cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/2531
title: Global patterns in monthly activity of influenza virus, respiratory syncytial virus, parainfluenza virus, and metapneumovirus: a systematic analysis

description: Background: Influenza virus (IFV), respiratory syncytial virus (RSV), parainfluenza virus (PIV), and metapneumovirus (MPV) are the most common viruses associated with acute lower respiratory infections in young children and the elderly. A global report of the monthly activity of these viruses is needed to inform public health strategies and programmes for their control. Methods: We conducted a systematic review of population-based studies supplemented by online data and unpublished research data reporting seasonality of IFV, RSV, PIV, and MPV. We calculated monthly annual average percentage (AAP) as the relative strength of virus activity. We defined duration of epidemics as the minimum number of months to account for 75% of annual positive samples, with each component month defined as an epidemic month. Furthermore, we modelled monthly AAP of IFV and RSV using site-specific temperature and relative humidity for the prediction of local average epidemic months. We also predicted global epidemic months of IFV and RSV on a 5° by 5° grid. The dataset contains the global seasonality of influenza virus, respiratory syncytial virus, parainfluenza virus, and human metapneumovirus. The data dictionary can be found in the second sheet of the excel file. R codes can be found in the word file. Funding: European Union Innovative Medicines Initiative: Respiratory Syncytial Virus Consortium in Europe (RESCEU)
description: The dataset contains the global seasonality of influenza virus, respiratory syncytial virus, parainfluenza virus, and human metapneumovirus. The data dictionary can be found in the second sheet of the excel file. R codes can be found in the word file.
DOI: 10.7488/ds/2879
title: Global burden of acute lower respiratory infection associated with human parainfluenza virus in children under five years for 2018: a systematic review and meta-analysis

description: We provide the datasets used in this study. The datasets include: (1) incidence rates of hPIV associated ALRI (see "ALRI" file); (2) hospitalisation rates of hPIV associated ALRI (see "Hos" file); (3) hospitalisation rates of hPIV with hypoxemia (see "sHos" file); (4) in-hospital case fatality ratios of hPIV associated ALRI (see "CFR" file); (5) proportion positives of hPIV in hospitalised ALRI (see "prop" file); (6) the main results in this study (see "Main table results" file). Background of this study: Acute lower respiratory infections (ALRI) are one of the leading causes of morbidity and mortality in children globally, accounting for 10% of mortality in children under five years in 2017.1 Human parainfluenza virus (hPIV), including four major serotypes (hPIV-1 to hPIV-4), has been long considered a common virus in childhood ALRI. However, there are no global burden estimates of hPIV-associated ALRI among children under five years due to the limited data on incidence and mortality of hPIV-associated ALRI that have been readily available in published literature, especially by narrow age groups. Using the published and unpublished data on laboratory-confirmed (culture, immunofluorescence assay, or molecular test) hPIV burden, we sought to estimate the global and regional number of hPIV-associated ALRI cases, hospitalisations, and mortality by age strata among children under five years for 2018. Two recent pooled analyses suggested that 43-87% of ALRI cases with laboratory-confirmed hPIV are attributable to hPIV in children under five years at population level (attributable fraction), with the attributable fraction varying by hPIV serotypes. To help better understand the contribution of hPIV in causing ALRI, we sought to estimate the global hPIV-attributable ALRI burden using type-specific data. These estimates should help guide health investment priorities and resource allocation. By raising awareness of the disease and healthcare burden they may also encourage and inform investment to accelerate the development of targeted prevention and treatment interventions. A few hPIV-3 candidate vaccines are under development, and have been assessed in phase I and II trials showing safety and immunogenicity in seronegative children above six months. A respiratory syncytial virus (RSV)/hPIV3 vaccine candidate has been assessed in a phase I trial, showing the possibility of using one vaccine to protect against both RSV and hPIV3 among young children. hPIV-1 and hPIV-2 candidate vaccines are also under development.
DOI: 10.7488/ds/2538
title: Data supporting the paper "From Head to Hind: Elucidating Function through Contrasting Morphometrics of Ancient and Modern Pedigree Dogs". This dataset was previously titled - Geometric Morphometrics in Canine Archaeozoology: Hallmarks of Present-Day Sight Hounds in the Bones of an Ancient Roman Dog
title: Geometric Morphometrics in Canine Archaeozoology: Hallmarks of Present-Day Sight Hounds in the Bones of an Ancient Roman Dog

