cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3712903
title: Link to dataset related to article "Dissection of acute stimulus-inducible nucleosome remodeling in mammalian cells"

description: Accessibility of the genomic regulatory information is largely controlled by the nucleosome-organizing activity of transcription factors (TFs). While stimulus-induced TFs bind to genomic regions that are maintained accessible by lineage-determining TFs, they also increase accessibility of thousands of <em>cis</em>-regulatory elements. Nucleosome remodeling events underlying such changes and their interplay with basal positioning are unknown. Here, we devised a novel quantitative framework discriminating different types of nucleosome remodeling events in micrococcal nuclease ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) data sets and used it to analyze nucleosome dynamics at stimulus-regulated <em>cis</em>-regulatory elements. At enhancers, remodeling preferentially affected poorly positioned nucleosomes while sparing well-positioned nucleosomes flanking the enhancer core, indicating that inducible TFs do not suffice to overrule basal nucleosomal organization maintained by lineage-determining TFs. Remodeling events appeared to be combinatorially driven by multiple TFs, with distinct TFs showing, however, different remodeling efficiencies. Overall, these data provide a systematic view of the impact of stimulation on nucleosome organization and genome accessibility in mammalian cells.
DOI: 10.5281/zenodo.3713039
title: Dataset related to article "Serum IFI16 and anti-IFI16 antibodies in psoriatic arthritis."

description: Nuclear interferon-inducible protein 16 (IFI16) and anti-IFI16 antibodies have been detected in subjects with several rheumatic diseases, often correlating with disease severity, and in this study we investigated their prevalence and clinical associations in psoriatic arthritis (PsA) compared to psoriasis (Pso). We tested sera and synovial fluids of patients with PsA for IFI16 protein levels by capture enzyme-linked immunosorbent assay (ELISA) and for anti-IFI16 immunoglobulin (Ig)G and IgA by ELISA, protein radio-immunoprecipitation and immunoprecipitation-Western blot of IgG. Sera from patients with Pso and healthy subjects were used as controls, and in a subgroup of patients with PsA we also studied sera after treatment with etanercept. IFI16 was detectable in the sera of 66% of patients with Pso, 46% with PsA and 19% of controls. Among PsA cases, 51% of IFI16-positive cases had elevated levels of C-reactive protein (CRP) compared to 31% of patients with undetectable IFI16. Anti-IFI16 of both IgG and IgA isoforms were detected with significantly higher frequency in PsA and Pso compared to healthy controls, with higher IgG titres in patients with elevated C-reactive protein (CRP) (P = 0·015). Immunoprecipitation confirmed the presence of anti-IFI16 IgG antibodies and these preferentially recognized epitopes outside the N-terminus of the protein. Lastly, IFI16 was detected in one of seven and anti-IFI16 in three of seven synovial fluids from patients with PsA. Therefore, IFI16 and anti-IFI16 are detectable in serum and synovial fluid of PsA patients, especially in cases of elevated CRP.
DOI: 10.5281/zenodo.3713040
title: Dataset related to article "Serum IFI16 and anti-IFI16 antibodies in psoriatic arthritis."

description: Nuclear interferon-inducible protein 16 (IFI16) and anti-IFI16 antibodies have been detected in subjects with several rheumatic diseases, often correlating with disease severity, and in this study we investigated their prevalence and clinical associations in psoriatic arthritis (PsA) compared to psoriasis (Pso). We tested sera and synovial fluids of patients with PsA for IFI16 protein levels by capture enzyme-linked immunosorbent assay (ELISA) and for anti-IFI16 immunoglobulin (Ig)G and IgA by ELISA, protein radio-immunoprecipitation and immunoprecipitation-Western blot of IgG. Sera from patients with Pso and healthy subjects were used as controls, and in a subgroup of patients with PsA we also studied sera after treatment with etanercept. IFI16 was detectable in the sera of 66% of patients with Pso, 46% with PsA and 19% of controls. Among PsA cases, 51% of IFI16-positive cases had elevated levels of C-reactive protein (CRP) compared to 31% of patients with undetectable IFI16. Anti-IFI16 of both IgG and IgA isoforms were detected with significantly higher frequency in PsA and Pso compared to healthy controls, with higher IgG titres in patients with elevated C-reactive protein (CRP) (P = 0·015). Immunoprecipitation confirmed the presence of anti-IFI16 IgG antibodies and these preferentially recognized epitopes outside the N-terminus of the protein. Lastly, IFI16 was detected in one of seven and anti-IFI16 in three of seven synovial fluids from patients with PsA. Therefore, IFI16 and anti-IFI16 are detectable in serum and synovial fluid of PsA patients, especially in cases of elevated CRP.
DOI: 10.5257/unesco/edulit/2020-02
title: Education Statistics (February 2020 Edition)

