cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1604778.v1
title: Green algal transcriptomes for phylogenetics and comparative genomics

description: <i></i><em>For technical details please see the README</em> <strong>Green algal transcriptomes for phylogenetics and comparative genomics.</strong> The incredible diversity of green plants traces its origins to a single, unicellular common ancestor. The Green Algal Tree of Life project (www.gratol.org) aims to reconstruct the evolutionary history of these globally important organisms. Here we provide the results of our transcriptome sequencing initiative. The 32 (from 31 species) high-coverage transcriptome assemblies, consisting of &gt;2.7 million contigs with a mean length ~1.3kb, provides a rich resource for phylogenetics and evolutionary comparative genomics. Our focus on high-coverage sequencing means that these transcriptomes include a larger fraction of the expressed genome, and more full-length coding sequences, than other previous and contemporary sequencing efforts. The recovery of a full-length homolog of the Arabidopsis BIG gene (a huge 5098 amino acid protein) provides an example of the completeness of these transcriptomes. With a dataset of over 1600 orthologs (&lt;10% missing sequences) we are identifying and isolating disparate evolutionary signals, and reconstructing deep phylogenetic relationships with unprecedented confidence. Transcriptome wide comparative analyses are revealing broad scale patterns of gene content evolution and implicating recurrent whole genome duplications in major evolutionary transitions. Detailed analyses of key molecular genetic mechanisms are providing insights into the origins and evolution of: developmental regulation of three-dimensional growth, plant hormones, photorespiration, and desiccation tolerance. <strong><em>At present no publication is available for citation purposes. We therefore ask that all users of this data cite it using the figshare DOI(s) as appropriate. In addition, until we have can provide a publication for citation purposes we ask that for large scale analyses of these data, users contact us to discuss their plans and thereby avoid conflict or overlap.</em></strong> <strong>PLEASE CITE:</strong><br>Cooper, Endymion; Delwiche, Charles (2016): Green algal transcriptomes for phylogenetics and comparative genomics. figshare.https://dx.doi.org/10.6084/m9.figshare.1604778 <em>For additional information please contact Professor Charles Delwiche (</em>delwiche@umd.edu<em>).</em> ​<i></i>
DOI: 10.6084/m9.figshare.24042981.v1
title: FTO-database.xlsx

description: three SNPs of FTO gene
DOI: 10.17632/vtjd68bmwt
title: Indonesian Food Image

description: 
The dataset is a diverse collection of colored images featuring various Indonesian foods. These images display a range of backgrounds where the foods are presented, including restaurants, roadside stalls, and traditional eateries. The collected images also include variations in the background objects, such as tableware like plates, bowls, forks, spoons, and knives, or additional condiments like soy sauce, chili sauce, and lime. This stage utilizes a Google Chrome extension called Fatkun to perform scraping of image files on the browser page. The browser page used is Google Images, and the search keyword is the names of the Indonesian food types. The Fatkun extension can save all the images on that browser page into a chosen directory. The Indonesian foods are divided into ten classes of images, namely; meatball soup (bakso), seasoned duck (bebek betutu), mixed vegetable salad with peanut sauce (gado-gado), jackfruit stew (gudeg), fried rice (nasi goreng), fishcake (pempek), black soup (rawon), spicy meat dish (rendang), skewered and grilled meat (sate), and traditional soup (soto).
DOI: 10.6084/m9.figshare.7012133.v1
title: Information of differently expressed high quality transcripts

description: Information of differently expressed high quality transcripts
DOI: 10.17632/bvmx85vf36
title: Measuring performance of investment strategies in ESG mutual funds. Evidence from fixed income flows to euro area

description: Research data related to the paper "Measuring performance of investment strategies in ESG mutual funds. Evidence from fixed income flows to euro area". Dataset: ESG and non-ESG euro area fixed income funds (names not reported). Sample: Dec17-Jun24. Frequency: daily. Source: Bloomberg. File extension: .xlsx.
DOI: 10.17632/hcvm3zrb95
title: Global high-resolution gridded dataset of N2O emission and mitigation potential (GhrdNEv1.0) from Maize and Wheat fields

