cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4542577
title: Supplementary Material for: Differential T-Helper Cell Polarization after Allergen-Specific Stimulation of Autologous Dendritic Cells in Polysensitized Allergic Patients

description: <b><i>Background:</i></b> Dendritic cells (DCs) play an important role in the induction and regulation of adaptive immune responses by polarizing T-helper (Th) cells. In allergic disease this response is dominated by Th2 cells. It is still unclear whether the activation of Th cells by DCs in atopic individuals is allergen specific. <b><i>Methods:</i></b> Monocyte-derived DCs (MoDCs) obtained from polysensitized patients were stimulated with purified Bet v 1, Phl p 5 and Act d 10, and the surface marker expression was analysed. Proliferation and cytokine profiles of autologous naïve CD4+ T cells co-cultured with allergen-pulsed MoDCs were assessed. <b><i>Results:</i></b> The addition of either Bet v 1 or Phl p 5 did not further increase the expression of surface markers from matured MoDCs in all study groups. In co-cultures, autologous naïve CD4+ T cells proliferated when DCs obtained from individuals allergic to birch and grass pollen were stimulated with Bet v 1 and Phl p 5, respectively. In the co-culture supernatants, significantly increased levels of IL-5 and IL-13 were detected. This effect correlated with the sensitization background and was absent when applying an unspecific allergen, Act d 10. The levels of IL-10 in supernatants of MoDCs and the levels of IL-10 and IFN-γ in supernatants of T cells remained unchanged upon stimulation with allergens. <b><i>Conclusions:</i></b> In this study we observed that allergen-specific stimulation of MoDCs induces T-cell proliferation and upregulation of Th2-type cytokines. Interestingly, this Th2 polarization was only observed in cells stimulated with the allergen to which the patients were sensitized.
DOI: 10.6084/m9.figshare.4542709.v5
title: Toward a Smell-aware Bug Prediction Model

description: Code smells are symptoms of poor design and implementation choices. Previous studies empirically assessed the impact of smells on code quality and clearly indicate their negative impact on maintainability, including a higher bug-proneness of components affected by code smells. In this paper, we capture previous findings on bug-proneness to build a specialized bug prediction model for smelly classes. Specifically, we evaluate the contribution of a measure of the severity of code smells (i.e., code smell intensity) by adding it to existing bug prediction models based on both product and process metrics, and comparing the results of the new model against the baseline models. Results indicate that the accuracy of a bug prediction model increases by adding the code smell intensity as predictor. We also compare the results achieved by the proposed model with the ones of an alternative technique which considers metrics about the history of code smells in files, finding that our model works generally better. However, we observed interesting complementarities between the set of buggy and smelly classes correctly classified by the two models. By evaluating the actual information gain provided by the intensity index with respect to the other metrics in the model, we found that the intensity index is a relevant feature for both product and process metrics-based models. At the same time, the metric counting the average number of code smells in previous versions of a class considered by the alternative model is also able to reduce the entropy of the model. On the basis of this result, we devise and evaluate a smell-aware combined bug prediction model that included product, process, and smell-related features. We demonstrate how such model classifies bug-prone code components with an F-Measure at least 13% higher than the existing state-of-the-art models.
DOI: 10.6084/m9.figshare.4542562
title: Patient empowerment: a systematic review of questionnaires measuring empowerment in cancer patients

description: <b>Background:</b> There is an increased attention to and demand for patient empowerment in cancer treatment and follow-up programs. Patient empowerment has been defined as feeling in control of or having mastery in relation to cancer and cancer care. This calls for properly developed questionnaires assessing empowerment from the user perspective. The aim of this review was to identify questionnaires and subscales measuring empowerment and manifestations of empowerment among cancer patients. <b>Materials and methods:</b> We conducted a systematic search of the PubMed, PsycINFO and CINAHL databases. Empowerment and multiple search terms associated with empowerment were included. We included peer-reviewed articles published in English, which described questionnaires measuring empowerment or manifestations of empowerment in a cancer setting. In addition, the questionnaire had to be a patient-reported outcome measure for adult cancer patients. <b>Results:</b> Database searches identified 831 records. Title and abstract screening resulted in 482 records being excluded. The remaining 349 full text articles were retrieved and assessed for eligibility. This led to the inclusion of 33 individual instruments measuring empowerment and manifestations of empowerment. Of these, only four were specifically developed to measure empowerment, and two were originally developed for the cancer setting, whereas the remaining two were developed elsewhere, but adapted to the cancer setting. The other 29 questionnaires were not intended to measure the concept of empowerment, but focused on patient-centered care, patient competence, self-efficacy, etc. However, they were included because part of the instrument (at least five items) was considered to measure empowerment or manifestations of empowerment. <b>Conclusion:</b> Our study provides an overview of the available questionnaires, which can be used by researchers and practitioners who wish to measure the concept of empowerment among cancer patients. Very few questionnaires were explicitly developed to explore empowerment, and the review brings to light a significant lack of questionnaires that measure patient empowerment comprehensively.
DOI: 10.6084/m9.figshare.4542562.v1
title: Patient empowerment: a systematic review of questionnaires measuring empowerment in cancer patients

