cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10260737.v1
title: Supplementary Material for: Enhancer of Zeste Homolog 2 in Colorectal Cancer Development and Progression

description: <b><i>Background:</i></b> Colorectal cancer (CRC) is the leading gastrointestinal malignancy. The development from premalignant intraepithelial lesions leading to invasive cancer is paradigmatic for the stepwise carcinogenesis of epithelial cancers, but the knowledge of the underlying mechanism of carcinogenesis and progression of CRC is still incomplete. The understanding of epigenetic mechanisms of carcinogenesis has led to new therapeutic approaches during the last years. <i>Enhancer of zeste homolog 2</i> (EZH2) is one central epigenetic silencer of the <i>polycomb repressor complex 2</i> (PRC2) that is already in clinical use as a novel drug target and is associated with poorer prognosis in several cancer entities. <b><i>Patients and Methods:</i></b> The protein expression of EZH2 and other members of the PRC2 as well as resulting posttranslational modifications were investigated by immunohistochemistry in 187 patients with CRC and in 94 patients with premalignant colorectal lesions and correlated with their clinical outcome. Furthermore, the corresponding mRNA expression levels were analyzed in 217 patients with rectal cancer that were enrolled in a prospective clinical trial. <b><i>Results:</i></b> We found a weak expression of EZH2 in normal colon mucosa that increased in low grade, peaked in high grade intraepithelial neoplasia, and decreased again in invasive CRC. The posttranslational modification caused by EZH2 as a measure of EZH2 activity showed the same behavior. Strong protein and mRNA expression of EZH2 were significantly correlated with favorable prognosis in both investigated cohorts. <b><i>Conclusion:</i></b> The expression and activity of EZH2 are associated with colorectal carcinogenesis and most expressed in intraepithelial high-grade lesions. Strong expression of EZH2 is associated with a significantly favorable prognosis in patients suffering from CRC.
DOI: 10.6084/m9.figshare.10260740.v2
title: Metadata record for: Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies

description: This dataset contains key characteristics about the data described in the Data Descriptor Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format<br><br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.10261016.v3
title: The new kid on the block: Immigrant males win big whereas females pay fitness cost after dispersal - data

description: The <b>data and code </b>for residents and immigrants (successful dispersers) and their offspring using 29 years of monitoring from North American red squirrels (<i>Tamiasciurus hudsonicus</i>) in Yukon, Canada. Data obtained with funding from the Natural Sciences and Engineering Council of Canada, Northern Scientific Training Program, and the National Science Foundation.<br><br>Published. <b>Martinig, A. R.</b>, A. G. McAdam, B. Danzter, J. E. Lane, D. W. Coltman, & S. Boutin. 2019.<i> </i>The new kid on the block: Immigrant males win big whereas females pay fitness cost after dispersal. Ecology Letters 23:430–438.<br>
DOI: 10.6084/m9.figshare.10260740.v1
title: Metadata record for: Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies

description: This dataset contains key characteristics about the data described in the Data Descriptor Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.10260710.v1
title: Supplementary Material for: Clinical Characteristics and Antifungal Susceptibility of <b><i>Candida nivariensis</i></b> from Vulvovaginal Candidiasis

