cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.12641454
title: PlasGO_dataset

description: Plasmid, as a mobile genetic element, plays a pivotal role in facilitating the transfer of traits, such as antimicrobial resistance, among the bacterial community. Annotating plasmid-encoded proteins with the widely used Gene Ontology (GO) vocabulary is a fundamental step in various tasks, including plasmid mobility classification. However, GO prediction for plasmid-encoded proteins faces two major challenges: the high diversity of functions and the limited availability of high-quality GO annotations. Thus, we introduce PlasGO, a tool that leverages a hierarchical architecture to predict GO terms for plasmid proteins. PlasGO utilizes a powerful protein language model to learn the local context within protein sentences and a BERT model to capture the global context within plasmid sentences. Additionally, PlasGO allows users to control the precision by incorporating a self-attention confidence weighting mechanism. We rigorously evaluated PlasGO and benchmarked it against six state-of-the-art tools in a series of experiments. The experimental results collectively demonstrate that PlasGO has achieved commendable performance. PlasGO significantly expanded the annotations of the plasmid-encoded protein database by assigning high-confidence GO terms to over 95% of previously unannotated proteins, showcasing impressive precision of 0.8229, 0.7941, and 0.8870 for the three GO categories, respectively, as measured on the novel protein test set. The PlasGO software implemented in Python, the curated RefSeq plasmid protein dataset used to train the PlasGO models and benchmark, and the pre-annotated high-confidence GO database generated by PlasGO are publicly available in this project.
DOI: 10.15468/dl.6vebye
title: Occurrence Download

description: A dataset containing 39736 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen, Fossil)",
 "Country is one of (United States of America, Canada, Mexico)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Ursus americanus Pallas, 1780"
 ]
}

 The dataset includes 39736 records from 84 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005302-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28311889
title: Abietane diterpenoids from <i>Phlegmariurus carinatus</i> and their cytotoxic activities

description: Two new abietane diterpenoids (<b>1</b> and <b>2</b>) and two known analogs (<b>3</b> and <b>4</b>) were isolated from the whole plants of <i>Phlegmariurus carinatus</i>. Their structures were determined by comprehensive spectroscopic methods (UV, IR, NMR, and HRESIMS). Moreover, all compounds were evaluated for their cytotoxic activities against U251 glioblastoma cells. Notably, compounds <b>1–4</b> exhibited potential cytotoxic activities with IC<sub>50</sub> values ranging from 19.81 to 81.49 μM. In addition, their stabilities were checked by HPLC in the preservation conditions and in the cell lines medium. The result showed that they were relatively stable in the preservation conditions, except for <b>3</b>, but that they were decomposed in the incubation process. Finally, the most possible structures of impurities <b>i1</b>, <b>i3</b> and <b>i4</b> were deduced by spectroscopic methods (UV, HRESIMS and MS/MS). This work provides potential insights for the development of abietane diterpenoids as candidate drugs for the treatment of glioma.
DOI: 10.6084/m9.figshare.28311889.v1
title: Abietane diterpenoids from <i>Phlegmariurus carinatus</i> and their cytotoxic activities

description: Two new abietane diterpenoids (<b>1</b> and <b>2</b>) and two known analogs (<b>3</b> and <b>4</b>) were isolated from the whole plants of <i>Phlegmariurus carinatus</i>. Their structures were determined by comprehensive spectroscopic methods (UV, IR, NMR, and HRESIMS). Moreover, all compounds were evaluated for their cytotoxic activities against U251 glioblastoma cells. Notably, compounds <b>1–4</b> exhibited potential cytotoxic activities with IC<sub>50</sub> values ranging from 19.81 to 81.49 μM. In addition, their stabilities were checked by HPLC in the preservation conditions and in the cell lines medium. The result showed that they were relatively stable in the preservation conditions, except for <b>3</b>, but that they were decomposed in the incubation process. Finally, the most possible structures of impurities <b>i1</b>, <b>i3</b> and <b>i4</b> were deduced by spectroscopic methods (UV, HRESIMS and MS/MS). This work provides potential insights for the development of abietane diterpenoids as candidate drugs for the treatment of glioma.
DOI: 10.6084/m9.figshare.27961622
title: Neural Bayes Estimators for Irregular Spatial Data Using Graph Neural Networks

