cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.18551380.v1
title: Monitored Natural Recovery of Contaminated Sediment in Cottonwood Bay, Texas

description: Monitored natural recovery (MNR) is a response action for contaminated sediment that relies on natural processes to reduce ecological and human health risks to acceptable levels over time. Multi-media long-term monitoring is necessary to verify remedy effectiveness and success. Whereas MNR has most often been employed together with other engineered remedies to address contaminated sediment, this case study describes an evaluation demonstrating the suitability of MNR with adaptive management as a stand-alone sediment remedial strategy for Cottonwood Bay, located in Dallas, Texas. Current risks at the Cottonwood Bay site are associated with human consumption of fish contaminated with polychlorinated biphenyls (PCBs). The lines of evidence used to evaluate MNR included documentation of source control; review of PCB burial/isolation and surface sediment recovery; evaluation of sediment deposition and sediment stability; and demonstration of decreasing temporal trends in fish tissue PCB concentrations. The multiple lines of evidence demonstrated that source control and natural recovery processes have contributed substantially to reduced concentrations of PCBs and metals in surface sediments and PCBs in fish. MNR has been approved by the Texas Commission on Environmental Quality (TCEQ) and is incorporated as a stand-alone remedy in the revised Remedial Action Plan (RAP) for Cottonwood Bay. A long-term monitoring plan is being implemented as part of an MNR response action to confirm decreasing trends in surface sediment and fish fillet PCB concentrations over time and to demonstrate the continued effectiveness of natural recovery processes.
DOI: 10.6084/m9.figshare.20510016
title: Human-in-the-loop labelled TissueNet data (Cellpose 2.0)

description: Training and testing images from TissueNet used in human-in-the-loop performance quantifications for Cellpose 2.0 (https://www.biorxiv.org/content/10.1101/2022.04.01.486764v1). <br> Labels are saved as _seg.npy files (see notebook for more details on how to use them for training: https://colab.research.google.com/github/MouseLand/cellpose/blob/main/notebooks/run_cellpose_2.ipynb). <br> See the license for the TissueNet images shared, please use their link for downloading the full dataset: https://datasets.deepcell.org/. And if you use TissueNet in your work cite their paper: https://www.nature.com/articles/s41587-021-01094-0.
DOI: 10.6084/m9.figshare.20101949.v1
title: Analysis of 3'UTRs in B. nonstop

description: To identify the 3'UTRs, we assembled the transcripts de novo using Trinity (https://doi.org/10.1038/nprot.2013.084) with both standard and 3'enriched transcriptomic reads. Then we mapped transcripts back to the genome using BLAST and chose those transcripts that were identical to the genome but had one or more of A at the 3' end of the transcript and analysed them using custom Python scripts.
DOI: 10.5285/e548efb8-84eb-78bc-e053-6c86abc08fe7
title: Citizen science derived data of microplastic distribution and composition on two Galápagos Island beaches, Ecuador.

description: Citizen science represents a promising option for monitoring visible microplastic (&gt; 1mm) contamination on sandy beaches across space and time. Here, high school and university students undertook supervised sampling surveys on two island beaches in the Galápagos Archipelago, Ecuador (Tortuga Bay, Santa Cruz and Punta Pitt, San Cristóbal) between 2019 and 2020. We employed a simple citizen science methodology using a standard unit (50 x 50 cm quadrat) sampled to a standardised depth (5 cm) and then sieved to 1 mm, to support microplastic monitoring efforts in the region. All suspected microplastics collected by citizen scientists from Tortuga Bay at known locations and times (n = 1,713) were analysed using FTIR spectroscopy. Due to COVID-19 travel restrictions, only ~10&percnt; of particles from Punta Pitt (n = 500; a random subsample across pooled particles, total n = 5,118) were submitted to researchers for polymer analysis. Consequently, exact coordinates and dates for each particle analysed from Punta Pitt cannot be specified, however space and time ranges are provided, along with the spatiotemporal data from all surveys. FTIR spectroscopy verified that 93&percnt; of particles collected by citizen scientists were plastic or rubber. These data revealed the highest abundance of microplastic contamination reported in the Galápagos of 0-2,524 particles m<sup>-2</sup>, with strong accumulation gradients measured on the two beaches. The gradients observed were parallel to the strandline at Punta Pitt, but perpendicular to the strandline at Tortuga Bay, where four-fold higher concentrations were recorded at the sea turtle nesting habitat on the back-beach dune. No significant seasonal trends were measured over the course of one year.
DOI: 10.6084/m9.figshare.20101949.v2
title: Analysis of 3'UTRs in B. nonstop

