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The Avon Longitudinal Study of Parents and Children (ALSPAC) is a prospective population-based cohort which recruited pregnant women in 1990-1992 and has followed these women, their partners (Generation 0; G0) and their offspring (Generation 1; G1) ever since. The study reacted rapidly and repeatedly to the coronavirus disease 2019 (COVID-19) pandemic, deploying multiple online questionnaires and a previous home-based antibody test in October 2020. A second antibody test, in collaboration with ten other longitudinal population studies, was completed by 4,622 ALSPAC participants between April and June 2021. Of 4,241 participants with a valid spike protein antibody test result (8.2% were void), indicating antibody response to either COVID-19 vaccination or natural infection, 3,172 were positive (74.8%). Generational differences were substantial, with 2,463/2,555 G0 participants classified positive (96.4%) compared to 709/1,686 G1 participants (42.1%). Of 4,199 participants with a valid nucleocapsid antibody test result (9.2% were void), suggesting potential and recent natural infection, 493 were positive (11.7%); 248/2,526 G0 participants (9.8%) and 245/1,673 G1 participants (14.6%) tested positive, respectively. We also compare results for this round of testing to that undertaken in October 2020. Future work will combine these test results with additional sources of data to identify participants’ COVID-19 infection and vaccination status. These ALSPAC COVID-19 serology data are being complemented with linkage to health records and Public Health England pillar testing results as they become available, in addition to four previous questionnaire waves and a prior antibody test. Data have been released as an update to the previous COVID-19 datasets. These comprise: 1) a standard dataset containing all participant responses to all four previous questionnaires with key sociodemographic factors; and 2) individual participant-specific release files enabling bespoke research across all areas supported by the study. This data note describes the second ALSPAC antibody test and the data obtained from it.

Objectives The main purpose of this publication is to help users (students, researchers, farmers, advisors, etc.) of weather data with agronomic purposes (e.g. crop yield forecast) to retrieve and process gridded weather data from different Application Programming Interfaces (API client) sources using R software. Data description This publication consists of a code-tutorial developed in R that is part of the data-curation process from numerous research projects carried out by the Ciampitti’s Lab, Department of Agronomy, Kansas State University. We make use of three weather databases for which specific libraries were developed in R language: (i) DAYMET (Thornton et al. in https://daymet.ornl.gov/, 2019; https://github.com/bluegreen-labs/daymetr), (ii) NASA-POWER (Sparks in J Open Source Softw 3:1035, 2018; https://github.com/ropensci/nasapower), and (iii) Climate Hazards Group InfraRed Precipitation with Station Data (CHIRPS) (Funk et al. in Sci Data 2:150066, 2015; https://github.com/ropensci/chirps). The databases offer different weather variables, and vary in terms of spatio-temporal coverage and resolution. The tutorial shows and explain how to retrieve weather data from multiple locations at once using latitude and longitude coordinates. Additionally, it offers the possibility to create relevant variables and summaries that are of agronomic interest such as Shannon Diversity Index (SDI) of precipitation, abundant and well distributed rainfall (AWDR), growing degree days (GDD), crop heat units (CHU), extreme precipitation (EPE) and temperature events (ETE), reference evapotranspiration (ET0), among others.

Objectives The ongoing Coronavirus disease 2019 (COVID-19) pandemic has drastically impacted the global health and economy. Computed tomography (CT) is the prime imaging modality for diagnosis of lung infections in COVID-19 patients. Data-driven and Artificial intelligence (AI)-powered solutions for automatic processing of CT images predominantly rely on large-scale, heterogeneous datasets. Owing to privacy and data availability issues, open-access and publicly available COVID-19 CT datasets are difficult to obtain, thus limiting the development of AI-enabled automatic diagnostic solutions. To tackle this problem, large CT image datasets encompassing diverse patterns of lung infections are in high demand. Data description In the present study, we provide an open-source repository containing 1000+ CT images of COVID-19 lung infections established by a team of board-certified radiologists. CT images were acquired from two main general university hospitals in Mashhad, Iran from March 2020 until January 2021. COVID-19 infections were ratified with matching tests including Reverse transcription polymerase chain reaction (RT-PCR) and accompanying clinical symptoms. All data are 16-bit grayscale images composed of 512 × 512 pixels and are stored in DICOM standard. Patient privacy is preserved by removing all patient-specific information from image headers. Subsequently, all images corresponding to each patient are compressed and stored in RAR format.

