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Quality of relationship between partners is associated with a wide range of physical and psychological outcomes like anxiety and depression. There are relatively few longitudinal studies with detailed and repeated measures for quality of relationship, particularly in both partners. The Avon Longitudinal Study of Parents and Children (ALSPAC) is a large birth cohort study in the UK with five post-partum repeated measures of quality of relationship between mothers and their partners assessed using the Intimate Bond Measure (IBM). The Measure includes two subscales named “Care” and “Control”. These were measured at 2.75, 6, 9, 12, and 18 years post-partum (baseline N for mothers: 8675; baseline N for partners: 5499). The aims of this data note are to provide a comprehensive overview on the existing IBM data in ALSPAC and to describe both its strengths and limitations for future users. The internal consistency of the subscales were high (Cronbach's alpha 0.95 and 0.88 for the Care and Control subscales) in both mothers and their partners at the baseline. In the Care subscale, all 12 items were highly correlated with the overall score (r>0.62) at the baseline, but in the Control subscale there were three items that had relatively low correlations with the total subscale (r

application/pdf, Objectives:Haemaphysalis longicornis is the most important tick species in Japan and has a wide range of vector capacity. Due to its veterinary and medical importance, this tick species has been used as a model for tick/vector biological studies. To identify the key molecules associated with physiological processes during blood feeding and embryogenesis, full‑length cDNA libraries were constructed using the fat body, hemocytes‑containing hemolymph, midgut, ovary and salivary glands of fed females and embryos of the laboratory colony of parthenogenetic H. longi-cornis. The sequences of cDNA from the salivary glands had been already released. However, the related information is still poor, and the other expressed sequence tags have not yet been deposited.Data description:A total of 39,113 expressed sequence tags were obtained and deposited at the DNA DataBank of Japan. There were 7745 sequences from embryos, 7385 from the fat body, 8303 from the hemolymph including hemocytes, 7385 from the midgut, and 8295 from the ovary. The data, including expressed sequence tags from the salivary glands was summarized into Microsoft Excel files. Sharing this data resource with the tick research community will be valuable for the identification of novel genes and advance the progress of tick research., Explanation of these data Data file 1_ESTs_Hl_Fat Body (Umemiya-Shirafuji et al.) (http://doi.org/10.24556/00004700) Data file 2_ESTs_Hl_Hemolymph (Umemiya-Shirafuji et al.) (http://doi.org/10.24556/00004701) Data file 3_ESTs_Hl_Midgut (Umemiya-Shirafuji et al.) (http://doi.org/10.24556/00004702) Data file 4_ESTs_Hl_Ovary (Umemiya-Shirafuji et al.) (http://doi.org/10.24556/00004703) Data file 5_ESTs_Hl_Salivary glands (Umemiya-Shirafuji et al.) (http://doi.org/10.24556/00004704) Data file 6_ESTs_Hl_Embryo (Umemiya-Shirafuji et al.) (http://doi.org/10.24556/00004705)

During the past decade, it became clear that the electric field elicited by non-invasive brain stimulation (NIBS) techniques such as transcranial direct current stimulation (tDCS) and transcranial magnetic stimulation (TMS) are substantially influenced by variations in individual head and brain anatomy. In addition to structural variations in the healthy, several psychiatric disorders are characterized by anatomical alterations that are likely to further constrain the intracerebral effects of NIBS. Here, we present high-resolution realistic head models derived from structural magnetic resonance imaging data of 19 healthy adults and 19 patients diagnosed with major depressive disorder (MDD). By using a freely available software package for modelling the electric fields induced by different NIBS protocols, we show that our head models are well-suited for assessing inter-individual and between-group variability in the magnitude and focality of tDCS-induced electric fields for two protocols targeting the left dorsolateral prefrontal cortex.