description: To identify the 3'UTRs, we assembled the transcripts de novo using Trinity (https://doi.org/10.1038/nprot.2013.084) with both standard and 3'enriched transcriptomic reads. Then we mapped transcripts back to the genome using BLAST and chose those transcripts that were identical to the genome but had one or more of A at the 3' end of the transcript and analysed them using custom Python scripts.
DOI: 10.5255/ukda-sn-855783
title: Improbable Dialogues: Local-level Peacebuilding in Colombia, Video Data, 2018-2022

description: The Improbable Dialogues project focussed on local-level conflicts and peacebuilding activities in three locations in Colombia: Buenaventura, Vista Hermosa, and Tibu. The nature of the data collected, which relates to ongoing conflicts, means that - in line with the project's Data Management Plan - the majority of the data is not suitable for public archiving, as doing so could create safety and security risks for those living in these communities. The exception are the public forums which were held online (due to COVID restrictions) and in which participants were warned that the sessions would be streamed publicly, and archived publicly. These contain rich data about peacebuilding processes, but do not provide details of conflict-related issues that could raise safety or security concerns.
DOI: 10.6084/m9.figshare.20101949.v3
title: Analysis of 3'UTRs in B. nonstop

description: To identify the 3'UTRs, we assembled the transcripts de novo using Trinity (https://doi.org/10.1038/nprot.2013.084) with both standard and 3'enriched transcriptomic reads. Then we mapped transcripts back to the genome using BLAST and chose those transcripts that were identical to the genome but had one or more of A at the 3' end of the transcript and analysed them using custom Python scripts.
DOI: 10.6084/m9.figshare.20484357.v2
title: Prevalence, causes and impacts of human trafficking in Asian countries: A scoping review

description: The purpose of this study is to collect evidence on human trafficking in Asian countries. A systematic review methodology was used to search online databases including Sage Journals Online, Wiley Online, Hein Online, Taylor & Francis Online, Web of Science, and Scopus literature to amalgamate information on this issue. For the purposes of this article, 64 studies met the inclusion criteria after searching and screening a total number of 1278 studies. The findings of this study were classified under three categories: prevalence of human trafficking in Asia, causes of human trafficking in Asia (poverty and unemployment, environmental and manmade disaster, weak policies and corruption), and impacts of human trafficking including social, health, physical, psychological impacts. <br>
DOI: 10.6084/m9.figshare.20510025
title: Network pharmacology approach to treat Cancer using eugenol

description: Computational method was utilized to predict the potential pathways and crucial genes involved in cancer using eugenol. STITCH, STRING, Cytoscape, MCODE, DAVID, PANTHER, Cytohubba databases are used for the study. Identified hub genes are validated using Survival analysis.
DOI: 10.6084/m9.figshare.20510025.v1
title: Network pharmacology approach to treat Cancer using eugenol

description: Computational method was utilized to predict the potential pathways and crucial genes involved in cancer using eugenol. STITCH, STRING, Cytoscape, MCODE, DAVID, PANTHER, Cytohubba databases are used for the study. Identified hub genes are validated using Survival analysis.
DOI: 10.21227/ryr1-yz94
title: Hysteresis data, residual force and haptic sensitivity data

description: The dataset 'sensitivityThreshold(haptic feedback).zip' contains the results of a haptic feedback sensitivity study comparing a novel laparoscopic grasper with 2 conventional graspers. Also grip preference of each participant was stored.The instrument sensitivity was validated by measuring the level at which participants could discriminate force differences applied at the grasper tip with an increasing force level, while the subjects were holding the new instrument and a conventional grasper at the handle grip. The force was increased and subjects reported at which force level they were able to feel an increase. The dataset 'balancingError.zip' consists of 10 repetitions of measurements on a balanced compliant laparoscopic grasper. It is the instrument's unloaded residual balancing error measured on a linear stage with load cell.
DOI: 10.5281/zenodo.6783043
title: LMAS Figures

description: LMAS is an automated workflow enabling the benchmarking of traditional and metagenomic prokaryotic de novo assembly software using defined mock communities. As proof of concept, the eight bacterial genomes and four plasmids, in tripled form, of the ZymoBIOMICS Microbial Community Standards are made available to be used as reference. Simulated raw sequence data of the mock communities with evenly distributed reads, generated from the reference genomes, with and without error, were obtained with inSilicoSeq. Project repository: https://github.com/cimendes/LMAS
DOI: 10.5281/zenodo.6786571
title: LMAS Figures

description: LMAS is an automated workflow enabling the benchmarking of traditional and metagenomic prokaryotic de novo assembly software using defined mock communities. As proof of concept, the eight bacterial genomes and four plasmids, in tripled form, of the ZymoBIOMICS Microbial Community Standards are made available to be used as reference. Simulated raw sequence data of the mock communities with evenly distributed reads, generated from the reference genomes, with and without error, were obtained with inSilicoSeq. Project repository: https://github.com/cimendes/LMAS
DOI: 10.5281/zenodo.6948708
title: LMAS Figures

