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81 results for “Assessment and Plan”
Structure Annotations of Assessment and Plan Sections from MIMIC-III
<p>Physicians record their detailed thought-processes about diagnoses and treatments as unstructured text in a section of a clinical note called the "assessment and plan". This information is more clinically rich than structured billing codes assigned for an encounter but harder to reliably extract given the complexity of clinical language and documentation habits. To structure these sections we collected a dataset of annotations over assessment and plan sections from the publicly available and de-identified MIMIC-III dataset, and developed deep-learning based models to perform this task, described in the associated paper available as a pre-print at: <a href="https://www.medrxiv.org/content/10.1101/2022.04.13.22273438v1">https://www.medrxiv.org/content/10.1101/2022.04.13.22273438v1</a></p> <p>When using this data please cite our paper:</p> <pre><code>@article {Stupp2022.04.13.22273438, author = {Stupp, Doron and Barequet, Ronnie and Lee, I-Ching and Oren, Eyal and Feder, Amir and Benjamini, Ayelet and Hassidim, Avinatan and Matias, Yossi and Ofek, Eran and Rajkomar, Alvin}, title = {Structured Understanding of Assessment and Plans in Clinical Documentation}, year = {2022}, doi = {10.1101/2022.04.13.22273438}, publisher = {Cold Spring Harbor Laboratory Press}, URL = {https://www.medrxiv.org/content/early/2022/04/17/2022.04.13.22273438}, journal = {medRxiv} }</code></pre> <p>The dataset, presented here, contains annotations of assessment and plan sections of notes from the publicly available and de-identified MIMIC-III dataset, marking the active problems, their assessment description, and plan action items. Action items are additionally marked as one of 8 categories (listed below). The dataset contains over 30,000 annotations of 579 notes from distinct patients, annotated by 6 medical residents and students. </p> <p>The dataset is divided into 4 partitions - a training set (481 notes), validation set (50 notes), test set (48 notes) and an inter-rater set. The inter-rater set contains the annotations of each of the raters over the test set. Rater 1 in the inter-rater set should be regarded as an intra-rater comparison (details in the paper). The labels underwent automatic normalization to capture entire word boundaries and remove flanking non-alphanumeric characters.</p> <p>Code for transforming labels into TensorFlow examples and training models as described in the paper will be made available at GitHub: <a href="https://github.com/google-research/google-research/tree/master/assessment_plan_modeling">https://github.com/google-research/google-research/tree/master/assessment_plan_modeling</a></p> <p>In order to use these annotations, the user additionally needs to obtain the text of the notes which is found in the NOTE_EVENTS table from MIMIC-III, access to which is to be acquired independently (<a href="http://mimic.mit.edu">https://mimic.mit.edu/</a>)</p> <p>Annotations are given as character spans in a CSV file with the following schema:</p> <table> <tbody> <tr> <td>Field</td> <td>Type</td> <td>Semantics</td> </tr> <tr> <td>partition</td> <td>categorical (one of [train, val, test, interrater]</td> <td>The set of ratings the span belongs to.</td> </tr> <tr> <td>rater_id</td> <td>int</td> <td>Unique id for each the raters</td> </tr> <tr> <td>note_id</td> <td>int</td> <td>The note’s unique note_id, links to the MIMIC-III notes table (as ROW-ID).</td> </tr> <tr> <td>span_type</td> <td>categorical (one of [PROBLEM_TITLE,<br> PROBLEM_DESCRIPTION, ACTION_ITEM]</td> <td>Type of the span as annotated by raters.</td> </tr> <tr> <td>char_start</td> <td>int</td> <td>Character offsets from note start</td> </tr> <tr> <td>char_end</td> <td>int</td> </tr> <tr> <td>action_item_type</td> <td>categorical (one of [MEDICATIONS, IMAGING, OBSERVATIONS_LABS, CONSULTS, NUTRITION, THERAPEUTIC_PROCEDURES, OTHER_DIAGNOSTIC_PROCEDURES, OTHER])</td> <td>Type of action item if the span is an action item (empty otherwise) as annotated by raters.</td> </tr> </tbody> </table>
Assessing Quality Variations in Early Career Researchers' Data Management Plans: Quantitative Data of the Content Analysis