description: With the adoption of the Sustainable Development Goals (SDGs), the UIS has been recognised as the official source of cross-nationally comparable data on education, as confirmed in the Education 2030 Framework for Action. The UIS has been given the mandate to work with partners to develop new indicators, statistical approaches and monitoring tools to better assess progress across the targets related to UNESCO's mandate, working in coordination with the Education 2030 Steering Committee.
DOI: 10.17632/nwr2j4pbhz.1
title: Data for: Consumer sentiment and time-varying betas: Testing the validity of the consumption CAPM on the Johannesburg Stock Exchange

description: Using all stocks listed in the Johannesburg Stock Exchange and macroeconomic data for South Africa, the dataset comprises the following series: 1. Monthly returns for 6 size-asset growth portfolios, following the Fama and French (1993) methodology. (Raw data source: Datastream database) 2. Monthly returns for 6 size-return on assets portfolios, following the Fama and French (1993) methodology. (Raw data source: Datastream database) 3. Monthly returns for 10 size-price to cash flow portfolios, following the Fama and French (1993) methodology. (Raw data source: Datastream database) 4. Monthly returns for 15 book-to-market equity portfolios, following the Fama and French (1993) methodology. (Raw data source: Datastream database) 5. Consumer Confidence Index (CCI) for South Africa. (Raw data source: OECD) 6. Private final consumption expenditure, in national currency and constant prices, non-seasonally adjusted, for South Africa. (Raw data source: OECD) 7. Fama and French (1993) factors (RM, SMB and HML), following the Fama and French (1993) methodology. (Raw data source: Datastream database) 8. Fama and French (2015) factors (RM, SMB, HML, RMW, and CMA), following the Fama and French (2015) methodology. (Raw data source: Datastream database) 9. Three-month interest rate of the Treasury Bill for South Africa. (Raw data source: OECD) We have produced all return series using the following data from Datastream: (i) total return index (RI series), (ii) market value (MV series), (iii) market-to-book equity (PTBV series), (iv) return on equity (WC08301 series), (v) total assets (WC02999 series), (vi) price-to-cash flow ratio (PC series), and (vii) tax rate (WC08346 series). We have used the generic rules suggested by Griffin, Kelly, & Nardari (2010) for excluding non-common equity securities from Datastream data. REFERENCES: Fama, E. F. and French, K. R. (1993). Common risk factors in the returns on stocks and bonds. Journal of Financial Economics, 33, 3–56. Fama, E. F. and French, K. R. (2015). A five-factor asset pricing model. Journal of Financial Economics, 116, 1–22. Griffin, J. M., Kelly, P., and Nardari, F. (2010). Do market efficiency measures yield correct inferences? A comparison of developed and emerging markets. Review of Financial Studies, 23, 3225–3277.
DOI: 10.25345/c52h6k
title: MassIVE MSV000085109 - A DNA-guided Argonaute Protein Functions in DNA Replication in Thermus thermophilus
title: In many eukaryotes, Argonaute proteins, guided by short RNA sequences, defend cells against transposons and viruses. In the eubacterium Thermus thermophilus, the DNA-guided Argonaute TtAgo defends against transformation by DNA plasmids. Here, we report that TtAgo also participates in DNA replication. In vivo, TtAgo binds 15-18 nt DNA guides derived from the chromosomal region where replication terminates and associates with proteins known to act in DNA replication. When gyrase, the sole T. thermophilus type II topoisomerase, is inhibited, TtAgo allows the bacterium to finish replicating its circular genome. In contrast, loss of both gyrase and TtAgo activity slows growth and produces long sausage-like filaments in which the individual bacteria are linked by DNA. Finally, wild-type T. thermophilus outcompetes an otherwise isogenic strain lacking TtAgo. We propose that the primary role of TtAgo is to help T. thermophilus disentangle the catenated circular chromosomes generated by DNA replication.
DOI: 10.17632/d79vb52nwd.4
title: Barrier database (AMBER-GB) for: A comprehensive assessment of stream fragmentation in Great Britain

