cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3204325
title: Self-contained ground-truths for cross-domain linkage

description: Cross-domain knowledge bases such as DBpedia, Freebase and YAGO have emerged as encyclopedic hubs in the Web of Linked Data. Despite enabling several practical applications in the Semantic Web, the large-scale, schema-free nature of such graphs often precludes research groups from employing them widely as evaluation test cases for entity resolution and instance-based ontology alignment applications. Although the ground-truth linkages between the three knowledge bases above are available, they are not amenable to resource-limited applications. One reason is that the ground-truth files are not self-contained, meaning that a researcher must usually perform a series of expensive joins (typically in MapReduce) to obtain usable information sets.<br> We constructed this resource by uploading several publicly licensed data resources to the public cloud and used simple Hadoop clusters to compile, and make accessible, three cross-domain self-contained test cases involving linked instances from DBpedia, Freebase and YAGO. Self-containment is enabled by virtue of a simple NoSQL JSON-like serialization format. Potential applications for these resources, particularly related to testing transfer learning research hypotheses, are described in more detail in a paper submission in the resource track at ISWC 2016.
DOI: 10.6084/m9.figshare.3205075.v13
title: NEON Data Institute 2016 - Remote Sensing Data Subsets - Domain 17 - California Field Sites

description: Teaching data subsets for the NEON Lower Teakettle (TEAK), San Joaquin Experimental Range (SJER), and Soaproot Saddle (SOAP) field sites in California (Domain 17). These data sets are used with the NEON Data Institute 2016.
DOI: 10.4225/03/572b2cd646b88
title: Falcons Diversification Evaluation Queries

description: The file contains list of queries used to evaluate search result diversification (fine-drained intent capture in top-k) on Falcons dataset. These queries are selected from TREC web track competitions.<br>
DOI: 10.6084/m9.figshare.3204325.v1
title: Self-contained ground-truths for cross-domain linkage

description: Cross-domain knowledge bases such as DBpedia, Freebase and YAGO have emerged as encyclopedic hubs in the Web of Linked Data. Despite enabling several practical applications in the Semantic Web, the large-scale, schema-free nature of such graphs often precludes research groups from employing them widely as evaluation test cases for entity resolution and instance-based ontology alignment applications. Although the ground-truth linkages between the three knowledge bases above are available, they are not amenable to resource-limited applications. One reason is that the ground-truth files are not self-contained, meaning that a researcher must usually perform a series of expensive joins (typically in MapReduce) to obtain usable information sets.<br> We constructed this resource by uploading several publicly licensed data resources to the public cloud and used simple Hadoop clusters to compile, and make accessible, three cross-domain self-contained test cases involving linked instances from DBpedia, Freebase and YAGO. Self-containment is enabled by virtue of a simple NoSQL JSON-like serialization format. Potential applications for these resources, particularly related to testing transfer learning research hypotheses, are described in more detail in a paper submission in the resource track at ISWC 2016.
DOI: 10.6084/m9.figshare.3205075.v15
title: NEON Data Institute 2016 - Remote Sensing Data Subsets - Domain 17 - California Field Sites

description: Teaching data subsets for the NEON Lower Teakettle (TEAK), San Joaquin Experimental Range (SJER), and Soaproot Saddle (SOAP) field sites in California (Domain 17). These data sets are used with the NEON Data Institute 2016.<br>This teaching data subset is used for several tutorials on the NEON website (neonscience.org). The dataset is for educational purposes, data for research purposes can be obtained from the NEON Data Portal (data.neonscience.org).<br>
DOI: 10.4225/03/572b2d2484472
title: BioPortal Diversification Evaluation Queries

description: The file contains list of queries used to evaluate search result diversification (fine-drained intent capture in top-k) on BioPortal dataset. The queries are selected from the BioPortal querylog.<br>
DOI: 10.4225/03/572b2d6edb7fc
title: Falcons Query Interpretation Evaluation Queries

description: The file contains list of queries used to evaluate our query interpretation approach (search result relevance) on Falcons dataset. These queries are selected from TREC web track competitions.
DOI: 10.6084/m9.figshare.3205075.v14
title: NEON Data Institute 2016 - Remote Sensing Data Subsets - Domain 17 - California Field Sites