ObjectiveIn March 2020, Iran tackled the first national wave of COVID-19 that was particularly felt in Mashhad, Iran’s second-most populous city. Accordingly, we performed a spatio-temporal study in this city to investigate the epidemiological aspects of the disease in an urban area and now wish to release a comprehensive dataset resulting from this study.Data descriptionThese data include two data files and a help file. Data file 1: “COVID-19_Patients_Data” contains the patient sex and age + time from symptoms onset to hospital admission; hospitalization time; co-morbidities; manifest symptoms; exposure up to 14 days before admission; disease severity; diagnosis (with or without RT-PCR assay); and outcome (recovery vs. death). The data covers 4000 COVID-19 patients diagnosed between 14 Feb 2020 and 11 May 2020 in Khorasan-Razavi Province. Data file 2: “COVID-19_Spatiotemporal_Data” is a digital map of census tract divisions of Mashhad, the capital of the province, and their population by gender along with the number of COVID-19 cases and deaths including the calculated rates per 100,000 persons. This dataset can be a valuable resource for epidemiologists and health policymakers to identify potential risk factors, control and prevent pandemics, and optimally allocate health resources.

Objectives Arachnids have fascinating and unique biology, particularly for questions on sex differences and behavior, creating the potential for development of powerful emerging models in this group. Recent advances in genomic techniques have paved the way for a significant increase in the breadth of genomic studies in non-model organisms. One growing area of research is comparative transcriptomics. When phylogenetic relationships to model organisms are known, comparative genomic studies provide context for analysis of homologous genes and pathways. The goal of this study was to lay the groundwork for comparative transcriptomics of sex differences in the brain of wolf spiders, a non-model organism of the pyhlum Euarthropoda, by generating transcriptomes and analyzing gene expression. Data description To examine sex-differential gene expression, short read transcript sequencing and de novo transcriptome assembly were performed. Messenger RNA was isolated from brain tissue of male and female subadult and mature wolf spiders (Schizocosa ocreata). The raw data consist of sequences for the two different life stages in each sex. Computational analyses on these data include de novo transcriptome assembly and differential expression analyses. Sample-specific and combined transcriptomes, gene annotations, and differential expression results are described in this data note and are available from publicly-available databases.

Objectives Bombyx mori is the key contributor to industrial silk production. The maximum production of silk occurs during 5th instar. The posterior silk glands in the larvae are responsible for the production of the main component of silk fibre—fibroin. The expression of genes and their regulation are dependent on the chromatin architecture. The nuclear matrix supports its structure and function by anchoring specific regions to regulate gene expression. The major constituent of the nuclear matrix, crucial to its structural and temporal maintenance, is its RNA. Therefore, the study of nuclear matrix RNA of the posterior silk glands on different days of 5th instar larval development is essential to understand its association to differential expression of genes. Data description The tissue-specific developmental association of nuclear matrix RNA (NuMat RNA) at the genome level has not been done so far for any organism. Bombyx mori, CSR2 X CSR4 is the most popular dihybrid strain in India. The nuclear matrix RNA was isolated from day 1, day 5 and day 7 of 5th instar posterior silk glands of Bombyx mori. The NuMat RNA was sequenced using Illumina platform. The reads obtained were processed and the datasets were deposited in NCBI.

Objectives Assessing the likelihood of success of induction of labour using cervical volume is an important research question. Data description We provide data generated in a prospective observational study which was carried out at North Colombo Teaching Hospital, Ragama, Sri Lanka. Study conducted to compare pre-induction digital cervical assessment, sonographic cervical length, and sonographic cervical volume with vaginal delivery rate within 24 h. Inductions with 100 singleton pregnancies at term were included.

Objectives The “Bolsa-Família” Program (PBF) is a Brazilian conditional cash-transfer program in which families should comply with health, education, and social assistance conditionalities. The program aims to fight poverty and hunger, promoting nutrition and health services for low-income populations. This paper presents a database on the coverage of monitoring and compliance with the PBF health conditionalities in Brazil from January 2005 to July 2021. Data description Database on the PBF conditioning cash-transfer program coverage in Brazil from 2005 to 2021. It comprises information on the number of families benefited, health conditionalities, and the follow-up on vaccination and nutrition of children under seven years old. The cities and semesters are the minimal aggregation units.