description: LMAS is an automated workflow enabling the benchmarking of traditional and metagenomic prokaryotic de novo assembly software using defined mock communities. As proof of concept, the eight bacterial genomes and four plasmids, in tripled form, of the ZymoBIOMICS Microbial Community Standards are made available to be used as reference. Simulated raw sequence data of the mock communities with evenly distributed reads, generated from the reference genomes, with and without error, were obtained with inSilicoSeq. Project repository: https://github.com/cimendes/LMAS
DOI: 10.5517/ccdc.csd.cc1zjs4f
title: CCDC 1833375: Experimental Crystal Structure Determination

description: Related Article: Ananyakumari Santra, Paula Brandao, Gopinath Mondal, Pradip Bera, Abhimanyu Jana, Indranil Bhattacharyya, Chandana Pramanik, Pulakesh Bera|2020|Inorg.Chim.Acta|501|119315|doi:10.1016/j.ica.2019.119315
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc299kck
title: CCDC 2124348: Experimental Crystal Structure Determination

description: Related Article: Thomas Déis, Jérémy Forté, Gilles Lemière and Louis Fensterbank|2022|Molecules|27|1767|doi:10.3390/molecules27061767
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc299kdl
title: CCDC 2124349: Experimental Crystal Structure Determination

description: Related Article: Thomas Déis, Jérémy Forté, Gilles Lemière and Louis Fensterbank|2022|Molecules|27|1767|doi:10.3390/molecules27061767
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc299kfm
title: CCDC 2124350: Experimental Crystal Structure Determination

description: Related Article: Thomas Déis, Jérémy Forté, Gilles Lemière and Louis Fensterbank|2022|Molecules|27|1767|doi:10.3390/molecules27061767
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc29gjx7
title: CCDC 2129139: Experimental Crystal Structure Determination

description: Related Article: Thomas Déis, Jérémy Forté, Gilles Lemière and Louis Fensterbank|2022|Molecules|27|1767|doi:10.3390/molecules27061767
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.20355381
title: Thermosensitive liposomes: a promising step toward localised chemotherapy

description: Many small molecules and biologic therapeutics have been developed for solid tumor therapy. However, the unique physiology of tumors makes the actual delivery of these drugs into the tumor mass inefficient. Such delivery requires transport from blood vessels, across the vasculature and into and through interstitial space within a tumor. This transportation is dependent on the physiochemical properties of the therapeutic agent and the biological properties of the tumor. It was hoped the application of nanoscale drug carrier systems would solve this problem. However, issues with poor tumor accumulation and limited drug release have impeded clinical impact. In response, these carrier systems have been redesigned to be paired with targetable external mechanical stimuli which can trigger much enhanced drug release and deposition. The pre-clinical and clinical progress of thermolabile drug carrier systems and the modalities used to trigger the release of their cargo are assessed. Combined application of mild hyperthermia and heat-responsive liposomal drug carriers has great potential utility. Clinical trials continue to progress this approach and serve to refine the technologies, dosing regimens and exposure parameters that will provide optimal patient benefit.
DOI: 10.6084/m9.figshare.20355381.v1
title: Thermosensitive liposomes: a promising step toward localised chemotherapy

description: Many small molecules and biologic therapeutics have been developed for solid tumor therapy. However, the unique physiology of tumors makes the actual delivery of these drugs into the tumor mass inefficient. Such delivery requires transport from blood vessels, across the vasculature and into and through interstitial space within a tumor. This transportation is dependent on the physiochemical properties of the therapeutic agent and the biological properties of the tumor. It was hoped the application of nanoscale drug carrier systems would solve this problem. However, issues with poor tumor accumulation and limited drug release have impeded clinical impact. In response, these carrier systems have been redesigned to be paired with targetable external mechanical stimuli which can trigger much enhanced drug release and deposition. The pre-clinical and clinical progress of thermolabile drug carrier systems and the modalities used to trigger the release of their cargo are assessed. Combined application of mild hyperthermia and heat-responsive liposomal drug carriers has great potential utility. Clinical trials continue to progress this approach and serve to refine the technologies, dosing regimens and exposure parameters that will provide optimal patient benefit.
DOI: 10.6084/m9.figshare.20510556
title: When did bumblebees reach South America? Unexpectedly old montane species may be explained by Mexican stopover (Hymenoptera: Apidae)