description: Teaching data subsets for the NEON Lower Teakettle (TEAK), San Joaquin Experimental Range (SJER), and Soaproot Saddle (SOAP) field sites in California (Domain 17). These data sets are used with the NEON Data Institute 2016.
DOI: 10.6084/m9.figshare.3204178
title: amrZ clean deletion strains in Pseudomonas stutzeri (DBL1052 and DBL1053)

description: A description for the creation of clean deletion mutants of amrZ in Pseudomonas stutzeri.
DOI: 10.6084/m9.figshare.3204181
title: Visualizing Count Data Regressions Using Rootograms

description: The rootogram is a graphical tool associated with the work of J. W. Tukey that was originally used for assessing goodness of fit of univariate distributions. Here, we extend the rootogram to regression models and show that this is particularly useful for diagnosing and treating issues such as overdispersion and/or excess zeros in count data models. We also introduce a weighted version of the rootogram that can be applied out of sample or to (weighted) subsets of the data, for example, in finite mixture models. An empirical illustration revisiting a well-known dataset from ethology is included, for which a negative binomial hurdle model is employed. Supplementary materials providing two further illustrations are available online: the first, using data from public health, employs a two-component finite mixture of negative binomial models; the second, using data from finance, involves underdispersion. An R implementation of our tools is available in the R package countreg. It also contains the data and replication code.
DOI: 10.6084/m9.figshare.3204184
title: FFT-Based Fast Computation of Multivariate Kernel Density Estimators With Unconstrained Bandwidth Matrices

description: The problem of fast computation of multivariate kernel density estimation (KDE) is still an open research problem. In our view, the existing solutions do not resolve this matter in a satisfactory way. One of the most elegant and efficient approach uses the fast Fourier transform. Unfortunately, the existing FFT-based solution suffers from a serious limitation, as it can accurately operate only with the constrained (i.e., diagonal) multivariate bandwidth matrices. In this article, we describe the problem and give a satisfactory solution. The proposed solution may be successfully used also in other research problems, for example, for the fast computation of the optimal bandwidth for KDE. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3204175
title: pMTN1907 Manual and Sequence

description: A genbank file containing pseudomolecule sequence for pMTN1907 plasmid<br>A PDF manual for creating deletions with pMTN1907<br>Please cite first description of pMTN1907 in reference:<br>Mol Plant Microbe Interact. 2012 Jul;25(7):877-88. doi: 10.1094/MPMI-08-11-0218.The molecular basis of host specialization in bean pathovars of Pseudomonas syringae.Baltrus DA1, Nishimura MT, Dougherty KM, Biswas S, Mukhtar MS, Vicente J, Holub EB, Dangl JL.<br>http://apsjournals.apsnet.org/doi/abs/10.1094/MPMI-08-11-0218
DOI: 10.6084/m9.figshare.3204178.v1
title: amrZ clean deletion strains in Pseudomonas stutzeri (DBL1052 and DBL1053)

description: A description for the creation of clean deletion mutants of amrZ in Pseudomonas stutzeri.
DOI: 10.6084/m9.figshare.3204184.v2
title: FFT-Based Fast Computation of Multivariate Kernel Density Estimators With Unconstrained Bandwidth Matrices

description: The problem of fast computation of multivariate kernel density estimation (KDE) is still an open research problem. In our view, the existing solutions do not resolve this matter in a satisfactory way. One of the most elegant and efficient approach uses the fast Fourier transform. Unfortunately, the existing FFT-based solution suffers from a serious limitation, as it can accurately operate only with the constrained (i.e., diagonal) multivariate bandwidth matrices. In this article, we describe the problem and give a satisfactory solution. The proposed solution may be successfully used also in other research problems, for example, for the fast computation of the optimal bandwidth for KDE. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3204181.v2
title: Visualizing Count Data Regressions Using Rootograms

