cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4775422
title: Phylogenetic structure of annual plant communities along an aridity gradient. Interacting effects of habitat filtering and shifting plant–plant interactions

description: The phylogenetic structure of communities (PSC) reveals how evolutionary history affects community assembly processes. However, there are important knowledge gaps on PSC patterns for annual communities and there is a need for studies along environmental gradients in dry ecosystems where several processes shape PSC. Here, we investigated the PSC of annual plants along an aridity gradient in Israel, including eight years, two spatial scales, the effects of shrubs on understory, and the phylogenetic signal of important traits. Increasing drought stress led to overdispersed PSC at the drier end of the gradient, indicating that species were less related than expected by chance. This was supported at a smaller spatial scale, where within the drier sites, communities in open – more arid – habitats were more overdispersed than those under nurse shrubs. Interestingly, some key traits related to drought resistance were not conserved in the phylogeny. Together, our findings suggested that while habitat filtering selected for drought resistance strategies, these strategies evolved independently along multiple contrasting evolutionary lineages. Our comprehensive PSC study provides strong evidence for the interacting effects of habitat filtering and plant–plant interactions, particularly highlighting that the conservative evolution of traits should not be assumed in future interpretations of PSC patterns.
DOI: 10.6084/m9.figshare.4775419
title: MATLAB .m file: Code for food chain model that generates simulated baseline data array. Surveillance scenario analysis code also included. No other data or code are required to replicate results from Towards an integrated food safety surveillance system: a simulation study to explore the potential of combining genomic and epidemiological metadata

description: Foodborne infection is a result of exposure to complex, dynamic food systems. The efficiency of foodborne infection is driven by ongoing shifts in genetic machinery. NGS technologies can provide high-fidelity data about the genetics of a pathogen. However, food safety surveillance systems do not currently provide similar high-fidelity epidemiological metadata to associate with genetic data. As a consequence, it is rarely possible to transform genetic data into actionable knowledge that can be used to genuinely inform risk assessment or prevent outbreaks. Big data approaches are touted as a revolution in decision support, and pose a potentially attractive method for closing the gap between the fidelity of genetic and epidemiological metadata for food safety surveillance. We therefore developed a simple food chain model to investigate the potential benefits of combining ‘big’ data sources, including both genetic and high-fidelity epidemiological metadata. Our results suggest that, as for any surveillance system, the collected data must be relevant and characterize the important dynamics of a system if we are to properly understand risk: this suggests the need to carefully consider data curation, rather than the more ambitious claims of big data proponents that unstructured and unrelated data sources can be combined to generate consistent insight. Of interest is that the biggest influencers of foodborne infection risk were contamination load and processing temperature, not genotype. This suggests that understanding food chain dynamics would likely more effectively generate insight into foodborne risk than prescribing the hazard in ever more detail in terms of genotype.
DOI: 10.6084/m9.figshare.4775431.v2
title: A planet population dichotomy from isotopic enrichment?

description: Talks given in Copenhagen, Leiden, Les Houches and Budapest.
DOI: 10.6084/m9.figshare.4775419.v1
title: MATLAB .m file: Code for food chain model that generates simulated baseline data array. Surveillance scenario analysis code also included. No other data or code are required to replicate results from Towards an integrated food safety surveillance system: a simulation study to explore the potential of combining genomic and epidemiological metadata