description: <b><i>Objectives:</i></b> The aim of this work is to evaluate the susceptibility profile of the isolates against antifungal drugs and the level of virulent genes and resistant genes mRNA expression of <i>Candida nivariensis</i>. <b><i>Methods:</i></b> We analyzed a collection of 9 <i>C. nivariensis</i> isolates from clinical isolates of <i>Candida glabrata</i> complex isolated from patients with vulvovaginal candidiasis (VVC). Antifungal susceptibilities of the isolates were assayed by using the broth microdilution method. The level of virulent genes and resistant genes mRNA expression was determined by using real-time PCR. <b><i>Results:</i></b> At day 7–14 and day 30–35 follow-up, mycological cure of VVC caused by <i>C. nivariensis</i> was 5 in 9 and 4 in 9 cases. The minimum inhibitory concentration geometric means of caspofungin, fluconazole, itraconazole, and amphotericin B in <i>C. nivariensis</i> isolates were higher than those in <i>Candida albicans</i> ATCC90028 (0.340, 1.852, 0.367, and 1.587 vs. 0.124, 0.140, 0.030, and 0.891 µg/mL; <i>p</i> &lt; 0.05). The level of resistant genes ERG11, CDR1, and CDR2 and virulent genes YPS1, AWP3, and EPA1 mRNA expression was higher in <i>C. nivariensis</i> isolates than that of <i>C. glabrata</i> (2.58 ± 0.78, 9.31 ± 5.19, 11.10 ± 0.76, 13.57 ± 0.54, 11.96 ± 2.93, and 14.40 ± 0.61 vs. 1.05 ± 1.19, 2.22 ± 0.27, 0.85 ± 0.48, 0.30 ± 0.37, 1.90 ± 0.43, and 2.40 ± 0.65). <b><i>Conclusion:</i></b> We conclude that patients infected with <i>C. nivariensis</i> were symptomatic and with a low mycological cure rate when treated with commonly used antifungal agents. Compared with <i>C. albicans</i>, <i>C. nivariensis</i> is more antifungal resistant and virulent.
DOI: 10.6084/m9.figshare.10260527
title: Supplementary Material for: Gastroenteropancreatic High-Grade Neuroendocrine Neoplasms: Histology and Molecular Analysis, Two Sides of the Same Coin

description: <b><i>Background:</i></b> In gastroenteropancreatic (GEP) high-grade neuroendocrine neoplasms (H-NENs), Ki-67 threshold of 55% defines three prognosis subclasses: neuroendocrine tumor (NET) G3, neuroendocrine carcinoma (NEC) &lt;55%, and NEC ≥55%. We investigated whether the molecular profiling of H-NENs differs among these subcategories and evaluated potential therapeutic targets, including PD-L1. <b><i>Methods:</i></b> In GEP-NEN patients, we evaluated: (i) 55% threshold for Ki-67 labeling index for further stratifying NEC and (ii) immunoreactivity and gene mutations by immunohistochemistry and targeted next-generation sequencing (T-NGS). <b><i>Results:</i></b> Fifteen NETs G3 and 39 NECs were identified. Ki-67 labeling index was &lt;55% in 9 NECs and ≥55% in 30 NECs. Gene mutations by NGS (<i>TP53</i>, 32.9%; <i>KRAS</i>, 5.5%; <i>BRAF</i>, 4.1%) were detected in 46.6% NENs, significantly enriched in NEC ≥55% (76.7%) compared to NEC &lt;55% (55.6%) or NET (20.0%). PD-L1 staining in tumor-infiltrating lymphocytes was observed in NEC ≥55% (36.7%; <i>p</i> = 0.03). Median OS was 4.3 years in NET G3, 1.8 years in NEC &lt;55%, and 0.7 years in NEC ≥55% (<i>p &lt;</i>0.0001); it was 2.3 years with NGS wild-type, 0.7 years with ≥1 mutation (<i>p &lt;</i>0.0001), 0.8 years in PD-L1-positive patients, and 1.7 years in PD-L1-negative subjects (<i>p</i> = 0.0004). In multivariate analysis, only the proposed subclassification approach yielded statistically significant differences between groups (NEC &lt;55% vs. NET G3, HR 14.1, 95% CI 2.2–89.8, <i>p</i> = 0.005; NEC ≥55% vs. NET G3, HR 25.8, 95% CI 3.9–169, <i>p</i> = 0.0007). <b><i>Conclusions:</i></b> These findings identify NEC ≥55% as a biologically and prognostically distinct subtype and pave the way for more personalized treatment.
DOI: 10.6084/m9.figshare.10260389
title: Supplementary table 2. Reconstructing the terrestrial flora and marine plankton of the Middle Devonian of Spain: implications for biotic interchange and palaeogeography.