description: The rootogram is a graphical tool associated with the work of J. W. Tukey that was originally used for assessing goodness of fit of univariate distributions. Here, we extend the rootogram to regression models and show that this is particularly useful for diagnosing and treating issues such as overdispersion and/or excess zeros in count data models. We also introduce a weighted version of the rootogram that can be applied out of sample or to (weighted) subsets of the data, for example, in finite mixture models. An empirical illustration revisiting a well-known dataset from ethology is included, for which a negative binomial hurdle model is employed. Supplementary materials providing two further illustrations are available online: the first, using data from public health, employs a two-component finite mixture of negative binomial models; the second, using data from finance, involves underdispersion. An R implementation of our tools is available in the R package countreg. It also contains the data and replication code.
DOI: 10.6084/m9.figshare.3204184.v1
title: FFT-Based Fast Computation of Multivariate Kernel Density Estimators with Unconstrained Bandwidth Matrices

description: The problem of fast computation of multivariate kernel density estimation (KDE) is still an open research problem. In our view, the existing solutions do not resolve this matter in a satisfactory way. One of the most elegant and efficient approach utilizes the fast Fourier transform. Unfortunately, the existing FFT-based solution suffers from a serious limitation, as it can accurately operate only with the constrained (i.e., diagonal) multivariate bandwidth matrices. In this paper we describe the problem and give a satisfactory solution. The proposed solution may be successfully used also in other research problems, for example for the fast computation of the optimal bandwidth for KDE.
DOI: 10.6084/m9.figshare.3204181.v1
title: Visualizing Count Data Regressions Using Rootograms

description: The rootogram is a graphical tool associated with the work of J. W. Tukey that was originally used for assessing goodness of fit of univariate distributions. Here we extend the rootogram to regression models and show that this is particularly useful for diagnosing and treating issues such as overdispersion and/or excess zeros in count data models. We also introduce a weighted version of the rootogram that can be applied out of sample or to (weighted) subsets of the data, e.g., in finite mixture models. An empirical illustration revisiting a well-known data set from ethology is included, for which a negative binomial hurdle model is employed. Supplementary materials providing two further illustrations are available online: the first, using data from public health, employs a two-component finite mixture of negative binomial models, the second, using data from finance, involves underdispersion. An <b>R</b> implementation of our tools is available in the <b>R</b> package <b>countreg</b>. It also contains the data and replication code.
DOI: 10.6084/m9.figshare.3204154
title: Single-Arm Phase II Survival Trial Design Under the Proportional Hazards Model

description: For designing single-arm phase II trials with time-to-event endpoints, a sample size formula is derived for the modified one-sample log-rank test under the proportional hazards model. The derived formula enables new methods for designing trials that allow a flexible choice of the underlying survival distribution. Simulation results showed that the proposed formula provides an accurate estimation of sample size. The sample size calculation has been implemented in an R function for the purpose of trial design. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3204154.v1
title: Single-Arm Phase II Survival Trial Design Under the Proportional Hazards Model

description: For designing single-arm phase II trials with time-to-event endpoints, a sample size formula is derived for the modified one-sample log-rank test under the proportional hazards model. The derived formula enables new methods for designing trials that allow a flexible choice of the underlying survival distribution. Simulation results showed that the proposed formula provides an accurate estimation of sample size. The sample size calculation has been implemented in an R function for the purpose of trial design. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3203938
title: WMFire RHESSys Assessment 1

description: Data generated by RHESSys for Santa Fe and HJ Andrews watersheds, used to run WMFire fire spread model for each watershed (SFNoFireRasters, HJNoFireRasters), as well as model results (IgnPoisRuns). Model results are organized by ignition rate (e.g., *01 has a mean monthly ignition rate of 0.10) and watershed.
DOI: 10.6084/m9.figshare.3203929
title: Making your research reproducible

description: Talk given at University of Cambridge Postdoc Masterclass April 27th 2016.<br>
DOI: 10.6084/m9.figshare.3203929.v1
title: Making your research reproducible

description: Talk given at University of Cambridge Postdoc Masterclass April 27th 2016.<br>
DOI: 10.6084/m9.figshare.3203782
title: supplementary figures_revised2.pptx