Indexado en Scopus Data on gender representation in food and beverage advertisements may allow for a better understanding of how the food industry is targeting different audiences based on gender. Nonetheless, scant research on food and beverage print advertising with a gender approach has been conducted. Therefore, we sought to assess the prevalence of gender focus in print advertisements found inside corner stores in two cities: Guatemala City, Guatemala, and Lima, Peru. Data description: We developed two complementary datasets as part of the study: (1) a dataset of digital photographs of 200 food and beverage print advertisements found in corner stores located near schools (100 ads per country selected according to criteria such as product type, image quality, and uniqueness); (2) a quantitative dataset with data of the content analysis of these photographs. We employed 19 variables to record the general information and gender assessment of the ads. These datasets should allow scholars and public officials to identify gender-specific marketing strategies of the food industry that might impact children’s and adolescents’ nutrition differently. Los datos sobre la representación de género en los anuncios de alimentos y bebidas pueden permitir una mejor comprensión de cómo la industria alimentaria se dirige a diferentes audiencias en función del género. No obstante, se han realizado escasas investigaciones sobre publicidad impresa de alimentos y bebidas con enfoque de género. Por lo tanto, buscamos evaluar la prevalencia del enfoque de género en los anuncios impresos que se encuentran dentro de las tiendas de la esquina en dos ciudades: Ciudad de Guatemala, Guatemala y Lima, Perú. Descripción de los datos: Desarrollamos dos conjuntos de datos complementarios como parte del estudio: (1) un conjunto de datos de fotografías digitales de 200 anuncios impresos de alimentos y bebidas que se encuentran en tiendas de esquina ubicadas cerca de las escuelas (100 anuncios por país seleccionados de acuerdo con criterios como el tipo de producto, calidad de imagen y singularidad); (2) un conjunto de datos cuantitativos con datos del análisis de contenido de estas fotografías. Empleamos 19 variables para registrar la información general y la valoración de género de los anuncios. Estos conjuntos de datos deberían permitir a académicos y funcionarios públicos identificar estrategias de marketing específicas de género de la industria alimentaria que podrían afectar la nutrición de niños y adolescentes de manera diferente. info:eu-repo/semantics/publishedVersion Revisión por pares

Objectives This data article aims to introduce the “XPolaris” R-package, designed to facilitate access to detailed soil data at any geographical location within the contiguous United States (CONUS). Without the need of advanced R-programming skills, XPolaris enables users to convert raster data from the POLARIS database into traditional spreadsheet format [i.e., Comma-Separated Values (CSV)] for further data analyses. Data description The core of this publication is a code-tutorial envisioned to assist users in retrieving soil raster data within the CONUS. All data is sourced from the POLARIS database, a 30-m probabilistic map of soil series and different soil properties [Chaney et al. Geoderma 274:54, 2016, Chaney et al. Water Resour Res 55:2916, 2019]. POLARIS represents an optimization of the Soil Survey Geographic (SSURGO) database, circumventing issues of spatial disaggregation, harmonizing, and filling spatial gaps. POLARIS was constructed using a machine learning algorithm, the Disaggregation and Harmonisation of Soil Map Units Through Resampled Classification Trees (DSMART-HPC) [Odgers et al. Geoderma 214:91, 2014]. Although the data is easily accessible in a raster format, retrieving large amounts of data can be time-consuming or require advanced programming skills.

Objective Passalora sequoiae (family Mycosphaerellaceae) causes a twig blight on Leyland cypress that requires numerous fungicide applications annually to minimize economic losses for ornamental plant nursery and Christmas tree producers. The objective was to generate a high-quality draft assembly of the genome of P. sequoiae as a resource for primer development to investigate genotype diversity. Data description We report here the genome sequence of P. sequoiae 9LC2 that was isolated from Leyland cypress ‘Leighton Green’ in 2017 in southern Mississippi, USA. The draft genome was obtained using Pacific Biosciences (PacBio) SMRT and Illumina HiSeq 2500 sequencing. Illumina reads were mapped to PacBio assembled contigs to determine base call consistency. Based on a total of 44 contigs with 722 kilobase (kb) average length (range 9.4 kb to 3.4 Mb), the whole genome size was estimated at 31,768,716 bp. Mapping of Illumina reads to PacBio contigs resulted in a 1000 × coverage and were used to confirm accuracy of the consensus sequences.