Objectives Tree legume species play an important role in forest restoration in the tropics. Understanding how different species adjust carbohydrate allocation and growth under distinct nutrient availability will enhance the success of restoring degraded areas. Data description A 2-year tropical forest plantation of the Forest Restoration Program of the Balbina Hydropower Dam was evaluated. Three non-N-fixing (Cenostigma tocantinum, Dipteryx odorata and Senna reticulata) and three N-fixing (Clitoria fairchildiana, Inga edulis and Acacia spp.) tree legume species were either fertilized or not fertilized. Growth rates and biomass allocation were calculated, and carbon (C) fractions and nitrogen (N), phosphorus (P) and nonstructural carbohydrate (NSC) concentrations were determined. Multiple nutrient additions increased the growth rates and aboveground biomass production of fertilized plants. According to the results presented, different species and N- fixers respond differently to fertilization regimes. The authors encourage the use of the presented data in meta-analysis studies that consider the fertilization or nutrient deficiency effects on growth, carbohydrate and nutrient responses. N-fixing species with high biomass growth and foliar N are important for restoring N and C cycles in nutrient-limited soils. Fertilization treatments are fundamental during the early stages of forest plantation development.

The modelling of electricity systems with substantial shares of renewable resources, such as solar power, wind power and hydropower, requires datasets on renewable resource profiles with high spatiotemporal resolution to be made available to the energy modelling community. Whereas such resources exist for solar power and wind power profiles on diurnal and seasonal scales across all continents, this is not yet the case for hydropower. Here, we present a newly developed open-access African hydropower atlas, containing seasonal hydropower generation profiles for nearly all existing and several hundred future hydropower plants on the African continent. The atlas builds on continental-scale hydrological modelling in combination with detailed technical databases of hydropower plant characteristics and can facilitate modelling of power systems across Africa.

Background The tufted duck is a non-model organism that experiences high mortality in highly pathogenic avian influenza outbreaks. It belongs to the same bird family (Anatidae) as the mallard, one of the best-studied natural hosts of low-pathogenic avian influenza viruses. Studies in non-model bird species are crucial to disentangle the role of the host response in avian influenza virus infection in the natural reservoir. Such endeavour requires a high-quality genome assembly and transcriptome. Findings This study presents the first high-quality, chromosome-level reference genome assembly of the tufted duck using the Vertebrate Genomes Project pipeline. We sequenced RNA (complementary DNA) from brain, ileum, lung, ovary, spleen, and testis using Illumina short-read and Pacific Biosciences long-read sequencing platforms, which were used for annotation. We found 34 autosomes plus Z and W sex chromosomes in the curated genome assembly, with 99.6% of the sequence assigned to chromosomes. Functional annotation revealed 14,099 protein-coding genes that generate 111,934 transcripts, which implies a mean of 7.9 isoforms per gene. We also identified 246 small RNA families. Conclusions This annotated genome contributes to continuing research into the host response in avian influenza virus infections in a natural reservoir. Our findings from a comparison between short-read and long-read reference transcriptomics contribute to a deeper understanding of these competing options. In this study, both technologies complemented each other. We expect this annotation to be a foundation for further comparative and evolutionary genomic studies, including many waterfowl relatives with differing susceptibilities to avian influenza viruses.

We present a genome assembly from an individual male Celastrina argiolus) (the holly blue; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 499 megabases in span. The majority (99.99%) of the assembly is scaffolded into 26 chromosomal pseudomolecules, with the Z sex chromosome assembled. Gene annotation of this assembly on Ensembl has identified 12,199 protein coding genes.

We present a genome assembly from an individual female Caprimulgus europaeus (the European nightjar; Chordata; Aves; Caprimulgiformes; Caprimulgidae). The genome sequence is 1,178 megabases in span. The majority of the assembly (99.33%) is scaffolded into 37 chromosomal pseudomolecules, including the W and Z sex chromosomes.

Background The National COVID-19 Chest Imaging Database (NCCID) is a centralized database containing mainly chest X-rays and computed tomography scans from patients across the UK. The objective of the initiative is to support a better understanding of the coronavirus SARS-CoV-2 disease (COVID-19) and the development of machine learning technologies that will improve care for patients hospitalized with a severe COVID-19 infection. This article introduces the training dataset, including a snapshot analysis covering the completeness of clinical data, and availability of image data for the various use-cases (diagnosis, prognosis, longitudinal risk). An additional cohort analysis measures how well the NCCID represents the wider COVID-19–affected UK population in terms of geographic, demographic, and temporal coverage. Findings The NCCID offers high-quality DICOM images acquired across a variety of imaging machinery; multiple time points including historical images are available for a subset of patients. This volume and variety make the database well suited to development of diagnostic/prognostic models for COVID-associated respiratory conditions. Historical images and clinical data may aid long-term risk stratification, particularly as availability of comorbidity data increases through linkage to other resources. The cohort analysis revealed good alignment to general UK COVID-19 statistics for some categories, e.g., sex, whilst identifying areas for improvements to data collection methods, particularly geographic coverage. Conclusion The NCCID is a growing resource that provides researchers with a large, high-quality database that can be leveraged both to support the response to the COVID-19 pandemic and as a test bed for building clinically viable medical imaging models.

