cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.35097/1821
title: Combined gridded carbonyl sulfide (OCS) dataset from MIPAS

description: :title = "OCS 60deg longitude 10deg latitude mean profiles from MIPAS single retrievals"; :institution = "Karlsruhe Institute of Technology - Institute for Meteorology and Climate Research"; :organization = "KIT/IMK-ASF"; :global_target_name = "OCS"; :source = "Satellite MIPAS on Envisat"; :type_of_data = "MEASUREMENTS"; :experiment = "MIPAS"; :platform = "SATELLITE"; :name_of_platform = "ENVISAT"; :original ungridded retrievals = "https://www.imk-asf.kit.edu/english/308.php" :data_version = "V5H_OCS_20,V5R_OCS_221,V5R_OCS_222,V5R_OCS_120"; :author = "SAT-group at KIT/IMK-ASF"; :institute = "KIT/IMK-ASF"; :address = "P.O.B. 3640, 76021 Karlsruhe, Germany"; :email = "norbert.glatthor@kit.edu, michael.hoepfner@kit.edu"; :distribution_statement = "Please follow data policy instructions for the use of this data, to be found on the data distribution site."; :references = "Glatthor et al., 2015 (https://doi.org/10.1002/2015GL066293), Glatthor et al., 2017 (https://doi.org/10.5194/acp-17-2631-2017) "; :comment = "Gridded from data which was retrieved from single scan retrievals"; :file_creation_time = "Wed Oct 9 18:31:05 2019"; :file_modification_time = " "; :file_modification_description = "negative values have been skipped for averaging";
DOI: 10.17026/dans-xrs-ycf6
title: Data from 'Rapid functional response tests for assessing impacts of alien snails on food crops'

description: In our paper 'Rapid functional response tests for assessing impacts of alien snails on food crops' (10.1016/j.ecolind.2020.107138 ), we used lab-derived data of consumption of crops by terrestrial snails to construct functional responses (FRs). The use of comparative functional response tests could give insight in the potential impact of alien herbivorous snails on agricultural crops and natural vegetation. It has been hypothesised that invasive alien snails are superior competitors for resources in comparison with common native species, due to higher attack rates and lower handling times of their food. In our study, food consumption of Cornu aspersum differed significantly for three crops: lettuce (Lactuca sativa), endive (Cichorium endivia var. latifolia) and common corn salad (Valerianella locusta). The functional responses for consumption of Lactuca sativa differed significantly between individuals collected from wild and from cultured populations of C. aspersum. Furthermore, the food consumption (in dry weight) of C. aspersum differed between tests with presence of an intraspecific and interspecific competitor (i.e., C. aspersum and Cepaea nemoralis, respectively). So, the interspecific and intraspecific competition for resources should be considered in risk assessments in order to generate more reliable impact predictions of alien snail species and to improve our understanding of their interactions with other grazers. In this repository, we provide the data of the consumption of these three different crops by Cornu aspersum originating from wild and from cultured populations . Furthermore, the data concerning the effect of a competitor on the consumption of lettuce is included.This dataset includes the following two data files:1. 'Functional_Response_All_data' includes all the data collected from functional response tests of Cornu aspersum individuals from cultured and wild populations feeding on three different type of crops.2. 'Competition_experiment_All_data' is a dataset including all the data concerning the potential impact of the presence of a competitor on lettuce consumption by Cornu aspersum.In both data sets weight and length of the snails is also provided.
DOI: 10.17026/dans-22w-ygkz
title: Dataset belonging to: Influence of photoperiod on thermal responses in body size, growth and development in Lycaena phlaeas (Lepidoptera: Lycaenidae)

