cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5909836.v1
title: Model Validation for Quantitative X-Ray Measurements

description: Soft–X-ray (SXR) brightness measurements contain information on a number of physics parameters in fusion plasmas; however, it is nearly impossible to extract the information without modeling. A validated forward model is therefore necessary for the accurate interpretation of SXR measurements and will be critical in the burning plasma era, where medium- and high-Z impurities are ever present. The Atomic Data and Analysis Structure (ADAS) database is a powerful interpretive tool that is extensively used to model and predict atomic spectra, level populations, and ionization balance for fusion plasmas. These predictions are in good agreement with experimental measurements. However, continuum radiation in the X-ray range, while also modeled in ADAS, has not been rigorously verified or tested against experimental data. We therefore performed a systematic comparison of ADAS to a simplified model called PFM. PFM only calculates continuum radiation but shows good agreement with experimental data when only continuum radiation is present. ADAS and the simplified model agree to within 1% to 2% indicating that ADAS is calculating continuum radiation correctly. We have also begun a validation of SXR brightness calculations from ADAS. The SXR brightness measurements modeled by ADAS agree well with experimental measurements from an extreme where the signal is dominated by line radiation continuously through another extreme where the signal is dominated by continuum emission. While this validation work is preliminary, it strongly suggests that ADAS accurately models the physics that lead to SXR radiation.
DOI: 10.6084/m9.figshare.5909827
title: NUCM Monte Carlo results - wet crust and dry mantle rheology

description: Monte Carlo results for NUCM simulations (Figures 6e-f-g-h and 7b). Rheology = dry mantle and wet crust, diffusion creep<br><b>Files:</b>Each line of the files (scores, thickness, enrichment factor and crustal radioelement content) corresponds to a model with given crustal parameters (crustal thickness in meters and enrichment factor) and the results obtained for this model.<br>Gaussian scores for the three constraints on elastic thickness are given in the files "score". To compute scores between 0 and 1, these scores have to be divided by the maximum of the corresponding gaussian (given in "Gaussian_maximum.csv": in order for the Noachian, the Southern polar cap and the Northern polar cap)<br>The file "MeltFormation" gives the difference in meters between the depth of the stagnant lid and the depth of melt formation in the Southern hemisphere. Models with present-day formation in the South are those where this difference is lower than 100 km.<br><br>
DOI: 10.6084/m9.figshare.5909827.v1
title: NUCM Monte Carlo results - wet crust and dry mantle rheology

description: Monte Carlo results for NUCM simulations (Figures 6e-f-g-h and 7b). Rheology = dry mantle and wet crust, diffusion creep<br><b>Files:</b>Each line of the files (scores, thickness, enrichment factor and crustal radioelement content) corresponds to a model with given crustal parameters (crustal thickness in meters and enrichment factor) and the results obtained for this model.<br>Gaussian scores for the three constraints on elastic thickness are given in the files "score". To compute scores between 0 and 1, these scores have to be divided by the maximum of the corresponding gaussian (given in "Gaussian_maximum.csv": in order for the Noachian, the Southern polar cap and the Northern polar cap)<br>The file "MeltFormation" gives the difference in meters between the depth of the stagnant lid and the depth of melt formation in the Southern hemisphere. Models with present-day formation in the South are those where this difference is lower than 100 km.<br><br>
DOI: 10.6084/m9.figshare.5909821
title: alignment.information.txt

description: Information of alignments of 2,636 orthologous loci in tab-delimited format.
DOI: 10.6084/m9.figshare.5909821.v1
title: alignment.information.txt

description: Information of alignments of 2,636 orthologous loci in tab-delimited format.
DOI: 10.6084/m9.figshare.5909812
title: fsc_input_files.zip

description: Input files of Fastsimcoal2 for demographic simulations/inferences in Fujisawa et al. (2018). The "model_comparison" folder includes est and tpl files for demographic inferences under multiple scenarios. The "simulation" folder includes par files for simulations with parameters estimated under the best demographic models.
DOI: 10.6084/m9.figshare.5909812.v1
title: fsc_input_files.zip

description: Input files of Fastsimcoal2 for demographic simulations/inferences in Fujisawa et al. (2018). The "model_comparison" folder includes est and tpl files for demographic inferences under multiple scenarios. The "simulation" folder includes par files for simulations with parameters estimated under the best demographic models.
DOI: 10.6084/m9.figshare.5909806
title: transcriptome_alignments.zip