We present a genome assembly from an individual male Abrostola tripartita (the spectacle; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 381 megabases in span. The majority of the assembly (99.99%) is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.

We present a genome assembly and annotation of an individual female Cercopithifilaria johnstoni, a parasitic filarial nematode that is transmitted by hard ticks (Ixodidae) to infect a broad range of native Australian murid and marsupial hosts. The genome sequence is 76.9 Mbp in length, and although in draft form (N50 = 99 kbp, N50[n] = 232), is largely complete based on universally conserved orthologs (BUSCOs; genome = 94.9%, protein = 96.5%) and relative to other related filarial species. These data represent the first genomic resources for the genus Cercopithifilaria, a group of parasites with a broad host range, and form the basis for comparative analysis with the human-infective parasite, Onchocerca volvulus, both of which are responsible for similar eye and skin pathologies in their respective hosts.

Objectives This study assessed changes in behaviors/attitudes related to the COVID-19. With the understanding that behaviors and vaccine decision-making could contribute to global spread of infectious diseases, this study collected several waves of internet-based surveys from individuals in the United States, mainland China, Taiwan, Malaysia, Indonesia, and India. The aims of this study were to (1) characterize the relationship between the epidemiology of disease and changes over time in risk perceptions, knowledge, and attitudes towards hygienic behaviors; (2) examine if risk perceptions affect acceptance of less-than-ideal vaccines; and (3) contrast adherence to public health recommendations across countries which have had different governmental responses to the outbreak. Data description We conducted cross-sectional online surveys in six countries from March 2020 to April 2021. By the end of June 2021, there will be six waves of surveys for the United States and China, and four waves for the rest of countries. There are common sets of questions for all countries, however, some questions were adapted to reflect local situations and some questions were designed intentionally for specific countries to capture different COVID-19 mitigation actions. Participants were asked about their adherence towards countermeasures, risk perceptions, and acceptance of a hypothetical vaccine for COVID-19.

Objectives The COVID-19 pandemic has impacted the mental health of people worldwide. Psychological resilience has been shown to buffer against the threat of the pandemic (i.e., COVID-19 fear) and sustain mental health. The extent to which psychological resilience factors impact mental health maintenance, however, is unclear, given broad differences in infection rates, prevention approaches, government interventions across different cultures and contexts. Our study examines resilience factors and how they protect individuals from COVID-19-related fear and sustain their mental health. Data description Data were collected from 1583 (Mage = 32.22, SD = 12.90, Range = 19–82) respondents from Japan, China, the United States, and Malaysia between October to November 2020. We collected data across age and sex, marital status, number of children, and occupations. We also accounted for stay-at-home measures, change in income, COVID-19 infection status, place of residence, and subjective social status in the study. Our variables included mental health-related and resilience constructs, namely (i) fear of COVID-19, (ii) depression, anxiety, and stress; (iii) present, past, and future life satisfaction, (iv) sense of control, (v) positive emotions, (vi) ego-resilience, (vii) grit, (viii) self-compassion, (ix) passion, and (x) relational mobility. All questionnaires were assessed for their suitability across the four countries with the necessary translation checks. Results from this study can be instrumental in examining the impact of multiple resilience factors and their interaction with demographic variables in shaping mental health outcomes.

We present a genome assembly from an individual male Canis lupus orion (the grey wolf, subspecies: Greenland wolf; Chordata; Mammalia; Carnivora; Canidae). The genome sequence is 2,447 megabases in span. The majority of the assembly (98.91%) is scaffolded into 40 chromosomal pseudomolecules, with the X and Y sex chromosomes assembled.

We present a genome assembly from an individual female Acronicta aceris (the sycamore; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 466 megabases in span. The complete assembly is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosome assembled.

