cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/3331
title: Blended learning for primary care physicians on chronic obstructive pulmonary disease (COPD): A feasibility study in Bangladesh

description: Quantitative data: The study participants were general practitioners (GPs) providing public and private primary healthcare services in Bangladesh. We administered the chronic obstructive pulmonary disease- physician’s practice assessment questionnaire (COPD-PPAQ) to the participants prior to the start of training and one month following completion of the training. We collected socio-demographic information such as age and gender, GP experience, workload, number of patients consulted per day, and previous experience of online training. At the end of course we collected knowledge and skills examination scores of participants. Qualitative data: All participants who completed the blended learning training were invited to participate in one of three focus groups with 18 participants facilitated by MNU and supported by a note-taker. The number of participants from urban, semi-rural and rural areas were nine, five and four respectively. Discussion addressed participants’ perceptions of blended learning, preferences compared to previous experiences of face-to-face or online learning, advantages/disadvantages of the blended learning. The three course trainers were interviewed individually to explore their views and opinions about the practicalities of delivering training using this approach. All discussions were digitally recorded and transcribed verbatim in the spoken language (Bengali). The emotional context such as pauses, laughter, emphasis and non-verbal communication were included as notes in the transcripts to aid analysis. Transcripts were translated (by MNU who led the focus groups) from Bengali to English for analysis.
DOI: 10.7488/ds/3447
title: All-purpose, all-sky photometric redshifts for the DESI Legacy Imaging Surveys DR8

description: This dataset contains the catalogues described in Duncan et al. (2022), which presents photometric redshift (photo-z) estimates for the Dark Energy Spectroscopic Instrument (DESI) Legacy Imaging Surveys, currently the most sensitive optical survey covering the majority of the extragalactic sky. Our photo-z methodology is based on a machine-learning approach, using sparse Gaussian processes augmented with Gaussian mixture models (GMMs) that allow regions of parameter space to be identified and trained separately in a purely data-driven way. The same GMMs are also used to calculate cost-sensitive learning weights that mitigate biases in the spectroscopic training sample. By design, this approach aims to produce reliable and unbiased predictions for all parts of the parameter space present in wide area surveys. Compared to previous literature estimates using the same underlying photometry, our photo-zs are significantly less biased and more accurate at z &gt; 1, with negligible loss in precision or reliability for resolved galaxies at z &lt; 1. Our photo-z estimates offer accurate predictions for rare high-value populations within the parent sample, including optically selected quasars at the highest redshifts (z &gt; 6), as well as X-ray or radio continuum selected populations across a broad range of flux (densities) and redshift. Deriving photo-z estimates for the full Legacy Imaging Surveys Data Release 8, the catalogues provided in this work offer photo-z estimates predicted to be of high quality for ≳9×10^8 galaxies over ∼19m,400 deg2 and spanning 0 &lt; z &lt; 7, offering one of the most extensive samples of redshift estimates ever produced.
description: The photometric redshift catalogues are presented as .csv files for each HEALPix Order 3 region of the sky, separated into Legacy Survey North (duncan22_lsdr8_pz_north.tar.gz; 123 files) and South (duncan22_lsdr8_pz_south.tar.gz; 349 files). A full description of catalogue format and columns can be found in Table 3 of the associated paper.
DOI: 10.7488/ds/2330
title: Details of Staphylococcus spp. isolates used in a Staphylococcus aureus Host-Adaptation Study
title: Supplementary Table 1 - Population Genomic Analysis of Bacterial Pathogen Niche Adaptation. PhD Thesis

description: A large-scale population genomic approach was used to provide a global perspective of the host-switching events that have defined the evolution of Staphylococcus aureus in the context of its host-species. To investigate the genetic basis of host-adaptation, we performed genome-wide association analysis, revealing an array of accessory genes linked to S. aureus host-specificity. In addition, positive selection analysis identified biological pathways encoded in the core genome that are under diversifying selection in different host-species, suggesting a role in host-adaptation. These findings provide a high-resolution view of the evolutionary landscape of a model multi-host pathogen and its capacity to undergo changes in host ecology by genetic adaptation.
DOI: 10.7488/ds/3060
title: Raw Files and Data Sets for paper "The Design of Carbon Fibre Composite Origami Airbrakes for Endeavour’s Darwin I Rocket"