description: <b>Background:</b> There is an increased attention to and demand for patient empowerment in cancer treatment and follow-up programs. Patient empowerment has been defined as feeling in control of or having mastery in relation to cancer and cancer care. This calls for properly developed questionnaires assessing empowerment from the user perspective. The aim of this review was to identify questionnaires and subscales measuring empowerment and manifestations of empowerment among cancer patients. <b>Materials and methods:</b> We conducted a systematic search of the PubMed, PsycINFO and CINAHL databases. Empowerment and multiple search terms associated with empowerment were included. We included peer-reviewed articles published in English, which described questionnaires measuring empowerment or manifestations of empowerment in a cancer setting. In addition, the questionnaire had to be a patient-reported outcome measure for adult cancer patients. <b>Results:</b> Database searches identified 831 records. Title and abstract screening resulted in 482 records being excluded. The remaining 349 full text articles were retrieved and assessed for eligibility. This led to the inclusion of 33 individual instruments measuring empowerment and manifestations of empowerment. Of these, only four were specifically developed to measure empowerment, and two were originally developed for the cancer setting, whereas the remaining two were developed elsewhere, but adapted to the cancer setting. The other 29 questionnaires were not intended to measure the concept of empowerment, but focused on patient-centered care, patient competence, self-efficacy, etc. However, they were included because part of the instrument (at least five items) was considered to measure empowerment or manifestations of empowerment. <b>Conclusion:</b> Our study provides an overview of the available questionnaires, which can be used by researchers and practitioners who wish to measure the concept of empowerment among cancer patients. Very few questionnaires were explicitly developed to explore empowerment, and the review brings to light a significant lack of questionnaires that measure patient empowerment comprehensively.
DOI: 10.6084/m9.figshare.4542454
title: Relationship between the molecular mass of cryoprotectants and weights of fresh (FM) and dry matter (DM) of empty beads of potato

description: Relationship between the molecular mass of cryoprotectants and weights of fresh (FM) and dry matter (DM) of empty beads of potato
DOI: 10.6084/m9.figshare.4542454.v1
title: Relationship between the molecular mass of cryoprotectants and weights of fresh (FM) and dry matter (DM) of empty beads of potato

description: Relationship between the molecular mass of cryoprotectants and weights of fresh (FM) and dry matter (DM) of empty beads of potato
DOI: 10.6084/m9.figshare.4542436
title: Diversity, distribution, and conservation of lizards (Reptilia: Squamata) in the Brazilian Amazonia

description: In the last decades research efforts studying Amazonian biodiversity have increased substantially, with many new localities surveyed, new specimens collected, and some new regional collections established. In our study, we revised, updated, and summarized the available data on the diversity, distribution, species richness, and conservation status of lizards from the Brazilian Amazonia. We recorded 138 species-level taxa of lizards in the Brazilian Amazonia that presented five general patterns of distribution, plus some cases of unique distributions. Species richness is unevenly distributed across the region, varying between one and 44 species in a single grid, with 37–44 species in the richest areas. Based on the overlap of occurrence area of each species with protected areas (strict nature reserves; managed resource protected areas; protected indigenous peoples’ territories) and deforested layers, we show that 58% of the analyzed species (<i>n</i> = 75) present more than 50% of their occurrence area outside of any protected area, and 20% (<i>n</i> = 26) of them present 33% or less occurrence in protected areas. Strict nature reserves (strictly protected areas) are responsible for the main protection (≥50% of the protected area) of only 3% of the species (<i>n</i> = 4). Indigenous peoples’ territories represent the main protection area for 31% of the species (<i>n</i> = 40). Ten species present more than 50% of their occurrence in area deforested, and for 12 species the range varied between 33 and 50% of habitat loss. Revising the International Union for Conservation of Nature conservation status categories for a regional assessment, three species were classified as EN (Endangered), six as VU (Vulnerable), and 15 as NT (Near Threatened). Species with occurrence in Southern Amazonia are the most threatened. We presented the core areas for conservation of species richness and discussed their conservation status. Habitat loss due to mechanized agriculture (mainly from soy plantation), pastures, fire, and infrastructure project (e.g. roads and hydroelectric dams) are the main threats to the lizard fauna. Southern Amazonia is the region with the highest human pressure and, at the same time, it is the least protected. We suggest a revision to the mosaic of interconnected conservation areas, mainly in Southern Amazonia, and recommend that new infrastructure projects in the region take preventive actions to mitigate the direct and indirect impacts on the local lizard fauna.
DOI: 10.6084/m9.figshare.4542433
title: Journal subscription expenditure in the UK 2015-16