description: Fasta formatted alignments of 2,636 orthologous loci used in phylogenetic and demographic analyses of Magicicada.
DOI: 10.6084/m9.figshare.5909806.v1
title: transcriptome_alignments.zip

description: Fasta formatted alignments of 2,636 orthologous loci used in phylogenetic and demographic analyses of Magicicada.
DOI: 10.6084/m9.figshare.5909788
title: Supplementary Material for: The Importance of Excluding Cutaneous T-Cell Lymphomas in Patients with a Working Diagnosis of Papuloerythroderma of Ofuji: A Case Series

description: Papuloerythroderma of Ofuji (PEO) is an erythroderma-like eruption with flat-topped papules that spare the skin folds (a “deck-chair sign” finding). Many infections, medications, and systemic diseases have been associated with PEO, including cutaneous T-cell lymphomas (CTCL). The relationship between the clinical presentation of PEO and CTCL remains poorly elucidated. Clinical, laboratory, and histopathological data were obtained from the Lymphoma Clinic at the Ottawa Hospital, Canada. We report 5 patients with deck-chair-sign-positive CTCL, mycosis fungoides, and Sézary syndrome variants. We contend that PEO should be viewed as a diagnosis of exclusion and that these patients should be monitored carefully for possible emergence of CTCL. Skin biopsy alone is not sufficient to exclude CTCL in these patients. A skin eruption demonstrating a positive deck-chair sign may signify systemic/leukemic CTCL and, therefore, warrants a thorough investigation, including skin biopsy, flow cytometry, and T-cell receptor clonality studies.
DOI: 10.6084/m9.figshare.5909788.v1
title: Supplementary Material for: The Importance of Excluding Cutaneous T-Cell Lymphomas in Patients with a Working Diagnosis of Papuloerythroderma of Ofuji: A Case Series

description: Papuloerythroderma of Ofuji (PEO) is an erythroderma-like eruption with flat-topped papules that spare the skin folds (a “deck-chair sign” finding). Many infections, medications, and systemic diseases have been associated with PEO, including cutaneous T-cell lymphomas (CTCL). The relationship between the clinical presentation of PEO and CTCL remains poorly elucidated. Clinical, laboratory, and histopathological data were obtained from the Lymphoma Clinic at the Ottawa Hospital, Canada. We report 5 patients with deck-chair-sign-positive CTCL, mycosis fungoides, and Sézary syndrome variants. We contend that PEO should be viewed as a diagnosis of exclusion and that these patients should be monitored carefully for possible emergence of CTCL. Skin biopsy alone is not sufficient to exclude CTCL in these patients. A skin eruption demonstrating a positive deck-chair sign may signify systemic/leukemic CTCL and, therefore, warrants a thorough investigation, including skin biopsy, flow cytometry, and T-cell receptor clonality studies.
DOI: 10.6084/m9.figshare.5909743
title: Correcting batch effects in case-control microbiome studies.

description: OTU table, representative sequences, and metadata from combined Baxter, Zeller, and Zackular studies (colorectal cancer case-control datasets). These data were processed using a standardized workflow (97% clustering of the V4 region of the 16S gene). For details see the preprint: https://www.biorxiv.org/content/early/2018/02/11/165910<br>
DOI: 10.6084/m9.figshare.5909743.v1
title: Correcting batch effects in case-control microbiome studies.

description: OTU table, representative sequences, and metadata from combined Baxter, Zeller, and Zackular studies (colorectal cancer case-control datasets). These data were processed using a standardized workflow (97% clustering of the V4 region of the 16S gene). For details see the preprint: https://www.biorxiv.org/content/early/2018/02/11/165910<br>
DOI: 10.6084/m9.figshare.5909644
title: Neuropathy in MS.xlsx

description: This data shows the peripheral neuropathy in MS patients
DOI: 10.6084/m9.figshare.5909611
title: Supplementary Material for: Benzodiazepines as a Monotherapy in Depressive Disorders: A Systematic Review