We present a genome assembly from an individual female Rana temporaria (the common frog; Chordata; Amphibia; Anura; Ranidae). The genome sequence is 4.11 gigabases in span. The majority of the assembly is scaffolded into 13 chromosomal pseudomolecules. Gene annotation of this assembly by the NCBI Eukaryotic Genome Annotation Pipeline has identified 23,707 protein coding genes.

We present a genome assembly from an individual male Bufo bufo (the common toad; Chordata; Amphibia; Anura; Bufonidae). The genome sequence is 5.04 gigabases in span. The majority of the assembly (99.1%) is scaffolded into 11 chromosomal pseudomolecules. Gene annotation of this assembly by the NCBI Eukaryotic Genome Annotation Pipeline has identified 21,517 protein coding genes.

Objectives The mangrove cricket, Apteronemobius asahinai, shows endogenous activity rhythms that synchronize with the tidal cycle (i.e., a free-running rhythm with a period of ~ 12.4 h [the circatidal rhythm]). Little is known about the molecular mechanisms underlying the circatidal rhythm. We present the draft genome of the mangrove cricket to facilitate future molecular studies of the molecular mechanisms behind this rhythm. Data description The draft genome contains 151,060 scaffolds with a total length of 1.68 Gb (N50: 27 kb) and 92% BUSCO completeness. We obtained 28,831 predicted genes, of which 19,896 (69%) were successfully annotated using at least one of two databases (UniProtKB/SwissProt database and Pfam database).

Background High-quality genomic resources facilitate investigations into behavioral ecology, morphological and physiological adaptations, and the evolution of genomic architecture. Lizards in the genus Sceloporus have a long history as important ecological, evolutionary, and physiological models, making them a valuable target for the development of genomic resources. Findings We present a high-quality chromosome-level reference genome assembly, SceUnd1.0 (using 10X Genomics Chromium, HiC, and Pacific Biosciences data), and tissue/developmental stage transcriptomes for the eastern fence lizard, Sceloporus undulatus. We performed synteny analysis with other snake and lizard assemblies to identify broad patterns of chromosome evolution including the fusion of micro- and macrochromosomes. We also used this new assembly to provide improved reference-based genome assemblies for 34 additional Sceloporus species. Finally, we used RNAseq and whole-genome resequencing data to compare 3 assemblies, each representing an increased level of cost and effort: Supernova Assembly with data from 10X Genomics Chromium, HiRise Assembly that added data from HiC, and PBJelly Assembly that added data from Pacific Biosciences sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq and single-nucleotide polymorphism calling, but the chromosome-level scaffolds provided by the addition of HiC data allowed synteny and whole-genome association mapping analyses. The subsequent addition of PacBio data doubled the contig N50 but provided negligible gains in scaffold length. Conclusions These new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.

Background Channa argus and Channa maculata are the main cultured species of the snakehead fish family, Channidae. The relationship between them is close enough that they can mate; however, their temperature adaptability is quite different. Results In this study, we sequenced and assembled the whole genomes of C. argus and C. maculata and obtained chromosome-level genome assemblies of 630.39 and 618.82 Mb, respectively. Contig N50 was 13.20 and 21.73 Mb, and scaffold N50 was 27.66 and 28.37 Mb, with 28,054 and 24,115 coding genes annotated for C. argus and C. maculata, respectively. Our analyses showed that C. argus and C. maculata have 24 and 21 chromosomes, respectively. Three pairs of chromosomes in C. argus correspond to 3 chromosomes in C. maculata, suggesting that 3 chromosomal fusion events occurred in C. maculata. Comparative analysis of their gene families showed that some immune-related genes were unique or expandable to C. maculata, such as genes related to herpes simplex infection. Analysis of the transcriptome differences related to temperature adaptation revealed that the brain and liver of C. argus rapidly produced more differentially expressed genes than C. maculata. Genes in the FoxO signalling pathway were significantly enriched in C. argus during the cooling process (P Conclusions C. maculata may have higher resistance to certain diseases, whereas C. argus has a faster and stronger response to low-temperature stress and thus has better adaptability to a low-temperature environment. This study provides a high-quality genome research platform for follow-up studies of Channidae and provides important clues regarding differences in the low-temperature adaptations of fish.

We present a genome assembly from an individual Lineus longissimus (the bootlace worm; Nemertea; Pilidiophora; Heteronemertea; Lineidae). The genome sequence is 391 megabases in span. The majority of the assembly is scaffolded into 19 chromosomal pseudomolecules.

