cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4240073.v1
title: Skyline documents for the article: A general method for targeted quantitative cross-linking mass spectrometry.

description: Skyline documents for the article: <b>A general method for targeted quantitative cross-linking mass spectrometry</b>.<br><b>Experiment Description</b>Varying amounts (50-1000 ng) of cross-linked BSA peptides were analyzed by LC-MS using a PRM method targeting 30 cross-linked peptide pairs. Cross-linked peptide pairs enriched from in vivo cross-linking of cultured human cells cultured in SILAC media and treated with varying concentrations of the Hsp90 inhibitor 17-AAG were analyzed by LC-MS using a PRM method to target at total of 12 precursor ions (light and heavy isotope versions for 6 cross-linked peptide pairs). Data was collected in the Bruce Laboratory at UW as well as at Cold Spring Harbor Laboratory (CSHL) during the 2016 Proteomics Course.<br><b>Sample Description</b>BSA was cross-linked with the protein interaction reporter cross-linker BDP-NHP. The protein was reduced, alkylated and digested with trypsin. The resulting peptide mixture was desalted with reversed phase solid phase extraction before LC-MS analysis. HeLa cells were cultured in SILAC media containing either isotopically light or heavy Lys and Arg. The cells were treated with varying concentrations of 17-AAG (100, 250, 500, 1000 nM) or a DMSO control for 18 h. The cells were harvested and mixed with a counterpart SILAC label DMSO control cell sample. The cells were then cross-linked with BDP-NHP followed by protein extraction with 8M urea. The protein was reduced, alkylated and digested with trypsin. Cross-linked peptides were enriched using a combination of strong cation exchange chromatography followed by avidin affinity chromatography before LC-MS analysis.<br><br>
DOI: 10.6084/m9.figshare.4240241.v11
title: CEDAR Overview BD2K 2016.pdf

description: Online biomedical repositories contain a wealth of freely available data submitted by the research community, but to reuse this data in further studies requires well-annotated associated metadata. There is a growing set of community-developed standards for creating this metadata, often in the form of templates; still, the difficulties of working with these standards are significant. The Center for Expanded Data Annotation and Retrieval (CEDAR) is building an end-to-end system to ease the authoring of metadata and the templates. This system targets the creation of higher quality metadata to facilitate data discovery, interoperability, and reuse. With our public release in September 2016, we now support many new features which make authoring easier.Template and Metadata Repository: We developed a standardized representation of metadata and the templates that describe them, together with Web-based services to store, search, and share these resources. Templates created using CEDAR technology are stored in our openly accessible community repository, and can now be shared with other people and groups. Researchers can search for templates to annotate their studies, and share their metadata with others. We’ve now added Web-based interfaces and REST APIs to facilitate access to templates, and all the metadata collected using those templates.Template and Metadata Editor: We developed highly interactive Web-based tools to simplify the process of authoring metadata and templates. The Template Editor allows users to create, search, and author templates. An upgraded feature provides interoperation with ontologies: interactive look-up services linked to NCBO’s BioPortal (bioportal.bioontology.org) let template authors find ontology terms to annotate fields in their templates and to define possible values of fields, including creating new terms and value sets. The Metadata Editor, which creates a forms-based acquisition interface from a template, has been redesigned so users can more easily populate metadata based on the template fields.
DOI: 10.6084/m9.figshare.4240061
title: Review of life cycle assessment on consumer electronic products: Developments and the way ahead