description: <b><i>Background:</i></b> The aim of this paper was to perform a systematic review and, when feasible, a meta-analysis of randomized controlled trials (RCT) which used benzodiazepines (BZD) as a monotherapy versus placebo, antidepressant drugs (AD), or both. <b><i>Methods:</i></b> Keyword searches were conducted for identifying RCT comparing BZD and AD, and/or placebo in the treatment of depression, using electronic databases from their inception up to April 2017. We selected reports of RCT in which BZD were compared to AD and/or placebo in the treatment of adult patients with a primary diagnosis of depressive disorder or anxious depression. When feasible, data were subjected to meta-analysis. <b><i>Results:</i></b> A total of 38 studies met the criteria for inclusion and were then included in the systematic review. Only 1 study concerned a newer AD, fluvoxamine. For the meta-analysis, we submitted data on response rate from 22 RCT, considering BZD versus placebo (8 comparisons) and BZD versus tricyclic antidepressants (TCA) (20 comparisons). There was a lack of significant differences as to response rate between BZD and placebo, as well as between BZD and TCA. Analysis of individual studies disclosed that, in more than half of the studies comparing BZD to TCA and/or placebo, BZD were significantly more effective than placebo and as effective as TCA. <b><i>Conclusions:</i></b> BZD are a therapeutic option in anxious depression and there are no indications that AD are preferable. There is a pressing need for RCT of adequate methodological quality and follow-up comparing BZD to second-generation AD and placebo in anxious depression.
DOI: 10.6084/m9.figshare.5909335
title: Supplementary Material for: Lysophosphatidic Acid Induces Ligamentum Flavum Hypertrophy Through the LPAR1/Akt Pathway

description: <b><i>Background/Aims:</i></b> Hypertrophic ligamentum flavum (LF) is a major cause of lumbar spinal stenosis. Our previous work showed that high levels of lysophosphatidic acid (LPA) expression are positively correlated with LF hypertrophy. This study aimed to further unveil how LPA regulates LF hypertrophy <b><i>Methods:</i></b> We studied LPAR1 expression in human LF cells using PCR and western blotting. Cell viability cell cycle, apoptosis rate and molecular mechanisms were assayed in LPAR1 knockdown or overexpression LF cells. LF hypertrophy and the molecular mechanism was confirmed in human samples and in <i>in vivo</i> studies. <b><i>Results:</i></b> The expression of LPA and its receptor LPAR1 is significantly higher in tissues or cells harvested from hypertrophic LF compared to healthy controls. Moreover, LPA promoted LF cell proliferation by interacting with LPAR1. This conclusion is supported by the fact that depletion or overexpression of LPAR1 changed the effect of LPA on LF cell proliferation. LPA also inhibits apoptosis in LF cells through the receptor LPAR1. Importantly, we demonstrated that the LPA-LPAR1 interaction initiated Akt phosphorylation and determined cell proliferation and apoptosis. Our <i>in vitro</i> findings were supported by our <i>in vivo</i> evidence that lyophilized LPA significantly induced LF hypertrophy via the LPAR1-Akt signaling pathway. More importantly, targeted inhibition of LPAR1 by Ki16425 with a gel sponge implant effectively reduced LPA-associated LF hypertrophy. Taken together, these data indicate that LPA binds to the receptor LPAR1 to induce LF cell proliferation and inhibit apoptosis by activating AKT signaling cascades. Targeting this signaling cascade with Ki16425 is a potential therapeutic strategy for preventing LF hypertrophy. <b><i>Conclusion:</i></b> LPA-LPAR1-Akt activation is positively correlated with the proliferation and survival of LF cells. LPAR1 could be a target for new drugs and the development of new therapeutic methods for treating LF hypertrophy.
DOI: 10.6084/m9.figshare.5909266
title: Pokhoday_etal_data

description: This is a dataset set of 24 participants which is described in a paper: Motor (but not auditory) attention affects syntactic choice by Pokhoday et al.
DOI: 10.6084/m9.figshare.5909266.v1
title: Pokhoday_etal_data

description: This is a dataset set of 24 participants which is described in a paper: Motor (but not auditory) attention affects syntactic choice by Pokhoday et al.
DOI: 10.6084/m9.figshare.5909194
title: RENE.zip

description: Replication package
DOI: 10.6084/m9.figshare.5909194.v1
title: RENE.zip

description: Replication package
DOI: 10.6084/m9.figshare.5909176
title: Manuscript submission data and R code archive for "Randomised Control Trials could be, and should be, more widely used in conservation: evidence from a Payment for Environmental Services evaluation"