description: Foodborne infection is a result of exposure to complex, dynamic food systems. The efficiency of foodborne infection is driven by ongoing shifts in genetic machinery. NGS technologies can provide high-fidelity data about the genetics of a pathogen. However, food safety surveillance systems do not currently provide similar high-fidelity epidemiological metadata to associate with genetic data. As a consequence, it is rarely possible to transform genetic data into actionable knowledge that can be used to genuinely inform risk assessment or prevent outbreaks. Big data approaches are touted as a revolution in decision support, and pose a potentially attractive method for closing the gap between the fidelity of genetic and epidemiological metadata for food safety surveillance. We therefore developed a simple food chain model to investigate the potential benefits of combining ‘big’ data sources, including both genetic and high-fidelity epidemiological metadata. Our results suggest that, as for any surveillance system, the collected data must be relevant and characterize the important dynamics of a system if we are to properly understand risk: this suggests the need to carefully consider data curation, rather than the more ambitious claims of big data proponents that unstructured and unrelated data sources can be combined to generate consistent insight. Of interest is that the biggest influencers of foodborne infection risk were contamination load and processing temperature, not genotype. This suggests that understanding food chain dynamics would likely more effectively generate insight into foodborne risk than prescribing the hazard in ever more detail in terms of genotype.
DOI: 10.6084/m9.figshare.4775422.v1
title: Phylogenetic structure of annual plant communities along an aridity gradient. Interacting effects of habitat filtering and shifting plant–plant interactions

description: The phylogenetic structure of communities (PSC) reveals how evolutionary history affects community assembly processes. However, there are important knowledge gaps on PSC patterns for annual communities and there is a need for studies along environmental gradients in dry ecosystems where several processes shape PSC. Here, we investigated the PSC of annual plants along an aridity gradient in Israel, including eight years, two spatial scales, the effects of shrubs on understory, and the phylogenetic signal of important traits. Increasing drought stress led to overdispersed PSC at the drier end of the gradient, indicating that species were less related than expected by chance. This was supported at a smaller spatial scale, where within the drier sites, communities in open – more arid – habitats were more overdispersed than those under nurse shrubs. Interestingly, some key traits related to drought resistance were not conserved in the phylogeny. Together, our findings suggested that while habitat filtering selected for drought resistance strategies, these strategies evolved independently along multiple contrasting evolutionary lineages. Our comprehensive PSC study provides strong evidence for the interacting effects of habitat filtering and plant–plant interactions, particularly highlighting that the conservative evolution of traits should not be assumed in future interpretations of PSC patterns.
DOI: 10.6084/m9.figshare.4775416
title: Long fuse phylogeny w species-level branching

description: The long fuse phylogeny from the amino acid supermatrix by Meredith et al. (Science, 2011), onto which I appended the intra-family branching patterns from the short fuse phylogeny by Bininda-Emonds et al. (Nature, 2007) and Fritz et al. (Ecology Letters 2009).
DOI: 10.6084/m9.figshare.4775431.v1
title: A planet population dichotomy from isotopic enrichment?

description: Talks given in Copenhagen, Leiden, ETH Zürich, Les Houches and Budapest.
DOI: 10.6084/m9.figshare.4775437.v1
title: GENESIS - the GENEric SImulation System for modelling state transitions.

description: This software is a highly-configurable way of modelling transitions between states, given known transition probabilities. It could therefore be used to model a disease progression and/or recovery in a population, or maybe an environmental process. You can have multiple branching and also bi-directional transitions. Full instructions are given in the README.txt file. You will need to have Perl installed, and a C++ 11 compiler. This software has been tested on both Windows and Linux. You need to have a “state transition table” called stt.txt, and an example is provided. You also need a configuration file config.txt, which sets the initial parameters for the program, and again an example is provided.
DOI: 10.6084/m9.figshare.4775437.v2
title: GENESIS - the GENEric SImulation System for modelling state transitions.

description: This software is a highly-configurable way of modelling transitions between states, given known transition probabilities. It could therefore be used to model a disease progression and/or recovery in a population, or maybe an environmental process. You can have multiple branching and also bi-directional transitions. Full instructions are given in the README.txt file. You will need to have Perl installed, and a C++ 11 compiler. This software has been tested on both Windows and Linux. You need to have a “state transition table” called stt.txt, and an example is provided. You also need a configuration file config.txt, which sets the initial parameters for the program, and again an example is provided.
DOI: 10.6084/m9.figshare.4775392
title: Genome phylogeny from Detecting taxonomic and phylogenetic signals in equid cheek teeth: towards new palaeontological and archaeological proxies