Objectives Genome sequences are a vital resource for accelerating the biological exploration of an organism of interest. Pythium destruens (a synonym of Pythium insidiosum) causes a difficult-to-treat infectious disease called pythiosis worldwide. Detection and management of pythiosis are challenging. Basic knowledge of the disease is lacking. Genomes of this organism isolated from different continents (i.e., Asia and the Americas) have been sequenced and publicly available. Here, we sequenced the genome of an Australian isolate of P. destruens. Genome data will facilitate the comparative analysis of this and related species at the molecular level. Data description Genomic DNA of the P. destruens strain ATCC 64221, isolated from a horse with pythiosis in Australia, was used to prepare one paired-end library (with 180-bp insert) for next-generation sequencing, using the Illumina HiSeq 2500 short-read platform. Raw reads were cleaned and assembled by several bioinformatics tools. A total of 20,860,454 processed reads, accounted for 2,614,890,553 total bases, can be assembled into a 37.8-Mb genome, consisting 13,060 contigs (average length: 2896 bases; range: 300–142,967), N50 of 11,370 bases, and 2.9% ‘N’ composition. The genome was determined 85.9% completeness, contained 14,424 predicted genes, and can be retrieved online at the NCBI/DDBJ databases under the accession number BCFQ01000000.1.

Objectives Advanced tools and resources are needed to efficiently and sustainably produce food for an increasing world population in the context of variable environmental conditions. The maize genomes to fields (G2F) initiative is a multi-institutional initiative effort that seeks to approach this challenge by developing a flexible and distributed infrastructure addressing emerging problems. G2F has generated large-scale phenotypic, genotypic, and environmental datasets using publicly available inbred lines and hybrids evaluated through a network of collaborators that are part of the G2F’s genotype-by-environment (G × E) project. This report covers the public release of datasets for 2014–2017. Data description Datasets include inbred genotypic information; phenotypic, climatic, and soil measurements and metadata information for each testing location across years. For a subset of inbreds in 2014 and 2015, yield component phenotypes were quantified by image analysis. Data released are accompanied by README descriptions. For genotypic and phenotypic data, both raw data and a version without outliers are reported. For climatic data, a version calibrated to the nearest airport weather station and a version without outliers are reported. The 2014 and 2015 datasets are updated versions from the previously released files [1] while 2016 and 2017 datasets are newly available to the public.

This data note describes a unique two-step methodology to construct six linked datasets covering the sequencing of Saccharomyces cerevisiae, Homo sapiens, and Sus scrofa genomes. The datasets were used as evidence in a project that investigated the history of genomic science. To design the datasets, we first retrieved all sequence submission data from the European Nucleotide Archive (ENA), including accession numbers associated with each of our three species. Second, we used these accession numbers to construct queries to retrieve peer-reviewed scientific publications that first described these sequence submissions in the scientific literature. For each species, this resulted in two associated datasets: 1) A .csv file documenting the PMID of each article describing new sequences, all paper authors, all institutional affiliations of each author, countries of institution, year of first submission to the ENA (when available), and the year of article publication, and 2) A .csv file documenting all institutions submitting to the ENA, number of nucleotides sequenced and years of submission to the database. We utilised these datasets to understand how institutional collaboration shaped sequencing efforts, and to systematically identify important institutions and changes in the structure of research communities throughout the history of genomics and across our three target species. This data note, therefore, should aid researchers who would like to use these data for future analyses by making the methodology that underpins it transparent. Further, by detailing our methodology, researchers may be able to utilise our approach to construct similar datasets in the future.