description: This fileset contains R code, data and metadata for a manuscript submission. We expect to create a new archive following reviewer comments. Please consult the README file for a more thorough description of contents.<br>
DOI: 10.6084/m9.figshare.5909164
title: Supplementary Material for: A Prospective Cohort Study in Patients with Type 2 Diabetes Mellitus for Validation of Biomarkers (PROVALID) – Study Design and Baseline Characteristics

description: <b><i>Background/Aims:</i></b> The prevalence of diabetes mellitus type 2 and kidney disease in these patients varies widely between European countries. <b><i>Methods:</i></b> In addition to store bio-samples the “Prospective cohort study in patients with type 2 diabetes mellitus for validation of biomarkers” collects information on history, physical status, laboratory measurements and medication in 4000 patients with diabetes mellitus type 2, being taken care of at the primary level of healthcare in 5 European countries (Austria, Hungary, Netherlands, Poland and Scotland). Next to comparing the rate of loss of eGFR between the countries, a further objective of the PROVALID study is to determine the 5-year cumulative incidence of renal and cardiovascular outcomes. <b><i>Results:</i></b> The mean age of the population recruited is 62.9±10 years, 54.6% are male and the mean BMI is 30.9±5.4 kg/m<sup>2</sup>. Metabolic control (median HBA1c 6.8 % (6.2; 7.5)) is achieved via administration of metformin in 67.4% of the patients and insulin in 30.3%. Median systolic and diastolic blood pressure at recruitment is 135 (125; 146) and 80 (72; 85) mmHg, 65.4% of subjects received RAAS blocking agents. Mean eGFR is 80.7±29.2 ml/min/1.73m<sup>2</sup> and median baseline albumin/creatinine ratio 8.3 mg (IQR: 3.8 and 25.1). <b><i>Conclusion:</i></b> PROVALID will provide information on incidence and progression of renal and cardiovascular disease and therapy in patients with type 2 diabetes mellitus in different European countries. Thus, in contrast to many other cohort studies we will be able to associate national clinical practise pattern with outcome in this highly vulnerable patient population.
DOI: 10.6084/m9.figshare.5909164.v1
title: Supplementary Material for: A Prospective Cohort Study in Patients with Type 2 Diabetes Mellitus for Validation of Biomarkers (PROVALID) – Study Design and Baseline Characteristics

description: <b><i>Background/Aims:</i></b> The prevalence of diabetes mellitus type 2 and kidney disease in these patients varies widely between European countries. <b><i>Methods:</i></b> In addition to store bio-samples the “Prospective cohort study in patients with type 2 diabetes mellitus for validation of biomarkers” collects information on history, physical status, laboratory measurements and medication in 4000 patients with diabetes mellitus type 2, being taken care of at the primary level of healthcare in 5 European countries (Austria, Hungary, Netherlands, Poland and Scotland). Next to comparing the rate of loss of eGFR between the countries, a further objective of the PROVALID study is to determine the 5-year cumulative incidence of renal and cardiovascular outcomes. <b><i>Results:</i></b> The mean age of the population recruited is 62.9±10 years, 54.6% are male and the mean BMI is 30.9±5.4 kg/m<sup>2</sup>. Metabolic control (median HBA1c 6.8 % (6.2; 7.5)) is achieved via administration of metformin in 67.4% of the patients and insulin in 30.3%. Median systolic and diastolic blood pressure at recruitment is 135 (125; 146) and 80 (72; 85) mmHg, 65.4% of subjects received RAAS blocking agents. Mean eGFR is 80.7±29.2 ml/min/1.73m<sup>2</sup> and median baseline albumin/creatinine ratio 8.3 mg (IQR: 3.8 and 25.1). <b><i>Conclusion:</i></b> PROVALID will provide information on incidence and progression of renal and cardiovascular disease and therapy in patients with type 2 diabetes mellitus in different European countries. Thus, in contrast to many other cohort studies we will be able to associate national clinical practise pattern with outcome in this highly vulnerable patient population.
DOI: 10.6084/m9.figshare.5909122
title: epicranialEEG_10rats.zip