description: The high-resolution N2O emission and mitigation potential dataset covers the globe (-179.9581 to 179.9812 degrees east and 83.59216 to -89.92174 degrees north) at 0.0833°x 0.0833° spatial resolution from maize and wheat fields at annual temporal resolution. It comprises estimation from four empirical N2O emission models; (a) CCAFS-MOT , (b) IPCC Tier-I , (c) IPCC Tier-II and (d) Tropical-N2O given in a NetCDF datasets. Description of the NetCDF data structure: Two data files are present containing estimated values from Maize and Wheat fields. The metadata in the individual NetCDF files describes the individual variables. The data has three dimensions namely "latitude", "longitude" and "Nreduction" in a global latitude-longitude coordinate. The "Nreduction" dimension variable has 5 levels (0%, 25%, 50%, 75%, 100%), describing the percentage amount of reduced excess nitrogen to each variable/model. The no data value is decoded by the value “-9999”. The variable names comprising the estimated values from the four empirical N2O emission models are described as follows. Where: (a) “N2O.ccafsMOT”: estimated emission values from CCAFS-MOT (b) “N2O.ipccTR1”: estimated emission values from IPCC Tier-I (c) “N2O.ipccTR2”: estimated emission values from IPCC Tier-II (d) “N2O.tropicalN2O”: estimated emission values from Tropical-N2O
DOI: 10.17632/np7g9398t7
title: PhD Project 

description: PhD stuff
DOI: 10.6084/m9.figshare.13244438.v1
title: Data from: Cost-effectiveness of four food waste interventions: is food waste reduction a "win-win?"

description: The data archived here are the raw data required to reproduce all analysis presented in a manuscript currently in press at <i>Resources, Conservation & Recycling</i>.<br>Read, Q. D. & Muth, M. K. (2020). Cost-effectiveness of four food waste interventions: is food waste reduction a "win-win?" <i>Resources, Conservation & Recycling</i>, in press.<br>This dataset is intended for use with the code archived at https://doi.org/10.5281/zenodo.4021655 . Please refer to the <b>README.md</b> file in that repository for instructions on how to download the data and reproduce the analysis.<br>The data archived in this repository are from a variety of different sources. As much as is practicable, they are presented here in their raw form as they were downloaded, without any processing. All processing steps can be replicated using the code archived in the accompanying code repository.<br><b>Abstract of manuscript</b><b><br></b>At least 30% of food is wasted during the journey from farm to processor to retailer to consumer in the United States, accounting for an estimated 20% of the environmental impact of the food system. The food waste problem is well characterized, but solutions are not: there has been little rigorous comparison of the costs and potential benefits of food waste reduction interventions. Food waste reduction is often described as a “win-win,” benefiting consumers, the environment, and businesses’ bottom line. We present a method for evaluating this claim by accounting for the costs and environmental benefits of food waste reduction. The procedure involves assembling data on costs and efficacy of the intervention, scaling the costs up to the national level, estimating the quantity and value of food waste averted, and finally estimating the potential averted environmental impact. We apply our method to four representative nationwide interventions: consumer education and public awareness campaigns, spoilage prevention packaging for produce and meat, standardization of date labels, and foodservice waste tracking systems. The estimated annual cost of each intervention varied from $126 to $595 million. The environmental cost-effectiveness of the interventions varied two- to threefold (for example, 6 to 16 kg CO<sub>2</sub> reduced per $1 invested). Outstanding questions include how to scale interventions to the national level and how to address the mismatch between who incurs the costs of implementation and who benefits. Our method can be adapted to waste interventions across the food system and in countries beyond the United States.<b><br></b><br>
DOI: 10.6084/m9.figshare.24762513.v4
title: HMEAs_dataset