description: Neural Bayes estimators are neural networks that approximate Bayes estimators in a fast and likelihood-free manner. Although they are appealing to use with spatial models, where estimation is often a computational bottleneck, neural Bayes estimators in spatial applications have, to date, been restricted to data collected over a regular grid. These estimators are also currently dependent on a prescribed set of spatial locations, which means that the neural network needs to be retrained for new datasets; this renders them impractical in many applications and impedes their widespread adoption. In this work, we employ graph neural networks (GNNs) to tackle the important problem of parameter point estimation from data collected over arbitrary spatial locations. In addition to extending neural Bayes estimation to irregular spatial data, the use of GNNs leads to substantial computational benefits, since the estimator can be used with any configuration or number of locations and independent replicates, thus, amortizing the cost of training for a given spatial model. We also facilitate fast uncertainty quantification by training an accompanying neural Bayes estimator that approximates a set of marginal posterior quantiles. We illustrate our methodology on Gaussian and max-stable processes. Finally, we showcase our methodology on a dataset of global sea-surface temperature, where we estimate the parameters of a Gaussian process model in 2161 spatial regions, each containing thousands of irregularly-spaced data points, in just a few minutes with a single graphics processing unit. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.27961622.v1
title: Neural Bayes Estimators for Irregular Spatial Data using Graph Neural Networks

description: Neural Bayes estimators are neural networks that approximate Bayes estimators in a fast and likelihood-free manner. Although they are appealing to use with spatial models, where estimation is often a computational bottleneck, neural Bayes estimators in spatial applications have, to date, been restricted to data collected over a regular grid. These estimators are also currently dependent on a prescribed set of spatial locations, which means that the neural network needs to be re-trained for new data sets; this renders them impractical in many applications and impedes their widespread adoption. In this work, we employ graph neural networks (GNNs) to tackle the important problem of parameter point estimation from data collected over arbitrary spatial locations. In addition to extending neural Bayes estimation to irregular spatial data, the use of GNNs leads to substantial computational benefits, since the estimator can be used with any configuration or number of locations and independent replicates, thus amortising the cost of training for a given spatial model. We also facilitate fast uncertainty quantification by training an accompanying neural Bayes estimator that approximates a set of marginal posterior quantiles. We illustrate our methodology on Gaussian and max-stable processes. Finally, we showcase our methodology on a data set of global sea-surface temperature, where we estimate the parameters of a Gaussian process model in 2161 spatial regions, each containing thousands of irregularly-spaced data points, in just a few minutes with a single graphics processing unit.
DOI: 10.6084/m9.figshare.27961622.v2
title: Neural Bayes Estimators for Irregular Spatial Data Using Graph Neural Networks

description: Neural Bayes estimators are neural networks that approximate Bayes estimators in a fast and likelihood-free manner. Although they are appealing to use with spatial models, where estimation is often a computational bottleneck, neural Bayes estimators in spatial applications have, to date, been restricted to data collected over a regular grid. These estimators are also currently dependent on a prescribed set of spatial locations, which means that the neural network needs to be retrained for new datasets; this renders them impractical in many applications and impedes their widespread adoption. In this work, we employ graph neural networks (GNNs) to tackle the important problem of parameter point estimation from data collected over arbitrary spatial locations. In addition to extending neural Bayes estimation to irregular spatial data, the use of GNNs leads to substantial computational benefits, since the estimator can be used with any configuration or number of locations and independent replicates, thus, amortizing the cost of training for a given spatial model. We also facilitate fast uncertainty quantification by training an accompanying neural Bayes estimator that approximates a set of marginal posterior quantiles. We illustrate our methodology on Gaussian and max-stable processes. Finally, we showcase our methodology on a dataset of global sea-surface temperature, where we estimate the parameters of a Gaussian process model in 2161 spatial regions, each containing thousands of irregularly-spaced data points, in just a few minutes with a single graphics processing unit. Supplementary materials for this article are available online.
DOI: 10.15468/dl.g4e8zp
title: Occurrence Download

description: A dataset containing 2053 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Crax alberti Fraser, 1852"
 ]
}

 The dataset includes 2053 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005304-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.25879705
title: Proportionate mortality following dysvascular partial foot amputation and how this compares to transtibial amputation: a systematic review

description: A large proportion of people die in the years following dysvascular partial foot amputation (PFA) or transtibial amputation (TTA) given the long-term consequences of peripheral vascular disease and/or diabetes. A critical appraisal of recent research is needed to understand the underlying cause of variation and synthesise data for use in consultations about amputation surgery and patient-facing resources. This systematic review aimed to describe proportionate mortality following dysvascular PFA and to compare this between PFA and TTA. The review protocol was registered in PROSPERO (CRD42023399161). Peer-reviewed studies of original research were included if they: were published in English between 1 January 2016, and 12 April 2024, included discrete cohorts with PFA, or PFA and TTA, and measured proportionate mortality following dysvascular amputation. Seventeen studies were included in the review. Following dysvascular PFA, proportionate mortality increased from 30 days (2.1%) to 1-year (13.9%), 3-years (30.1%), and 5-years (42.2%). One study compared proportionate mortality 1-year after dysvascular PFA and TTA, showing a higher relative risk of dying after TTA (RR 1.51). Proportionate mortality has not changed in recent years. These results are comparable to a previous systematic review that included studies published before 31 December 2015.Implications for rehabilitationIt is important to ensure data describing mortality in the years following dysvascular partial foot or transtibial amputation is up to date and accurate.Evidence about proportionate mortality has not changed in recent years and the results are comparable to previous systematic reviews.Data describing mortality outcomes can be used in decision aids that support conversations about the choice of amputation level. It is important to ensure data describing mortality in the years following dysvascular partial foot or transtibial amputation is up to date and accurate. Evidence about proportionate mortality has not changed in recent years and the results are comparable to previous systematic reviews. Data describing mortality outcomes can be used in decision aids that support conversations about the choice of amputation level.
DOI: 10.6084/m9.figshare.25879705.v1
title: Proportionate mortality following dysvascular partial foot amputation and how this compares to transtibial amputation: a systematic review