description: This dataset contains raw data of adult weight, growth rate, development time, ommatidium measurements and threshold weight of small copper used for analyses and figures in the research described in: Influence of photoperiod on thermal responses in body size, growth and development in Lycaena phlaeas (Lepidoptera: Lycaenidae). (2022) by Semsar-kazerouni, Siepel, and Verberk. In this paper, we investigated how temperature and photoperiod modify body size in the small copper, and whether size responses are related to responses in growth and development, threshold weight and cell size. Details about the experimental procedures are given in the Materials and Methods section of the paper. We have also included the R scripts for data analyses in this dataset. A brief description of the data files and column descriptions can be found below.
DOI: 10.17026/dans-xnf-a6n8
title: Dataset-Psychosocial well-being needs of alcohol/drug sufferers and therapeutic architectural solutions in rehabilitation centre, Nigeria: a cross-sectional study

description: The data uploaded here describes the study result that presents a correlation between ADSs' recovery rates and a well-designed therapeutic environment. So, there is a need for evidence-based design (EBD) of rehabilitation centres with full compliments of a therapeutic architectural environment and integration of mental health services into routine care in sub-Saharan Africa.Limitations include that analyses were cross-sectional and thus may not deduce causal directions, and the authors based the result on self-report.The study was a case study of four rehabilitation centres in Nigeria’s busiest cities; Lagos, Abuja, Port Harcourt, and Enugu. The authors collected data via survey questionnaires, an in-depth interview guide, an observation guide, and a checklist of TACs in a healthcare facility.The authors interviewed twelve selected sufferers and specialists from the four (4) rehabilitation centres and Three (3) interviewees from each of the rehabilitation facilities (The 12 participants were purposively selected from the four (4) randomly selected rehabilitation facilities in the four busiest cities (Lagos, Abuja, Port-Harcourt and Enugu) across four (south-west, north-central, south-south and south-east) of the six geopolitical zones in Nigeria. The authors selected 3 out of the 12 participants from the four facilities. The three participants comprised: 1. the chief consultant, 2. a specialist nurse and 3. an alcohol drug sufferer (ADS). Therefore, three from ADRS-RC, Lagos, three (3) from NLSHRC, Abuja, three (3) from 180DC, Port Harcourt and three (3) from NPHS, Enugu total of 12 participants). Also, the study used observation guides and checklists to record data on the available TACs in the four facilities that influence the patient's psychosocial well-being. The authors used a semi-structured questionnaire to identify the psychosocial well-being needs (PWNs) of ADSs. The breakdown of the number of questionnaires administered and the responses are in table 1. The authors designed these questionnaires to be completed by the patients (ADSs).Four research assistants undertook the data gathering process for twelve weeks during the morning and evening, during weekends (Fridays to Sundays). Data collection started on July 15 and ended on September 30, 2022.
DOI: 10.17026/dans-xg9-vzpx
title: Data underlying the publication: The potential of soil amendment with insect exuviae and frass to control the cabbage root fly

description: In a set of greenhouse experiments, exuviae and frass of different insect species were added to soil. Soil was mixed with black soldier fly or mealworm exuviae in Experiment 1, with black soldier fly exuviae or frass in Experiment 2 and with house cricket exuviae or frass in Experiment 3. Exuviae and frass treatments were compared to treatments with synthetic fertilizer. Brussels sprouts plants were grown in amended soil for five weeks before being infested with cabbage root fly larvae. For Experiment 1, insect and plant performance were assessed by recording cabbage root fly survival and larval biomass and plant shoot and root biomass, respectively. In Experiments 2 and 3, cabbage root fly survival, adult fly biomass and eclosion time and seed germination and plant shoot biomass were recorded.
DOI: 10.17026/dans-xry-juty
title: Data with Facultative annual life cycles in seagrasses

description: Supplementary Information S1: Seagrasses with vegetative quiescent phases, Supplementary Information S2: Facultative annual species, Supplementary Information S3. Table with reproductive traits of Zostera marina populations, comparing annual populations with the nearest perennial population
DOI: 10.17026/dans-25z-w37w
title: Coralline algal explosion in an overgrazed seagrass meadow:coralline algal growth and cover