description: Supplementary table 2 - Chitinozoan presence-absence data
DOI: 10.6084/m9.figshare.10260392
title: Supplementary table 3. Reconstructing the terrestrial flora and marine plankton of the Middle Devonian of Spain: implications for biotic interchange and palaeogeography.

description: Supplementary table 3 - Phytoplankton presence-absence data
DOI: 10.6084/m9.figshare.10260392.v1
title: Supplementary table 3. Reconstructing the terrestrial flora and marine plankton of the Middle Devonian of Spain: implications for biotic interchange and palaeogeography.

description: Supplementary table 3 - Phytoplankton presence-absence data
DOI: 10.6084/m9.figshare.10260386
title: Supplementary table 1. Reconstructing the terrestrial flora and marine plankton of the Middle Devonian of Spain: implications for biotic interchange and palaeogeography.

description: Supplementary table 1 - Spore presence-absence data
DOI: 10.6084/m9.figshare.10260389.v1
title: Supplementary table 2. Reconstructing the terrestrial flora and marine plankton of the Middle Devonian of Spain: implications for biotic interchange and palaeogeography.

description: Supplementary table 2 - Chitinozoan presence-absence data
DOI: 10.6084/m9.figshare.10260386.v1
title: Supplementary table 1. Reconstructing the terrestrial flora and marine plankton of the Middle Devonian of Spain: implications for biotic interchange and palaeogeography.

description: Supplementary table 1 - Spore presence-absence data
DOI: 10.6084/m9.figshare.10260359
title: miclic breakout

description: miclic breakout
DOI: 10.5281/zenodo.4001641
title: Aalborg Energy Vision scenarios

description: EnergyPLAN scenario files
DOI: 10.5281/zenodo.3629264
title: Aalborg Energy Vision scenarios

description: EnergyPLAN scenario files
DOI: 10.6084/m9.figshare.10260035
title: Supplementary Material for: Breastfeeding and Atopic Dermatitis Risk: A Systematic Review and Meta-Analysis of Prospective Cohort Studies

description: <b><i>Objectives:</i></b> The effect of breastfeeding on atopic dermatitis (AD) remains controversial. To determine the association ­between breastfeeding and AD, we conducted an updated meta-analysis of prospective cohort studies. <b><i>Methods:</i></b> A comprehensive search of PubMed, EMBASE, MEDLINE and Cochrane Library was conducted. Studies meeting the predetermined criteria were evaluated by 2 authors independently. The pooled relative risk (RR) adjusted for confounders with its 95% CI was calculated by a random-effects model. Heterogeneity was explored by subgroup analysis and meta-regression. <b><i>Results:</i></b> A total of 27 studies were included for meta-analysis. The pooled estimates for the effect of total and exclusive breastfeeding on AD were 1.01 (95% CI 0.93–1.10) and 0.99 (95% CI 0.88–1.11), respectively. Heterogeneity was substantial across studies (total: <i>p</i> &lt; 0.01 or <i>I</i><sup>2</sup> = 65.2%; exclusive: <i>p</i> &lt; 0.01 or <i>I</i><sup>2</sup> = 72.3%). There was a weak evidence for a protective effect of breastfeeding against AD in cohorts with atopic heredity (total: RR 0.85, 95% CI 0.74–0.98; exclusive: RR 0.83, 95% CI 0.70–0.97). In cohorts without atopic heredity, the effect shifted to the risk side when limited to exclusive breastfeeding (RR 1.19, 95% CI 1.02–1.40) while it dropped towards null when limited to total breastfeeding (RR 1.11, 95% CI 0.94–1.31). <b><i>Conclusions:</i></b> There is no association between AD and breastfeeding, regardless of total or exclusive breastfeeding patterns. There is some evidence for a protective function of exclusive and total breastfeeding in a cohort with atopic heredity. The effect shifts to the risk side in cohorts without atopic heredity. However, these findings should be interpreted with caution because heterogeneity is evident.
DOI: 10.6084/m9.figshare.10260011
title: Supplementary Material for: Pain, Anxiety, Depression, and Quality of Life in Patients with Vulvodynia