Objectives To measure depressive severity of 85 Thai adolescents by using the the Beck Depression Inventory-II and the Patient Health Questionnaire-9 and to record the resting-state EEG of these participants. Data description The current data note provides raw data of behavioral (i.e., group, BDI-II score, and PHQ-9 score) and electrophysiological parameters (i.e., absolute and relative EEG powers over 64 electrode sites) of 30, 27, and 28 participants with minimal, mild, and moderate depression, respectively. These data are especially useful to investigate the behavioral and electrophysiological markers of adolescents with subclinical depression. It can also be utilized in comparative analysis among age groups, and races.

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 Information was collected to identify anxiety in dental patients visiting a dental clinic using the Dental Anxiety Scale, their level of psychological distress using the Brief Symptom Inventory-18 and identifying a correlation between these groups as well as the gender and age. Data description This data contains a set of 1550 patients’ answers to questionnaires taken before dental treatment in a dental clinic. It is divided into male and female patients as well as according to their age. The level of Dental Anxiety can be interpreted by answers chosen in the Dental Anxiety Scale (DAS) and the level of psychological distress by answers chosen in the Brief Symptom Inventory-18 (BSI-18). This dataset should help to encourage more research in the field of dental anxiety and we hope to see more comparisons with our data in the future or in different regions of the world.

Objectives Black Bengal goat (Capra hircus), a member of the Bovidae family with the unique traits of high prolificacy, skin quality and low demand for food is the most socioeconomically significant goat breed in Bangladesh. Furthermore, the aptitude of adaptation and disease resistance capacity of it is highly notable which makes its whole genome information an area of research interest. Data description The genomic DNA of a local (Chattogram, Bangladesh) healthy male Black Bengal goat (Capra hircus) was extracted and then sequenced. Sequencing was completed using the Illumina HiSeq 2500 sequencing platform and the draft assembly was generated using the “ARS1” genome as the reference. MAKER gene annotation pipeline was utilized to annotate 26,458 gene models. Genome completeness was assessed using BUSCO (Benchmarking Universal Single-Copy Orthologs) which showed 82.5% completeness of the assembled genome.

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.

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.

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 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.

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.

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.

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).

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 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.

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.

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.

Objectives Respiratory tract diseases (RTDs) are among the top five leading causes of death worldwide. Mortality rates due to respiratory tract diseases (MRRTDs) follow a spatial pattern and this may suggest a potential link between environmental risk factors and MRRTDs. Spatial analysis of RTDs mortality data in an urban setting can provide new knowledge on spatial variation of potential risk factors for RTDs. This will enable health professionals and urban planners to design tailored interventions. We aim to release the datasets of MRRTDs in the city of Tehran, Iran, between 2008 and 2018. Data description The Research data include four datasets; (a) mortality dataset which includes records of deaths and their attributes (age, gender, date of death and district name where death occurred), (b) population data for 22 districts (age groups with 5 years interval and gender by each district). Furthermore, two spatial datasets about the city are introduced; (c) the digital boundaries of districts and (d) urban suburbs of Tehran.

Objective Nuclear Factor One X (NFIX) is a transcription factor expressed by neural stem cells within the developing mouse brain and spinal cord. In order to characterise the pathways by which NFIX may regulate neural stem cell biology within the developing mouse spinal cord, we performed an microarray-based transcriptomic analysis of the spinal cord of embryonic day (E)14.5 Nfix−/− mice in comparison to wild-type controls. Data description Using microarray and differential gene expression analyses, we were able to identify differentially expressed genes in the spinal cords of E14.5 Nfix−/− mice compared to wild-type controls. We performed microarray-based sequencing on spinal cords from n = 3 E14.5 Nfix−/− mice and n = 3 E14.5 Nfix+/+ mice. Differential gene expression analysis, using a false discovery rate (FDR) p-value of p ± 1.5, revealed 1351 differentially regulated genes in the spinal cord of Nfix−/− mice. Of these, 828 were upregulated, and 523 were downregulated. This resource provides a tool to interrogate the role of this transcription factor in spinal cord development.