description: In a Mexican Caribbean Bay, a seagrass-coralline algae mutualism protects the seagrass Thalassia testudinum from green turtle overgrazing. We postulate that the state of the seagrass meadow in this bay depends on the strengths of the interactions among seagrasses, green turtles, and coralline algae. Spatio-temporal changes in coralline algae cover, growth rates under conditions mimicking seagrass presence and absence, and mortality under conditions of a well-developed coralline algal mat and not algal mat developed were performed. The grazing protection mutualism between seagrasses and coralline algae came into existence under a co-occurrence of increasing grazing pressure and rapid population growth
DOI: 10.17026/dans-z2r-8av6
title: Removing 10 cm of degraded peat mitigates unwanted effects of peatland rewetting: a mesocosm study

description: This data file is part of the scientific article that demonstrates that 5 to 10 cm of topsoil removal (TSR) may already reduce undesirable methane emissions and nutrient release of rewetting former agricultural peatlands. The two experiments ran at Radboud University facilities using peat soil cores from two sites in the Netherlands. This file includes (see codebook below for details) data obtained during the two experiments.
DOI: 10.17026/dans-xct-m758
title: Invertebrate communities across wader habitats in Europe

description: Grassland breeding waders have been steadily declining across Europe. Recent studies indicating a dramatic decline in grassland invertebrates abundance and biomass, the key food of most grassland wader chicks, suggest a likely driver of the demise of waders. While agricultural intensification is generally inferred as the main cause for arthropod decline, there is surprisingly little information on the relationship between land use intensity and total arthropod abundance in grasslands. Here, we explored those relationships across several key wader breeding habitats by surveying ground-active, aerial and soil-dwelling invertebrate communities in five European countries that range from natural undisturbed bogs to intensively managed grasslands. Using maximum vegetation growth and soil moisture content, we investigated how they shape the size of the invertebrate community within and across different countries. We found predominantly positive relationships between grassland invertebrate abundance, biomass and body weight with increasing vegetation growth and soil moisture. Maximum vegetation growth was strongly positively related to ground-active invertebrate abundance and biomass and abundance of soil-dwelling invertebrates (mainly earthworms). Body weight of aerial invertebrates furthermore increased with increasing maximum vegetation growth. Our results provide little support for the hypothesis that agricultural practices associated with intensification of grassland management result in an abundance decline of invertebrate prey for wader chicks. Conservation practices aiming to enhance wader chick survival require a careful balancing act between maintaining habitat productivity to secure high prey abundance and keeping productivity low enough to maintain open swards that do not need to be cut before chicks have fledged.
DOI: 10.17026/dans-xsv-355j
title: Wader breeding densities across European habitats

description: Wading birds can be found breeding in a myriad of habitats and ecosystems across Europe that vary widely in their land-use intensity. Over the past few decades, wader breeding populations have declined steeply in habitats ranging from natural undisturbed ecosystems to intensively managed farmland. Most conservation science has focused on factors determining local population size and trends which leave cross-continental patterns and the associated consequences for large-scale conservation strategies unexplored. Here, we review the key factors underlying population decline. We find land-use intensification in western Europe and mostly agricultural extensification and abandonment in northern, central and eastern Europe to be important drivers. Additionally, predation seems to have increased throughout the breeding range and across all habitats. Using collected breeding density data from published and grey literature, we explore habitat specificity of wader species and, of the most widely distributed species, how breeding densities change across a land-use intensity gradient. We found that two-thirds of all examined wader species have relatively narrow breeding habitat preferences, mostly in natural and undisturbed ecosystems, while the remaining species occurred in most or all habitats. The most widespread generalist species (black-tailed godwit, northern lapwing, common redshank, Eurasian oystercatcher, common snipe and ruff) demonstrated peak breeding densities at different positions along the land-use intensity gradient. To conserve both diverse wader communities and viable meta-populations of species, a diversity of habitats should be targeted ranging in land-use intensity from natural ecosystems to medium-intensity farmland. Alongside, strategies should be designed to moderate predation of wader clutches and chicks.
DOI: 10.17026/dans-xhh-8925
title: Enhancing gene regulatory networks inference through hub-based data integration