description: This dataset contains raw files, raw extractable data and processed data for the paper, "The Design of Carbon Fibre Composite Origami Airbrakes for Endeavour’s Darwin I Rocket". Included are STEP files of the folded and unfolded flasher structures as are M files related to computations conducted in relation to rocket stability and the perimeter truss. The STEP files can be reused for new solid mechanics and CFD simulations. An M file used to create graphs for this paper is also included as are calculations of raw data in relevant excel files. The user may wish to refer to any of the files shared for updating and improvement, or as a template for new simulations or calculations to further this work, or in different work where templates such as these may be useful. The abstract of the paper follows: "This paper concerns the conceptual design of a carbon fibre composite airbrake intended for use on the Endeavour Darwin I rocket. The airbrake design is based on a Flasher origami model and we research its actuation mechanism, its ability to increase drag, and its mechanical behaviour when actuated. The aim of this work was to improve upon the current ‘Pancake’ airbrake model and we find that the origami Flasher generates six times more drag at a given torque. The Flasher is designed to be built of quasi-isotropic CFRP resting on a carbon fibre woven membrane. When subjected to distributed loads from drag, the Flasher presses into the membrane material causing it to stress at levels of 1.4 GPa. Taking into account a safety factor of 1.2 for the rocket airbrake, this stress lies far below the failure stress of the carbon fibre woven membrane. In this work, the composite Flasher origami airbrake design offers improvements in drag and weight reduction, and will withstand drag forces when actuated."
description: Please see README.txt file.
DOI: 10.7488/ds/1563
title: "Increased Abundance of M cells in the Gut Epithelium Dramatically Enhances Oral Prion Disease Susceptibility"

description: Data supporting Donaldson et al "Increased Abundance of M cells in the Gut Epithelium Dramatically Enhances Oral Prion Disease Susceptibility" (In Submission).
DOI: 10.7488/ds/307
title: Construction of a modular arsenic resistance operon in E. coli and the production of arsenic nanoparticles: Figure 7 original images

description: ICP-OES data for arsenic depletion by various strains of E. coli. Includes raw data and data after processing.
DOI: 10.7488/ds/368
title: Infection avoidance behaviour during foraging is sex-specific and depends on prior exposure to a viral pathogen

description: Data for Infection avoidance behaviour of Drosophila melanogaster during foraging is sex-specific and depends on prior exposure to a viral pathogen. This data is referred to in Vale (2015) submitted to BMC Evolutionary Biology.
DOI: 10.7488/ds/2890
title: Impact of preventive chemotherapy survey during a national helminth control program dataset: perception, knowledge, attitudes and practices (KAP) outcome data.

description: The impact of preventive chemotherapy project was a study to determine the perception and knowledge, attitudes and practices (KAP) on Zimbabwe’s national helminth control programme conducted between 2012 and 2017. It focused on schistosomiasis (a parasitic disease affecting tropical and subtropical communities without access to safe drinking water and adequate sanitation provision) in the school children treated with the antihelminthic drug praziquantel, as well as schoolteachers and village health workers (VHW). School children (n= 409) from Grades 6 and 7 who had the full benefit of the 6 years of MDA from 2012 to 2017 were recruited, in addition to 36 schoolteachers and 22 VHW who were serving the schools. A structured questionnaire developed in English, translated into the local language Shona, and validated prior to the study was administered to all participants. The questions focused on the perceived impact of the preventive chemotherapy programme for schistosomiasis on individual/overall health, school attendance and performance, as well as KAP. Data were captured electronically on android platforms using the Open Data Kit. Full details are given in Mutapi et al., 2020 (Title: Positive impact of preventative chemotherapy during a national helminth control program: perception and KAP)
description: File name: Impact_survey outcome data.xlsx Description: This includes the full outcome data for the study. File name: Impact Survey Data Dictionary.xlsx Description: This is a data dictionary describing each variable its associated codes and a summary of values for each variable
DOI: 10.7488/ds/2930
title: Schistosomiasis and the host metabolome in preschool-aged children: Schistosoma haematobium infection outcome data