Objective Labeo catla (catla), one of the three Indian major carps, is native to the Indo-Gangetic riverine system of India as well as the rivers of Pakistan, Bangladesh, Nepal and Myanmar. Its higher growth rate and compatibility with other major carps, specific surface feeding habit, and consumer preference have increased its popularity in carp polyculture systems among the fish farmers in Indian subcontinent. Recent advancement in sequencing technology coupled with massive parallel sequencing platforms has facilitated accelerated genetic improvement in aquaculture species through integration of genomics tools. A draft genome and allied resources are lacking in catla. Therefore, in the present study, we have performed de-novo assembly of Labeo catla for the first time. Data description A male farm reared catla was used for extracting high molecular weight genomic DNA followed by sequencing in Oxford Nanopore and Illumina platforms. Approximately, 80× coverage of sequence data was assembled adopting the hybrid assembly strategy. The assembled genome size of catla was 1.01 Gb containing 5345 scaffolds with N50 value 0.7 Mb and more than 92% BUSCO completeness. Gene annotation resulted in 25,812 predicted genes.

Objectives The genus Bacillus comprises spore-forming rod-shaped Gram-positive bacteria, which usually grow aerobically or anaerobically. Members of this genus are common environmental microorganisms. Also, they can be monitored in the food production chain. Genome sequence of Bacillus sp. strain EE-W1 will provide helpful information to understand its ecology and genetics. Draft genome data may be useful in the field of using Bacillus species in industrial biotechnology. Also, these data can be a useful resource for the study of comparative genomics. Data description Here, we present the draft genome sequence of Bacillus sp. strain EE-W1 isolated from a biogas reactor, Kazan, Russia. The assembled genome size was 5,769,164 bp, with a GC content 35.1%. This draft genome data can be accessed at DDBJ/ENA/GenBank under the accession WIPE00000000.

Objectives In the bovine placenta, intimate fetomaternal contact is restricted to placentomes. Within the placentomes fetal chorionic villi interdigitate with corresponding maternal caruncular crypts. The trophoblast epithelium covering the chorionic villi consists of 80% uninucleate trophoblast cells (UTCs) and 20% trophoblast giant cells (TGCs). TGCs migrate toward the endometrium and fuse with endometrial cells to form short-lived fetomaternal hybrid cells. Thereby the TGCs transport molecules of fetal origin across the placental barrier into the maternal compartment. The UTC/TGC ratio is constant during pregnancy because UTCs can differentiate into new TGCs to replace spent TGCs. However, our understanding of this differentiation process was sparse. Therefore, we collected the data to study the gene expression profiles in UTCs and TGCs and to identify differently expressed genes between the two trophoblast cell populations. Using Gene Ontology analysis, we wanted to identify biological processes and pathways that play an important role in the differentiation of UTCs into TGCs. Data description Bovine placentas were from days 118 to 130 of gestation. We obtained virtually pure UTCs and TGCs using a fluorescence-activated cell sorting (FACS) method. Total RNA was extracted from the UTC and TGC isolates, labeled and hybridized to Affymetrix Bovine Gene 1.0 ST Arrays.

Objectives Text classification is a recurrent goal in machine learning projects and a typical task in crowdsourcing platforms. Hybrid approaches, leveraging crowdsourcing and machine learning, work better than either in isolation and help to reduce crowdsourcing costs. One way to mix crowd and machine efforts is to have algorithms highlight passages from texts and feed these to the crowd for classification. In this paper, we present a dataset to study text highlighting generation and its impact on document classification. Data description The dataset was created through two series of experiments where we first asked workers to (i) classify documents according to a relevance question and to highlight parts of the text that supported their decision, and on a second phase, (ii) to assess document relevance but supported by text highlighting of varying quality (six human-generated and six machine-generated highlighting conditions). The dataset features documents from two application domains: systematic literature reviews and product reviews, three document sizes, and three relevance questions of different levels of difficulty. We expect this dataset of 27,711 individual judgments from 1851 workers to benefit not only this specific problem domain, but the larger class of classification problems where crowdsourced datasets with individual judgments are scarce.