description: Artificial barriers are one of the main threats to river ecosystems, resulting in habitat fragmentation and loss of connectivity. Yet, the abundance and distribution of most artificial barriers, excluding high head dams, is poorly documented. We provide a global assessment of the distribution and typology of artificial barriers in Great Britain, and estimate for the first time the extent of river fragmentation. To this end, barrier data were compiled from existing databases and were ground truthed by field surveys in England, Scotland and Wales to derive a correction factor for barrier density across Great Britain. Field surveys indicate that existing barrier databases underestimate barrier density by 68%, particularly in the case of low-head structures (&lt;1 m) which are often missing from current records. Field-corrected barrier density estimates ranged from 0.48 barriers/km in Scotland to 0.63 barriers/km in Wales, and 0.75 barriers/km in England. Corresponding estimates of stream fragmentation, measured as mean barrier-free length, were 12.30 km in Scotland, 6.68 km in Wales and 5.29 km in England, reflecting different anthropogenic pressures. Our study indicates that 97% of the river network in Great Britain is fragmented and none of the rivers are free of artificial barriers. Update. Version 3. Data added from OSM Dams and GOOD2 following the same method. GOOD2: 65 dams OSM: 47 dams, 1 weir New total 23731 barriers.
DOI: 10.17632/zfp6nzy87w.1
title: Potential benefits of Reverse Blending: A case study of the fertilizer industry

description: These data represent the dataset used for the study of Reverse Blending impact on the production system of a leading fertilizer producer.
DOI: 10.6073/pasta/238742e7d0297f52185376f25cf2a3e7
title: North Temperate Lakes LTER: Macrophyte Rating - Madison Lakes Area 1995 - current

description: Aquatic macrophytes are sampled from a boat at stations located at depths from 1 to 4 meters at 0.5-m intervals along transects perpendicular to the lake shoreline of the four primary study lakes in the Madison area (Lakes Mendota, Monona, and Wingra, and Fish Lake) from June to August. A weighted, double-headed garden rake is cast off the front left, front right, rear left, and rear right of the boat and then dragged approximately 2 meters across the bottom by means of an attached line. For each rake cast, filamentous algae and any aquatic macrophyte species present are assigned a density rating from 0-5 based on the extent of coverage of the upper rake head. Determination of extent of coverage involves judgment of the surveyor as to the number of rake teeth and area of teeth covered by each species. It is necessary to separate plants to assess individual species coverage. Ratings from the 4 rake casts at each station can be averaged to compute an overall density rating for each species found at the station.1 to 4 meters at 0.5-m intervals along transects perpendicular to the lake shoreline of the four primary study lakes in the Madison area (Lakes Mendota, Monona, and Wingra, and Fish Lake) from June to August. A weighted, double-headed garden rake is cast off the front left, front right, rear left, and rear right of the boat and then dragged approximately 2 meters across the bottom by means of an attached line. In addition (see related data set: Macrophyte Weight --- Madison Lakes Area), the total plant mass and the total filamentous algae mass in each tow is measured. To the maximum extent possible, water is squeezed from the plants to minimize the amount of water present in the final weight. Weights are recorded in the boat using field scales. Weights from the 4 rake casts at each station can be averaged to compute overall average weights for plant mass and for filamentous algae mass at the station. Sampling Frequency: annually during summer Number of sites: 4
DOI: 10.14469/hpc/6993
title: Reversed phase chromatography mass-spectrometry (negative mode) in urine