description: Life cycle assessment (LCA) has grown rapidly and is now well established within the electronics industry. The growing number of journal publications, conferences, and special issues is a proof for the same. A number of literature reviews have been published till now in this area focusing on different aspects. This study has identified 134 significant journal articles to conduct a systematic and narrative literature review. This review covers a wide range of product categories and analyzes the usefulness of LCA as a decision-making tool within the electronics industry which has not been explored fully in previous reviews conducted in this area of research. For this purpose, we organized LCA studies into 10 main product categories. A narrative review was employed to summarize the significant findings from the LCA studies. Although the central objective of all the studies was to evaluate the environmental impact created by the product, the focus and methods employed differed. A systematic review was used to categorize the overall frameworks used in the studies. The studies were classified based on their research purpose, types of approach, LCIA methods used, system boundaries involved, data collection methods, and data analysis levels. Within the subcategory of research purpose, three research domains were identified and the studies were classified accordingly. Generally it has been revealed that use phase, end of life, and production phase are the dominant phases in that order. However discrepancies occur owing to functional units, data usage, and assumptions made. All these and more make benchmarking difficult. Finally we identified gaps that merit attention in future research. It is also hoped that this review is a good resource for anyone interested in doing research on LCA of electronic products, helping them identify current research trends, provide suggestions for future research, and stimulate interest in creating new research directions.
DOI: 10.6084/m9.figshare.4240061.v1
title: Review of life cycle assessment on consumer electronic products: Developments and the way ahead

description: Life cycle assessment (LCA) has grown rapidly and is now well established within the electronics industry. The growing number of journal publications, conferences, and special issues is a proof for the same. A number of literature reviews have been published till now in this area focusing on different aspects. This study has identified 134 significant journal articles to conduct a systematic and narrative literature review. This review covers a wide range of product categories and analyzes the usefulness of LCA as a decision-making tool within the electronics industry which has not been explored fully in previous reviews conducted in this area of research. For this purpose, we organized LCA studies into 10 main product categories. A narrative review was employed to summarize the significant findings from the LCA studies. Although the central objective of all the studies was to evaluate the environmental impact created by the product, the focus and methods employed differed. A systematic review was used to categorize the overall frameworks used in the studies. The studies were classified based on their research purpose, types of approach, LCIA methods used, system boundaries involved, data collection methods, and data analysis levels. Within the subcategory of research purpose, three research domains were identified and the studies were classified accordingly. Generally it has been revealed that use phase, end of life, and production phase are the dominant phases in that order. However discrepancies occur owing to functional units, data usage, and assumptions made. All these and more make benchmarking difficult. Finally we identified gaps that merit attention in future research. It is also hoped that this review is a good resource for anyone interested in doing research on LCA of electronic products, helping them identify current research trends, provide suggestions for future research, and stimulate interest in creating new research directions.
DOI: 10.6084/m9.figshare.4240241.v12
title: CEDAR Overview BD2K 2016.pdf

description: Online biomedical repositories contain a wealth of freely available data submitted by the research community, but to reuse this data in further studies requires well-annotated associated metadata. There is a growing set of community-developed standards for creating this metadata, often in the form of templates; still, the difficulties of working with these standards are significant. The Center for Expanded Data Annotation and Retrieval (CEDAR) is building an end-to-end system to ease the authoring of metadata and the templates. This system targets the creation of higher quality metadata to facilitate data discovery, interoperability, and reuse. With our public release in September 2016, we now support many new features which make authoring easier.Template and Metadata Repository: We developed a standardized representation of metadata and the templates that describe them, together with Web-based services to store, search, and share these resources. Templates created using CEDAR technology are stored in our openly accessible community repository, and can now be shared with other people and groups. Researchers can search for templates to annotate their studies, and share their metadata with others. We’ve now added Web-based interfaces and REST APIs to facilitate access to templates, and all the metadata collected using those templates.Template and Metadata Editor: We developed highly interactive Web-based tools to simplify the process of authoring metadata and templates. The Template Editor allows users to create, search, and author templates. An upgraded feature provides interoperation with ontologies: interactive look-up services linked to NCBO’s BioPortal (bioportal.bioontology.org) let template authors find ontology terms to annotate fields in their templates and to define possible values of fields, including creating new terms and value sets. The Metadata Editor, which creates a forms-based acquisition interface from a template, has been redesigned so users can more easily populate metadata based on the template fields.
DOI: 10.6084/m9.figshare.4240031
title: Fair Topologies: Community Structures and Network Hubs Contribute to the Emergence of Fairness Norms