description: This dataset contains payments made by UK higher education institutions for access to academic journals from eight publishers in 2015 and 2016. The data was obtained by sending Freedom of Information requests to 153 institutions through the website whatdotheyknow.com.<br><br>The total expenditure on these eight publishers in 2016 was £103m.<br><br>* Updated 24 January 2017 with data for five institutions.<br>* Updated 20 February 2017 with data for nine institutions.<br>* Updated 19 April 2017 with data for two institutions.<br>* Updated 26 April 2017 after checking all figures for inclusion of VAT and currency conversion from EUR to GBP.<br>* Updated 9 May 2017 with figures for Elsevier expenditure by University of Leeds. <br>
DOI: 10.6084/m9.figshare.4542439
title: Raw_data_all_ISI_rats.mat

description: Stimulation response data from all animals used in this study.
DOI: 10.6084/m9.figshare.4542436.v1
title: Diversity, distribution, and conservation of lizards (Reptilia: Squamata) in the Brazilian Amazonia

description: In the last decades research efforts studying Amazonian biodiversity have increased substantially, with many new localities surveyed, new specimens collected, and some new regional collections established. In our study, we revised, updated, and summarized the available data on the diversity, distribution, species richness, and conservation status of lizards from the Brazilian Amazonia. We recorded 138 species-level taxa of lizards in the Brazilian Amazonia that presented five general patterns of distribution, plus some cases of unique distributions. Species richness is unevenly distributed across the region, varying between one and 44 species in a single grid, with 37–44 species in the richest areas. Based on the overlap of occurrence area of each species with protected areas (strict nature reserves; managed resource protected areas; protected indigenous peoples’ territories) and deforested layers, we show that 58% of the analyzed species (<i>n</i> = 75) present more than 50% of their occurrence area outside of any protected area, and 20% (<i>n</i> = 26) of them present 33% or less occurrence in protected areas. Strict nature reserves (strictly protected areas) are responsible for the main protection (≥50% of the protected area) of only 3% of the species (<i>n</i> = 4). Indigenous peoples’ territories represent the main protection area for 31% of the species (<i>n</i> = 40). Ten species present more than 50% of their occurrence in area deforested, and for 12 species the range varied between 33 and 50% of habitat loss. Revising the International Union for Conservation of Nature conservation status categories for a regional assessment, three species were classified as EN (Endangered), six as VU (Vulnerable), and 15 as NT (Near Threatened). Species with occurrence in Southern Amazonia are the most threatened. We presented the core areas for conservation of species richness and discussed their conservation status. Habitat loss due to mechanized agriculture (mainly from soy plantation), pastures, fire, and infrastructure project (e.g. roads and hydroelectric dams) are the main threats to the lizard fauna. Southern Amazonia is the region with the highest human pressure and, at the same time, it is the least protected. We suggest a revision to the mosaic of interconnected conservation areas, mainly in Southern Amazonia, and recommend that new infrastructure projects in the region take preventive actions to mitigate the direct and indirect impacts on the local lizard fauna.
DOI: 10.6084/m9.figshare.4542418
title: New draft item

description: The raw values behind graphs, statistical averages, or figures presented in the study of Evaluation of complex toxicity of canbon nanotubes and sodium pentachlorophenol based on earthworm coelomocytes test were uploaded to a stable public repository Figshare as required.
DOI: 10.6084/m9.figshare.4542439.v1
title: Raw_data_all_ISI_rats.mat

description: Stimulation response data from all animals used in this study.
DOI: 10.6084/m9.figshare.4542418.v2
title: New draft item

description: The raw values behind graphs, statistical averages, or figures presented in the study of Evaluation of complex toxicity of canbon nanotubes and sodium pentachlorophenol based on earthworm coelomocytes test were uploaded to a stable public repository Figshare as required.
DOI: 10.6084/m9.figshare.4542418.v1
title: New draft item

description: The raw values behind graphs, statistical averages, or figures presented in the study of Evaluation of complex toxicity of canbon nanotubes and sodium pentachlorophenol based on earthworm coelomocytes test were uploaded to a stable public repository Figshare as required.
DOI: 10.6084/m9.figshare.4542433.v1
title: Journal subscription expenditure in the UK 2015-16

description: *Note: this is a work in progress - the data is not yet complete and may contain inaccuracies regarding the inclusion of VAT. Please check original sources on whatdotheyknow.com before quoting individual figures*<br><br>This dataset contains payments made by UK higher education institutions for access to academic journals from eight publishers in 2015 and 2016. The data was obtained by sending Freedom of Information requests to 153 institutions through the website whatdotheyknow.com.<br><br>The current total expenditure on these eight publishers in 2016 is £95m.<br>
DOI: 10.6084/m9.figshare.4542405
title: A GPU-Based Solution to Fast Calculation of Betweenness Centrality on Large Weighted Networks

