cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5510098
title: Interactive Visualization of Hierarchically Structured Data

description: We introduce methods for visualization of data structured along trees, especially hierarchically structured collections of time series. To this end, we identify questions that often emerge when working with hierarchical data and provide an R package to simplify their investigation. Our key contribution is the adaptation of the visualization principles of focus-plus-context and linking to the study of tree-structured data. Our motivating application is to the analysis of bacterial time series, where an evolutionary tree relating bacteria is available a priori. However, we have identified common problem types where, if a tree is not directly available, it can be constructed from data and then studied using our techniques. We perform detailed case studies to describe the alternative use cases, interpretations, and utility of the proposed visualization methods.
DOI: 10.6084/m9.figshare.5510098.v1
title: Interactive Visualization of Hierarchically Structured Data

description: We introduce methods for visualization of data structured along trees, especially hierarchically structured collections of time series. To this end, we identify questions that often emerge when working with hierarchical data and provide an R package to simplify their investigation. Our key contribution is the adaptation of the visualization principles of focus-plus-context and linking to the study of tree-structured data. Our motivating application is to the analysis of bacterial time series, where an evolutionary tree relating bacteria is available a priori. However, we have identified common problem types where, if a tree is not directly available, it can be constructed from data and then studied using our techniques. We perform detailed case studies to describe the alternative use cases, interpretations, and utility of the proposed visualization methods.
DOI: 10.6084/m9.figshare.5510104.v1
title: Stochastic Spanning

description: This study develops and implements methods for determining whether introducing new securities or relaxing investment constraints improves the investment opportunity set for all risk averse investors. We develop a test procedure for “stochastic spanning” for two nested portfolio sets based on subsampling and linear programming. The test is statistically consistent and asymptotically exact for a class of weakly dependent processes. A Monte Carlo simulation experiment shows good statistical size and power properties in finite samples of realistic dimensions. In an application to standard datasets of historical stock market returns, we accept market portfolio efficiency but reject two-fund separation, which suggests an important role for higher-order moment risk in portfolio theory and asset pricing. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5510101.v2
title: Estimation of Models With Multiple-Valued Explanatory Variables

description: We study estimation and inference when there are multiple values (“matches”) for the explanatory variables and only one of the matches is the correct one. This problem arises often when two datasets are linked together on the basis of information that does not uniquely identify regressor values. We offer a set of two intuitive conditions that ensure consistent inference using the average of the possible matches in a linear framework. The first condition is the exogeneity of the false match with respect to the regression error. The second condition is a notion of exchangeability between the true and false matches. Conditioning on the observed data, the probability that each match is correct is completely unrestricted. We perform a Monte Carlo study to investigate the estimator’s finite-sample performance relative to others proposed in the literature. Finally, we provide an empirical example revisiting a main area of application: the measurement of intergenerational elasticities in income. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5509531
title: Supporting Files to "An Illumina metabarcoding pipeline for fungi"

description: Example data to article "Bálint*, M., Schmidt*, P.-A., Sharma, R., Thines, M. & Schmitt, I. (2014): An Illumina metabarcoding pipeline for fungi. Ecology and Evolution, 4: 2642-2653."
DOI: 10.6084/m9.figshare.5510101.v1
title: Estimation of Models with Multiple-Valued Explanatory Variables

description: We study estimation and inference when there are multiple values (“matches”) for the explanatory variables and only one of the matches is the correct one. This problem arises often when two datasets are linked together on the basis of information that does not uniquely identify regressor values. We offer a set of two intuitive conditions which ensure consistent inference using the average of the possible matches in a linear framework. The first condition is the exogeneity of the false match with respect to the regression error. The second condition is a notion of exchangeability between the true and false matches. Conditioning on the observed data, the probability that each match is correct is completely unrestricted. We perform a Monte Carlo study to investigate the estimator's finite-sample performance relative to others proposed in the literature. Finally, we provide an empirical example revisiting a main area of application: the measurement of intergenerational elasticities in income.
DOI: 10.17028/rd.lboro.5509528
title: Experimental data - modelling the bending response of soft pneumatic actuators

description: File contains the experimental data generated from testing the soft bending actuators with embedded flex sensor at varying input conditions. The data was split and used for training and testing an empirical model describing the bending response of the soft actuators, for prediction and control purposes.
DOI: 10.6084/m9.figshare.5509525
title: SeymourCommsBio2017_Data.xlsx