Objectives Universal stool banks provide stool to physicians for use in treating recurrent Clostridioides difficile infection via fecal microbiota transplantation. Stool donors providing the material are rigorously screened for diseases and disorders with a potential microbiome etiology, and they are likely healthier than the controls in most microbiome datasets. 16S rRNA sequencing was performed on samples from a selection of stool donors at a large stool bank, OpenBiome, to characterize their gut microbial community and to compare samples across different timepoints and sequencing runs. Data description 16S rRNA sequencing was performed on 200 samples derived from 170 unique stool donations from 86 unique donors. Samples were sequenced on 11 different sequencing runs. We are making this data available because rigorously screened, likely very healthy stool donors may be useful for characterizing and understanding microbial community differences across different populations and will help shed light into the how the microbiome community promotes health and disease.

Objectives Hospitalized patients who presented within the last 24 h with a bacterial infection were recruited. Participants were assigned into sepsis and uncomplicated infection groups. In addition, healthy volunteers were recruited as controls. RNA was prepared from whole blood, depleted from beta-globin mRNA and sequenced. This dataset represents a highly valuable resource to better understand the biology of sepsis and to identify biomarkers for severe sepsis in humans. Data description The data presented here consists of raw and processed transcriptome data obtained by next generation RNA sequencing from 105 peripheral blood samples from patients with uncomplicated infections, patients who developed sepsis, septic shock patients, and healthy controls. It is provided as raw sequenced reads and as normalized log2 transformed relative expression levels. This data will allow performing detailed analyses of gene expression changes between uncomplicated infections and sepsis patients, such as identification of differentially expressed genes, co-regulated modules as well as pathway activation studies.

Over the past decade, there have been several attempts to standardize cross-linguistic datasets. Since language comparison is a notoriously difficult endeavor, it requires tools that facilitate standardization and are convenient to use. The Concepticon is based on a toolkit provided for cross-linguistic comparison and offers a reference catalog for comparable concepts that appear in concept lists. While curating the Concepticon, we found that a variety of studies in distinct research fields collected information on word properties. However, until recently, no resource existed that contained these data to enable the comparison of the different word properties across languages. This gap was filled by the Database of Norms, Ratings, and Relations (NoRaRe), which is an extension of the Concepticon. Here, we present the major release of both resources - Concepticon Version 3.0 and NoRaRe Version 1.0 - which represents an important step in our data development. We show that extending and adapting the data curation workflow in Concepticon to NoRaRe is useful for the standardization of cross-linguistic datasets. In addition, combining datasets from different research fields enables studies grounded in language comparison. Concepticon and NoRaRe include lexical data for various languages, tools for test-driven data curation, and the possibility for data reuse. The first major release of NoRaRe is also accompanied by a new web application that allows convenient access to the data.

Objectives Recently natural language interfaces (e.g., chatbots) have gained enormous attention. Such interfaces execute underlying application programming interfaces (APIs) based on the user's utterances to perform tasks (e.g., reporting weather). Supervised approaches for building such interfaces rely upon a large set of user utterances paired with APIs. Collecting such pairs is typically starts with obtaining initial utterances for a given API method. Generating initial utterances can be considered as a machine translation task in which an API method is translated into an utterance. However, the key challenge is the lack of training samples for training domain-independent translation models. In this paper, we propose a dataset for training supervised models to generate initial utterances for APIs. Data description The dataset contains 14,370 pairs of API methods and utterances. It is built automatically by converting method descriptions of a large number of APIs to user utterances; and it is cleaned manually to ensure quality. The dataset is also accompanied with a set of microservices (e.g., translating API methods to utterances) which can facilitate the process of collecting training samples for building natural language interfaces.

Objectives Induction of labour (IOL), or starting labour artificially, can be a lifesaving intervention for pregnant women and their babies, and rates are rising significantly globally. As rates increase, it becomes increasingly important to fully evaluate all available data, especially that from low income settings where the potential benefits and harms are greater. The goal of this paper is to describe the datasets collected as part of the Induction with Foley OR Misoprostol (INFORM) Study, a randomised trial comparing two of the recommended methods of cervical ripening for labour induction, oral misoprostol and Foley catheter, in women being induced for hypertension in pregnancy, at two sites in India during 2013–15. Data description This dataset includes comprehensive data on 602 women who underwent IOL for hypertensive disorders in pregnancy. Women were randomly assigned to cervical ripening with oral misoprostol or a transcervical Foley catheter in two government hospitals in India. The main dataset has 367 variables including monitoring during the induction of labour, medications administered, timing and mode of delivery, measures of neonatal morbidity and mortality, maternal mortality and morbidity, maternal satisfaction and health economic data. The dataset is anonymised and available on ReShare.

