cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4484435.v4
title: SPATIAL ANALYSIS OF HANDWRITTEN TEXTS AS AN INDICATOR OF COGNITIVE CONTROL

description: We compared the heterogeneity of handwritten texts in tasks with different cognitive demands; transcription and exposition about an autobiographical episode. The heterogeneity of texts was analyzed with lacunarity, a non-linear measure of geometric patterns. Lacunarity of handwritten texts was significantly lower in transcription than in exposition. These effects were verified in a task that compared a veridical and a fictitious version of a personal event. Lacunarity was lower in veridical than fictitious texts. We contend that differences in lacunarity of handwritten texts reveal the degree of automaticity in handwriting.
DOI: 10.6084/m9.figshare.4484108
title: Current knowledge of Umbrian macrofungi (central Italy)

description: An annotated checklist of 1016 species of fungi (Ascomycota and Basidiomycota), which have been recorded in 95 different localities, from 1990 to 2015, is presented for Umbria (Italy). The checklist was compiled from records of Umbrian fungi in scientific publications, unpublished lists and personal observations. This work represents the first comprehensive checklist of macrofungi for Umbria. Even if not complete, an exhaustive overview of the current knowledge of the mycobiota of Umbria is presented. Although a large amount of the regional territory has still to be explored for mycological diversity, this study offers an important support in compiling red-lists of endangered macrofungi, as well as to identify indicator species of particular habitats to be considered for wildlife reserves, as is currently done in many European countries.
DOI: 10.6084/m9.figshare.4484108.v1
title: Current knowledge of Umbrian macrofungi (central Italy)

description: An annotated checklist of 1016 species of fungi (Ascomycota and Basidiomycota), which have been recorded in 95 different localities, from 1990 to 2015, is presented for Umbria (Italy). The checklist was compiled from records of Umbrian fungi in scientific publications, unpublished lists and personal observations. This work represents the first comprehensive checklist of macrofungi for Umbria. Even if not complete, an exhaustive overview of the current knowledge of the mycobiota of Umbria is presented. Although a large amount of the regional territory has still to be explored for mycological diversity, this study offers an important support in compiling red-lists of endangered macrofungi, as well as to identify indicator species of particular habitats to be considered for wildlife reserves, as is currently done in many European countries.
DOI: 10.6084/m9.figshare.4484141.v1
title: GeneSeqToFamily.zip

description: Supporting data for GeneSeqToFamily, the Ensembl Compara GeneTrees pipeline as a Galaxy workflow<br>
DOI: 10.6084/m9.figshare.4484141.v2
title: GeneSeqToFamily.zip

description: Supporting data for GeneSeqToFamily, the Ensembl Compara GeneTrees pipeline as a Galaxy workflow<br>
DOI: 10.6084/m9.figshare.4484141.v4
title: GeneSeqToFamily.zip

description: Supporting data for GeneSeqToFamily, the Ensembl Compara GeneTrees pipeline as a Galaxy workflow<br>
DOI: 10.6084/m9.figshare.4484141.v5
title: GeneSeqToFamily.zip

description: Supporting data for GeneSeqToFamily, the Ensembl Compara GeneTrees pipeline as a Galaxy workflow<br>
DOI: 10.6073/pasta/bf8d12b8f9da9ae82bb5474b9fdd6e38
title: Jornada Basin LTER Cross-scale Interactions Study (CSIS) Block 11 meteorological station: 30-minute summary data: 2017 - ongoing

description: This data package contains 30-minute air temperature, relative humidity, and wind summary data from Jornada Basin LTER Cross Scale Interactions Study (CSIS) Block-1 met station. Average air temperature, relative humidity, wind speed, wind direction, and precipitation are measured and calculated at an automated meteorological station connected to a 900 MHz spread spectrum wireless network. Wind speed is measured at 37cm, 75 cm, 150 cm, and 300 cm, wind direction at approximately 3m, and air temperature and relative humidity at approximate 2.5m. Measurements are aggregated at intervals of 5, 30, 60 minutes and daily, with precipitation additionally provided with 1 second aggregation during precipitation events. The met station variables measured include air temperature, precipitation, relative humidity, wind direction, wind speed. Precipitation is not measured at Block 1 and Block 12 because of proximity to Block 2 and Block 13, respectively. This is an ONGOING dataset.
DOI: 10.6084/m9.figshare.4484141.v6
title: GeneSeqToFamily.zip