description: One of the main research topics in computational biology is Gene Regulatory Network (GRN) reconstruction that refers to inferring the relationships between genes involved in regulating cell conditions in response to internal or external stimuli. To this end, most computational methods use only transcriptional gene expression data to reconstruct gene regulatory network, but recent studies suggest that gene expression data must be integrated with other types of data to obtain more accurate models predicting real relationships between genes. In this study, a diffusion-based method is enhanced to integrate biological data of network types besides structural prior knowledge. The Random Walk with Restart algorithm (RWR) with an emphasis on hub nodes is executed separately on each network, and then jointly optimizes low-dimensional feature vectors for network nodes by diffusion component analysis. Next, these feature vectors are used to infer gene regulatory networks. Fourteen centrality measures are studied for the detection of hub nodes to be used in the RWR algorithm, and the best centrality measure having the greatest effect on the improvement of gene network inference is selected. A case study for the Saccharomyces cerevisiae and E. coli networks shows that using the proposed features in comparison with gene expression data alone results in 0.02 to 0.08 units improvement in Area Under Receiver Characteristic Operator (AUROC) criteria across different gene regulatory network inference methods. Furthermore, the proposed method was applied to the esophageal cancer data to infer its gene regulatory network. The proposed framework substantially improves accuracy and scalability of GRN inference. The fused features and the best centrality measure detected can be used to provide functional insights about genes or proteins in various biological applications. Moreover, it can be served as a general framework for network data and structural data integration and analysis problems in various scientific disciplines including biology.
DOI: 10.17026/dans-zsc-kfr7
title: Factors influencing the implementation of Home-Based Stroke Rehabilitation: professionals’ perspective

description: Semi-structured focus groups were conducted to explore the perspectives of health and social care professionals involved in stroke rehabilitation. Directed content analysis was performed to analyze the transcripts of recorded conversations.
DOI: 10.17026/dans-26p-7drn
title: Estimating fine-scale visibility in a temperate forest landscape using airborne laser scanning

description: The data set contains several tiles of ALS point cloud data which covers the scanning area of corresponding TLS point cloud data. This data set was used to estimate fine-scale visibility in a temperate forest landscape in the paper: "Estimating fine-scale visibility in a temperate forest landscape using airborne laser scanning" https://doi.org/10.1016/j.jag.2021.102478
DOI: 10.17026/dans-zxb-cyvu
title: Black-tailed Godwit abundancies across key European breeding habitats

description: he endangered continental Black-tailed Godwit (Limosa limosa limosa) is a migratory ground-nesting wader breeding in a wide variety of open, wet habitats across Europe. Conservation research has concentrated on the causes of population decline, but we know surprisingly little about whether any resources limit local breeding populations and, if so, whether these are resources for the adults or the chicks. We collected data from 63 key breeding sites in five countries across Europe to test whether, after correcting for differences in surveyed areas, the size of Godwit breeding populations was related to environmental variables (vegetation biomass, soil moisture) or food resources for adult birds (soil invertebrates) or chicks (vegetation dwelling arthropods) measured during different times of the reproductive cycle. We found the number of Godwit territories to be positively related to arthropod abundance during the chick-hatching period. We found additional, weaker support for a positive relation between Godwit territory numbers and the abundance of soil-dwelling invertebrates (mostly earthworms) at clutch laying, but not at chick-hatching. These relationships were observed across countries, while we found little support for relationships within countries, possibly due to the smaller range in conditions that exist within countries. Both vegetation growth and soil moisture weren’t related to Godwit territory numbers. Our results suggest that food abundance for chicks, and to a lesser extent adult birds, are key factors determining the size of local Godwit breeding populations. Conservation management aiming to enhance local Godwit populations should therefore consider the impacts of management strategies on the arthropod prey of chicks.
DOI: 10.17026/dans-z9t-zhpu
title: Analyse dose response for gene expression and phenotype