Objectives Existing information on Arctic marine food web structure is fragmented. Integrating data across research programs is an important strategy for building a baseline understanding of food web structure and function in many Arctic regions. Naturally-occurring stable isotope ratios of nitrogen (δ15N) and carbon (δ13C) measured directly in the tissues of organisms are a commonly-employed method for estimating food web structure. The objective of the current dataset was to synthesize disparate δ15N, and secondarily δ13C, data in the Canadian Beaufort continental shelf region relevant to trophic and ecological studies at the local and pan-Arctic scales. Data description The dataset presented here contains nitrogen and carbon stable isotope ratios (δ15N, δ13C) measured in marine organisms from the Canadian Beaufort continental shelf region between 1983 and 2013, gathered from 27 published and unpublished sources with associated sampling metadata. A total of 1077 entries were collected, summarizing 8859 individual organisms/samples representing 333 taxa across the Arctic food web, from top marine mammal predators to primary producers.

We present a genome assembly from an individual male Euproctis similis (the yellow-tail; Arthropoda; Insecta; Lepidoptera; Lymantriidae). The genome sequence is 508 megabases in span. The majority of the assembly is scaffolded into 22 chromosomal pseudomolecules, with the Z sex chromosome assembled.

Aim: Generation of an R-group replacement system for compound optimization in medicinal chemistry. Materials & methods: From bioactive compounds, analogue series (ASs) were systematically extracted and from these ASs, all R-groups were isolated and further analyzed. Exemplary results & data: From more than 17,000 ASs, more than 50,000 unique R-groups were isolated. For the 500 most frequently used R-groups, preferred replacements were identified and organized in hierarchies. All original data and an R-group replacement database are made available in an open access deposition. Limitations & next steps: The searchable database has no limitations and can easily be modified using the source data we provide. The next step will be applying this R-group resource in practical medicinal chemistry projects as decision support., Graphical abstract For a representative frequently used R-group (blue, left), four pathways with a preferred first (green) and second (pink) replacement are depicted (from left to right). Such R-group replacements were systematically derived from thousands of series of bioactive compounds., Lay abstract To optimize the biological activity of small molecules in medicinal chemistry, series of analogues are generated by introducing substituents (R-groups) at different positions. The choice of R-groups largely depends on the experience of individual chemists. We have computationally isolated a large number of R-groups from currently available analogue series. Frequently used R-groups and their preferred replacements were identified and organized in a searchable database for medicinal chemists to aid in R-group selection.

Objective The incidence of ductal carcinoma in situ (DCIS) is increasing due to more widespread mammographic screening. DCIS, the earliest form of breast cancer, is non-invasive at the time of detection. If DCIS tissues are left undetected or untreated, it can spread to the surrounding breast tissue. Thus, surgical resection is the standard treatment. Understanding the mechanism underlying the non-invasive property of DCIS could lead to more appropriate medical treatments, including nonsurgical options. Data description We conducted a microarray-based genome-wide transcriptome analysis using DCIS specimens obtained by puncture from surgical specimens immediately after surgery.

Objective Reported rainfall data from multiple rain gauges and its corresponding estimate from Dual-Polarization (Dual-Pol) radar is presented here. The ordered set of data pairs were collected from multiple peer reviewed publications spanning across the last decade. Data description Taken from multiple sources, the data set represents several radar sites and rain gauge sites combined for 12,734 data points. The data is relevant in various applications of hydrometeorology and engineering as well as weather forecasting. Further, the importance of accuracy in radar precipitation estimates continues to increase, necessitating the incorporation of as much data as possible.

Objective Patients with thalassemia major (TM) have the highest mortality rate due to heart failure induced by myocardial iron overload. However, T2* weighted MR imaging is currently a gold standard approach for measuring iron overload. Examining ventricular volumes with magnetic resonance imaging (MR imaging) and measuring myocardial iron overload in TM patients allows for an early prediction of heart failure. This dataset includes cardiac MR images of TM patients and the control group with clinical and echocardiographic data. This dataset may be useful to researchers investigating myocardial iron overload. This dataset can also be used for medical image processing applications, such as ventricle segmentation. Data description This study provides open-source cardiac MR images of 50 subjects and clinical and echocardiographic data. From February 2016 to January 2019, all images and clinical data were obtained from the MRI department of a general hospital in Mashhad, Iran. All the images are 16-bit gray-scale and stored in DICOM format. All patient-specific information is removed from image headers to preserve patient privacy. In addition, all images associated with each subject are compressed and saved in the RAR format.