description: <b><i>Background/Aims:</i></b> The term vulvodynia refers to vulvar pain of unknown origin lasting at least 3 months. Psychiatric comorbidities are a common feature and, along with pain, may severely affect patients’ wellbeing. We aimed to determine the characteristics of pain in vulvodynia, to correlate characteristics with symptoms of anxiety and depression, and to analyse the impact of these factors on patients’ quality of life. <b><i>Methods:</i></b> This cross-sectional observational study analysed pain, anxiety, and depression and the effects of these factors on quality of life. Pain, anxiety, and depression were assessed using validated tools in 110 women. <b><i>Results:</i></b> Statistical analyses found correlations between pain and anxiety and between anxiety and worsened quality of life. Patients often reported stinging, burning, pain, itching, and dyspareunia, pointing to the importance of temporal, localisation, punctate pressure, thermal, tactile sensitivity, and emotional tension characteristics. Most patients had severe pain related to psychiatric comorbidities and decreased quality of life. <b><i>Conclusion:</i></b> Using descriptors of pain quality and assessing anxiety and depression might help to define subgroups of patients that may benefit from different therapeutic approaches and thus enable treatments to be tailored to individual patients.
DOI: 10.6084/m9.figshare.10260011.v1
title: Supplementary Material for: Pain, Anxiety, Depression, and Quality of Life in Patients with Vulvodynia

description: <b><i>Background/Aims:</i></b> The term vulvodynia refers to vulvar pain of unknown origin lasting at least 3 months. Psychiatric comorbidities are a common feature and, along with pain, may severely affect patients’ wellbeing. We aimed to determine the characteristics of pain in vulvodynia, to correlate characteristics with symptoms of anxiety and depression, and to analyse the impact of these factors on patients’ quality of life. <b><i>Methods:</i></b> This cross-sectional observational study analysed pain, anxiety, and depression and the effects of these factors on quality of life. Pain, anxiety, and depression were assessed using validated tools in 110 women. <b><i>Results:</i></b> Statistical analyses found correlations between pain and anxiety and between anxiety and worsened quality of life. Patients often reported stinging, burning, pain, itching, and dyspareunia, pointing to the importance of temporal, localisation, punctate pressure, thermal, tactile sensitivity, and emotional tension characteristics. Most patients had severe pain related to psychiatric comorbidities and decreased quality of life. <b><i>Conclusion:</i></b> Using descriptors of pain quality and assessing anxiety and depression might help to define subgroups of patients that may benefit from different therapeutic approaches and thus enable treatments to be tailored to individual patients.
DOI: 10.6084/m9.figshare.10260017
title: Collection of Power Traces

description: This file contains the template power patterns used by our simulation approach.
DOI: 10.6084/m9.figshare.10260005
title: Selection of the optimal personalized treatment from multiple treatments with multivariate outcome measures

description: In this work, we propose a novel method for individualized treatment selection when the treatment response is multivariate. For the <i>K</i> treatment (<i>K ≥</i>2) scenario we compare quantities that are suitable indexes based on outcome variables for each treatment conditional on patient-specific scores constructed from collected covariate measurements. Our method covers any number of treatments and outcome variables, and it can be applied for a broad set of models. The proposed method uses a rank aggregation technique to estimate an ordering of treatments based on ranked lists of treatment performance measures such as smooth conditional means and conditional probability of a response for one treatment dominating others. The method has the flexibility to incorporate patient and clinician preferences to the optimal treatment decision on an individual case basis. A simulation study demonstrates the performance of the proposed method in finite samples. We also present data analyses using HIV and Diabetes clinical trials data to show the applicability of the proposed procedure for real data.
DOI: 10.6084/m9.figshare.10260017.v1
title: Collection of Power Traces