description: Supporting data and archaeological reports described by Schoenebeck et al. 2019. Anatomical Record (in submission). Skeletal data related to the comparative morphological analysis of an ancient Roman dog found in Warmington, England against the morphologies of modern pedigree dog skeletons housed in the NMBE (Bern, Switzerland). Data includes raw coordinate data and measurements, as well as their derivatives.
DOI: 10.7488/ds/2754
title: CKCS CEL data

description: The dataset is microrarray data collected from canine RNA samples. The experimental design of this project is to perform comparative analysis (unpaired one-way ANOVA) between normal canine mitral valves, late stage Myxomatous mitral valves from a mixed breed population and late stage Myxomatous mitral valves from Cavalier King Charles Spaniels (CKCS). At the time of deposit, the data creators are working on a draft manuscript with which this dataset is associated, whose draft title is "Comparative transcriptomic profiling of myxomatous mitral valve disease in the cavalier King Charles spaniel".
DOI: 10.7488/ds/2985
title: Boran BovineHD SNP data

description: BovineHD SNP (single nucleotide polymorphism) data for 82 Boran cattle.
description: Plink standard file format.
DOI: 10.7488/ds/2056
title: Data on the composition of four balanced and four unbalanced series of E12.5 fetal mouse chimaeras

description: This is numerical data used to compare the composition of different series of fetal mouse chimaeras. Eight series of chimaeras were created as matched pairs in four studies and the composition of each chimaeric conceptus was evaluated by electrophoresis of glucose phosphate isomerase (GPI) markers. These data show that BALB/c embryos tend to contribute poorly to mouse chimaeras [references 1, 3, 4] and this appears to be mediated, in part, by a maternal effect [reference 2]. 1. West, J.D., Flockhart, J.H., 1994. Genotypically unbalanced diploid ↔diploid foetal mouse chimaeras: possible relevance to human confined mosaicism. Genet Res 63, 87-99. DOI: https://doi.org/10.1017/S0016672300032195 2. West, J.D., Flockhart, J.H., Kissenpfennig, A., 1995. A maternal genetic effect on the composition of mouse aggregation chimaeras. Genet Res 65, 29-40. DOI: https://doi.org/10.1017/S0016672300032985 3. Tang, P.-C. & West, J.D., 2001. Size regulation does not cause the composition of mouse chimaeras to become unbalanced. Int. J. Dev. Biol. 45, 583-590. 4. MacKay, G.E., Keighren, M.A., Wilson, L., Pratt, T., Flockhart, J.H., Mason, J.O., Price, D.J., West, J.D., 2005. Evaluation of the mouse TgTP6.3 tauGFP transgene as a lineage marker in chimeras. J. Anat. 206, 79-92. DOI: 10.1111/j.0021-8782.2005.00370.x
description: 1 Excel Workbook (with 4 spreadsheets): Data from 8 series of fetal mouse chimaeras. Spreadsheet 1: Chimaera Series XM and XR. (From West & Flockhart, 1994). Spreadsheet 2: Chimaera Series XP and XN. (From West et al 1995). Spreadsheet 3: Chimaera Series PCT-V and PCT-VI. (From Tang & West 2001). Spreadsheet 4: Chimaera Series GMA and GMB. (From MacKay et al 2005). 1 “Read Me” file (pdf format). 1 “Read Me” file (docx format).
DOI: 10.7488/ds/2750
title: Comparative profiling of murine CLN1 Thalamus and Cortex at early and late disease timepoints

description: CLN1 disease or Infantile neuronal ceroid lipofuscinosis is a fatal inherited neurodegenerative lysosomal storage disease of early childhood with no currently available therapy. CLN1 disease is caused by mutations in the CLN1 gene, which encodes the enzyme Palmitoyl Protein Thioesterase-1 (PPT-1). We recently found significant spinal pathology in Ppt1-deficient (Ppt1-/-) mice and human CLN1 disease, that contributes to clinical outcome, and precedes the onset of similar changes in the brain of these mice. To further understand the underlying mechanisms that cause such regional vulnerability, we used quantitative proteomic profiling to analyze the cortex and spinal cord tissue from wildtype (WT) and Ppt1-/- mice at early (3 months) and late (7 month) timepoints respectively. Tandem Mass Tagged (TMT) proteomic analysis revealed a significant early inflammatory response as well as changes in mitochondrial function, cell-signalling pathways and developmental processes in the spinal cords of Ppt1-/- mice at 3 months, as compared to their wildtype counterparts. Taken together, these early and progressive pathological and related proteomic changes in this largely unexplored region of the CNS may help explain the limited success of previous brain-directed therapies for CLN1 disease. More importantly, these data fundamentally change our understanding of the progressive, site-specific disease pathogenesis in CLN1 disease, and highlight the importance of early inflammation. This will greatly impact our approach to the timing and targeting of future therapeutic trials for the neuronal ceroid lipofuscinoses (NCLs). The proteomic data generated in the process of this research has been uploaded for general access here.
DOI: 10.7488/ds/3792
title: cAge and bAge EWAS - Epigenome-wide association study of chronological age (linear and quadratic) and of survival