description: A large proportion of people die in the years following dysvascular partial foot amputation (PFA) or transtibial amputation (TTA) given the long-term consequences of peripheral vascular disease and/or diabetes. A critical appraisal of recent research is needed to understand the underlying cause of variation and synthesise data for use in consultations about amputation surgery and patient-facing resources. This systematic review aimed to describe proportionate mortality following dysvascular PFA and to compare this between PFA and TTA. The review protocol was registered in PROSPERO (CRD42023399161). Peer-reviewed studies of original research were included if they: were published in English between 1 January 2016, and 12 April 2024, included discrete cohorts with PFA, or PFA and TTA, and measured proportionate mortality following dysvascular amputation. Seventeen studies were included in the review. Following dysvascular PFA, proportionate mortality increased from 30 days (2.1%) to 1-year (13.9%), 3-years (30.1%), and 5-years (42.2%). One study compared proportionate mortality 1-year after dysvascular PFA and TTA, showing a higher relative risk of dying after TTA (RR 1.51). Proportionate mortality has not changed in recent years. These results are comparable to a previous systematic review that included studies published before 31 December 2015.Implications for rehabilitationIt is important to ensure data describing mortality in the years following dysvascular partial foot or transtibial amputation is up to date and accurate.Evidence about proportionate mortality has not changed in recent years and the results are comparable to previous systematic reviews.Data describing mortality outcomes can be used in decision aids that support conversations about the choice of amputation level. It is important to ensure data describing mortality in the years following dysvascular partial foot or transtibial amputation is up to date and accurate. Evidence about proportionate mortality has not changed in recent years and the results are comparable to previous systematic reviews. Data describing mortality outcomes can be used in decision aids that support conversations about the choice of amputation level.
DOI: 10.6084/m9.figshare.25858110
title: “I think it was helpful but not as helpful as it could have been” - a qualitative study of the experiences and perspectives of using fitness apps among manual wheelchair users with spinal cord injury

description: To gain knowledge of the experiences and perceptions of using fitness apps by full-time wheelchair users with spinal cord injury (SCI) and to explore experiences and perceptions of using these apps in relation to barriers to and facilitators of physical activity (PA). A qualitative design was employed. Semi-structured interviews were conducted with ten manual wheelchair users with SCI. Data were analysed using reflexive thematic analysis. Four themes were developed: 1) <i>App functionality and experience</i>, 2) <i>Enhancing motivation</i>, 3) <i>Precursors to engagement</i> and 4) <i>Knowledge gaps</i>. Experience and perception were strongly influenced by app design, particularly the presence or absence of features tailored for wheelchair users. Many apps incorporated the use wearable or mountable sensors. Fitness apps were perceived to increase motivation, although, this had its limitations. Conversely, apps were reported to have limited influence on commonly reported barriers to PA. Furthermore, the data highlighted gaps in knowledge which created barriers to effective app use. Fitness apps were perceived to increase motivation to engage in PA in manual wheelchair users with SCI. However, more needs to be done to further develop app features for wheelchair users with SCI and to address remaining barriers to engagement. Fitness apps may provide additional motivation for manual wheelchair users with Spinal Cord Injury (SCI) to increase their levels of physical activity (PA).Fitness apps should be used in conjunction with other supports to enable these individuals to overcome additional barriers to PA.When recommending the use of fitness apps, health and fitness professionals need to consider the unique motivations of each client in order to select an app that best enhances their motivation.A collaborative approach needs to be taken by health and fitness professionals and individuals with SCI to create greater awareness of the benefits and limitations of apps and to advocate the need for more app features tailored for wheelchair users with SCI. Fitness apps may provide additional motivation for manual wheelchair users with Spinal Cord Injury (SCI) to increase their levels of physical activity (PA). Fitness apps should be used in conjunction with other supports to enable these individuals to overcome additional barriers to PA. When recommending the use of fitness apps, health and fitness professionals need to consider the unique motivations of each client in order to select an app that best enhances their motivation. A collaborative approach needs to be taken by health and fitness professionals and individuals with SCI to create greater awareness of the benefits and limitations of apps and to advocate the need for more app features tailored for wheelchair users with SCI.
DOI: 10.6084/m9.figshare.25858110.v1
title: “I think it was helpful but not as helpful as it could have been” - a qualitative study of the experiences and perspectives of using fitness apps among manual wheelchair users with spinal cord injury