description: CT values and copy number (CN) values from the eDNA experiment detailed in Seymour <i>et al</i>. (2017) Communication Biology. Columns are 1) Site 2) Channel ID 3) Sample replicate ID 4) Hour that the sample was taken 5) <i>Daphnia magna</i> CT value 6) <i>Daphnia magna</i> CN value 7) <i>Ephemera danica</i> CT value 8) <i>Ephemera danica</i> CN value 9) <i>Anguilla anguilla</i> CT value 10) <i>Anguilla anguilla</i> CN value
DOI: 10.6084/m9.figshare.5509531.v1
title: Supporting Files to "An Illumina metabarcoding pipeline for fungi"

description: Example data to article "Bálint*, M., Schmidt*, P.-A., Sharma, R., Thines, M. & Schmitt, I. (2014): An Illumina metabarcoding pipeline for fungi. Ecology and Evolution, 4: 2642-2653."
DOI: 10.17028/rd.lboro.5509528.v1
title: Experimental data - modelling the bending response of soft pneumatic actuators

description: File contains the experimental data generated from testing the soft bending actuators with embedded flex sensor at varying input conditions. The data was split and used for training and testing an empirical model describing the bending response of the soft actuators, for prediction and control purposes.
DOI: 10.6084/m9.figshare.5509510
title: Omega3_cognitionUntitled Item

description: Dataset for the placebo-controlled double-blind randomized trial of a supplementation rich in omega-3 PUFA in patients aged 75 or more years. <br>PLEASE BEFORE USING THIS DATA SET CONTACT TO MAIRA BES-RASTROLLO (mbes@unav.es)
DOI: 10.6084/m9.figshare.5509525.v1
title: SeymourCommsBio2017_Data.xlsx

description: CT values and copy number (CN) values from the eDNA experiment detailed in Seymour <i>et al</i>. (2017) Communication Biology. Columns are 1) Site 2) Channel ID 3) Sample replicate ID 4) Hour that the sample was taken 5) <i>Daphnia magna</i> CT value 6) <i>Daphnia magna</i> CN value 7) <i>Ephemera danica</i> CT value 8) <i>Ephemera danica</i> CN value 9) <i>Anguilla anguilla</i> CT value 10) <i>Anguilla anguilla</i> CN value
DOI: 10.6084/m9.figshare.5509501
title: Comparison of Vai script (pdf version)

description: This dataset is a comprehensive diachronic comparison of the Vai script of Liberia, as derived from sixteen sources dated between 1834 and 2005. It can be viewed as a webpage at https://ftp.shh.mpg.de/kelly/Vai.html.<br>A sortable docx version can also be downloaded from figshare. <br>Please note that a subset of these graphemes have been traced as svg vector images. You can download them here: https://doi.org/10.6084/m9.figshare.5897158.v1<br>The same graphemes with a black background can be found here: https://doi.org/10.6084/m9.figshare.5901337.v1
DOI: 10.6084/m9.figshare.5509510.v1
title: Omega3_cognitionUntitled Item

description: Dataset for the placebo-controlled double-blind randomized trial of a supplementation rich in omega-3 PUFA in patients aged 75 or more years. <br>PLEASE BEFORE USING THIS DATA SET CONTACT TO MAIRA BES-RASTROLLO (mbes@unav.es)
DOI: 10.6084/m9.figshare.5509459
title: The Role of Savings and Credit in Coping with Idiosyncratic Household Shocks

description: This study examines the effect of access to formal banking services on households’ ability to smooth consumption in response to illness of adult workers. The institutional peculiarities of Indonesia’s largest commercial bank are exploited to separately estimate the effects of access to formal credit from savings. The means by which households smooth consumption differs depending on their access to formal services. Those with access to formal credit increase borrowing from banks, while those with access only to formal savings, but not credit, draw down on savings. Households without access to formal banking services end up liquidating productive assets.
DOI: 10.6084/m9.figshare.5509459.v1
title: The Role of Savings and Credit in Coping with Idiosyncratic Household Shocks

description: This study examines the effect of access to formal banking services on households’ ability to smooth consumption in response to illness of adult workers. The institutional peculiarities of Indonesia’s largest commercial bank are exploited to separately estimate the effects of access to formal credit from savings. The means by which households smooth consumption differs depending on their access to formal services. Those with access to formal credit increase borrowing from banks, while those with access only to formal savings, but not credit, draw down on savings. Households without access to formal banking services end up liquidating productive assets.
DOI: 10.6084/m9.figshare.5509465
title: Assemblies of icefishes