description: The absence of nationwide distribution data regarding heavy metal emissions into the atmosphere poses a significant constraint in environmental research and public health assessment. In response to the critical data deficiency, we have established a dataset covering Cr, Cd, As, and Pb emissions into the atmosphere (HMEAs, unit: ton) across 367 municipalities in China. Initially, we collected HMEAs data and covariates such as industrial emissions, vehicle emissions, meteorological variables, among other 10 indicators. Following this, nine machine learning models, including Linear Regression (LR), Ridge, Bayesian Ridge (Bayesian), K-Neighbors Regressor (KNN), MLP Regressor (MLP), Random Forest Regressor (RF), LGBM Regressor (LGBM), Lasso, and ElasticNet, were assessed using coefficient of determination (R2), root-mean-square error (RMSE) and Mean Absolute Error (MAE) on the testing dataset. RF and LGBM models were chosen, due to their favorable predictive performance (R<sup>2</sup>: 0.58–0.84, lower RMSE/MAE), confirming their robustness in modelling. This dataset serves as a valuable resource for informing environmental policies, monitoring air quality, conducting environmental assessments, and facilitating academic research.
DOI: 10.6084/m9.figshare.28596155.v1
title: Supplementary Material for: Filgotinib to treat acute severe refractory ulcerative colitis: A case report and review of the literature

description: INTRODUCTION
Acute severe ulcerative colitis (ASUC) is a serious complication affecting 9%-15% of patients with UC within 3 months of diagnosis and up to 28% of patients during the course of the disease. Despite the use of infliximab and calcineurin inhibitors, the rate of colectomy remains high both during the hospitalization and in the 5 years after an acute episode. 
We present a case of ASUC that was unresponsive to conventional therapies but was successfully treated with filgotinib.
CASE PRESENTATION
A 21-year-old male with a recent diagnosis of UC presented to our hospital with a severe flare. He received rescue therapy of high-dose intravenous steroids and 10 mg/kg infliximab. We observed little clinical and biochemical benefit. The patient declined the surgical option. Therefore, we decided to start a second rescue therapy with a new and rapid-acting Janus kinase inhibitor, filgotinib, due to its characteristics and pharmacokinetic profile of rapid absorption and metabolism. The patient showed an immediate clinical and biochemical response at 48 h, an endoscopic response at week 3, and an endoscopic remission at week 10. No recurrence was observed after 12 months of follow-up. The patient is in clinical remission with a good quality of life.
CONCLUSION
Filgotinib may be an effective second-line therapy in an emergency setting such as ASUC in patients unresponsive to conventional therapy.
DOI: 10.17632/dkxpvp3xh7
title: Data for: Detection of cervical cancer cells based on strong feature CNN-SVM network

description: 1. Due to the large number of pictures, we just selected some of them for display. 2. Original negative sample and Original positive sample are raw data collected from our cooperative unit. We used 100 cervical liquid based cell slides in total, for the sake of simplicity, we have selected a positive and a negative sample for publication, so that you can see the appearance of our raw data which has not been processed. 3. Processed training material are the images which have been processed after binarization, image segmentation and image classification. This folder contains 400 epithelial cells , they are the images of single cells after a series of processes. epithelial cells has been divided into two categories including 200 cancerous epithelial cells and 200 normal epithelial cells, as the names you can see, these are the typical samples we used in the paper.
DOI: 10.6084/m9.figshare.12452795.v1
title: Dataset used for CANYON-MED training and validation

description: Dataset used for training and validating the CANYON-MED neural networks. One dataset per trained parameter. "categ" describes the training or validation use.<br>
DOI: 10.6084/m9.figshare.4476188.v1
title: Supplemental data for "Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses"

description: Supplementary data, including gene trees from both the site-only and gene-only resampling pseudoreplicates, the phylogenetic trees inferred for each resampling pseudoreplicate, trees with reference clades, and a Microsoft Excel file containing the raw and summarized data.
DOI: 10.17632/bkh2h24jh3
title: Images from Meso- and Bathypelagic Surveys in the Gully Marine Protected Area: III: Fish of the 2009 Survey

description: During 2007–10, Canada’s Department of Fisheries and Oceans conducted four midwater-trawl surveys, at meso- and bathypelagic depths, in The Gully – a large submarine canyon incised into the Scotian Shelf, east of Sable Island, the core of which has been within a Marine Protected Area since 2004. The surveys followed a fixed-station, depth-stratified design, with replicate sets both in daylight and at night. Most sampling used International Young Gadoid Pelagic Trawls (IYGPTs) –open nets with 60 m² mouth area– worked on double-oblique profiles. From the 2008 survey, the trawls were fitted with rigid (“aquarium”) codends and successfully took a number of delicate specimens in exceptional condition. Full details of the field methodologies have been presented by Kenchington et al. (2009, 2014). Catches of the abundance- or biomass-dominant fish species have been published by Thompson and Kenchington (2016) and Kenchington et al. (2018, 2020a). The ceratioid anglerfishes have been published by Kenchington et al. (2020b) and DNA barcodes derived from selected specimens by Kenchington et al. (2017). 