description: Supporting data for GeneSeqToFamily, the Ensembl Compara GeneTrees pipeline as a Galaxy workflow<br>
DOI: 10.6084/m9.figshare.4484141.v7
title: GeneSeqToFamily.zip

description: Supporting data for GeneSeqToFamily, the Ensembl Compara GeneTrees pipeline as a Galaxy workflow<br>
DOI: 10.6084/m9.figshare.4484141.v8
title: GeneSeqToFamily.zip

description: Supporting data for GeneSeqToFamily, the Ensembl Compara GeneTrees pipeline as a Galaxy workflow<br>
DOI: 10.6084/m9.figshare.4484141.v9
title: GeneSeqToFamily.zip

description: Supporting data for GeneSeqToFamily, the Ensembl Compara GeneTrees pipeline as a Galaxy workflow<br>
DOI: 10.6084/m9.figshare.4484141.v10
title: GeneSeqToFamily.zip

description: Supporting data for GeneSeqToFamily, the Ensembl Compara GeneTrees pipeline as a Galaxy workflow<br>
DOI: 10.6084/m9.figshare.4484141.v11
title: GeneSeqToFamily.zip

description: Supporting data for GeneSeqToFamily, the Ensembl Compara GeneTrees pipeline as a Galaxy workflow<br>
DOI: 10.6084/m9.figshare.4484141.v12
title: GeneSeqToFamily.zip

description: Supporting data for GeneSeqToFamily, the Ensembl Compara GeneTrees pipeline as a Galaxy workflow<br>
DOI: 10.6084/m9.figshare.4484141.v13
title: GeneSeqToFamily.zip

description: Supporting data for GeneSeqToFamily, the Ensembl Compara GeneTrees pipeline as a Galaxy workflow<br>
DOI: 10.6084/m9.figshare.4484141.v15
title: GeneSeqToFamily.zip

description: Supporting data for GeneSeqToFamily, the Ensembl Compara GeneTrees pipeline as a Galaxy workflow<br>
DOI: 10.6084/m9.figshare.4484141.v14
title: GeneSeqToFamily.zip

description: Supporting data for GeneSeqToFamily, the Ensembl Compara GeneTrees pipeline as a Galaxy workflow<br>
DOI: 10.6084/m9.figshare.4483889
title: Configuration scripts, logs and summary of results for modified H.264/AVC encoder with PsuedoSSIM model for sub-block (4x4, 8x8) prediction

description: This contains the encoder settings, scripts, logs and encoded video sequences produced by the JM H.264/AVC encoder and modified H.264/AVC encoder with PseudoSSIM model for sub-block (4x4 and 8x8) prediction.Please note that version 18.4 was used of JM H.264/AVC.The modifed code is available in the references below.<br><br>
DOI: 10.6084/m9.figshare.4483889.v1
title: Configuration scripts, logs and summary of results for modified H.264/AVC encoder with PsuedoSSIM model for sub-block (4x4, 8x8) prediction

description: This contains the encoder settings, scripts, logs and encoded video sequences produced by the JM H.264/AVC encoder and modified H.264/AVC encoder with PseudoSSIM model for sub-block (4x4 and 8x8) prediction.Please note that version 18.4 was used of JM H.264/AVC.The modifed code is available in the references below.<br><br>
DOI: 10.6084/m9.figshare.4483850
title: Supplementary Material for: Test-Retest Reliability of Scotopic and Mesopic Fundus-Controlled Perimetry Using a Modified MAIA (Macular Integrity Assessment) in Normal Eyes