description: We develop an efficient parallel GPU-based approach to boost the calculation of betweenness centrality on very large and weighted networks. Comprehensive and systematic evaluations on both synthetic and real-world networks demonstrate that our solution can arrive the performance of 30x to 150x speedup over the CPU implementation by integrating the work-efficient and warp-centric strategies. <br>READMEThis program compute node or edge betweenness centrality on weighted networks.<br>Graph formatThe first line has two columns, the first item is the number of nodes and the second one is the number of edges. The following lines are weighted edges that contain three columns. The first two items are the node pair and the last item is the weight of the link. One edge appears only once, e.g., if "0 1 0.5" is in the file, the edge "1 0 0.5" must not show up. You can find an example file named "graph.txt".Installation:<br>We use "tclap" as the command line tool which should be installed in the first step. Then you can compile BC.cu and main.cu to get the executable program.You can run the executable program without params to see the usage document.<br>
DOI: 10.6084/m9.figshare.4542433.v2
title: Journal subscription expenditure in the UK 2015-16

description: *Note: this is a work in progress - the data is not yet complete and may contain inconsistencies regarding the inclusion of VAT. Please check original sources on whatdotheyknow.com before quoting individual figures*<br><br>This dataset contains payments made by UK higher education institutions for access to academic journals from eight publishers in 2015 and 2016. The data was obtained by sending Freedom of Information requests to 153 institutions through the website whatdotheyknow.com.<br><br>The current total expenditure on these eight publishers in 2016 is £99m.<br><br>* Updated 24 January 2017 with data for five new institutions.<br>
DOI: 10.6084/m9.figshare.4542433.v3
title: Journal subscription expenditure in the UK 2015-16

description: *Note: this is a work in progress - the data is not yet complete and may contain inconsistencies regarding the inclusion of VAT. Please check original sources on whatdotheyknow.com before quoting individual figures*<br><br>This dataset contains payments made by UK higher education institutions for access to academic journals from eight publishers in 2015 and 2016. The data was obtained by sending Freedom of Information requests to 153 institutions through the website whatdotheyknow.com.<br><br>The current total expenditure on these eight publishers in 2016 is £101m.<br><br>* Updated 24 January 2017 with data for five institutions.<br>* Updated 20 February 2017 with data for nine institutions.
DOI: 10.6084/m9.figshare.4542433.v4
title: Journal subscription expenditure in the UK 2015-16

description: *Note: this is a work in progress - the data is not yet complete and may contain inconsistencies regarding the inclusion of VAT. Please check original sources on whatdotheyknow.com before quoting individual figures*<br><br>This dataset contains payments made by UK higher education institutions for access to academic journals from eight publishers in 2015 and 2016. The data was obtained by sending Freedom of Information requests to 153 institutions through the website whatdotheyknow.com.<br><br>The current total expenditure on these eight publishers in 2016 is £102m.<br><br>* Updated 24 January 2017 with data for five institutions.<br>* Updated 20 February 2017 with data for nine institutions.<br>* Updated 19 April 2017 with data for two institutions.<br>
DOI: 10.6084/m9.figshare.4542433.v5
title: Journal subscription expenditure in the UK 2015-16

description: This dataset contains payments made by UK higher education institutions for access to academic journals from eight publishers in 2015 and 2016. The data was obtained by sending Freedom of Information requests to 153 institutions through the website whatdotheyknow.com.<br><br>The total expenditure on these eight publishers in 2016 was £102m.<br><br>* Updated 24 January 2017 with data for five institutions.<br>* Updated 20 February 2017 with data for nine institutions.<br>* Updated 19 April 2017 with data for two institutions.<br>* Updated 26 April 2017 after checking all figures for inclusion of VAT and currency conversion from EUR to GBP.<br>
DOI: 10.6084/m9.figshare.4541776
title: TP53.sorted.bed

description: BED formatTP53
DOI: 10.6084/m9.figshare.4541725
title: CosmicCodingMuts.chr.sort.head.vcf

description: COSMICv77VCF file of all coding mutations in the current release.<br>
DOI: 10.6084/m9.figshare.4541776.v1
title: TP53.sorted.bed

description: BED formatTP53
DOI: 10.6084/m9.figshare.4541725.v1
title: CosmicCodingMuts.chr.sort.head.vcf

description: COSMICv77VCF file of all coding mutations in the current release.<br>
DOI: 10.6084/m9.figshare.4541632
title: Orion Scores

description: The Orion scores in BED files for all autosomal chromosomes, across the portion of the non-repetitive genome that was covered in our sample. Coordinates are in hg19. The scores were compressed using bgzip and specific coordinates can be extracted using tabix (http://www.htslib.org/doc/tabix.html).