description: These datasets correspond to the manuscript “Refining epigenetic prediction of chronological and biological age“. Here, we include the summary statistics for an epigenome-wide association study (EWAS) of age, considering both CpG (linear) and CpG^2 (quadratic) associations, as well as for an EWAS of survival (using a fixed effects Cox Proportional Hazards Model; results for a mixed effects model to account for relatedness included in Supplementary Table 4 of manuscript). Also included are goodness of fit F-test results comparing models accounting and not accounting for a quadratic CpG association, as well as mean and SD of CpG M-values in the Generation Scotland cohort. Further methodological details, including quality control steps, software used, and covariates adjusted for, are described in the accompanying manuscript. Analyses were conducted using the Generation Scotland cohort (N = 18,413).
DOI: 10.7488/ds/148
title: Identification of miRNAs associated with the follicular-luteal transition in the ruminant ovary

description: Little is known about the involvement of microRNAs (miRNAs) in the follicular-luteal transition. The aim of this study was to identify genome-wide changes in miRNAs associated with follicular differentiation in sheep. miRNA libraries were produced from samples collected at defined stages of the ovine oestrous cycle and representing healthy growing follicles (diameter, 4.0-5.5 mm) pre-ovulatory follicles (6.0-7.0 mm), early corpora lutea (day 3 post-oestrus) and late corpora lutea (day 9). A total of 189 miRNAs reported in sheep or other species and an additional 23 novel miRNAs were identified by sequencing these libraries. miR-21, miR-125b, let-7a and let-7b were the most abundant miRNAs overall, accounting for 40% of all miRNAs sequenced. Examination of changes in cloning frequencies across development identified nine different miRNAs which expression decreased in association with the follicular-luteal transition and eight miRNAs which expression increased during this transition. Expression profiles were confirmed by Northern analyses, and experimentally validated targets were identified using miRTarBase. A majority of the 29 targets identified represented genes known to be actively involved in regulating follicular differentiation in vivo. Finally, luteinisation of follicular cells in vitro resulted in changes in miRNA levels that were consistent with those identified in vivo, and these changes were temporally associated with changes in levels of putative miRNA targets in granulosa cells. In conclusion, this is the first study to characterise genome-wide miRNA profiles during different stages of follicle and luteal development. Our data identifies a subset of miRNAs which are potentially important regulators of the follicular-luteal transition.
description: Sequence and tissue distribution of ovine miRNA
DOI: 10.7488/ds/2901
title: Community health worker-based mobile health (mHealth) approaches for improving management and caregiver knowledge of common childhood infections: A systematic review
DOI: 10.7488/ds/3053
title: Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome
title: Human ATAC-seq narrow peaks from FGFR3 sorted adult spermatogonial cells

description: ATAC-Seq reports local chromatin accessibility and provides a snapshot of active regulatory regions and genomic regions occupied by DNA-binding proteins in a given tissue. We used ATAC-Seq to identify open chromatin sites in FGFR3-positive spermatogonial cells isolated from dissociated human testicular samples. FGFR3 is most highly expressed in self-renewing spermatogonial stem cells, with low expression also being detected in early differentiating spermatogonia; its expression thus overlaps with the onset of PRDM9 expression in pre-meiotic spermatogonia. Open chromatin in FGFR3-positive cells was identified using standard peak detection analysis with MACS2 software.
description: See README.txt for data processing and format details. * Replicate_1.narrowPeak.bed - replicate 1 data containing merged reads of patient H.5 libraries 1 and 4 (FGFR3 positive large high side-scatter spermatogonial cells). * Replicate_2.narrowPeak.bed - replicate 2 data containing merged reads of patient H.5 libraries 2 and 5 (FGFR3 positive large spermatogonial cells). * Replicate_3.narrowPeak.bed - replicate 3 data containing merged reads of patient H.7 and H.10 (FGFR3 positive large spermatogonial cells).
DOI: 10.7488/ds/2988
title: Average male and female mouse brain TSPO atlases, generated using TSPO PET radiotracer [18F]LW223 (normalised to injected dose)