description: File Family Speciesfish_57.scf/utg.fasta.gz Eleginopsidae Eleginops maclovinusfish_58.scf/utg.fasta.gz Nototheniidae Patagonotothen guntherifish_59.scf/utg.fasta.gz Nototheniidae Trematomus newnesifish_60.scf/utg.fasta.gz Nototheniidae Pleuragramma antarcticumfish_62.scf/utg.fasta.gz Artedidraconidae Artedidraco skottsbergifish_63.scf/utg.fasta.gz Harpagiferidae Harpagifer kerguelensisfish_64.scf/utg.fasta.gz Bathydraconidae Gymnodraco acuticeps
DOI: 10.6084/m9.figshare.5509465.v2
title: Assemblies of icefishes

description: File Family Speciesfish_57.scf/utg.fasta.gz Eleginopsidae Eleginops maclovinusfish_58.scf/utg.fasta.gz Nototheniidae Patagonotothen guntherifish_59.scf/utg.fasta.gz Nototheniidae Trematomus newnesifish_60.scf/utg.fasta.gz Nototheniidae Pleuragramma antarcticumfish_62.scf/utg.fasta.gz Artedidraconidae Artedidraco skottsbergifish_63.scf/utg.fasta.gz Harpagiferidae Harpagifer kerguelensisfish_64.scf/utg.fasta.gz Bathydraconidae Gymnodraco acuticeps
DOI: 10.6084/m9.figshare.5509429
title: R-CNN VGG nail plate detect model

description: Requirements- Linux (Ubuntu)<br>- NVIDIA GPU (GTX-1050 or better)<br>- BVLC PyCaffe<br>- py-faster RCNNs<br><br>Download- VGG-16 nail part detection model<br>- demo_nail.py<br><br>How to use1. It is difficult to compile a CPU-mode faster-rcnn on Windows operating system at present. <br>NVidia GPU with CUDA and cuDNN is required because it takes too much time to conduct CNNs training without GPU<br>We recommend to install py-faster-rcnn program (https://github.com/rbgirshick/py-faster-rcnn) which operated on Linux (http://ubuntu.com).<br>Installation Tutorial by Huangying : https://huangying-zhan.github.io/2016/09/22/detection-faster-rcnn.html<br><br>2. Download (VGG-16 nail part detection model) <br>Model - VGG-16 nail part detection ; 2 outputs(class) : #0 background #1 nail<br><br>The VGG-16 nail part model was trained using information about the crop location on the nail part from the Asan A2 dataset as instructed by the following tutorials.<br>http://sgsai.blogspot.kr/2016/02/training-faster-r-cnn-on-custom-dataset.html<br>https://github.com/deboc/py-faster-rcnn/tree/master/help<br><br>3. We modified demo.py of py-faster-rcnn (https://github.com/rbgirshick/py-faster-rcnn/blob/master/tools/demo.py) to get the following image.<br><br>Download our demo_nail.py ( #1 Main Server; US East ) <br>
DOI: 10.6084/m9.figshare.5509432
title: Model - Hand and Foot Image Selector

description: Requirements- BVLC PyCaffe for Python example<br><br>Download- Caffe Model + Python source + WIN64 EXE example :<br><br>How to useResNet-152; 3 outputs : #0 handfoot photos #1 others #2 index photos<br><br>We created a Windows 64bit executable using pyinstaller (http://www.pyinstaller.org).<br>Example)1) Windows 64bit EXE example<br>c:\handfoot\demo.bat<br><br>2) Python example ; requirements - PyCaffe<br>handfoot.bat [source_path] [result_prefix]
DOI: 10.6084/m9.figshare.5509441
title: Model - Fine Image Selector

description: Requirements- BVLC PyCaffe<br><br>Download- Model Fine image selector :<br><br>How to useResNet-152; 6 outputs<br>#0 nail<br>#1 non-focused or tilted nail<br>#2 skin photo, not nail<br>#3 skin photo, not nail<br>#4 index photo, or EMR screenshot<br>#5 non-skin photo, general internet images<br>
DOI: 10.6084/m9.figshare.5509435
title: Codes_for_Plos.zip

description: Empirical analysis of vegetation dynamics and the possibility of a catastrophic desertification transition. - Codes<br>The tif files are a sample of the real DATA of area number 1.<br>
DOI: 10.6084/m9.figshare.5509429.v1
title: R-CNN VGG nail plate detect model