description: These data are freely provided for scientific non-profit use, by the Functional Brain Mapping Laboratory of the University of Geneva, Switzerland.<br>When using these data in publications please cite: <br>Plomp, G., Quairiaux, C., Michel, C.M., Astolfi, L., 2014. The physiological plausibility of time-varying Granger-causal modeling: normalization and weighting by spectral power. NeuroImage. doi:10.1016/j.neuroimage.2014.04.016<br><br><br>#---------- Data info<br>10 datasets of EEG recorded from p21 Wistar rats with electrodes positioned on the cranium. <br>These data were originally published in Quairiaux et al. (2010), where a full description of the methods can be found.<br>50 Left/Right (Gauche/Droite, excuse my French) whisker stimulations (some lacking in one animal).<br>Signals were referenced to an electrode placed above the cerebellum, online filtered 1-500 Hz, and digitized at 2 kHz.<br><br>Each directory contains data files from one animal: Epochs for left ('G') and right ('D') stimulation plus an average for each condition.<br>Each file contains 15-channel epicranial EEG, the reference electrode has been removed.<br>Stimulus onset is at time-frame 120.<br>The EEG files (.eph) are plain text files with a header: nr of channels, nr of time frames, sampling rate (Hz).<br>Openable in Cartool software, freely available here: https://sites.google.com/site/fbmlab/cartool<br><br>Electrode layout file: electrodeLayout_15chan.els<br>A text file with 15 electrode coordinates, can be linked to the .eph files for topographic ERP views using Cartool software.<br><br>The electrode layout is shown in rodent_15ch_electrodeLayout_left-right.PNG<br>For left stimuli, e4 is the electrode over contralateral S1, for right stimuli it is e12. <br><br>#---------- Animal names and numbers<br>1. IC070523<br>2. RN060616A<br>3. RN060707A<br>4. RN060707B<br>5. RN060714C<br>6. RN060728A<br>7. RN060728B<br>8. RN0609122<br>9. RN060915A2<br>10. RN070129C2<br><br><br>#---------- References<br>Plomp, G, Quairiaux, C, Michel, CM, Astolfi, L (2014) The physiological plausibility of time-varying Granger-causal modeling: normalization and weighting by spectral power. NeuroImage. doi:10.1016/j.neuroimage.2014.04.016<br>Quairiaux C, Mégevand P, Kiss JZ, Michel CM (2011) Functional development of large-scale sensorimotor cortical networks in the brain. J Neurosci 31:9574–9584.<br><br>
DOI: 10.6084/m9.figshare.5909101
title: PCGF5 is required for neural differentiation of embryonic stem cells

description: The data information for investigating the PCGF5 function during mESC neural differentation.
DOI: 10.6084/m9.figshare.5909101.v1
title: PCGF5 is required for neural differentiation of embryonic stem cells

description: The data information for investigating the PCGF5 function during mESC neural differentation.
DOI: 10.6084/m9.figshare.5909005
title: Dataset for: Capturing the multifactorial nature of ARDS- “Two-hit” approach to model murine acute lung injury

description: Severe acute respiratory distress syndrome (ARDS) presents typically with an initializing event, followed by the need for mechanical ventilation. Most animal models of ALI are limited by the fact that they focus on a singular cause of acute lung injury (ALI) and therefore fail to mimic the complex, multifactorial pathobiology of ARDS. To better capture this scenario, we provide a comprehensive characterization of models of ALI combining two injuries: intra tracheal (i.t.) instillation of LPS or hypochloric acid (HCl) followed by ventilator-induced lung injury (VILI). We hypothesized, that mice pre-treated with LPS or HCl prior to VILI and thus receiving a (“ two-hit injury”) will sustain a super additive lung injury when compared to VILI. Mice were allocated to following treatment groups: control with i.t. NaCl, ventilation with low peak inspiratory pressure (PIP), i.t. HCl, i.t. LPS, VILI (high PIP), HCl i.t. followed by VILI and LPS i.t. followed by VILI. Severity of injury was determined by protein content and MPO activity in bronchoalveolar lavage (BAL), expression of inflammatory cytokines and histopathology. Mice subjected to VILI after HCl or LPS instillation displayed augmented lung injury, compared to singular lung injury. However, mice that received i.t. LPS prior to VILI showed significantly increased inflammatory lung injury compared to animals that underwent i.t. HCl followed by VILI. The two hit lung injury models described, resulting in additive but differential acute lung injury recaptures the clinical relevant multifactorial etiology of ALI and could be a valuable tool in translational research.