description: Nexus file of the genome wide phylogeny for 10 Equus taxa.
DOI: 10.6084/m9.figshare.4775395
title: Specimens details from Detecting taxonomic and phylogenetic signals in equid cheek teeth: towards new palaeontological and archaeological proxies

description: Information for the 345 specimens of the morphometric dataset regarding Museum location, identifiers in the collection, sex, age and geographic origin.
DOI: 10.6084/m9.figshare.4775398
title: Preview-type source file of FEBio simulation for cellular structure with closed hexagonal prismatic cells of neo-Hookean material. from Microstructure-based hyperelastic models for closed-cell solids

description: A comparison between model (continuous line) and simulation (dashed line) of the effective elastic modulus. The cell-core is 10 times softer than the cell walls for structure 1, 20 times softer than the cell walls for structure 2, and 100 times softer than the walls for structure 3. The closed hexagonal prismatic cells and their inclusions are shown at 20\% (right) tension in the vertical direction (colour bar showing the displacement in the same direction) is shown.
DOI: 10.6084/m9.figshare.4775392.v1
title: Genome phylogeny from Detecting taxonomic and phylogenetic signals in equid cheek teeth: towards new palaeontological and archaeological proxies

description: Nexus file of the genome wide phylogeny for 10 Equus taxa.
DOI: 10.6084/m9.figshare.4775395.v1
title: Specimens details from Detecting taxonomic and phylogenetic signals in equid cheek teeth: towards new palaeontological and archaeological proxies

description: Information for the 345 specimens of the morphometric dataset regarding Museum location, identifiers in the collection, sex, age and geographic origin.
DOI: 10.6084/m9.figshare.4775398.v1
title: Preview-type source file of FEBio simulation for cellular structure with closed hexagonal prismatic cells of neo-Hookean material. from Microstructure-based hyperelastic models for closed-cell solids

description: A comparison between model (continuous line) and simulation (dashed line) of the effective elastic modulus. The cell-core is 10 times softer than the cell walls for structure 1, 20 times softer than the cell walls for structure 2, and 100 times softer than the walls for structure 3. The closed hexagonal prismatic cells and their inclusions are shown at 20\% (right) tension in the vertical direction (colour bar showing the displacement in the same direction) is shown.
DOI: 10.6084/m9.figshare.4775389
title: Preview-type source file of FEBios simulation for cellular structure with closed cubic cells of neo-Hookean material. from Microstructure-based hyperelastic models for closed-cell solids

description: A comparison between model (continuous line) and simulation (dashed line) of the effective elastic modulus. The cell-core is 10 times softer than the cell walls for structure 1, 20 times softer than the cell walls for structure 2, and 100 times softer than the walls for structure 3. The closed cubical cells and their inclusions are shown at 20\% (right) tension in the vertical direction (colour bar showing the displacement in the same direction).
DOI: 10.6084/m9.figshare.4775437.v3
title: GENESIS - the GENEric SImulation System for modelling state transitions.

description: This software is a highly-configurable way of modelling transitions between states, given known transition probabilities. It could therefore be used to model a disease progression and/or recovery in a population, or maybe an environmental process. You can have multiple branching and also bi-directional transitions. Full instructions are given in the README.txt file. You will need to have Perl installed, and a C++ 11 compiler. This software has been tested on both Windows and Linux. You need to have a “state transition table” called stt.txt, and an example is provided. You also need a configuration file config.txt, which sets the initial parameters for the program, and again an example is provided.
DOI: 10.6084/m9.figshare.4775389.v1
title: Preview-type source file of FEBios simulation for cellular structure with closed cubic cells of neo-Hookean material. from Microstructure-based hyperelastic models for closed-cell solids

description: A comparison between model (continuous line) and simulation (dashed line) of the effective elastic modulus. The cell-core is 10 times softer than the cell walls for structure 1, 20 times softer than the cell walls for structure 2, and 100 times softer than the walls for structure 3. The closed cubical cells and their inclusions are shown at 20\% (right) tension in the vertical direction (colour bar showing the displacement in the same direction).
DOI: 10.6084/m9.figshare.4775437.v4
title: GENESIS - the GENEric SImulation System for modelling state transitions.