description: Requirements- Linux (Ubuntu)<br>- NVIDIA GPU (GTX-1050 or better)<br>- BVLC PyCaffe<br>- py-faster RCNNs<br><br>Download- VGG-16 nail part detection model : <br>- demo_nail.py : #1 Main Server; US East <br><br>How to use1. It is difficult to compile a CPU-mode faster-rcnn on Windows operating system at present. <br>NVidia GPU with CUDA and cuDNN is required because it takes too much time to conduct CNNs training without GPU<br>We recommend to install py-faster-rcnn program (https://github.com/rbgirshick/py-faster-rcnn) which operated on Linux (http://ubuntu.com).<br>Installation Tutorial by Huangying : https://huangying-zhan.github.io/2016/09/22/detection-faster-rcnn.html<br><br>2. Download (VGG-16 nail part detection model) : #1 OneDrive (483 Mbytes)<br>Model - VGG-16 nail part detection ; 2 outputs(class) : #0 background #1 nail<br><br>The VGG-16 nail part model was trained using information about the crop location on the nail part from the Asan A2 dataset as instructed by the following tutorials.<br>http://sgsai.blogspot.kr/2016/02/training-faster-r-cnn-on-custom-dataset.html<br>https://github.com/deboc/py-faster-rcnn/tree/master/help<br><br>3. We modified demo.py of py-faster-rcnn (https://github.com/rbgirshick/py-faster-rcnn/blob/master/tools/demo.py) to get the following image.<br><br>Download our demo_nail.py ( #1 Main Server; US East ) <br>
DOI: 10.6084/m9.figshare.5508643
title: All Sample Descriptions and Locations

description: List of sample names, coordinates and descriptions, plus Google Earth .kmz file of sample locations.
DOI: 10.6084/m9.figshare.5508634
title: SUPPLEMENTARY FILE for LESSONS LEARNT FROM EPIDEMIOLOGICAL INVESTIGATION OF LASSA FEVER OUTBREAK.zip

description: This is the data available for the manuscript "<b>Lessons learnt from epidemiological investigation of Lassa fever outbreak in a southwest state of Nigeria December 2015 to April 2016</b>"<br><br>The data provided was used to derived the results section of the manuscript
DOI: 10.6084/m9.figshare.5508622
title: Testing the event witnessing status of micro-bloggers

description: This directory contains the minimum supporting annotation for experiments described in the following paper: Truelove, Marie, Vasardani, Maria and Winter, Stephan (forthcoming). Testing the event witnessing status of micro-bloggers from evidence in their micro-blogs.<br>
DOI: 10.6084/m9.figshare.5508622.v1
title: Testing the event witnessing status of micro-bloggers

description: This directory contains the minimum supporting annotation for experiments described in the following paper: Truelove, Marie, Vasardani, Maria and Winter, Stephan (forthcoming). Testing the event witnessing status of micro-bloggers from evidence in their micro-blogs.<br>
DOI: 10.6084/m9.figshare.5508634.v1
title: SUPPLEMENTARY FILE for LESSONS LEARNT FROM EPIDEMIOLOGICAL INVESTIGATION OF LASSA FEVER OUTBREAK.zip

description: This is the data available for the manuscript "<b>Lessons learnt from epidemiological investigation of Lassa fever outbreak in a southwest state of Nigeria December 2015 to April 2016</b>"<br><br>The data provided was used to derived the results section of the manuscript
DOI: 10.6084/m9.figshare.5508223
title: Predator Mitigation Efficacy_Supplemental Raw Data

description: This is a raw data set that is a supplement to the Scientific Reports paper titled "Rancher-reported efficacy of lethal and non-lethal livestock predation mitigation strategies for a suite of carnivores". This study was conducted under IRB approval to protect human subjects and no subject identifiers are available within this data set to protect the anonymity of participants. The first tab presents meta-data and the second tab presents raw data.
DOI: 10.6084/m9.figshare.5508223.v1
title: Predator Mitigation Efficacy_Supplemental Raw Data

description: This is a raw data set that is a supplement to the Scientific Reports paper titled "Rancher-reported efficacy of lethal and non-lethal livestock predation mitigation strategies for a suite of carnivores". This study was conducted under IRB approval to protect human subjects and no subject identifiers are available within this data set to protect the anonymity of participants. The first tab presents meta-data and the second tab presents raw data.
DOI: 10.6084/m9.figshare.5508079
title: An Efficient Sampling Algorithm for Network Motif Detection