description: reversed-phase chromatography (denoted R in NPC assays) targets small moderately polar molecules, ionised in negative mode
DOI: 10.17632/8d4p844ryd.1
title: Influence of CDKAL1 expression on the survival of patients with non-metastatic nasopharyngeal carcinoma
DOI: 10.17632/yrb99wgpsc.2
title: Turnout and Territorial Reform: Data from Submunicipal governments in Portugal

description: data from the national electoral commission and from the National Institute of Statistics.
DOI: 10.17632/c84p4nhtvm.1
title: Data Repository for "Influence of effective stress and pore fluid pressure on fault strength and slip localization in calcite gouges"

description: This dataset contains the experimental data found in the manuscript entitled "Influence of effective stress and pore fluid pressure on fault strength and slip localization in calcite gouges". The data is ordered according to the figures and tables in which they are found. Each folder containing the data includes a readme file describing the content of the files as well.
DOI: 10.5281/zenodo.3712918
title: Mass spectrometry data for interactive volcano plots - van der Weegen et al., 2020

description: These datasets are generated by Yana van der Weegen et al. (2020) and part of the publication "The sequential and cooperative action of CSB, CSA and UVSSA targets the TFIIH complex to DNA damage-stalled RNA polymerase II" to be published in Nature Communications. The CSV files are used as input to generate (interactive) volcano plots, using the web app VolcanoNoseR. The code is archived here: https://zenodo.org/record/3625858 The most up-to-date version of the interactive web app is available here: https://huygens.science.uva.nl/VolcaNoseR/
DOI: 10.5281/zenodo.3712919
title: Mass spectrometry data for interactive volcano plots - van der Weegen et al., 2020

description: These datasets are generated by Yana van der Weegen et al. (2020) and part of the publication "The sequential and cooperative action of CSB, CSA and UVSSA targets the TFIIH complex to DNA damage-stalled RNA polymerase II" to be published in Nature Communications. The CSV files are used as input to generate (interactive) volcano plots, using the web app VolcanoNoseR. The code is archived here: https://zenodo.org/record/3625858 The most up-to-date version of the interactive web app is available here: https://huygens.science.uva.nl/VolcaNoseR/
DOI: 10.5066/p93z8uy7
title: National Water Model V2.0 retrospective for selected NWIS gage locations (1993-2018)

description: This dataset contains modeled hourly streamflow in cubic meters per second at each of about eighteen thousand selected operational and water-quality stream gage locations. It was assembled from publicly available retrospective V2.0 National Water Model outputs. The streamflow variable was extracted from model output files and the data were reshaped to optimize read performance. The stream gage locations were derived from several ongoing USGS project gages for evaluation of streamflow, water quality, and real-time monitoring, however only National Water Model identifiers and NHDPlus catchment outlet locations are used to identify model results. Relationships between NWIS gages and National Water Model prediction locations were not reviewed for release at the time of publication of this data. Please contact the author for up to date information. All processing resources used for data reformatting and extraction can be found in this repository: https://code.usgs.gov/water/nwm_subset. This supporting code also contains Docker images that are capable of processing real-time National Water Model outputs into similar formats as this dataset and provide data services via the THREDDS Data Server. The retrospective is available in one NetCDF file. These data conform to the NetCDF-CF Discrete Sampling Geometry conventions. The retrospective data are available from public cloud data outlets (Such as: https://registry.opendata.aws/nwm-archive/). More information on these data are available from the National Water Model v2 release notes here. https://www.weather.gov/media/notification/scn19-42natl_water_model.pdf. The contents of that pdf have been archived with this dataset.
DOI: 10.5281/zenodo.3713255
title: Traceability Solutions for Supporting Intermingled-Bilingual Artifacts

description: Bilingual software engineering dataset for issues and commits
DOI: 10.5281/zenodo.3713256
title: Traceability Solutions for Supporting Intermingled-Bilingual Artifacts