description: This software is a highly-configurable way of modelling transitions between states, given known transition probabilities. It could therefore be used to model a disease progression and/or recovery in a population, or maybe an environmental process. A test suite is included. You can have multiple branching and also bi-directional transitions. Full instructions are given in the README.txt file. You will need to have Perl installed, and a C++ 11 compiler. This software has been tested on both Windows and Linux. You need to have a “state transition table” called stt.txt, and an example is provided. You also need a configuration file config.txt, which sets the initial parameters for the program, and again an example is provided.
DOI: 10.6084/m9.figshare.4775377
title: Geometric morphometric dataset from Detecting taxonomic and phylogenetic signals in equid cheek teeth: towards new palaeontological and archaeological proxies

description: 356 x and y coordinates extracted from the enamel outline of the 4 mandibular cheek teeth digitized for each of the 345 specimens. Anatomic and Taxonomic factors are provided.
DOI: 10.6084/m9.figshare.4775377.v2
title: Geometric morphometric dataset from Detecting taxonomic and phylogenetic signals in equid cheek teeth: towards new palaeontological and archaeological proxies

description: 356 x and y coordinates extracted from the enamel outline of the 4 mandibular cheek teeth digitized for each of the 345 specimens. Anatomic and Taxonomic factors are provided.
DOI: 10.6084/m9.figshare.4775437.v5
title: GENESIS - the GENEric SImulation System for modelling state transitions.

description: This software is a highly-configurable way of modelling transitions between states, given known transition probabilities. It could therefore be used to model a disease progression and/or recovery in a population, or maybe an environmental process. A test suite is included. You can have multiple branching and also bi-directional transitions. Full instructions are given in the README.txt file. You will need to have Perl installed, and a C++ 11 compiler. This software has been tested on both Windows and Linux. You need to have a “state transition table” called stt.txt, and an example is provided. You also need a configuration file config.txt, which sets the initial parameters for the program, and again an example is provided.
DOI: 10.6084/m9.figshare.4775377.v1
title: Geometric morphometric dataset from Detecting taxonomic and phylogenetic signals in equid cheek teeth: towards new palaeontological and archaeological proxies

description: 356 x and y coordinates extracted from the enamel outline of the 4 mandibular cheek teeth digitized for each of the 345 specimens. Anatomic and Taxonomic factors are provided.
DOI: 10.6084/m9.figshare.4775437.v7
title: GENESIS - the GENEric SImulation System for modelling state transitions.

description: This software is a highly-configurable way of modelling transitions between states, given known transition probabilities. It could therefore be used to model a disease progression and/or recovery in a population, or maybe an environmental process. A test suite is included. You can have multiple branching and also bi-directional transitions. Full instructions are given in the README.txt file. You will need to have Perl installed, and a C++ 11 compiler. This software has been tested on both Windows and Linux. You need to have a “state transition table” called stt.txt, and an example is provided. You also need a configuration file config.txt, which sets the initial parameters for the program, and again an example is provided.
DOI: 10.6084/m9.figshare.4775437.v6
title: GENESIS - the GENEric SImulation System for modelling state transitions.