description: To gain knowledge of the experiences and perceptions of using fitness apps by full-time wheelchair users with spinal cord injury (SCI) and to explore experiences and perceptions of using these apps in relation to barriers to and facilitators of physical activity (PA). A qualitative design was employed. Semi-structured interviews were conducted with ten manual wheelchair users with SCI. Data were analysed using reflexive thematic analysis. Four themes were developed: 1) <i>App functionality and experience</i>, 2) <i>Enhancing motivation</i>, 3) <i>Precursors to engagement</i> and 4) <i>Knowledge gaps</i>. Experience and perception were strongly influenced by app design, particularly the presence or absence of features tailored for wheelchair users. Many apps incorporated the use wearable or mountable sensors. Fitness apps were perceived to increase motivation, although, this had its limitations. Conversely, apps were reported to have limited influence on commonly reported barriers to PA. Furthermore, the data highlighted gaps in knowledge which created barriers to effective app use. Fitness apps were perceived to increase motivation to engage in PA in manual wheelchair users with SCI. However, more needs to be done to further develop app features for wheelchair users with SCI and to address remaining barriers to engagement. Fitness apps may provide additional motivation for manual wheelchair users with Spinal Cord Injury (SCI) to increase their levels of physical activity (PA).Fitness apps should be used in conjunction with other supports to enable these individuals to overcome additional barriers to PA.When recommending the use of fitness apps, health and fitness professionals need to consider the unique motivations of each client in order to select an app that best enhances their motivation.A collaborative approach needs to be taken by health and fitness professionals and individuals with SCI to create greater awareness of the benefits and limitations of apps and to advocate the need for more app features tailored for wheelchair users with SCI. Fitness apps may provide additional motivation for manual wheelchair users with Spinal Cord Injury (SCI) to increase their levels of physical activity (PA). Fitness apps should be used in conjunction with other supports to enable these individuals to overcome additional barriers to PA. When recommending the use of fitness apps, health and fitness professionals need to consider the unique motivations of each client in order to select an app that best enhances their motivation. A collaborative approach needs to be taken by health and fitness professionals and individuals with SCI to create greater awareness of the benefits and limitations of apps and to advocate the need for more app features tailored for wheelchair users with SCI.
DOI: 10.6084/m9.figshare.25902756
title: How do users define success with a lower limb prosthesis? A focus group study

description: In this study, we sought to examine how lower limb prosthesis users define success, what constructs they associate with success, and what barriers and facilitators contribute to achieving success. Purposively sampled lower limb prosthesis users were recruited to participate in a focus group study. Verbatim transcripts from focus groups were analyzed using inductive thematic analysis. Identified constructs were mapped to existing outcome measures, and a conceptual framework for success with a lower limb prosthesis was proposed. Thirty-one lower limb prosthesis users participated in one of five focus groups. Five themes were developed: <i>keep moving forward, despite ups and downs; being able to live MY normal life and do the things I want to do with ease; learning what works for me and how to manage my prosthesis; only I can define my success;</i> and <i>what about my mental health?</i> Several constructs that do not align with existing measures were identified, including prosthetic attention, grief/loss after amputation, and trust in prosthesis. Facilitators for success described by participants included peer connection, finding the right prosthetist, and mental health support. According to lower limb prosthesis users, success must be patient-driven, individually defined, and continually reassessed. According to prosthesis users, success with a lower limb prosthesis should be patient-driven, individually defined, and continually reassessed.Lower limb prosthesis users described facilitators for success to include peer connection, finding the right prosthetist, mental health support, and access to appropriate prosthetic technology.Constructs described by lower limb prosthesis users as relating to success that are currently difficult to measure include prosthetic attention, grief/loss after amputation, prosthesis management, ability to blend in, and trust in the prosthesis. According to prosthesis users, success with a lower limb prosthesis should be patient-driven, individually defined, and continually reassessed. Lower limb prosthesis users described facilitators for success to include peer connection, finding the right prosthetist, mental health support, and access to appropriate prosthetic technology. Constructs described by lower limb prosthesis users as relating to success that are currently difficult to measure include prosthetic attention, grief/loss after amputation, prosthesis management, ability to blend in, and trust in the prosthesis.