Identification of fish specimens is ongoing (in 2022), while damage in the nets means that not all can be identified to species. It is, nevertheless, sure that specimens from in excess of 240 fish species were captured. Many of those have rarely been seen and most had never been photographed in fresh condition. Thus, a variety of camera systems were taken to sea on the surveys and an attempt made to create images of every species captured. The resulting collection has been catalogued and lightly edited, while erring on the side of retaining any image that might prove useful in the future. Almost all of those retained are in their original formats and resolutions, though some copies subsequently edited for publication have been added. Because of file-size limits, the present collection includes only the 498 catalogued images of fish specimens from the 2009 survey, together with a copy of the entire catalogue of fish images. Individual files are uniquely numbered (from F09001 to F09498), with corresponding entries in the catalogue. The latter presents the contents of each image (typically only a species name, though some entries have more details) and such other image-specific details as are available. Not all images can be linked to particular specimens but, for those which can be, catalogue entries include cross-references to the survey-program’s catch database, which provides further details on the specimens concerned.

All images © His Majesty the King in Right of Canada, 2022.

Amongst the named authors, the surveys were led by Trevor Kenchington, who also catalogued the images and, working with Cam Lirette, presented them here. Specimen identifications at sea and most of those ashore were by Daphne Themelis, while Merlin Best and Andrew Cogswell captured the images at sea.
DOI: 10.17632/x4mxnjmc76
title: Supplementary Tables and Methods

description: Supplemental Methods
DOI: 10.4121/uuid:a0addfda-2044-4541-a450-fdcc9fe16d17
title: BPI Challenge 2015 Municipality 1

description: Data for municipality 1 Parent item: BPI Challenge 2015 This data is provided by five Dutch municipalities. The data contains all building permit applications over a period of approximately four years. There are many different activities present, denoted by both codes (attribute concept:name) and labels, both in Dutch (attribute taskNameNL) and in English (attribute taskNameEN). The cases in the log contain information on the main application as well as objection procedures in various stages. Furthermore, information is available about the resource that carried out the task and on the cost of the application (attribute SUMleges). The processes in the five municipalities should be identical, but may differ slightly. Especially when changes are made to procedures, rules or regulations the time at which these changes are pushed into the five municipalities may differ. Of course, over the four year period, the underlying processes have changed. The municipalities have a number of questions, namely: What are the roles of the people involved in the various stages of the process and how do these roles differ across municipalities? What are the possible points for improvement on the organizational structure for each of the municipalities? The employees of two of the five municipalities have physically moved into the same location recently. Did this lead to a change in the processes and if so, what is different? Some of the procedures will be outsourced from 2018, i.e. they will be removed from the process and the applicant needs to have these activities performed by an external party before submitting the application. What will be the effect of this on the organizational structures in the five municipalities? Where are differences in throughput times between the municipalities and how can these be explained? What are the differences in control flow between the municipalities? There are five different log files available in this collection. Events are labeled with both a code and a Dutch and English label. Each activity code consists of three parts: two digits, a variable number of characters, and then three digits. The first two digits as well as the characters indicate the subprocess the activity belongs to. For instance ‘01_HOOFD_xxx’ indicates the main process and ‘01_BB_xxx’ indicates the ‘objections and complaints’ (‘Beroep en Bezwaar’ in Dutch) subprocess. The last three digits hint on the order in which activities are executed, where the first digit often indicates a phase within a process. Each trace and each event, contain several data attributes that can be used for various checks and predictions. Furthermore, some employees may have performed tasks for different municipalities, i.e. if the employee number is the same, it is safe to assume the same person is being identified.
DOI: 10.6084/m9.figshare.7570445.v1
title: Additional file 3: of Secretome analysis of Strongyloides venezuelensis parasitic stages reveals that soluble and insoluble proteins are involved in its parasitism

description: Table S2. List of proteins identified in the Strongyloides venezuelensis parasitic female excretory/secretory (E/S) soluble fraction. (XLSX 36 kb)
DOI: 10.6084/m9.figshare.7667030.v3
title: Sequencing design, alignment and methylation statistics calculated from the data described in the manuscript 'Temporally replicated reduced representation bisulfite sequencing data on dna methylation patterns in Great tit'.