description: Figures and datasets for Gangadhara et al 2016 BMC Cancer
DOI: 10.6084/m9.figshare.3203785
title: Categorías, esquemas y sombras: el caso del fideicomiso peruano

description: Se busca definir el rol que cumplen las categorías y los esquemas dentro del proceso cognitivo del ser humano; el papel obstructivo que juegan los conceptos legales en el Civil Law; y, la noción filosófica y legal de “derecho”. Todos estos campos son analizados en el ámbito del fideicomiso peruano, especialmente el organizacional.<br>
DOI: 10.6084/m9.figshare.3203785.v1
title: Categorías, esquemas y sombras: el caso del fideicomiso peruano

description: Se busca definir el rol que cumplen las categorías y los esquemas dentro del proceso cognitivo del ser humano; el papel obstructivo que juegan los conceptos legales en el Civil Law; y, la noción filosófica y legal de “derecho”. Todos estos campos son analizados en el ámbito del fideicomiso peruano, especialmente el organizacional.<br>
DOI: 10.6084/m9.figshare.3203782.v1
title: supplementary figures_revised2.pptx

description: Figures and datasets for Gangadhara et al 2016 BMC Cancer
DOI: 10.6084/m9.figshare.3203803.v2
title: Investigating Open Access Attitudes by Discipline at Mississippi State University

description: Presented at Institutional Repository Day (April 29, 2016) at University of Southern Mississippi.
DOI: 10.6084/m9.figshare.3203740
title: Failure pattern and survival after breast conserving therapy. Long-term results of the Danish Breast Cancer Group (DBCG) 89 TM cohort

description: Based on the results from the DBCG 82 trial, breast conserving therapy (BCT) has been implemented as standard in Denmark since 1989, and today constitutes more than 70% of the primary treatment. Our aim was to evaluate the implementation of BCT as a routine procedure in patients treated according to the DBCG 89 program and compare recurrence pattern and survival both overall and when separated in age groups, with the results from the randomized DBCG 82 TM trial. <b>Material and methods</b>: A total of 1847 patients treated between 1989 and 1999 were included in a retrospective population-based cohort study. Data from the DBCG database were completed via search through the Danish Pathology Data Bank and medical records. <b>Results</b>: Median follow-up time was 17 years. At 20 years the cumulative incidences of local recurrence (LR) and disease-specific mortality (DSM) were 15.3% and 25.8%, respectively. Twenty-year overall survival (OS) and recurrence-free survival were 63.7% and 43.1%, respectively. Subdivided by age groups cumulative incidences at 20 years were LR: 18.9%, 10.5% and 12.4%, and DSM: 28.9%, 18.9% and 28.4% in young (≤45 years), middle-aged (46–55 years) and older (≥56 years) women, respectively. In an adjusted analysis age maintained a significant and independent effect on both LR and DSM. <b>Conclusion</b>: The DBCG 82 TM program was successfully implemented. The women treated with BCT in the DBCG 89 program displayed equal failure pattern and improved survival in comparison with women from the DBCG 82 TM protocol. Occurrence of first failure and mortality varied with age; demonstrated by increased risk of LR, DM and DSM in the young patients and increased risk of DM and DSM in the older patients, compared to the middle-aged patients.
DOI: 10.6084/m9.figshare.3203740.v1
title: Failure pattern and survival after breast conserving therapy. Long-term results of the Danish Breast Cancer Group (DBCG) 89 TM cohort