description: [18F]LW223 is a novel Positron Emission Tomography (PET) radiotracer which can be used to detetect 18kDa translocator protein (TSPO) distribution in vivo. Murine brain TSPO atlases were generated using average SUV at 90-120 minutes post-[18F]LW223 injection in healthy male (n=9, age 14.7 ± 6.2 weeks, mean ± SD) and female (n=5, age 11.6 ± 2.5 weeks, mean ± SD) C57Bl6/J mice. Three average atlases are available to download as NIfTI (.nii) files: 1) averge male TSPO atlas; 2) average female TSPO atlas; 3) average TSPO atlas of both sexes. The atlases were smoothed using 0.2 mm Gaussian filter.
DOI: 10.35078/bnuebx
title: Replication Data for: Ficha epidemiológica de localidade: Distrito: Caratinga | Município: Chalé

description: Levantamento Triatomínico com operações de campo ocorridas em Minas Gerais pela Superintendência de Campanhas de Saúde Pública (SUCAM) e FUNASA (Fundação Nacional de Saúde), no período de 1979 a 1999, objetivando a busca da presença de vetores da doença de Chagas ou de vestígios dessa presença. A partir dela são orientadas as operações com inseticida (pt) Triatomine survey with field operations carried out in Minas Gerais by the Public Health Campaigns Superintendence (SUCAM) and FUNASA (National Health Foundation), from 1979 to 1999, aiming to search for the presence of Chagas disease vectors or traces of that presence. From it, operations with insecticide are guided (en) Encuesta de triatominos con operaciones de campo realizada en Minas Gerais por la Superintendencia de Campañas de Salud Pública (SUCAM) y FUNASA (Fundación Nacional de Salud), de 1979 a 1999, con el objetivo de buscar la presencia de vectores de la enfermedad de Chagas o rastros de esa presencia. Desde ella se orientan las operaciones con insecticida (es)
DOI: 10.7488/ds/1341
title: Lineage tracing in the adult mouse corneal epithelium supports the limbal epithelial stem cell hypothesis with intermittent periods of stem cell quiescence
title: Lineage tracing in the adult mouse corneal epithelium_Dora et al_DataShare

description: The limbal epithelial stem cell (LESC) hypothesis proposes that LESCs in the corneal limbus maintain the corneal epithelium both during normal homeostasis and wound repair. The alternative corneal epithelial stem cell (CESC) hypothesis proposes that LESCs are only involved in wound repair and CESCs in the corneal epithelium itself maintain the corneal epithelium during normal homeostasis. We used tamoxifen-inducible, CreER-loxP lineage tracing to distinguish between these hypotheses. Clones of labelled cells were induced in adult CAGG-CreER;R26R-LacZ reporter mice and their distributions analysed after different chase periods. Short-lived clones, derived from labelled transient amplifying cells, were shed during the chase period and long-lived clones, derived from stem cells, expanded. At 6 weeks, labelled clones appeared at the periphery, extended centripetally as radial stripes and a few reached the centre by 14 weeks. Stripe numbers depended on the age of tamoxifen treatment. Stripes varied in length, some were discontinuous, few reached the centre and almost half had one end at the limbus. Similar stripes extended across the cornea in CAGG-CreER;R26R-mT/mG reporter mice. The distributions of labelled clones are inconsistent with the CESC hypothesis and support the LESC hypothesis if LESCs cycle between phases of activity and quiescence, each lasting several weeks.
DOI: 10.7488/ds/2989
title: ATEC manuscript 3 - supporting data: "Combining Process Modelling and LAI Observations to Diagnose Winter Wheat Nitrogen Status and Forecast Yield"