<p>The data includes the numerical results of the ranking of the data management plans created during the Basics of Research Data Management (BRDM) courses worth 3 ECTS credits in the years 2020 - 2022. The ranking was made using the Finnish DMP Evaluation Guidance (https://doi.org/10.5281/zenodo.4729831). Additionally, the data contains the results of the analysis of the best RDM practices included in the DMPs.</p> <p>Note 1: The comma-separated coded CSV version 1 (5.2.2024) may not open correctly on MacOS. You can use the comma-delimited CSV file version 2 or 3 (31.5.2024).</p> <p>Note 2: Versions 1 (Quality_variations_in_ECRs_DMPs_data) and 3 (Quality_variations_in_ECRs_DMPs_data_ver_3) contain evaluations of DMPs, best practices for data management, as well as methods for data sharing, storage, and preservation. In version 2 (Quality_variations_in_ECRs_DMPs_data_ver_2), the methods for data sharing, storage, and preservation are missing.</p> <p>Data is related to the research article https://doi.org/10.2218/ijdc.v18i1.873.</p>
FISHPASS ASSESSMENT PLAN LONG-TERM MONITORING OF HYDROLOGIC AND WATER QUALITY DATA
The Great Lakes Fishery Commissions’ (GLFC) FishPass project seeks to reconnect the waterscape for only desired species (i.e., selective passage) by integrating a multitude of existing and novel passage techniques and technologies. The probability of a fish passing through a sorting system is dependent on environmental conditions and a fish’s motivation ─ its internal state in relation to environmental stimuli. While fish decision making abilities introduce complexity to the sorting operations, they also provide an opportunity to exploit behavioral tendencies and abilities to achieve selective sorting. The FishPass Assessment Plan details a monitoring program aimed at quantifying fish movement and sorting capabilities associated with both individual mechanisms and integrated sorting systems. The results of the monitoring program will be used to inform future adjustments to the selection of techniques and technologies and their configuration to optimize passage of desirable species while blocking and/or removing undesirable species. A key component to the Assessment Plan is the long-term monitoring of abiotic variables in and around FishPass. This data set contains the hydrologic (e.g., river discharge, water level) and water quality data (e.g., temperature, specific conductivity, conductivity, and turbidity) collected at mostly static stations throughout the Boardman/Ottaway River. The dataset is updated annually. These data are collected until the initiation and/or substantial completion of the FishPass structure. Collection of this type of data are expected to continue after FishPass construction completion but modifications to the extent and location of monitoring stations are anticipated. As a result, a new dataset will be updated in the future containing all long term hydrologic and water quality monitoring post construction. R. Swanson, GLFC Assessment Biologist, is primarily responsible for maintaining the monitoring equipment, data retrieval, quality assuran
Ecosystem-based marine spatial planning assessment tool video tutorial
<p><span>Aiming at promoting the capacity building of competent authorities, scientists and consultants, a novel tool is proposed for assessing the alignment of marine spatial planning processes with ecosystem-based approach principles and to guide its operationalization.</span></p> <p><span>The EB-MSP assessment tool is developed with the ambition of providing a fit-for-purpose tool to overcome the ecosystem-based marine spatial planning implementation barriers reported by experts and managers.</span></p> <p><span>The EB-MSP assessment tool is designed to apply to any spatial plan, regardless of its stage of development: assessment of existing plans, plans in progress; or different national plans in a transboundary region.</span></p> <p><span>The EB-MSP tool can be accessed at https://aztidata.es/EB-MSP</span></p> <p><span>The EB-MSP assessment tool leads users through a step-by-step procedure for evaluating a specific plan.</span></p> <p><span>Upon first access, the user must register. This way, the users can conduct multiple assessments in a single session or different sessions, and can retrieve the information from previous sessions.</span></p> <p><span>The evaluation can be conducted by documenting the actions adopted during the planning process stages, or by examining how ecosystem-based marine spatial planning cross-cutting topics, have been incorporated into the plan.</span></p> <p><span>The user has to provide information about 130 statements that reflect the actions or tasks adopted during the planning process.