description: <b><i>Purpose:</i></b> To assess the intrasession test-retest reliability of scotopic cyan and scotopic red fundus-controlled perimetry (FCP) in normal subjects using a modified MAIA “microperimeter” (macular integrity assessment) device. <b><i>Methods:</i></b> Forty-seven normal eyes of 30 subjects (aged 33.8 years) underwent duplicate mesopic (achromatic stimuli, 400-800 nm), scotopic cyan (505 nm), and scotopic red (627 nm) FCP, using a grid of 49 stimuli over 14° of the central retina. Test-retest reliability for pointwise sensitivity (PWS), stability of fixation, reaction time and test duration were analyzed using mixed-effects models. <b><i>Results:</i></b> PWS test-retest reliability was good among all 3 types of retinal sensitivity assessments (coefficient of repeatability of 4.75 dB for mesopic, 5.26 dB for scotopic cyan, and 4.06 dB for scotopic red testing). While the mean sensitivity decreased with eccentricity for both mesopic and scotopic red testing, it was highest at 7° eccentricity for the scotopic cyan assessment (p &lt; 0.001). <b><i>Conclusions:</i></b> The modified MAIA device allows for reliable scotopic FCP in normal subjects. Our findings suggest that testing of scotopic cyan sensitivity largely reflects rod function.
DOI: 10.6084/m9.figshare.4483841
title: Minimum Distance Estimation for the Generalized Pareto Distribution

description: The generalized Pareto distribution (GPD) is widely used for extreme values over a threshold. Most existing methods for parameter estimation either perform unsatisfactorily when the shape parameter <i>k</i> is larger than 0.5, or they suffer from heavy computation as the sample size increases. In view of the fact that <i>k</i> &gt; 0.5 is occasionally seen in numerous applications, including two illustrative examples used in this study, we remedy the deficiencies of existing methods by proposing two new estimators for the GPD parameters. The new estimators are inspired by the minimum distance estimation and the <i>M</i>-estimation in the linear regression. Through comprehensive simulation, the estimators are shown to perform well for all values of <i>k</i> under small and moderate sample sizes. They are comparable to the existing methods for <i>k</i> &lt; 0.5 while perform much better for <i>k</i> &gt; 0.5.
DOI: 10.6084/m9.figshare.4483826
title: Cap.6 - Eco Chamber data.xlsx

description: migrants
DOI: 10.6084/m9.figshare.4483841.v1
title: Minimum Distance Estimation for the Generalized Pareto Distribution

description: The generalized Pareto distribution (GPD) is widely used for extreme values over a threshold. Most existing methods for parameter estimation either perform unsatisfactorily when the shape parameter <i>k</i> is larger than 0.5, or they suffer from heavy computation as the sample size increases. In view of the fact that <i>k</i> &gt; 0.5 is occasionally seen in numerous applications, including two illustrative examples used in this study, we remedy the deficiencies of existing methods by proposing two new estimators for the GPD parameters. The new estimators are inspired by the minimum distance estimation and the <i>M</i>-estimation in the linear regression. Through comprehensive simulation, the estimators are shown to perform well for all values of <i>k</i> under small and moderate sample sizes. They are comparable to the existing methods for <i>k</i> &lt; 0.5 while perform much better for <i>k</i> &gt; 0.5.
DOI: 10.6084/m9.figshare.4483820
title: Supplementary Material for: The HDM2 (MDM2) Inhibitor NVP-CGM097 Inhibits Tumor Cell Proliferation and Shows Additive Effects with 5-Fluorouracil on the p53-p21-Rb-E2F1 Cascade in the p53wild type Neuroendocrine Tumor Cell Line GOT1