Objectives During the COVID-19 pandemic, most countries implemented lockdowns that motivated changes in the dietary patterns, physical activity, and body mass index (BMI) of consumers worldwide, as well as the emergence of new food marketing strategies in social media. We sought to design and validate a methodology for monitoring and evaluating the Facebook marketing strategies of multinational fast-food chains in response to the COVID-19 pandemic. Data description We developed three datasets. First, a dataset with the Uniform Resource Locators (URLs) of 1015 Facebook posts of five fast-food chains present in Argentina, Bolivia, Guatemala, and Peru. Second, a dataset of 106 content-analyzed posts we used in a pilot to determine intercoder reliability using statistical tests. Third, a dataset of a final sample of the 1015 content-analyzed posts that we used to determine the variables most frequently used. Following a mixed-methods approach, we developed 29 variables that recorded general information, as well as the marketing strategies we identified in the posts, including 14 COVID-19 specific variables. These data should help to monitor the social media marketing strategies that fast-food chains have introduced during the COVID-19 lockdowns, thus providing initial evidence about how they could be contributing to an unhealthy food environment.

Objective Navigation is the most important feature of homing pigeons, however no integrated response to genetic mechanism of navigation has been reported. The generated data herein represent whole-genome resequencing data for homing pigeon and three other breeds of rock pigeons. Selective sweep analysis between homing pigeon and other breeds of rock pigeon can provide new insight about identification of candidate genes and biological pathways for homing pigeon ability. Data description Whole-genomes sequence data related to 95 birds from four breeds of rock pigeons including, 29 feral pigeons, 24 Shiraz tumblers, 24 Persian high flyers and 18 homing pigeons were provided. More than 6.94 billion short reads with coverage (average ≈7.50 x) and 407.1 Gb data were produced. Whole genome sequencing was carried out on the Illumina Hiseq 2000 platform using a 350 bp library size and 150 bp paired-end read lengths. The whole genome sequencing data have been submitted at the NCBI SRA Database (PRJNA532675). The presented data set can provide useful genomic information to explain the genetic mechanism of navigation ability of homing pigeons and also testing other genetic hypothesis by genomic analysis.

Background The shuttles hoppfish (mudskipper), Periophthalmus modestus, is one of the mudskippers, which are the largest group of amphibious teleost fishes, which are uniquely adapted to live on mudflats. Because mudskippers can survive on land for extended periods by breathing through their skin and through the lining of the mouth and throat, they were evaluated as a model for the evolutionary sea-land transition of Devonian protoamphibians, ancestors of all present tetrapods. Results A total of 39.6, 80.2, 52.9, and 33.3 Gb of Illumina, Pacific Biosciences, 10X linked, and Hi-C data, respectively, was assembled into 1,419 scaffolds with an N50 length of 33 Mb and BUSCO score of 96.6%. The assembly covered 117% of the estimated genome size (729 Mb) and included 23 pseudo-chromosomes anchored by a Hi-C contact map, which corresponded to the top 23 longest scaffolds above 20 Mb and close to the estimated one. Of the genome, 43.8% were various repetitive elements such as DNAs, tandem repeats, long interspersed nuclear elements, and simple repeats. Ab initio and homology-based gene prediction identified 30,505 genes, of which 94% had homology to the 14 Actinopterygii transcriptomes and 89% and 85% to Pfam familes and InterPro domains, respectively. Comparative genomics with 15 Actinopterygii species identified 59,448 gene families of which 12% were only in P. modestus. Conclusions We present the high quality of the first genome assembly and gene annotation of the shuttles hoppfish. It will provide a valuable resource for further studies on sea-land transition, bimodal respiration, nitrogen excretion, osmoregulation, thermoregulation, vision, and mechanoreception.

Objectives Extensive efforts have been made to characterize the rumen microbiome under various conditions. However, few studies have addressed the long-term impacts of ruminal microbiome dysbiosis and the extent of host control over microbiome stability. These data can also inform host-microbial symbioses. The objective was to develop preliminary data to measure the changes that occur in the rumen bacterial communities following a rumen content exchange to understand the effects major perturbations may impart upon the rumen microbiome, which may be host-driven. Data description We report here an initial rumen content exchange between two SimAngus (Simmental/Angus) non-pregnant, non-lactating cows of ~ 6 years of age weighing 603.4 ± 37.5 kg. To measure bacterial community succession and acclimation following the exchange, rumen content was collected via rumen cannula at the beginning of the study immediately prior to and following the rumen content exchange, and weekly for 12 weeks. The V4 hypervariable region of the 16S rRNA gene was targeted for DNA sequencing and bacterial analysis. Over 12 weeks, numerous genera and diversity varied, before partial return to pre-exchange metrics. These preliminary data help support potential host control for the rumen microbiome, aiding in efforts to define bovine host-microbe relationships.