description: The rise of high-throughput methods has allowed for screens with millions of single compounds and thousands of (binary) compound combinations. Investigating compounds in combination is cost and labor intensive. This has motivated recent investigations to predict synergistic combinations from information of the compound targets, the known pathways and the gene expression response to single compounds. Even though these predictive models are reasonably successful (AUCs around 0.9), there is room for improvement. Importantly, these models are often evaluated with data sets collected for other purposes. In particular, there exists currently no large-scale data set of molecular events underlying synergy. Such data would allow for an improvement of synergy prediction from molecular data in terms of model validation and development. The L1000 platform has proven to be a powerful tool for gene expression based hypothesis generation and small molecule screening. The assay has been used extensively to investigate the transcriptional signatures of small molecule perturbations, but there is not yet a well-validated experimental workflow for studying compounds in combination. We combined a cell-viability readout with an L1000-based gene expression readout on a diverse set of compounds.We implemented the code to fit dose-response curves to L1000 data and phenotype readouts such as from a Cell-Titer Glow assay or Incucyte. The code contains many visualization tools to visualize the plate-layout of 384 well plates, fit dose-response curves of the drc or GRdrc of L1000 or phenotype data, apply outlier detection based on GAMs or dr4pl method, and other functions useful for the analysis of cell viability data and gene expression.This code was generated for the analyses conducted in "Lederer, S., Lyons, N., Dijkstra, (unpublished). 'Investigating Compound Interactions - from Gene Expression to Phenotype', unpubished work"
DOI: 10.17026/dans-zj5-3pfq
title: PROFILES registry: Quality of life non-Hodgkin lymphoma May 2010

description: The PROFILES registry offers scientific data in the area of medical psychology and more specific on quality of life of cancer survivors. The PROFILES registry is open to academics anywhere in the world for scientific purposes, free of charge. The archive can be found on the following website: http://www.profilesregistry.nlIn 2010 a questionnaire has been composed treating the subjects health-related quality of life, use of health care and satisfaction with care in patients who had been diagnosed with non-Hodgkin lymphoma.The questionnaire was submitted to 655 patients who were diagnosed with non-Hodgkin lymphoma between 1999 and 2009. 508 patients completed the questionnaire.Questionnaires used:- General Questions- Work- Lifestyle- Activities- Cancer and Care- Comorbidity- Work- Insurance- EORTC-QLQ-C30 (version 3)- EORTC-disease specific lymfoom (CLL)(in development)- FAS- HADS- IOC1/IOC2/IOC1+items2
DOI: 10.17026/dans-2bd-ufvk
title: Toward co-design of an AI solution for detection of diarrheal pathogens in drinking water within resource-constrained contexts

description: Water images
DOI: 10.17026/dans-z8a-7p5p
title: Safe-by-Design: Stakeholders' perceptions and expectations of how to deal with risks of emerging biotechnologies

description: Advanced gene editing techniques such as CRISPR/Cas have increased the pace of developments in the field of industrial biotechnology. Such techniques imply new possibilities when working with living organisms, possibly leading to uncertain risks. In the Netherlands, current policy fails to address these uncertain risks because risk classification is determined process-wise (i.e. GMO and non-GMO), there is a strong focus on quantifiable risks, and the linearity within current governance (science – policy – society) hinders iterative communication between stakeholders, leaving limited room to anticipate uncertainties at an early stage of development. A suggested concept to overcome these shortcomings is the Safe-by-Design (SbD) approach, which, theoretically, allows stakeholders to iteratively incorporate safety measures throughout a technology’s development process, creating a more dynamic environment for the anticipation of uncertain risks. Although this concept originates from chemical engineering and is already widely applied in nanotechnology, for the field of biotechnology, there is no agreed upon definition (yet). To explore the possibilities of SbD for future governance of biotechnology, we should gain insight in how various stakeholders perceive notions of risk, safety and inherent safety, and what this implies for the applicability of SbD for risk governance in industrial biotechnology in the Netherlands. Our empirical research reveals three main themes: (1) diverging expectations with regard to safety and risks, and to establishing an acceptable level of risk; (2) different applications of SbD and inherent safety, namely product- and process-wise; and (3) unclarity in allocating responsibilities to stakeholders in the development process of a biotechnology and within society.