description: <b><i>Background/Aims:</i></b> The tumor suppressor p53 is depleted in many tumor cells by the E3 ubiquitin ligase mouse double minute 2 homolog (MDM2) through MDM2/p53 interaction. A novel target for inhibiting p53 degradation and for causing reexpression of p53<sup>wild type</sup> is inhibition of MDM2. The small molecule NVP-CGM097 is a novel MDM2 inhibitor. We investigated MDM2 inhibition as a target in neuroendocrine tumor cells in vitro. <b><i>Methods:</i></b> Human neuroendocrine tumor cell lines from the pancreas (BON1), lung (NCI-H727), and midgut (GOT1) were incubated with the MDM2 inhibitor NVP-CGM097 (Novartis) at concentrations from 4 to 2,500 nM. <b><i>Results:</i></b> While p53<sup>wild type</sup> GOT1 cells were sensitive to NVP-CGM097, p53<sup>mutated</sup> BON1 and p53<sup>mutated</sup> NCI-H727 cells were resistant to NVP-CGM097. Incubation of GOT1 cells with NVP-CGM097 at 100, 500, and 2,500 nM for 96 h caused a significant decline in cell viability to 84.9 ± 9.2% (<i>p</i> &lt; 0.05), 77.4 ± 6.6% (<i>p</i> &lt; 0.01), and 47.7 ± 9.2% (<i>p</i> &lt; 0.01). In a Western blot analysis of GOT1 cells, NVP-CGM097 caused a dose-dependent increase in the expression of p53 and p21 tumor suppressor proteins and a decrease in phospho-Rb and E2F1. Experiments of co-incubation of NVP-CGM097 with 5-fluorouracil, temozolomide, or everolimus each showed additive antiproliferative effects in GOT1 cells. NVP-CGM097 and 5-fluorouracil increased p53 and p21 expression in an additive manner. <b><i>Conclusions:</i></b> MDM2 inhibition seems a promising novel therapeutic target in neuroendocrine tumors harboring p53<sup>wild type</sup>. Further investigations should examine the potential role of MDM2 inhibitors in neuroendocrine tumor treatment.
DOI: 10.6084/m9.figshare.4483823
title: Data for PseudoSSIM model for sub-block (4x4, 8x8) prediction using covariance in H.264/AVC

description: Data for PseudoSSIM model for sub-block (4x4, 8x8) prediction using covariance in H.264/AVC <br> Code book: "BlockSize","SSIM","OneMinSSIM1k","Covariance","AbsMeanDiff","PseudoSSIM","TradDist","OneMinSSIM","LogCovar" <br> "BlockSize", 8 for 8x8, 4 for 4x4 "SSIM", Structural Similarity (SSIM) measure "OneMinSSIM1k", 1-SSIM times 1000, to make it an integer "Covariance", statistical component of SSIM "AbsMeanDiff", additional measure of calculating difference between original and reconstructed "PseudoSSIM", proposed measure "TradDist", L1 norm of Sum of Absolute Transform Difference, (SATD) "OneMinSSIM", 1-SSIM used make SSIM score zero based "LogCovar", Log value of covariance scaled against a maximum covariance score observed, ~13k. <br>
DOI: 10.6084/m9.figshare.4483838
title: Robust Parameter Designs in Computer Experiments Using Stochastic Approximation

description: Robust parameter designs are widely used to produce products/processes that perform consistently well across various conditions known as noise factors. Recently, the robust parameter design method is implemented in computer experiments. The structure of conventional product array design becomes unsuitable due to its extensive number of runs and the polynomial modeling. In this article, we propose a new framework robust parameter design via stochastic approximation (RPD-SA) to efficiently optimize the robust parameter design criteria. It can be applied to general robust parameter design problems, but is particularly powerful in the context of computer experiments. It has the following four advantages: (1) fast convergence to the optimal product setting with fewer number of function evaluations; (2) incorporation of high-order effects of both design and noise factors; (3) adaptation to constrained irregular region of operability; (4) no requirement of statistical analysis phase. In the numerical studies, we compare RPD-SA to the Monte Carlo sampling with Newton–Raphson-type optimization. An “Airfoil” example is used to compare the performance of RPD-SA, conventional product array designs, and space-filling designs with the Gaussian process. The studies show that RPD-SA has preferable performance in terms of effectiveness, efficiency and reliability.
DOI: 10.6084/m9.figshare.4483826.v2
title: Cap.6 - Eco Chamber data.xlsx