description: This software is a highly-configurable way of modelling transitions between states, given known transition probabilities. It could therefore be used to model a disease progression and/or recovery in a population, or maybe an environmental process. A test suite is included. You can have multiple branching and also bi-directional transitions. Full instructions are given in the README.txt file. You will need to have Perl installed, and a C++ 11 compiler. This software has been tested on both Windows and Linux. You need to have a “state transition table” called stt.txt, and an example is provided. You also need a configuration file config.txt, which sets the initial parameters for the program, and again an example is provided.
DOI: 10.6084/m9.figshare.4775338
title: Relative change in stream discharge from a tropical watershed improves predictions of fecal bacteria in near-shore environments

description: Statistical models poorly predict bacteria in near-shore environments of tropical islands due to inaccuracies in runoff and discharge characterization of storm events. Intense, short duration storms on small, steeply sloped watersheds produce high rates of runoff, resulting in rapid pulses of discharge that influence the physical and physiological conditions of the fate and transport of pathogens. As such, increasing rates of discharge are expected to have a different influence on sediment transport and pathogen load compared to decreasing rates of discharge. Regression modeling was used to examine the affect of antecedent streamflow on the interaction between environmental parameters and two fecal indicator bacteria, enterococci and <i>Clostridium perfringens</i>. Including the relative change in discharge incorporates a proximate representation of the energy available to transport particulates, improving predictions of near-shore water quality. Understanding factors that influence pathogen loads improves management of watersheds and protects public health.
DOI: 10.6084/m9.figshare.4775320
title: Beliefs and habits: staff experiences with key word signing in special schools and group residential homes

description: Even though use of aided augmentative and alternative communication (AAC) by staff has been extensively researched, few studies relate to unaided AAC strategies such as key word signing (KWS). We explored the KWS views of two groups: direct support staff in group residential homes and teachers from special education secondary schools. We examined transcripts from individual semi-structured interviews with five direct support staff and five teachers using thematic analysis. Participants discussed consistency of KWS use and reasons for implementing KWS. Compared to direct support staff, teachers described more use of KWS throughout the day with more individuals with intellectual disability. Teachers discussed use of KWS to facilitate students’ present and future interactions, while direct support staff primarily discussed immediate effects. Participants experienced KWS implementation as a learning process and aimed to turn the use of manual signs into a routine habit. This required considerable self-monitoring, and the effort that this continuous self-feedback required, combined with environmental factors, could hinder KWS implementation. These preliminary findings suggest that preservice KWS training and on-site KWS assistance may need to be enhanced.
DOI: 10.6084/m9.figshare.4775308
title: Outcome for children treated for medulloblastoma and supratentorial primitive neuroectodermal tumor (CNS-PNET) – a retrospective analysis spanning 40 years of treatment

description: <b>Background:</b> Medulloblastoma (MB) and supratentorial primitive neuroectodermal tumor of the central nervous system (CNS-PNET) are among the most common pediatric brain tumors. The diagnosis, treatment, and outcome of MB/CNS-PNET patients treated during the last four decades at Oslo University Hospital (OUH) are described. <b>Material and methods:</b> All patients younger than 20 years of age diagnosed and treated for MB/CNS-PNET at OUH between 1 January 1974 and 31 December 2013 were identified. <b>Results:</b> We found 175 patients. In 13 of them, the diagnosis was changed upon histopathological review and in 4 patients part of the treatment was administered at other hospitals. Thus, 158 patients were included for further analysis. Eight patients did not receive adjuvant therapy because of a dismal clinical condition. The overall 5-year survival rate for MB and CNS-PNET was 54%, for MB 57%, and for CNS-PNET 41%. Gross total resection (GTR) was achieved in 118 patients and 5-year overall survival for patients with GTR versus those with non-GTR differed significantly with 64% versus 22%. Cytological examination of the cerebrospinal fluid was performed in 52 patients. A total of 126 patients received radiotherapy as part of the primary treatment and 24 did not due to young age. Median time from surgery to start of radiotherapy was 33 days. Duration of radiotherapy was more than 48 days in 22% of patients. At the time of analysis, 63 patients were alive and disease-free, one alive with disease, and 94 patients were deceased; 84 of these due to MB/CNS-PNET and 10 due to supposed late effects from the treatment. <b>Conclusions:</b> Survival was comparable to data from other population-based studies. The importance of GTR for survival was corroborated. Reporting real-world data remains crucial to know the true outcome of patients treated outside clinical trials.