description: Sequence and alignment information for the 63 libraries used in the manuscript 'Temporally replicated reduced representation bisulfite sequencing data on dna methylation patterns in Great tit'.
DOI: 10.17632/48y87jd66d
title: Sorption and Desorption of Cyantraniliprole in Soils 

description: Cyantraniliprole is an anthranilic diamide insecticide used in seed treatment, but the insecticide can come into direct contact with the soil. In this work, the equilibrium sorption of the insecticide in soils with different attributes was studied. The sorption was low, characterizing the high leaching potential of the insecticide.

The SigmaPlot files are disponible.
DOI: 10.17632/bw255hcw7h
title: Single molecule imaging uncovers rules governing nonsense-mediated mRNA decay. Hoek et al.
DOI: 10.17632/wg2px6dj3v
title: Data for: Expected Stock Price Crash Risk and Bank Loan Pricing: Evidence from China's Listed Firms
DOI: 10.6084/m9.figshare.14984415.v1
title: Trans Cohorts Metabolomic Modulation Following Long-Term Successful Therapy in HIV-Infection

description: Metabolomics and proteomics data
DOI: 10.17632/mgb7ftwr9d
title: Mapping patterns of thought onto brain activity during movie-watching Data and Scripts

description: Data and scripts for Wallace et al., 2024 for reproducibility can be found here. The study set out to map patterns of thought to brain activity during movie watching. 

The research experiment was exploratory in nature - so there were no explicit hypotheses. However, we set out to look at whether or not variations in thought patterns during movie watching, consisting of three 11-minute clips from Citizenfour, Little Miss Sunshine, and 500 Days of Summer, by leveraging a novel sampling technique using multi-dimensional experience sampling (mDES). We were able to accomplish this by using previously-collected fMRI data (n = 44) from the naturalistic neuroimaging database (Aliko et al., 2020) where participants were scanned while watching the films, and using a separate sample of participants (n = 120) to come into the lab to watch the same films and respond to mDES probes. 
 
Our first analysis consisted of a PCA which decomposed the experience sampling data into 4 components of thought. Based on the mDES item loadings, we labelled the thought patterns 'Episodic Knowledge', 'Intrusive Distraction', 'Verbal Detail', and 'Sensory Engagement.' We found that 'Episodic Knowledge' was most reported during 500 Days of Summer, specifically predicted better comprehension performance for this movie, and was related to activity in the visual cortex, specifically in the dorsal medial regions. 'Intrusive Distraction' was associated with reduced activity in the frontoparietal network, was highly reported during Citizenfour, and predicted poorer overall comprehension performance across the movies. 'Verbal Detail' was associated with reduced activity in the auditory cortex, most reported during Citizenfour. Lastly, "Sensory Engagement" was related to multi-modal sensory engagement in auditory and visual cortexes, predicted better overall comprehension performance, and was most highly reported during 500 Days of Summer. These results highlight the critical role that sensory systems play in the multi-modal experience of movie-watching and place important constraints on the contribution of systems in association cortex, like the default network.

The raw mDES data is available, as well as the full dataset with the PCA components, gradient scores and demographic information. The relevant brain maps from the imaging analyses are also included.
DOI: 10.6084/m9.figshare.21905166.v2
title: Data for "Extra-pair paternity, breeding density and synchrony in natural cavities versus nestboxes in two passerine birds"

description: Data for "Extra-pair paternity, breeding density and synchrony in natural cavities versus nestboxes in two passerine birds":"nests_blue_tits.xlsx" contains nest data for blue tits;"nests_great_tits.xlsx" contains nest data for great tits and"nestlings.xlsx" contains nestling data for both blue and great tits."genotypes_blue_tits.csv" contains genotypes for blue tits."genotypes_great_tits.csv" containes genotypes for great tits.