Objectives Salmonella bacteria can induce the unfolded protein response, a cellular stress response to misfolding proteins within the endoplasmic reticulum. Salmonella can exploit the host unfolded protein response leading to enhanced bacterial replication which was in part mediated by the induction and/or enhanced endo-reticular membrane synthesis. We therefore wanted to establish a quantitative confocal imaging assay to measure endo-reticular membrane expansion following Salmonella infections of host cells. Data description High-content screening confocal fluorescence microscopic image set of Salmonella infected HeLa cells is presented. The images were collected with a PerkinElmer Opera LX high-content screening system in seven 96-well plates, 50 field-of-views and DAPI, endoplasmic reticulum tracker channels and Salmonella mCherry protein in each well. Totally 93,300 confocal fluorescence microscopic images were published in this dataset. An ImageJ high-content image analysis workflow was used to extract features. Cells were classified as infected and non-infected, the mean intensity of endoplasmic reticulum tracker under Salmonella bacteria was calculated. Statistical analysis was performed by an R script, quantifying infected and non-infected cells for wild-type and ΔsifA mutant cells. The dataset can be further used by researchers working with big data of endoplasmic reticulum fluorescence microscopic images, Salmonella bacterial infection images and human cancer cells.

Objectives Transcription of eukaryotic protein-coding genes by RNA polymerase II (pol II) is highly regulated at initiation, elongation and termination. Transcription is also coordinated with co-transcriptional processing of the emerging pre-mRNA by capping, splicing, and cleavage and polyadenylation. Polyadenylation (poly(A)) site recognition, which defines the end of the mRNA, relies on the cleavage and polyadenylation (CPA) complex. It was previously observed that knocking-down proteins of the CPA complex affects not only recognition of the poly(A) site but also results in increased pausing of pol II at the beginning of genes. This finding suggests that the CPA complex plays a role in regulating pol II turnover after transcription initiation. Data description To explore this possibility, we knocked-down a subunit of the cleavage factor I (CFIm), CFIm68, which is part of the CPA complex and involved in alternative polyadenylation, and performed pol II ChIP-seq in absence or presence of a transcription elongation inhibitor. In addition, we performed pol II ChIP-qPCR on a subset of protein coding genes after knocking down CFIm68.

Objective: The objective of this experiment was to identify transcripts in baker’s yeast (Saccharomyces cerevisiae) that could have originated from previously non-coding genomic regions, or de novo. We generated this data to be able to compare the transcriptomes of different species of Ascomycota. Data description: We generated high-depth RNA sequencing data for 11 species of yeast: Saccharomyces cerevisiae, Saccharomyces paradoxus, Saccharomyces mikatae, Saccharomyces kudriavzevii, Saccharomyces bayanus, Naumovia castelii, Kluyveromyces lactis, Lachancea waltii, Lachancea thermotolerans, Lachancea kluyveri, and Schizosaccharomyces pombe. Using RNA-Seq from yeast grown in rich and oxidative conditions we created genome-guided de novo assemblies of the transcriptomes for each species. We included synthetic spike-in transcripts in each sample to determine the lower limit of detection of the sequencing platform as well as the reliability of our de novo transcriptome assembly pipeline. We subsequently compared the de novo transcripts assemblies to the reference gene annotations and generated assemblies that comprised both annotated and novel transcripts. The work was funded by the following grants: (1) BFU2015-65235-P Ministerio de Economía e Innovación (Spanish Government)-FEDER (EU). (2) BFU2015-68351-P Ministerio de Economía e Innovación (Spanish Government)-FEDER (EU). (3) MDM-2014-0370 “Maria de Maeztu” Programme for Units of Excellence in R&D (Spanish Government). (4) 2017SGR1054 Agència de Gestió d’Ajuts Universitaris i de Recerca Generalitat de Catalunya. (5) 2017SGR01020 Agència de Gestió d’Ajuts Universitaris i de Recerca Generalitat de Catalunya. (6) Predoctoral fellowship (FI, Generalitat de Catalunya) to WRB. Grants 1, 3 and 4 were used to cover lab expenses and to obtain the RNA samples from yeast cultures. Grants 2 and 5 were used for RNA sequencing. Grant 6 covered the salary of WRB. These funding bodies had no role in the design of the study, collection of the data, analysis of the results, or writing of the manuscript.

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.