description: Based on the results from the DBCG 82 trial, breast conserving therapy (BCT) has been implemented as standard in Denmark since 1989, and today constitutes more than 70% of the primary treatment. Our aim was to evaluate the implementation of BCT as a routine procedure in patients treated according to the DBCG 89 program and compare recurrence pattern and survival both overall and when separated in age groups, with the results from the randomized DBCG 82 TM trial. <b>Material and methods</b>: A total of 1847 patients treated between 1989 and 1999 were included in a retrospective population-based cohort study. Data from the DBCG database were completed via search through the Danish Pathology Data Bank and medical records. <b>Results</b>: Median follow-up time was 17 years. At 20 years the cumulative incidences of local recurrence (LR) and disease-specific mortality (DSM) were 15.3% and 25.8%, respectively. Twenty-year overall survival (OS) and recurrence-free survival were 63.7% and 43.1%, respectively. Subdivided by age groups cumulative incidences at 20 years were LR: 18.9%, 10.5% and 12.4%, and DSM: 28.9%, 18.9% and 28.4% in young (≤45 years), middle-aged (46–55 years) and older (≥56 years) women, respectively. In an adjusted analysis age maintained a significant and independent effect on both LR and DSM. <b>Conclusion</b>: The DBCG 82 TM program was successfully implemented. The women treated with BCT in the DBCG 89 program displayed equal failure pattern and improved survival in comparison with women from the DBCG 82 TM protocol. Occurrence of first failure and mortality varied with age; demonstrated by increased risk of LR, DM and DSM in the young patients and increased risk of DM and DSM in the older patients, compared to the middle-aged patients.
DOI: 10.6084/m9.figshare.3203521
title: Do forest resources help increase rural household income and alleviate rural poverty? Empirical evidence from Bhutan

description: About 73% of Bhutan’s land area is currently under forest coverage, and the forest occupies a potentially important position in promoting rural livelihood and thereby alleviating the poverty of people living in and around the forest. This study uses data from the Bhutan Living Standard Survey to examine the relative contribution of wood and non-wood-based forest products to rural household income and poverty alleviation. It uses a propensity score matching approach to correct for potential sample selection bias that may arise due to systematic differences between households who exploit forest resources and those who do not. Our results show that rural households with forestry related activities have a higher income and are less prone to poverty than those who do not exploit forest resources. However, the increase in income due to forestry activities is in general limited, although this increase may be substantial for the poorest households, representing up to 25% of their income. Our results also confirm the global trend that wood-based forest products are more economically rewarding than non-wood forest products. We conclude with some policy implications underlining the potential of the development of forest activities for the betterment of the rural poor in Bhutan.
DOI: 10.6084/m9.figshare.3203422
title: Designing and validation of a yoga-based intervention for obsessive compulsive disorder

description: Some yoga-based practices have been found to be useful for patients with obsessive compulsive disorder (OCD). The authors could not find a validated yoga therapy module available for OCD. This study attempted to formulate a generic yoga-based intervention module for OCD. A yoga module was designed based on traditional and contemporary yoga literature. The module was sent to 10 yoga experts for content validation. The experts rated the usefulness of the practices on a scale of 1–5 (5 = extremely useful). The final version of the module was pilot-tested on patients with OCD (<i>n</i> = 17) for both feasibility and effect on symptoms. Eighty-eight per cent (22 out of 25) of the items in the initial module were retained, with modifications in the module as suggested by the experts along with patients’ inputs and authors’ experience. The module was found to be feasible and showed an improvement in symptoms of OCD on total Yale-Brown Obsessive-Compulsive Scale (YBOCS) score (<i>p</i> = 0.001). A generic yoga therapy module for OCD was validated by experts in the field and found feasible to practice in patients. A decrease in the symptom scores was also found following yoga practice of 2 weeks. Further clinical validation is warranted to confirm efficacy.
DOI: 10.6084/m9.figshare.3203521.v1
title: Do forest resources help increase rural household income and alleviate rural poverty? Empirical evidence from Bhutan

description: About 73% of Bhutan’s land area is currently under forest coverage, and the forest occupies a potentially important position in promoting rural livelihood and thereby alleviating the poverty of people living in and around the forest. This study uses data from the Bhutan Living Standard Survey to examine the relative contribution of wood and non-wood-based forest products to rural household income and poverty alleviation. It uses a propensity score matching approach to correct for potential sample selection bias that may arise due to systematic differences between households who exploit forest resources and those who do not. Our results show that rural households with forestry related activities have a higher income and are less prone to poverty than those who do not exploit forest resources. However, the increase in income due to forestry activities is in general limited, although this increase may be substantial for the poorest households, representing up to 25% of their income. Our results also confirm the global trend that wood-based forest products are more economically rewarding than non-wood forest products. We conclude with some policy implications underlining the potential of the development of forest activities for the betterment of the rural poor in Bhutan.