</span></p> <p><span>For each action, six complementary fields of information have to be provided by the user:</span></p> <ol> <li><span><span><span> </span></span></span><span>the degree of implementation of the action; </span></li> <li><span><span><span> </span></span></span><span>the relevance of the action for the assessed planning site; </span></li> <li><span><span><span> </span></span></span><span>the main source of knowledge base supporting the action; </span></li> <li><span><span><span> </span></span></span><span>the respondent's confidence; </span></li> <li><span><span><span> </span></span></span><span>approaches, tools and methods implemented; and </span></li> <li><span><span><span> </span></span></span><span>justification of the responses</span></li> </ol> <p><span>Once the assessment is performed, the results are displayed as dynamic graphs that can be downloaded.</span></p> <p><span>The responses are also stored in a table, which can be downloaded as an Excel spreadsheet.</span></p>
Assessment of risk and vulnerability to disasters by field protocols and classification trees: an analysis of the Municipal Risk Reduction Plans (MRRP) of São Bernardo do Campo and Franco da Rocha (2020-2021), in Brazil
<p><span>Most disaster risk assessment methodologies were developed by natural science professionals. The UN Sendai Framework confirms the need to include these methods as interweaving complex networks of socially vulnerable financial processes, especially in developing countries. This work aimed to analyze the experience of including social vulnerability information in field protocols of the Municipal Risk Reduction Plans (MRRP) of São Bernardo do Campo and Franco da Rocha (2020-2021). A georeferenced database was structured with data from field protocols on risk sectors and then the relationship between vulnerability and risk was analyzed using the classification tree method. The results show that the geotechnical and social vulnerability variables relevant to risk attribution are largely overlapping over the sectors, but that the integrated analysis of the two dimensions allows a better interpretation of the risk level. However, the models with information from field protocols cannot replace a broader holistic assessment by the specialist in the field. Finally, qualitative reflections are made on the limitations and potential of including aspects of vulnerability in the specific case study.</span></p>
Fig. 8 in Action Plan For The Fire-Bellied Toad Bombina Bombina In Latvia: Assessment Of The Implementation For Ten Years, Releasing From Aquaculture And Restoration Of Habitats In 2006-2016
Fig. 8. Fitted linear model of the relationship between Actions' implementation before and after BAP.
Fig. 7 in Action Plan For The Fire-Bellied Toad Bombina Bombina In Latvia: Assessment Of The Implementation For Ten Years, Releasing From Aquaculture And Restoration Of Habitats In 2006-2016
Fig. 7. Box-and-Whicker plots for Species Conservation and Habitats Conservation Sub-actions' implementation in points before and after BAP.
Habitat Assessment and Restoration Planning (HARP) Model for the Snohomish and Stillaguamish River Basins
<p>Model code (R) to accompany the 2023 NOAA report "Habitat Assessment and Restoration Planning (HARP) Model for the Snohomish and Stillaguamish River Basins"</p>
Fig. 5 in Action Plan For The Fire-Bellied Toad Bombina Bombina In Latvia: Assessment Of The Implementation For Ten Years, Releasing From Aquaculture And Restoration Of Habitats In 2006-2016
Fig. 5. Invasive fish Perccottus glenii from pond of B.bombina (Ainavas).
Fig. 6. B in Action Plan For The Fire-Bellied Toad Bombina Bombina In Latvia: Assessment Of The Implementation For Ten Years, Releasing From Aquaculture And Restoration Of Habitats In 2006-2016
Fig. 6. B.bombina populations found in Latvia before and after BAP.
Fig. 1. B in Action Plan For The Fire-Bellied Toad Bombina Bombina In Latvia: Assessment Of The Implementation For Ten Years, Releasing From Aquaculture And Restoration Of Habitats In 2006-2016
Fig. 1. B.bombina tadpoles in aquaculture in the Latgales Zoo.
Fig.3 in Action Plan For The Fire-Bellied Toad Bombina Bombina In Latvia: Assessment Of The Implementation For Ten Years, Releasing From Aquaculture And Restoration Of Habitats In 2006-2016
Fig.3. Two new micro-reserves Strauti and Katriniski, established for B.bombina after BAP.
Fig. 4. Optimized pond for B in Action Plan For The Fire-Bellied Toad Bombina Bombina In Latvia: Assessment Of The Implementation For Ten Years, Releasing From Aquaculture And Restoration Of Habitats In 2006-2016
Fig. 4. Optimized pond for B.bombina population in Katriniski.