description: A problem for understanding bumblebee biogeography is that if bumblebees dispersed from Asia through North America to South America, if they are poor at long-distance dispersal with establishment over sea, and if the land bridge between North and South America was not established until <i>c.</i> 3 Ma BP, then there is an apparent conflict with the divergence among currently endemic South American lineages having been dated as early as 15–17 Ma. Using the first complete phylogenetic trees for all known and accepted extant species of the groups involved, we show how this conflict could be resolved. We suggest that characterizing bumblebees as being associated generally with temperate flower-rich meadows conflates divergent habitat specializations between two early lineages, associated with northern lowland grasslands and with southern montane grasslands respectively, which may have driven divergences in behaviour and in biogeographic processes. First, for most of the lowland grassland group of bumblebees, estimated dates of divergence are consistent with dispersal to South America via the land-bridge corridor that opened at <i>c.</i> 3 Ma, followed by extant endemic lineages diverging <i>in situ</i> within South America. In contrast, for the second group that occupies montane grassland habitats (and for a few montane lineages of the ‘lowland’ group), we suggest that dispersal to South America at <i>c.</i> 3 Ma could be consistent with older divergence for currently endemic species if: (1) many of the extant South American lineages had already diverged outside the region before 3 Ma in neighbouring Mesoamerica; and (2) they had been constrained within the high mountains there, dispersing southwards into South America only once the isthmus corridor had become established; and (3) some of those ancestral montane lineages had become extirpated from Mesoamerica during subsequent warm climatic fluctuations. This interpretation re-emphasizes that biogeographic studies need to consider habitat-specific dispersal models that change through time.
DOI: 10.6084/m9.figshare.20510556.v1
title: When did bumblebees reach South America? Unexpectedly old montane species may be explained by Mexican stopover (Hymenoptera: Apidae)

description: A problem for understanding bumblebee biogeography is that if bumblebees dispersed from Asia through North America to South America, if they are poor at long-distance dispersal with establishment over sea, and if the land bridge between North and South America was not established until <i>c.</i> 3 Ma BP, then there is an apparent conflict with the divergence among currently endemic South American lineages having been dated as early as 15–17 Ma. Using the first complete phylogenetic trees for all known and accepted extant species of the groups involved, we show how this conflict could be resolved. We suggest that characterizing bumblebees as being associated generally with temperate flower-rich meadows conflates divergent habitat specializations between two early lineages, associated with northern lowland grasslands and with southern montane grasslands respectively, which may have driven divergences in behaviour and in biogeographic processes. First, for most of the lowland grassland group of bumblebees, estimated dates of divergence are consistent with dispersal to South America via the land-bridge corridor that opened at <i>c.</i> 3 Ma, followed by extant endemic lineages diverging <i>in situ</i> within South America. In contrast, for the second group that occupies montane grassland habitats (and for a few montane lineages of the ‘lowland’ group), we suggest that dispersal to South America at <i>c.</i> 3 Ma could be consistent with older divergence for currently endemic species if: (1) many of the extant South American lineages had already diverged outside the region before 3 Ma in neighbouring Mesoamerica; and (2) they had been constrained within the high mountains there, dispersing southwards into South America only once the isthmus corridor had become established; and (3) some of those ancestral montane lineages had become extirpated from Mesoamerica during subsequent warm climatic fluctuations. This interpretation re-emphasizes that biogeographic studies need to consider habitat-specific dispersal models that change through time.
DOI: 10.25502/d4eh-s362/d
title: Baseline data for the CSAT project-Mali

description: The West African Sahel and dry savannahs cover a large northern sector of the sub-region from Nigeria through Benin, Niger, Burkina Faso, Mali, to Senegal where natural resource limitations, especially water scarcity and land degradation, are expected to be exacerbated by climate change. The main goal of the proposed project is to introduce climate smart agricultural technologies and innovations in the Sahel and dry savannah regions of Mali and Niger that will improve rural livelihoods and food security. In the first of the two components of the project, we will use innovation platforms (IPs) to scale out exisitng technologies along the value  chain of key commodities. In Niger the delivery mechanisms that the current Norwegian project (RED/SAACC-Niger) is applying will also be adopted. In the second project component  we  will conduct research  to develop and adapt additional technological options to expand the pool from which farmers and other value chain actors get to choose from.
DOI: 10.6084/m9.figshare.20510346
title: Data for the paper "Nature benefit hypothesis: role of personal nature experiences in enhancing pro-biodiversity behaviours"

description: The full description of the dataset is described in the manuscript.
DOI: 10.6084/m9.figshare.20510337.v1
title: drosera_spatulata_decontaminated_FSCR.fasta.gz

description: .........
DOI: 10.6084/m9.figshare.20510337
title: drosera_spatulata_decontaminated_FSCR.fasta.gz

description: .........
DOI: 10.25500/edata.bham.00000862
title: Research data supporting “Limited Impact of Diesel Particle Filters on Road Traffic Emissions of Ultrafine Particles”