description: migrants
DOI: 10.6084/m9.figshare.4483838.v2
title: Robust Parameter Designs in Computer Experiments Using Stochastic Approximation

description: Robust parameter designs are widely used to produce products/processes that perform consistently well across various conditions known as noise factors. Recently, the robust parameter design method is implemented in computer experiments. The structure of conventional product array design becomes unsuitable due to its extensive number of runs and the polynomial modeling. In this article, we propose a new framework robust parameter design via stochastic approximation (RPD-SA) to efficiently optimize the robust parameter design criteria. It can be applied to general robust parameter design problems, but is particularly powerful in the context of computer experiments. It has the following four advantages: (1) fast convergence to the optimal product setting with fewer number of function evaluations; (2) incorporation of high-order effects of both design and noise factors; (3) adaptation to constrained irregular region of operability; (4) no requirement of statistical analysis phase. In the numerical studies, we compare RPD-SA to the Monte Carlo sampling with Newton–Raphson-type optimization. An “Airfoil” example is used to compare the performance of RPD-SA, conventional product array designs, and space-filling designs with the Gaussian process. The studies show that RPD-SA has preferable performance in terms of effectiveness, efficiency and reliability.
DOI: 10.6084/m9.figshare.4483826.v1
title: Eco Chamber data.xlsx

description: migrants
DOI: 10.6084/m9.figshare.4483805
title: thca

description: thca
DOI: 10.6084/m9.figshare.4483838.v1
title: Robust Parameter Designs in Computer Experiments using Stochastic Approximation

description: Robust parameter designs are widely used to produce products/processes that perform consistently well across various conditions known as noise factors. Recently, the robust parameter design method is implemented in computer experiments. The structure of conventional product array design becomes unsuitable due to its extensive number of runs and the polynomial modeling. In this paper, we propose a new framework “Robust Parameter Design via Stochastic Approximation” (RPD-SA) to efficiently optimize the robust parameter design criteria. It can be applied to general robust parameter design problems, but is particularly powerful in the context of computer experiments. It has the following four advantages: 1. fast convergence to the optimal product setting with fewer number of function evaluations; 2. incorporation of high-order effects of both design and noise factors; 3. adaptation to constrained irregular region of operability; 4. no requirement of statistical analysis phase. In the numerical studies, we compare RPD-SA to the Monte Carlo sampling with Newton Raphson-type optimization. An “Airfoil” example is used to compare the performance of RPD-SA, conventional product array designs, and space-filling designs with Gaussian Process. The studies show that RPD-SA has preferable performance in terms of effectiveness, efficiency and reliability. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.4483805.v1
title: thca

description: thca
DOI: 10.6084/m9.figshare.4483730
title: Finding reference: a comparison of modelling approaches for predicting macroinvertebrate community index benchmarks

description: Reference benchmarks are needed to assess the contemporary status of rivers and to establish restoration targets. We developed predictive models to estimate site-specific reference values for a macroinvertebrate community index (MCI), which is used to indicate a range of human impacts on wadeable streams. We compared three statistical modelling approaches – general linear, boosted regression tree (BRT) and random forest (RF) – and tested the effect of spatial scale on predictive accuracy by developing national and regional BRT models. Using fitted flexible models (BRT, RF) and resetting predictors to reflect natural state provided the most accurate predictions of reference condition. Variation in reference MCI predictions from national and regional models was within the range observed from methodological and temporal variability. The proportion of native vegetation in upstream catchments was the primary predictor of MCI scores in all models, while secondary predictors varied regionally.
DOI: 10.6084/m9.figshare.4483724
title: From single video sequence - Observations of L1 (SAD, SATD) and L2 (SSE) vs Structural Similarity (SSIM) for Intra and Inter coded frames