Raw_data_Combining several indicators to assess the effectiveness of tailor-made health plans in pig farms
<p>Raw data for a paper submitted to Peer Community In Animal Science. </p>
Brazilian Starter Data Kit Update to Support the Paper "Integrated Long-Term Expansion Planning and Short-Term Operation Assessment for Decarbonisation Pathways in Brazil Considering Utility-Scale Storage"
<p>This dataset presents updates on the Brazilian starter data kit, considering current load profile data and specific renewable energy sources production, using public data from official Brazilian power system agents. The dataset contains the input data and respective files to run OSeMOSYS and Flextool, including the utility-scale storage model. Additionally, this dataset contains the results of the study "Integrated Long-Term Expansion Planning and Short-Term Operation Assessment for Decarbonisation Pathways in Brazil Considering Utility-Scale Storage". This study evaluates the increase in variable renewable energy in Brazil and its integration with Storage systems. </p>
A predictive approach to assess urban biodiversity and plan for future development scenarios
Open the record for dataset details and reuse information.
Combining seascape connectivity with cumulative impact assessment in support of ecosystem-based marine spatial planning
<p>1. Cumulative impact assessment (CIA) is a promising approach to guide marine spatial planning (MSP) and management. One limitation of CIA is the neglect of seascape connectivity, which may spread the impact of localised pressures to ambient areas, e.g. through lost dispersal and recruitment of organisms.</p> <p>2. We here, for the first time, incorporate seascape connectivity into a traditional CIA model using a connectivity matrix, exemplified by dispersal of propagules estimated through biophysical modelling. Two <i>connectivity impacts</i>are identified: the <i>source impact</i> represents downstream areas losing recruits because of reduced larval dispersal from sites affected by the pressure, and the <i>sink impact</i> represents loss of recruits originating from upstream areas prevented from settlement in the site affected by the local pressure.</p> <p>3. By including seascape connectivity into the Swedish MSP-guiding CIA tool Symphony we demonstrate how to practically account for remote effects of local environmental impact. Our example on blue mussel shows how reducing mussel fitness in a given area may have impacts on mussels far from the acting pressures. Overall, results indicate that connectivity impact for blue mussels plays a minor role in most areas, less than 10% of the ordinary cumulative impact. However, in some smaller areas, e.g. on offshore banks and the Danish Straits, seascape connectivity may increase ordinary cumulative impact with 20-30%. In an example of scenario-based CIA analyses of MSP projections, we demonstrate how impacts of particular management actions, e.g. shipping rerouting and wind power developments, can be tracked far from the original area of influence.</p> <p>4. Depending on the dispersal ability of ecosystem components, a local pressure may impact a considerable area through seascape connectivity, transgressing management units and national borders. Although the mean connectivity impact may be modest for a single ecosystem component, the consideration of seascape connectivity across multiple ecosystem components may significantly alter the mapping of cumulative impact and the assessment of different MSP scenarios.</p> <p>5. Synthesis and applications.<span><span><span><span><span><span><span><span><span><span><span> Our extension of Cumulative Impact Assessment offers a new method for mapping and practically integrating seascape connectivity with ecosystem-based MSP and other spatial instruments for policy making, such as marine protected areas.</span></span></span></span></span></span></span></span></span></span></span></p>
Bibliometric assessment of marine spatial planning publications (2003-2019)
<p>Dataset of marine spatial planning (MSP) publications for the period 2003 - 2019.</p>
Data from: Habitat risk assessment for regional ocean planning in the U.S. Northeast and Mid-Atlantic
Coastal habitats provide important benefits to people, including habitat for species targeted by fisheries and opportunities for tourism and recreation. Yet, such human activities also can imperil these habitats and undermine the ecosystem services they provide to people. Cumulative risk assessment provides an analytical framework for synthesizing the influence of multiple stressors across habitats and decision-support for balancing human uses and ecosystem health. To explore cumulative risk to habitats in the U.S. Northeast and Mid-Atlantic Ocean Planning regions, we apply the open-source InVEST Habitat Risk Assessment model to 13 habitats and 31 stressors in an exposure-consequence framework. In doing so, we advance the science priorities of EBM and both regional planning bodies by synthesizing the wealth of available data to improve our understanding of human uses and how they affect marine resources. We find that risk to ecosystems is greatest first, along the coast, where a large number of stressors occur in close proximity and secondly, along the continental shelf, where fewer, higher consequence activities occur. Habitats at greatest risk include soft and hard-bottom nearshore areas, tidal flats, soft-bottom shelf habitat, and rocky intertidal zones—with the degree of risk varying spatially. Across all habitats, our results indicate that rising sea surface temperatures, commercial fishing, and shipping consistently and disproportionally contribute to risk. Further, our findings suggest that management in the nearshore will require simultaneously addressing the temporal and spatial overlap as well as intensity of multiple human activities and that management in the offshore requires more targeted efforts to reduce exposure from specific threats. We offer a transparent, generalizable approach to evaluating cumulative risk to multiple habitats and illustrate the spatially heterogeneous nature of impacts along the eastern Atlantic coast and the importance of spatial scale in estimating such impacts. These results offer a valuable decision-support tool by helping to constrain the decision space, focus attention on habitats and locations at the greatest risk, and highlight effect management strategies.