description: This data has been used in the following paper: p, li { white-space: pre-wrap; } <pre>Fair Topologies: Community Structures and Network Hubs Contribute to the Emergence of Fairness Norms</pre>
DOI: 10.6084/m9.figshare.4240031.v2
title: Fair Topologies: Community Structures and Network Hubs Contribute to the Emergence of Fairness Norms

description: This data has been used in the following paper: p, li { white-space: pre-wrap; } <pre>Fair Topologies: Community Structures and Network Hubs Contribute to the Emergence of Fairness Norms</pre>
DOI: 10.6084/m9.figshare.4240031.v1
title: Variations in fairness norms can be attributed to variations in social network structures

description: This data has been used in the following paper: Variations in fairness norms can be attributed to variations in social network structures
DOI: 10.6084/m9.figshare.4239929
title: Involvement of STH7 in light-adapted development in <i>Arabidopsis thaliana</i> promoted by both strigolactone and karrikin

description: Strigolactones (SLs) and karrikins (KARs) regulate photomorphogenesis. GR24, a synthetic SL and KAR<sub>1</sub>, a KAR, inhibit the hypocotyl elongation of <i>Arabidopsis thaliana</i> in a weak light. GR24 and KAR<sub>1</sub> up-regulate the expression of <i>STH7</i>, encoding a transcription factor belonging to the double B-box zinc finger subfamily. In this study, we used <i>STH7</i>-overexpressing (<i>STH7ox</i>) lines and functionally defective <i>STH7</i> (<i>STH7</i>-<i>SRDX</i>) mutants to investigate roles of SLs and KARs in photomorphogenesis of <i>Arabidopsis</i>. Hypocotyl elongation of <i>STH7</i>-<i>SRDX</i> mutants was less sensitive to both GR24 and KAR<sub>1</sub> treatment than that of wild-type <i>Arabidopsis</i> under weak light conditions. Furthermore, the chlorophyll and anthocyanin content was increased in <i>STH7ox</i> lines when de-etiolated with light and GR24-treated plants had enhanced anthocyanin production. GR24 and KAR<sub>1</sub> treatment significantly increased the expression level of photosynthesis-related genes <i>LHCB1</i> and <i>rbcS</i>. The results strongly suggest that SL and KAR induce photomorphogenesis of <i>Arabidopsis</i> in an STH7-dependent manner. Strigolactone response is mediated by D14 and KAI2 while karrikin response is mediated by only KAI2.
DOI: 10.6084/m9.figshare.4239830
title: Size, Composition, and Source Profiles of Inhalable Bioaerosols from Colorado Dairies

description: Agricultural particulate pollution is a global health risk among workers and nearby residents. This particulate matter contains a wide range of chemical and biological constituents (bioaerosols) with aerodynamic diameters consistent with the inhalable fraction. Due to sampling and analytical limitations, major gaps exist in understanding the relative contribution of large particles (i.e., 10-100 µm) and their physiological relevance in respiratory disease. We evaluated the full distribution of dairy inhalable particulate matter (IPM) using a novel high-volume cascade impactor that segregated airborne dust into four aerodynamic size fractions: &gt;30, 10-30, 3-10, and &lt;3 μm. We analyzed these size-fractionated particles using multiple chemical and biological methods, including high-throughput DNA sequencing, to better understand the heterogeneity of bioaerosols, in particular: (1) bacterial communities, (2) opportunistic pathogens, and (3) inflammatory potential. Based on particulate mass, a bimodal size distrubution was observed with one mode under 3 µm and a second mode above 30 µm. Correlations between inhalable particulate matter and bacterial chemical markers were statistically signficant indicating that large particles need to be considered during assessements otherwise a large proportion of exposure (and health outcomes) may go unnoticed. Further, bacteria in bioaerosols were derived predominantly from animal sources, but other noteworthy sources included birds, water, soil, and humans. Taxa such as <i>Staphlyococcus</i>,<i> Pseudomonas</i>, and <i>Streptococcus</i> were identified, which have important implications in infectious disease in the context of the lung and nasal microbiome. This is the first study to characterize the full size distribution of airborne particles emitted by agricultural dairy operations. The size, composition, and speciation of IPM in this study suggest that both small and large particles are of concern and more research is needed to better understand health effects in the upper respiratory system, including the nasopharyngeal region.
DOI: 10.6084/m9.figshare.4239929.v1
title: Involvement of STH7 in light-adapted development in <i>Arabidopsis thaliana</i> promoted by both strigolactone and karrikin