description: Millions of preschool-aged children (PSAC), i.e. aged 5 years and below, in sub-Saharan Africa suffer from a neglected tropical disease caused by helminth parasitic worms, known as schistosomiasis (commonly referred to as bilharzia or snail fever). This was a study to determine the changes in host metabolic profiles, in response to the first Schistosoma haematobium infection and treatment in Zimbabwean preschool-aged children. The species S. haematobium is the most common, and accounts for about two-thirds of all schistosomiasis cases in Africa. Eighty-three children (age range, 2–5 years old) confirmed schistosome-negative (as determined by parasitological diagnosis, guardian interviews and examination of medical records) were recruited at baseline (T0). Children were followed up after three months for parasitological diagnosis of their first S. haematobium infection, as determined by microscopic egg counts in urine (T2). Children positive for infection were treated with the antihelminthic drug praziquantel, and treatment efficacy was checked three months after treatment (T3). Blood samples were taken at each time point (i.e. T0, T2, and T3) and serum metabolite profiles were measured by capillary electrophoresis mass spectrometry. The change in serum metabolite profiles (∆T) were compared between schistosome-infected versus uninfected children. This dataset is linked as part of the manuscript "Schistosoma haematobium infection is associated with alterations in energy and purine-related metabolism in preschool-aged children" Osakunor DNM, Mduluza T, Osei-Hyiaman D, Burgess K, Woolhouse MEJ, et al. (2020) Schistosoma haematobium infection is associated with alterations in energy and purine-related metabolism in preschool-aged children. PLOS Neglected Tropical Diseases 14(12): e0008866. https://doi.org/10.1371/journal.pntd.0008866
DOI: 10.7488/ds/2261
title: Mobius Assembly: a versatile Golden-Gate framework towards universal DNA assembly

description: Synthetic biology builds upon the foundation of engineering principles, prompting innovation and improvement in biotechnology via a design-build-test-learn cycle. A community-wide standard in DNA assembly would enable bio-molecular engineering at the levels of predictivity and universality in design and construction that are comparable to other engineering fields. Golden Gate Assembly technology, with its robust capability to unidirectionally assemble numerous DNA fragments in a one-tube reaction, has the potential to deliver a universal standard framework for DNA assembly. While current Golden Gate Assembly frameworks (e.g. MoClo and Golden Braid) render either high cloning capacity or vector toolkit simplicity, the technology can be made more versatile – simple, streamlined, and cost/labor-efficient, without compromising capacity. Here we report the development of a new Golden Gate Assembly framework named Mobius Assembly, which combines vector toolkit simplicity with high cloning capacity. It is based on a two-level, hierarchical approach and utilizes a low-frequency cutter to reduce domestication requirements. Mobius Assembly embraces the standard overhang designs designated by MoClo, Golden Braid, and Phytobricks and is largely compatible with already available Golden Gate part libraries. In addition, dropout cassettes encoding chromogenic proteins were implemented for cost-free visible cloning screening that color-code different cloning levels. As proofs of concept, we have successfully assembled up to 16 transcriptional units of various pigmentation genes in both operon and multigene arrangements. Taken together, Mobius Assembly delivers enhanced versatility and efficiency in DNA assembly, facilitating improved standardization and automation.
description: * Plasmid sequences (Zip file) * List of primers (Excel file)
DOI: 10.7488/ds/3458
title: Introducing blood flow in kidney explants by engraftment onto the chick chorioallantoic membrane is not sufficient to induce arterial smooth muscle cell development