Assessing Multiple Values of Nature in National Biodiversity Strategies and Action Plans: Coded Data
<p>We coded eleven National Biodiversity Strategies and Action Plans (NBSAPs) for the human values for nature (instrumental, instrinsic, and relational) expressed in the NBSAPs. The 11 country NBSAPs coded were: Angola, Australia, Bhutan, Czech Republic, Egypt, Germany, Guyana, Malaysia, Russia, Saint Vincent and the Grenadines, and Turkey. Each sentence, <span>defined as an orthographic unit beginning with a capital letter and ending with a full stop, was provided a value code (instrumental, intrinsic, relational, unspecified, ‘not value orientation statement', or uncertain) depending on the value orientation of the statement. Coding criteria for each code is given below: </span></p> <p><span><span> </span></span></p> <table> <tbody> <tr> <td> <p><strong><span>Code</span></strong></p> </td> <td> <p><strong><span>Description</span></strong></p> </td> </tr> <tr> <td> <p><span>Instrumental</span></p> </td> <td> <p><span><span>●<span> </span></span></span><span>Nature is described as valuable or useful for humans ends</span></p> <p><span><span>●<span> </span></span></span><span>Mentions of provisioning services, regulating services, economic benefits, natural capital, stocks and harvests, use of nature (tourism/recreation was tagged as instrumental unless an explicit relational aspect mentioned)</span></p> </td> </tr> <tr> <td> <p><span>Intrinsic</span></p> </td> <td> <p><span><span>●<span> </span></span></span><span>Nature is described as valuable regardless of humans</span></p> <p><span><span>●<span> </span></span></span><span>Nature is valuable for natural (nonhuman) ends (e.g., forests must be preserved as habitats for animals)</span></p> <p><span><span>●<span> </span></span></span><span>Nature as having a right to exist undisturbed by humans</span></p> </td> </tr> <tr> <td> <p><span>Relational</span></p> </td> <td> <p><span><span>●<span> </span></span></span><span>Meaningful relationships with nature </span></p> <p><span><span>●<span> </span></span></span><span>Links between nature and culture, identity, traditions, traditional knowledge, fairness, environmental justice and rights, sharing, future generations, heritage, responsibilities, human beings as a part of nature, and quality of life</span></p> <p><span><span>●<span> </span></span></span><span>References to personified nature (e.g. “Mother Earth”)</span></p> </td> </tr> <tr> <td> <p><span>Unspecified</span></p> </td> <td> <p><span><span>●<span> </span></span></span><span>Value or importance of nature is implied, but no direct link to instrumental, intrinsic, or relational values (e.g., “our coastal and marine areas house important ecosystems”; “we have safeguarded all our key ecosystems, species and genetic diversity”)</span></p> </td> </tr> <tr> <td> <p><span>Not value orientation statement</span></p> </td> <td> <p><span><span>●<span> </span></span></span><span>Sentence does not imply value, or value statement does not link to nature. Purely biophysical language that is only descriptive (e.g., “There are an estimated 15,000 species of plants in the country”).</span></p> </td> </tr> </tbody> </table> <p> </p> <p>For a detailed overview of the methods, please refer the paper published in People and Nature.</p>
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