description: Strigolactones (SLs) and karrikins (KARs) regulate photomorphogenesis. GR24, a synthetic SL and KAR<sub>1</sub>, a KAR, inhibit the hypocotyl elongation of <i>Arabidopsis thaliana</i> in a weak light. GR24 and KAR<sub>1</sub> up-regulate the expression of <i>STH7</i>, encoding a transcription factor belonging to the double B-box zinc finger subfamily. In this study, we used <i>STH7</i>-overexpressing (<i>STH7ox</i>) lines and functionally defective <i>STH7</i> (<i>STH7</i>-<i>SRDX</i>) mutants to investigate roles of SLs and KARs in photomorphogenesis of <i>Arabidopsis</i>. Hypocotyl elongation of <i>STH7</i>-<i>SRDX</i> mutants was less sensitive to both GR24 and KAR<sub>1</sub> treatment than that of wild-type <i>Arabidopsis</i> under weak light conditions. Furthermore, the chlorophyll and anthocyanin content was increased in <i>STH7ox</i> lines when de-etiolated with light and GR24-treated plants had enhanced anthocyanin production. GR24 and KAR<sub>1</sub> treatment significantly increased the expression level of photosynthesis-related genes <i>LHCB1</i> and <i>rbcS</i>. The results strongly suggest that SL and KAR induce photomorphogenesis of <i>Arabidopsis</i> in an STH7-dependent manner. Strigolactone response is mediated by D14 and KAI2 while karrikin response is mediated by only KAI2.
DOI: 10.6084/m9.figshare.4239830.v1
title: Size, Composition, and Source Profiles of Inhalable Bioaerosols from Colorado Dairies

description: Agricultural particulate pollution is a global health risk among workers and nearby residents. This particulate matter contains a wide range of chemical and biological constituents (bioaerosols) with aerodynamic diameters consistent with the inhalable fraction. Due to sampling and analytical limitations, major gaps exist in understanding the relative contribution of large particles (i.e., 10-100 µm) and their physiological relevance in respiratory disease. We evaluated the full distribution of dairy inhalable particulate matter (IPM) using a novel high-volume cascade impactor that segregated airborne dust into four aerodynamic size fractions: &gt;30, 10-30, 3-10, and &lt;3 μm. We analyzed these size-fractionated particles using multiple chemical and biological methods, including high-throughput DNA sequencing, to better understand the heterogeneity of bioaerosols, in particular: (1) bacterial communities, (2) opportunistic pathogens, and (3) inflammatory potential. Based on particulate mass, a bimodal size distrubution was observed with one mode under 3 µm and a second mode above 30 µm. Correlations between inhalable particulate matter and bacterial chemical markers were statistically signficant indicating that large particles need to be considered during assessements otherwise a large proportion of exposure (and health outcomes) may go unnoticed. Further, bacteria in bioaerosols were derived predominantly from animal sources, but other noteworthy sources included birds, water, soil, and humans. Taxa such as <i>Staphlyococcus</i>,<i> Pseudomonas</i>, and <i>Streptococcus</i> were identified, which have important implications in infectious disease in the context of the lung and nasal microbiome. This is the first study to characterize the full size distribution of airborne particles emitted by agricultural dairy operations. The size, composition, and speciation of IPM in this study suggest that both small and large particles are of concern and more research is needed to better understand health effects in the upper respiratory system, including the nasopharyngeal region.
DOI: 10.6084/m9.figshare.4239782
title: LPGs for biomedical application.pdf