description: Kidney explant cultures are an important tool to gain insights into developmental processes, insights that can be used to develop strategies for engineering kidneys from stem cells. However, explants are not connected to a perfused vascular system. This limits their survival and limits physiological studies, for example of blood filtration, the main function of the kidney. Previous studies have shown that grafting kidneys on to avian chorioallantoic membrane (CAM) can establish perfusion and enable glomerular vascularization, but the realism and maturity of the resultant vasculature has not been examined. Here we show that vasculature of kidney explants grafted on to CAM is very different from natural kidney vasculature, showing excessive growth of endothelial cells, absence of a hierarchical arterio-venous network, and no vascular smooth muscle cell recruitment. The model therefore has serious limits. This dataset contains images of embryonic kidneys that were grafted onto the chick chorioallantoic membrane in order to evaluate the realism of the forming vasculature. # Note on opening image files # The .nd2 image files can be opened using an ImageJ plugin. At the time of writing, either the ImageJ Nikon ND2 Reader plugin for Windows or the Bio-formats plugin for other platforms, see https://imagej.nih.gov/ij/plugins/nd2-reader.html .
DOI: 10.7488/ds/3498
title: THE INDO AND ROUNDO DATASETS OF VEHICLE OCCLUSIONS

description: The dataset contains the occlusions for the "Bendplatz", "Frankenburg" and "Heckstrasse" scenarios in the inD [1] dataset, and for "Neuweiler" in the rounD [2] dataset. The occlusions are stored from the perspective of each of the vehicles alive in each of the frames contained in the recordings in [1] and [2]. More information about the dataset, and the references to the inD and rounD datasets, can be found in the README.txt below and at https://arxiv.org/abs/2206.14163
description: The dataset is structured as follows: - bendplatz_json: this zip folder contains the occlusions, stored in JSON format, for the episodes set in the "Bendplatz" junction. - frankenburg_json: this zip folder contains the occlusions, stored in JSON format, for the episodes set in the "Frankenburg" junction. - heckstrasse_json: this zip folder contains the occlusions, stored in JSON format, for the episodes set in the "Heckstrasse" junction. - neuweiler_json: this zip folder contains the occlusions, stored in JSON format, for the episodes set in the "Neuweiler" roundabout. - bendplatz_pickle: this zip folder contains the occlusions, stored in pickle format, for the episodes set in the "Bendplatz" junction. - frankenburg_pickle: this zip folder contains the occlusions, stored in pickle format, for the episodes set in the "Frankenburg" junction. - heckstrasse_pickle: this zip folder contains the occlusions, stored in pickle format, for the episodes set in the "Heckstrasse" junction. - neuweiler_pickle: this zip folder contains the occlusions, stored in pickle format, for the episodes set in the "Neuweiler" roundabout. - README.txt: text file containing information on how the occlusions are stored in the individual episode files. To see the mapping between the episode id we use and the recording id from the original inD and rounD datasets, please see the README.txt file.
DOI: 10.7488/ds/3406
title: Slovenian, Croatian, and Serbian Parliamentary Network Values (EU Accession)

description: This data set is made up of three smaller data sets each containing a list of Members of Parliament (MPs) in the Slovenian, Croatian, and Serbian parliaments during their respective EU accession processes. The data includes both the names of the MPs and their various roles in parliament, their party affiliations, and their membership in various parliamentary bodies. This data was collected for the PhD Thesis "It's Not What You Know: Europeanization and Informal Networks in Former Yugoslavia" to act as the base data set for the construction of social networks maps.
description: The three links are to the Croatian, Slovenian, and Serbian parliamentary websites from which the data was gathered before being collated into this form.
DOI: 10.7488/ds/3450
title: Data for "Interpreted machine learning in fluid dynamics" Lellep et al., Journal of Fluid Mechanics, 2022
title: Interpreted machine learning in fluid dynamics