description: We propose a sequential importance sampling strategy to estimate subgraph frequencies and detect network motifs. The method is developed by sampling subgraphs sequentially node by node using a carefully chosen proposal distribution. Viewing the subgraphs as rooted trees, we propose a recursive formula that approximates the number of subgraphs containing a particular node or set of nodes. The proposal used to sample nodes is proportional to this estimated number of subgraphs. The method generates subgraphs from a distribution close to uniform, and performs better than competing methods. We apply the method to four real-world networks and demonstrate outstanding performance in practical examples. Supplemental materials for the article are available online.
DOI: 10.6084/m9.figshare.5508079.v1
title: An Efficient Sampling Algorithm for Network Motif Detection

description: We propose a sequential importance sampling strategy to estimate subgraph frequencies and detect network motifs. The method is developed by sampling subgraphs sequentially node by node using a carefully chosen proposal distribution. Viewing the subgraphs as rooted trees, we propose a recursive formula that approximates the number of subgraphs containing a particular node or set of nodes. The proposal used to sample nodes is proportional to this estimated number of subgraphs. The method generates subgraphs from a distribution close to uniform, and performs better than competing methods. We apply the method to four real-world networks and demonstrate outstanding performance in practical examples. Supplemental materials for the article are available online.
DOI: 10.6084/m9.figshare.5508043
title: Leptin alone and in combination with interleukin-1-beta induced cartilage degradation potentially inhibited by EPA and DHA

description: Osteoarthritis (OA) is the most common form of arthritis. Obesity has been believed to be an important risk factor for OA development and the progression of not only load-bearing joints, but low-load-bearing joints as well. Increased leptin has been the focus of a link between obesity and OA. In this study, the effects of pathological (100ng/ml) or supra-pathological (10μg/ml) concentrations of leptin alone or in combination with IL1β on cartilage metabolisms were studied in porcine cartilage explant. The involved mechanisms were examined in human articular chondrocytes (HACs). Moreover, the protective effect of omega-3 polyunsaturated acids, eicosapentaenoic acid (EPA) or docosahexaenoic acid (DHA) was also investigated. Leptin (10μg/ml) alone or in combination with IL1β could induce cartilage destruction, although lower concentrations had no effect. Leptin activated NFκB, ERK, JNK and p38 in HACs, which led to the induction of MMP3, MMP13 and ADAMTS4 secretions. The combined effect could further induce those enzymes through the additive effect on activation of NFκB and JNK. Interestingly, both EPA and DHA could inhibit cartilage damage induced by leptin plus IL1β by reducing the activation of NFκB and JNK, which led to the decrease of ADAMTS4 secretion. Altogether, only a supra-pathological concentration of leptin alone or in combination with IL1β could induce cartilage destruction, whereas a pathological one could not. This effect could be inhibited by EPA and DHA. To gain greater understanding of the link between leptin and OA, the effect of different levels of leptin on several states of OA cartilage requires further investigation.
DOI: 10.6084/m9.figshare.5508043.v1
title: Leptin alone and in combination with interleukin-1-beta induced cartilage degradation potentially inhibited by EPA and DHA

description: Osteoarthritis (OA) is the most common form of arthritis. Obesity has been believed to be an important risk factor for OA development and the progression of not only load-bearing joints, but low-load-bearing joints as well. Increased leptin has been the focus of a link between obesity and OA. In this study, the effects of pathological (100ng/ml) or supra-pathological (10μg/ml) concentrations of leptin alone or in combination with IL1β on cartilage metabolisms were studied in porcine cartilage explant. The involved mechanisms were examined in human articular chondrocytes (HACs). Moreover, the protective effect of omega-3 polyunsaturated acids, eicosapentaenoic acid (EPA) or docosahexaenoic acid (DHA) was also investigated. Leptin (10μg/ml) alone or in combination with IL1β could induce cartilage destruction, although lower concentrations had no effect. Leptin activated NFκB, ERK, JNK and p38 in HACs, which led to the induction of MMP3, MMP13 and ADAMTS4 secretions. The combined effect could further induce those enzymes through the additive effect on activation of NFκB and JNK. Interestingly, both EPA and DHA could inhibit cartilage damage induced by leptin plus IL1β by reducing the activation of NFκB and JNK, which led to the decrease of ADAMTS4 secretion. Altogether, only a supra-pathological concentration of leptin alone or in combination with IL1β could induce cartilage destruction, whereas a pathological one could not. This effect could be inhibited by EPA and DHA. To gain greater understanding of the link between leptin and OA, the effect of different levels of leptin on several states of OA cartilage requires further investigation.
DOI: 10.6084/m9.figshare.5508016
title: Traits of tick species from the genus Ixodes

description: These data describe anatomical, life history, and ecological traits about tick species in the genus <i>Ixodes</i>.