description: Gratings (LPGs) sensors are tiny periodic in-fiber structure inscribed along the optical fiber. It formed by longitudinal periodic refractive index and/or structural modulation along an optical fiber, which induces resonant coupling between the fundamental mode and co-propagating cladding modes. As higher order modes are strongly attenuated, a series of resonant dips can be observed in the transmissionspectrum. Dependent on fabrication parameters and the hosting fibers resonant wavelengths can be sensitive to the temperature, strain, bending, pressure, curvature et cetera. LPG executes an evanescent wave, which makes a best candidate for the chemical sensors or biosensors. Bare LPGs already used to monitor the respiratory volumes whereas a LPGs coated with different analytes like zinc oxide, gold, silver, TiO2 has been demonstrated for the recognition of bacteria, a platform for DNA/Aptamerdetection, cancer tissue detections and other biomedical applications. Recently Partridge et al. reported that LPGs coated with hemoglobin can be applicable for dissolved oxygen sensing.These LPG fabricated for biomedical applications
DOI: 10.6084/m9.figshare.4239782.v1
title: LPGs for biomedical application.pdf

description: Gratings (LPGs) sensors are tiny periodic in-fiber structure inscribed along the optical fiber. It formed by longitudinal periodic refractive index and/or structural modulation along an optical fiber, which induces resonant coupling between the fundamental mode and co-propagating cladding modes. As higher order modes are strongly attenuated, a series of resonant dips can be observed in the transmissionspectrum. Dependent on fabrication parameters and the hosting fibers resonant wavelengths can be sensitive to the temperature, strain, bending, pressure, curvature et cetera. LPG executes an evanescent wave, which makes a best candidate for the chemical sensors or biosensors. Bare LPGs already used to monitor the respiratory volumes whereas a LPGs coated with different analytes like zinc oxide, gold, silver, TiO2 has been demonstrated for the recognition of bacteria, a platform for DNA/Aptamerdetection, cancer tissue detections and other biomedical applications. Recently Partridge et al. reported that LPGs coated with hemoglobin can be applicable for dissolved oxygen sensing.These LPG fabricated for biomedical applications
DOI: 10.6084/m9.figshare.4239728
title: Evidence-Based Guidelines for Fatigue Risk Management in EMS: Formulating Research Questions and Selecting Outcomes

description: <b>Background</b>: Greater than half of Emergency Medical Services (EMS) personnel report work-related fatigue, yet there are no guidelines for the management of fatigue in EMS. A novel process has been established for evidence-based guideline (EBG) development germane to clinical EMS questions. This process has not yet been applied to operational EMS questions like fatigue risk management. The objective of this study was to develop content valid research questions in the Population, Intervention, Comparison, and Outcome (PICO) framework, and select outcomes to guide systematic reviews and development of EBGs for EMS fatigue risk management. <b>Methods</b>: We adopted the National Prehospital EBG Model Process and Grading of Recommendations Assessment, Development, and Evaluation (GRADE) framework for developing, implementing, and evaluating EBGs in the prehospital care setting. In accordance with steps one and two of the Model Process, we searched for existing EBGs, developed a multi-disciplinary expert panel and received external input. Panelists completed an iterative process to formulate research questions. We used the Content Validity Index (CVI) to score relevance and clarity of candidate PICO questions. The panel completed multiple rounds of question editing and used a CVI benchmark of ≥0.78 to indicate acceptable levels of clarity and relevance. Outcomes for each PICO question were rated from 1 = less important to 9 = critical. <b>Results</b>: Panelists formulated 13 candidate PICO questions, of which 6 were eliminated or merged with other questions. Panelists reached consensus on seven PICO questions (<i>n</i> = 1 diagnosis and <i>n</i> = 6 intervention). Final CVI scores of relevance ranged from 0.81 to 1.00. Final CVI scores of clarity ranged from 0.88 to 1.00. The mean number of outcomes rated as critical, important, and less important by PICO question was 0.7 (SD 0.7), 5.4 (SD 1.4), and 3.6 (SD 1.9), respectively. Patient and personnel safety were rated as critical for most PICO questions. PICO questions and outcomes were registered with PROSPERO, an international database of prospectively registered systematic reviews. <b>Conclusions</b>: We describe formulating and refining research questions and selection of outcomes to guide systematic reviews germane to EMS fatigue risk management. We outline a protocol for applying the Model Process and GRADE framework to create evidence-based guidelines