Case Report of Esophageal Ulcer

description: Background: Erosive injury to the upper gastrointestinal tract caused by therapeutic oral iron supplements is a rare occurrence. Although erosive injury to the mucosa of the upper gastrointestinal (GI) tract is commonly associated with overdoses of oral iron supplements, similar injuries can also occur with doses within the normal therapeutic range. Reports have documented upper gastrointestinal disorders induced by iron, primarily affecting the stomach and occasionally the esophagus. Iron preparations are initially absorbed as ferrous iron and then oxidized to ferric iron. Excess ferric iron, surpassing the binding capacity of transferrin, a binding protein, leads to cellular damage. Ferric iron directly corrodes the gastrointestinal mucosa and disrupts various cellular processes by generating free radicals and initiating lipid peroxidation.Case Description:A 55-year-old female with dysphagia, pain and anorexia showed linear to circumferential ulcers covered extensively with white slough around the central esophagus with thickened and erythematous mucosa with focal erosions on esophagogastroduodenoscopy. Conclusions:This case highlights a rare case report of Iron- Induced esophageal ulcer found incidentally and the significance of acknowledging that iron preparations can harm the esophageal mucosa especially in an Indian population where anemia is fairly predominant.
DOI: 10.6084/m9.figshare.28707107.v2
title: Source data for AJP-GI manuscript

description: Source data for AJP-GI manuscript.
DOI: 10.6084/m9.figshare.28771409.v2
title: LLM-assisted Graph-RAG Information Extraction from IFC Data

description: In this research, we utilise the capabilities of LLMs to parse the IFC data with Graph Retrieval-Augmented Generation (Graph-RAG) technique to retrieve building object properties and their relations. We will show that, despite limitations due to the complex hierarchy of the IFC data, the Graph-RAG parsing enhances generative LLMs like GPT-4o with graph-based knowledge, enabling natural language query-response retrieval without the need for a complex pipeline.IFC data has become the general building information standard for collaborative work in the construction industry. However, IFC data can be very complicated because it allows for multiple ways to represent the same product information. In this research, we utilise the capabilities
of LLMs to parse the IFC data with Graph Retrieval-Augmented Generation (Graph-RAG) technique to retrieve building object properties and their relations. We will show that, despite limitations due to the complex hierarchy of the IFC data, the Graph-RAG parsing enhances generative LLMs like GPT-4o with graph-based knowledge, enabling natural language query-response retrieval without the need for a complex pipeline.
DOI: 10.6084/m9.figshare.9911927.v2
title: Shuanggou peridotite (JGR-2019JB017552R).xlsx

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