description: This file contains the template power patterns used by our simulation approach.
DOI: 10.6084/m9.figshare.10260038.v1
title: 346 journal articles related to volunteered geographic information (VGI) and the Python codes for performing the latent Dirichlet allocation (LDA) topic modeling

description: The files include: (1) The detailed attributes of 346 volunteered geographic information (VGI)-related articles published in 24 international refereed journals in GIScience between 20 November 2007 and 20 November 2017. (2) The Python codes for performing the latent Dirichlet allocation (LDA) topic modeling, which can be used to classify the articles into a given number of topics based on their abstracts. The data and codes support the findings of our article entitled ‘Volunteered geographic information research in the first decade: a narrative review of selected journal articles in GIScience’.<br>
DOI: 10.6084/m9.figshare.10259999
title: Equation J(kS,zeta)

description: Supplementary material to the contribution <b>"Spatially dependent friction - a way of adjusting bottleneck flow in cellular models"</b> to <i>Traffic and Granular Flow 2019</i>.<br>The file <b>Eq_JkSzeta.mat</b> contains all neceassary variables to reproduce the <b>Equation (3)</b> in the contribution: <b><i>J = J</i>(<i>kS, zeta</i>)</b>. The formula is contained in the symbolical variable <b>'J'</b>, which is symbolic expression in variables <b>'p'</b> and <b>'z'</b>, where<i>p</i> = exp{<i>kS</i>} in [1, +<i>Infty</i>),<i>z</i> = <i>zeta</i> in [0, 1].<br>The workspace is primarily designed for MATLAB software, however, it can be imported to other mathematical softwares as well.In MATLAB use<b>load('Eq_JkSzeta.mat')</b><br>The value of the flow can be reached by substitution<b>j = subs(J, {'p', 'z'}, [pval, zval]);</b><br><b>Example:</b> to get stationary flow for <i>kS</i> = 3 and <i>zeta</i> = 0.55 do<b>load('Eq_JkSzeta.mat')</b> % load variables to workspace<b>j = subs(J, {'p', 'z'}, [exp(3), 0.55]);</b> % substitute values to the formula<b>j = double(j);</b> % convert symbolical expresion to double
DOI: 10.6084/m9.figshare.10260005.v1
title: Selection of the optimal personalized treatment from multiple treatments with multivariate outcome measures

description: In this work, we propose a novel method for individualized treatment selection when the treatment response is multivariate. For the <i>K</i> treatment (<i>K ≥</i>2) scenario we compare quantities that are suitable indexes based on outcome variables for each treatment conditional on patient-specific scores constructed from collected covariate measurements. Our method covers any number of treatments and outcome variables, and it can be applied for a broad set of models. The proposed method uses a rank aggregation technique to estimate an ordering of treatments based on ranked lists of treatment performance measures such as smooth conditional means and conditional probability of a response for one treatment dominating others. The method has the flexibility to incorporate patient and clinician preferences to the optimal treatment decision on an individual case basis. A simulation study demonstrates the performance of the proposed method in finite samples. We also present data analyses using HIV and Diabetes clinical trials data to show the applicability of the proposed procedure for real data.
DOI: 10.6084/m9.figshare.10259999.v1
title: Equation J(kS,zeta)