description: Observations of L1 (Sum of Absolute Difference (SAD), Sum of Absolute Transform Difference (SATD)) and L2 (Sum of Squared Errors (SSE)) against Structural Similarity (SSIM) at sub-block (4x4) and (8x8) on H.264/AVC. This taken during Intra and Inter coding. Limited to a single video, Foreman, see paper. <br> Please note the following when dataset is unzipped: SAD and SSE is marked out on the folder name, however SATD is marked as PsuedoSSIM. The observations are recorded within file that have an extension/end with .dat (dot dat). <br> Codebook: Below are the headings and an overall description. BlockSize SSIM OneMinSSIM1k Covariance AbsMeanDiff PseudoSSIM TradDist Only the first two columns and the last column were used for the paper referenced. BlockSize – this will be 4 for 4x4, 8 for 8x8. SSIM – SSIM score as calculated using the implementation found within JM H.264/AVC. TradDist – This would refer to L1 or L2 norm of SA(T)D or SSE respectively. <br>OneMinSSIM1k, Covariance, AbsMeanDiff and PseudoSSIM refer to the development of the PsuedoSSIM score, a model to map traditional distortion metric assessment to SSIM values. This is concept is explained in: http://dx.doi.org/10.1109/BMSB.2013.6621695
DOI: 10.6084/m9.figshare.4483730.v1
title: Finding reference: a comparison of modelling approaches for predicting macroinvertebrate community index benchmarks

description: Reference benchmarks are needed to assess the contemporary status of rivers and to establish restoration targets. We developed predictive models to estimate site-specific reference values for a macroinvertebrate community index (MCI), which is used to indicate a range of human impacts on wadeable streams. We compared three statistical modelling approaches – general linear, boosted regression tree (BRT) and random forest (RF) – and tested the effect of spatial scale on predictive accuracy by developing national and regional BRT models. Using fitted flexible models (BRT, RF) and resetting predictors to reflect natural state provided the most accurate predictions of reference condition. Variation in reference MCI predictions from national and regional models was within the range observed from methodological and temporal variability. The proportion of native vegetation in upstream catchments was the primary predictor of MCI scores in all models, while secondary predictors varied regionally.
DOI: 10.6084/m9.figshare.4483493
title: From multiple video sequences - Observations of L1 (Sum of Absolute Transform Difference (SATD)) and Structural Similarity (SSIM) at sub-block (4x4) and (8x8) on H.264/AVC

description: Observations of L1 (Sum of Absolute Transform Difference (SATD)) and Structural Similarity (SSIM) at sub-block (4x4) and (8x8) on H.264/AVC Codebook:Below are the headings and an overall description.BlockSize SSIM OneMinSSIM1k Covariance AbsMeanDiff PseudoSSIM TradDistOnly the first two columns and the last column were used for the paper referenced.BlockSize – this will be 4 for 4x4, 8 for 8x8.SSIM – SSIM score as calculated using the implementation found within JM H.264/AVC.TradDist – This would refer to L1 or L2 norm of SA(T)D or SSE respectively.<br> OneMinSSIM1k, Covariance, AbsMeanDiff and PseudoSSIM refer to the development of the PsuedoSSIM score, a model to map traditional distortion metric assessment to SSIM values.This is concept is explained in: http://dx.doi.org/10.1109/BMSB.2013.6621695
DOI: 10.6084/m9.figshare.4483478
title: SeqID and Rawdata from DNA measurements ft item

description: The Sequence Identities (SeqID) with linked samples and their respective DNA absorbance measurements from Infinite M1000 PRO and DNA concentrations from Qubit ® 2.0 Fluorometer are presented in excel.
DOI: 10.6084/m9.figshare.4483484
title: ContigsReference.fasta

description: Contigs with SNPs in linkage map. Detailed information in: <br>Palomar et al. 2017. Comparative high-density linkage mapping reveals conserve genome structure but variation in levels of heterochiasmy and location of recombination cold spots in the common frog. G3: genes, genomes, genetics.