Objective M. morganii is a gram-negative, non-lactose fermenting and an opportunistic pathogen frequently associated with nosocomial infections. Although first isolated in 1906 from a pediatric fecal sample, not many M. morganii isolates have been sequenced. The objective of this work is to determine the complete genome sequence of an XDR M. morganii strain (SMM01) isolated from the urine of a patient with urinary and fecal incontinence and to characterize its antimicrobial resistance profile. Data description Here, we report the complete genome sequence of M. morganii SMM01 generated from the hybrid assembly of Illumina HiSeq X and Nanopore MinION reads. The assembly is 100% complete with genome size of 39,30,130 bp and GC content of 51%. Genomic features include 3617 CDS, 18 rRNAs, 78 tRNAs, 4 ncRNAs and 60 pseudogenes. Antimicrobial resistance profile was characterized by the presence of genes conferring resistance to aminoglycosides, β-lactams, fluoroquinolones, chloramphenicol, and tetracyclines. Secondary metabolite biosynthetic gene clusters like NRPS, T1PKS, thiopeptide, beta-lactone, and bacteriocin were identified. The genome data described here would be the first complete genome of an Indian M. morganii isolate providing crucial information on antimicrobial resistance patterns, paving the way for further comparative genome analyses.

Objectives Four-dimensional flow CMR allows for a comprehensive assessment of the blood flow kinetic energy of the ventricles of the heart. In comparison to standard two-dimensional image acquisition, 4D flow CMR is felt to offer superior reproducibility, which is important when repeated examinations may be required. The objective was to evaluate the inter-observer and intra-observer reproducibility of blood flow kinetic energy assessment using 4D flow of the left ventricle in 20 healthy volunteers across two centres in the United Kingdom and the Netherlands. Data description This dataset contains 4D flow CMR blood flow kinetic energy data for 20 healthy volunteers with no known cardiovascular disease. Presented is kinetic energy data for the entire cardiac cycle (global), the systolic and diastolic components, in addition to blood flow kinetic energy for both early and late diastolic filling. This data is available for reuse and would be valuable in supporting other research, such as allowing for larger sample sizes with more statistical power for further analysis of these variables.

Objectives Pistacia genus belongs to the flowering plants in the cashew family and contains at least 11 species. The whole-genome resequencing data of different species from Pistacia genus are described herein. The data reported here will be useful for better understand the adaptive evolution, demographic history, genetic diversity, population structure, and domestication of pistachio. Data description Genomic DNA was isolated from fresh leaves and used to construct libraries with insert size of 350 bp. Sequence libraries were made and sequenced on the Illumina Hiseq 4000 platform to produce 150 bp paired-end reads. A total number of 4,851,118,730 billion reads (ranging from 33,305,900 to 34,990,618 reads per sample) were created across all samples. We produced a total of 727.67 Gbp data which have been deposited in the Genome Sequence Archive (GSA) database with the Accession of CRA000978. All of the data are also available as the sequence read archive (SRA) format in the National Center for Biotechnology Information (NCBI) with identifier of SRP189222, mirroring our deposited data in GSA.

Objectives The “Integrating a neonatal healthcare package for Malawi” (IMCHA#108030) project conducted mixed-methods to understand facility-based implementation factors for newborn health innovations in low-resourced health settings. The objective of the two datasets was to evaluate: (a) capacity of quality newborn care in three districts in southern Malawi, and (b) barriers and facilitators the scale up of bubble continuous positive airway pressure (CPAP), a newborn health innovation to support babies with respiratory distress. Data description The Integrated Maternal, Neonatal and Child Quality of Care Assessment and Improvement Tool (version April-2014) is a standardized facility assessment tool developed by the World Health Organization (WHO) that examines quality as well as quantity and availability. The facility survey is complemented by a qualitative dataset of illustrative quotes from health service providers and supervisors on bubble CPAP implementation factors. Research was conducted in one primary health centre (facility assessment only), three district-level hospitals (both) and a tertiary hospital (qualitative only) in southern Malawi. These datasets may be used by other researchers for insights into health systems of low-income countries and implementation factors for the roll-out of neonatal health innovations as well as to frame future research questions or preliminary exploratory research on similar topics.