description: Supplementary material to the contribution <b>"Spatially dependent friction - a way of adjusting bottleneck flow in cellular models"</b> to <i>Traffic and Granular Flow 2019</i>.<br>The file <b>Eq_JkSzeta.mat</b> contains all neceassary variables to reproduce the <b>Equation (3)</b> in the contribution: <b><i>J = J</i>(<i>kS, zeta</i>)</b>. The formula is contained in the symbolical variable <b>'J'</b>, which is symbolic expression in variables <b>'p'</b> and <b>'z'</b>, where<i>p</i> = exp{<i>kS</i>} in [1, +<i>Infty</i>),<i>z</i> = <i>zeta</i> in [0, 1].<br>The workspace is primarily designed for MATLAB software, however, it can be imported to other mathematical softwares as well.In MATLAB use<b>load('Eq_JkSzeta.mat')</b><br>The value of the flow can be reached by substitution<b>j = subs(J, {'p', 'z'}, [pval, zval]);</b><br><b>Example:</b> to get stationary flow for <i>kS</i> = 3 and <i>zeta</i> = 0.55 do<b>load('Eq_JkSzeta.mat')</b> % load variables to workspace<b>j = subs(J, {'p', 'z'}, [exp(3), 0.55]);</b> % substitute values to the formula<b>j = double(j);</b> % convert symbolical expresion to double
DOI: 10.6084/m9.figshare.10259984
title: Table DR5. Weathering history and landscape evolution of Western Ghats (India) from <sup>40</sup>Ar/<sup>39</sup> Ar dating of supergene K–Mn oxides

description: Analytical results obtained for each irradiated and dated cryptomelane grains analysed using laser energy (in power %) of the spectrometer Argus VI.The concentrations (in molar volume, V) of <sup>36</sup>Ar, <sup>37</sup>Ar, <sup>38</sup>Ar, <sup>39</sup>Ar and <sup>40</sup>Ar with their respective 1σ error are provided for each step heating. The amount of <sup>40</sup>Ar* (%), of <sup>39</sup>Ar released (% <sup>39</sup>Ar) and the K/Ca ratio (derived from <sup>39</sup>Ar/<sup>37</sup>Ar) are also given, and also the sample parameters and the irradiation constants. Finally, this table show ratios <sup>40</sup>Ar*/<sup>39</sup>Ark used to determine the corresponding apparent ages with their associated 2σerror. The different J-Factor values are also provided for each irradiated grains.
DOI: 10.6084/m9.figshare.10259984.v1
title: Table DR5. Weathering history and landscape evolution of Western Ghats (India) from <sup>40</sup>Ar/<sup>39</sup> Ar dating of supergene K–Mn oxides

description: Analytical results obtained for each irradiated and dated cryptomelane grains analysed using laser energy (in power %) of the spectrometer Argus VI.The concentrations (in molar volume, V) of <sup>36</sup>Ar, <sup>37</sup>Ar, <sup>38</sup>Ar, <sup>39</sup>Ar and <sup>40</sup>Ar with their respective 1σ error are provided for each step heating. The amount of <sup>40</sup>Ar* (%), of <sup>39</sup>Ar released (% <sup>39</sup>Ar) and the K/Ca ratio (derived from <sup>39</sup>Ar/<sup>37</sup>Ar) are also given, and also the sample parameters and the irradiation constants. Finally, this table show ratios <sup>40</sup>Ar*/<sup>39</sup>Ark used to determine the corresponding apparent ages with their associated 2σerror. The different J-Factor values are also provided for each irradiated grains.
DOI: 10.6084/m9.figshare.10259960
title: Second Storey Additions Perth

description: Oakwoodbuilders specialize in second storey additions Perth, Australia. This kind of service can increase the value of your home. A significant advantage of adding additional storeys is that they can be designed and transform your single storey house into an extra spacious without taking up any further room in your area. So if you have not much outdoor living space, then add an extra storey with the help of Oakwodbuilders experienced and professional team.
DOI: 10.6084/m9.figshare.10259960.v1
title: Second Storey Additions Perth

description: Oakwoodbuilders specialize in second storey additions Perth, Australia. This kind of service can increase the value of your home. A significant advantage of adding additional storeys is that they can be designed and transform your single storey house into an extra spacious without taking up any further room in your area. So if you have not much outdoor living space, then add an extra storey with the help of Oakwodbuilders experienced and professional team.