description: Bilingual software engineering dataset for issues and commits
DOI: 10.5281/zenodo.3713092
title: Study replicability dataset 1

description: This dataset contains all data collected to conduct the studies on Chapter 2 and 5 of Ph.D. thesis "Augmented fine-grained defect prediction for code review" Bug prediction is aimed at identifying software artifacts that are more likely to be defective in the future. Most approaches defined so far target the prediction of bugs at class/file level. Nevertheless, past research has provided evidence that this granularity is too coarse-grained for its use in practice. As a consequence, researchers have started proposing defect prediction models targeting a finer granularity (particularly method-level granularity), providing promising evidence that it is possible to operate at this level. Particularly, models mixing product and process metrics provided the best results. We present a study in which we first replicate previous research on method-level bug-prediction, by using different systems and timespans. Afterwards, based on the limitations of existing research, we (1) re-evaluate method-level bug prediction models more realistically and (2) analyze whether alternative features based on textual aspects, code smells, and developer-related factors can be exploited to improve method-level bug prediction abilities. Key results of our study include that (1) the performance of the previously proposed models, tested using the same strategy but on different systems/timespans, is confirmed; but, (2) when evaluated with a more practical strategy, all the models show a dramatic drop in performance, with results close to that of a random classifier. Finally, we find that (3) the contribution of alternative features within such models is limited and unable to improve the prediction capabilities significantly. As a consequence, our replication and negative results indicate that method-level bug prediction is still an open challenge.
DOI: 10.5281/zenodo.3713174
title: Mass spectrometry data for interactive volcano plots - by van der Weegen et al.

description: These datasets are generated by Yana van der Weegen et al. (2020) and part of the publication "The sequential and cooperative action of CSB, CSA and UVSSA targets the TFIIH complex to DNA damage-stalled RNA polymerase II" to be published in Nature Communications. The CSV files are used as input to generate (interactive) volcano plots, using the web app VolcanoNoseR. The code is archived here: https://zenodo.org/record/3625858 The most up-to-date version of the interactive web app is available here: https://huygens.science.uva.nl/VolcaNoseR/
DOI: 10.5281/zenodo.3712941
title: Dataset related to article "Oocyte Cryopreservation in Oncological Patients: Eighteen Years Experience of a Tertiary Care Referral Center."

description: <strong>Objective:</strong> The aim of the present study is to report our experience on elective women fertility preservation before cancer treatment. <strong>Study Design:</strong> This is a single-center retrospective observational study, including all patients who underwent elective fertility preservation before oncological treatment between January 2001 and March 2019 at our Institute. <strong>Results:</strong> Of a total of 568 women who received fertility counseling, 244 (42.9%) underwent 252 oocyte retrieval cycles after controlled ovarian stimulation for cryopreservation. The majority of patients were diagnosed with breast cancer (59.9%), followed by women affected by Hodgkin's and non-Hodgkin's lymphoma (27.4%). A minority comprised patients diagnosed with other malignancies that affected soft tissues (2.8%), ovary borderline type (2.4%), digestive system (1.6%), leukemia (1.6%), uterine cervix (1.2%). The remaining 3.1% were affected by other cancer types. The mean age of the cohort was 31.3 ± 6.4 years and the mean oocyte retrieval was 13.5± 8.4. Of 11 women who returned to attempt a pregnancy, three performed two thawed cycles. We obtained four pregnancies from 24 embryo transfers (Pregnancy Rate 36.4% for couple): two miscarriages and two live births. Overall, 95.7% of oocytes are still in storage. <strong>Conclusions:</strong> A close collaboration between Cancer and Fertility Center in a tertiary care hospital is essential to provide a good health service in oncological patients. Offering fertility preservation is no longer considered optional and must be included in every therapeutic program for women who receive an oncological diagnosis in their reproductive age. Oocyte cryopreservation appears to be a good opportunity for fertility preservation. Our results, although they are obtained in a small sample, are encouraging, even if only 4.5% of patients returned to use their gametes.