description: This dataset is the supplementary data for the publication https://arxiv.org/abs/2102.05541. Machine Learning (ML) is becoming increasingly popular in fluid dynamics. Powerful ML algorithms such as neural networks or ensemble methods are notoriously difficult to interpret. Here, we introduce the novel Shapley additive explanations (SHAP) algorithm (Lundberg & Lee, Advances in Neural Information Processing Systems, 2017, pp. 4765–4774), a game-theoretic approach that explains the output of a given ML model in the fluid dynamics context. We give a proof of concept concerning SHAP as an explainable artificial intelligence method providing useful and human-interpretable insight for fluid dynamics. To show that the feature importance ranking provided by SHAP can be interpreted physically, we first consider data from an established low-dimensional model based on the self-sustaining process (SSP) in wall-bounded shear flows, where each data feature has a clear physical and dynamical interpretation in terms of known representative features of the near-wall dynamics, i.e. streamwise vortices, streaks and linear streak instabilities. SHAP determines consistently that only the laminar profile, the streamwise vortex and a specific streak instability play a major role in the prediction. We demonstrate that the method can be applied to larger fluid dynamics datasets by a SHAP evaluation on plane Couette flow in a minimal flow unit focussing on the relevance of streaks and their instabilities for the prediction of relaminarisation events. Here, we find that the prediction is based on proxies for streak modulations corresponding to linear streak instabilities within the SSP. That is, the SHAP analysis suggests that the break-up of the self-sustaining cycle is connected with a suppression of streak instabilities.
DOI: 10.7488/ds/3500
title: Costs of management of acute respiratory infections in older adults: extracted cost data

description: The data that are presented in the excel sheet are the cost data extracted from the individual studies that contribute to the metaanalysis. Background: Acute respiratory infections (ARIs) accounted for an estimated 3.9 million deaths worldwide in 2015, of which 56% occurred in adults aged 60 years or older. We aimed to identify the cost of ARI management in older adults (≥50 years) in order to develop an evidence base to assist decision-making for resource allocation and inform clinical practice. Methods: We searched 8 electronic databases including Global Health, Medline and EMBASE for studies published between 1 January 2000 and 31 December 2021. Total management costs per patient per ARI episode were extracted and meta-analysis was conducted by WHO region and World Bank income level. All costs were a converted and inflated to Euros (€) (2021 average exchange rate). Results: A total of 42 publications were identified for inclusion, reporting cost data for 8,082,752 ARI episodes in older adults across 20 countries from 2001 to 2021. The majority (86%) of studies involved high-income countries based in Europe, North America and Western Pacific. The mean cost per episode was €17,803.9 for inpatient management and €128.9 for outpatient management. Compared with costs reported for patients aged &lt;65 years, inpatient costs were €154.1, €7,018.8 and €8,295.6 higher for patients aged 65-74 years, 75-84 years and over 85 years. ARI management of at-risk patients with comorbid conditions and patients requiring higher level of care, incurred substantially higher costs for hospitalization - €735.9 and €1,317.3 respectively. Conclusions: ARIs impose a substantial economic burden on health systems, governments, patients and societies. This study identified high ARI management costs in older adults, reinforcing calls for investment by global health players to quantify and address the scale of the challenge. There are large gaps in data availability from low-income countries, especially from South East Asia and Africa regions.
DOI: 10.7488/ds/3759
title: Contactless Interfacial Rheology: Probing Shear at Liquid-Liquid Interfaces without an Interfacial Geometry via Fluorescence Microscopy

description: Interfacial rheology is important for understanding properties such as Pickering emulsion or foam stability. Currently, the response is measured using a probe directly attached to the interface. This can both disturb the interface and is coupled to flow in the bulk phase, limiting its sensitivity. We have developed a contactless interfacial method to perform interfacial shear rheology on liquid/liquid interfaces with no tool attached directly to the interface. This is achieved by shearing one of the liquid phases and measuring the interfacial response via confocal microscopy. Using this method we have measured steady shear material parameters such as interfacial elastic moduli for interfaces with solid-like behaviour and interfacial viscosities for fluid-like interfaces. The accuracy of this method has been verified relative to a double-wall ring geometry. Moreover, using our contactless method we are able to measure lower interfacial viscosities than those that have previously been reported using a double-wall ring geometry. A further advantage is the simultaneous combination of macroscopic rheological analysis with microscopic structural analysis. Our analysis directly visualizes how the interfacial response is strongly correlated to the particle surface coverage and their interfacial assembly. Furthermore, we capture the evolution and irreversible changes in the particle assembly that correspond with the rheological response to steady shear. A Jupyter Notebook for image analysis is available here: https://datashare.ed.ac.uk/handle/10283/4746.
description: The dataset contains the figures related to the publication https://arxiv.org/abs/2012.07057