description: Climate, nitrogen (N) and leaf area index (LAI) are key determinants of crop yield. N additions can enhance yield but must be managed efficiently to reduce pollution. Complex process models estimate N status by simulating soil-crop N interactions, but such models require extensive inputs that are seldom available. Through model-data fusion (MDF), we combine climate and LAI time-series with an intermediate-complexity model to infer leaf N and yield. The DALEC-Crop model was calibrated for wheat leaf N and yields across field experiments covering N applications ranging from 0 to 200 kg N ha−1 in Scotland, UK. Requiring daily meteorological inputs, this model simulates crop C cycle responses to LAI, N and climate. The model, which includes a leaf N-dilution function, was calibrated across N treatments based on LAI observations, and tested at validation plots. We showed that a single parameterization varying only in leaf N could simulate LAI development and yield across all treatments—the mean normalized root-mean-square-error (NRMSE) for yield was 10%. Leaf N was accurately retrieved by the model (NRMSE = 6%). Yield could also be reasonably estimated (NRMSE = 14%) if LAI data are available for assimilation during periods of typical N application (April and May). Our MDF approach generated robust leaf N content estimates and timely yield predictions that could complement existing agricultural technologies. Moreover, EO-derived LAI products at high spatial and temporal resolutions provides a means to apply our approach regionally. Testing yield predictions from this approach over agricultural fields is a critical next step to determine broader utility.
description: A description of datasets available for download with this item is provided in README.txt.
DOI: 10.7488/ds/3001
title: Source data and scripts for "A systematic approach to inserting split inteins for Boolean logic gate engineering and basal activity reduction"

description: Split inteins are powerful tools for seamless ligation of synthetic split proteins. Yet, their use remains limited because the already intricate split site identification problem is often complicated by the requirement of extein junction sequences. To address this, we augment a mini-Mu transposon-based screening approach and devise the intein-assisted bisection mapping (IBM) method. IBM robustly reveals clusters of split sites on five proteins, converting them into AND or NAND logic gates. We further show that the use of inteins expands functional sequence space for splitting a protein. We also demonstrate the utility of our approach over rational inference of split sites from secondary structure alignment of homologous proteins, and that basal activities of highly active proteins can be mitigated by splitting them. Our work offers a generalizable and systematic route towards creating split protein-intein fusions for synthetic biology.
description: Secondary structures of mCherry, TEM-1 beta-lactamase and TetR are obtained from Protein Data Bank, with accession codes of PDB: 2H5Q, PDB: 1ZG4, and PDB: 4AC0, respectively
DOI: 10.7488/ds/2245
title: Data on selection against BALB/c strain cells in mouse chimaeras

description: The data are numerical data used to produce Figs. 2, 3 & 4 and Supplementary Tables S1, S2 & S3 in a manuscript entitled "Selection against BALB/c strain cells in mouse chimaeras" by Tang P-C, Mackay GE, Flockhart JH, Keighren MA, Kopakaki A and West JD. The study seeks to explain why BALB/c strain embryos tend to contribute poorly to mouse aggregation chimaeras. BALB/c cells were not preferentially allocated to any extraembryonic lineages in chimaeras but their contribution decreased between E4.5 and E8.5. The development of BALB/c strain preimplantation embryos lagged behind embryos from some other strains and the contribution that BALB/c and other embryos made to chimaeras correlated with their developmental stage at E2.5. This relationship suggests that the poor contribution of BALB/c embryos to aggregation chimaeras is at least partly a consequence of generalised selection related to slow or delayed preimplantation development.
DOI: 10.7488/ds/3501
title: Edinburgh virtual multiphase flow imaging dataset

description: This dataset is for publication "Digital twin enables quantitative multiphase flow imaging with low-cost tomography". ABSTRACT: Multiphase flow is ubiquitous in nature, industry, and research. Quantitative multiphase flow imaging is the key to understanding this complex phenomenon. However, there are as yet no low-cost, scalable imaging techniques to achieve quantitative multiphase flow imaging for a wide range of scenarios. Here we report a digital twin (DT) framework that unlocks the real-time quantitative multiphase flow imaging capability of electrical tomography (ET) that is non-invasive, non-radioactive, scalable, and low-cost. The DT framework, building upon a synergistic integration of the 3D field coupling model, deep learning, and edge computing, allows ET to dynamically learn the flow features in the virtual space and implement the learned model in the physical device, thus providing unprecedented resolution and accuracy in the real world. The DT framework is demonstrated on dynamic gas-liquid two-phase flows, showing step-change performance compared to the state of the art. It can be readily extended to various tomography modalities and multiphase flows at different scales for precise flow visualization and characterization.