cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6282992
title: Photoacclimation and photoregulation strategies of <i>Corallina</i> (Corallinales, Rhodophyta) across the NE Atlantic

description: This study characterizes the photoacclimation and photoregulation mechanisms that allow calcified macroalgae of the genus <i>Corallina</i> (Corallinales, Rhodophyta) to dominate rock pool habitats across the NE Atlantic despite the highly variable irradiance regimes experienced. Rapid light curves (RLCs) were performed with pulse amplitude modulation (PAM) fluorometry <i>in situ</i> across a full seasonal cycle in the UK intertidal with <i>C. officinalis</i> and <i>C. caespitosa</i>. Latitudinal comparisons were performed across the full extent of <i>C. officinalis</i>’ range in the NE Atlantic (Iceland–northern Spain), and for <i>C. caespitosa</i> in northern Spain. <i>Ex situ</i> RLCs with dark recovery were further employed to assess the optimal, as compared with actual, photophysiology across seasons and latitudes. <i>Corallina</i> species were shown to photoacclimate at seasonal timescales to changing irradiance, increasing light-harvesting during low-light autumn/winter periods and protecting photosystems during high-light summer conditions. Seasonal photoacclimation was achieved through alteration in the number of photosystem (PS) units (PSII and light harvesting antennae) over time. Non-photochemical quenching (NPQ) served as an important photoregulation mechanism utilized by <i>Corallina</i> to prevent or minimize photoinhibition over shorter time scales (seconds–hours), though the efficiency of NPQ was dependent on the seasonal-acclimated state. With increasing latitude the efficiency of photoregulation decreased, representing potential differential photoadaptation of <i>Corallina</i> across species ranges in the NE Atlantic. In contrast, highly conserved inter-specific patterns in photophysiological responses to irradiance were apparent. This study demonstrates the photophysiological mechanisms allowing <i>Corallina</i> to optimize use of the variable irradiance conditions apparent in rock pool environments, when and how they are employed, and their limitations.
DOI: 10.6084/m9.figshare.6282992.v1
title: Photoacclimation and photoregulation strategies of <i>Corallina</i> (Corallinales, Rhodophyta) across the NE Atlantic

description: This study characterizes the photoacclimation and photoregulation mechanisms that allow calcified macroalgae of the genus <i>Corallina</i> (Corallinales, Rhodophyta) to dominate rock pool habitats across the NE Atlantic despite the highly variable irradiance regimes experienced. Rapid light curves (RLCs) were performed with pulse amplitude modulation (PAM) fluorometry <i>in situ</i> across a full seasonal cycle in the UK intertidal with <i>C. officinalis</i> and <i>C. caespitosa</i>. Latitudinal comparisons were performed across the full extent of <i>C. officinalis</i>’ range in the NE Atlantic (Iceland–northern Spain), and for <i>C. caespitosa</i> in northern Spain. <i>Ex situ</i> RLCs with dark recovery were further employed to assess the optimal, as compared with actual, photophysiology across seasons and latitudes. <i>Corallina</i> species were shown to photoacclimate at seasonal timescales to changing irradiance, increasing light-harvesting during low-light autumn/winter periods and protecting photosystems during high-light summer conditions. Seasonal photoacclimation was achieved through alteration in the number of photosystem (PS) units (PSII and light harvesting antennae) over time. Non-photochemical quenching (NPQ) served as an important photoregulation mechanism utilized by <i>Corallina</i> to prevent or minimize photoinhibition over shorter time scales (seconds–hours), though the efficiency of NPQ was dependent on the seasonal-acclimated state. With increasing latitude the efficiency of photoregulation decreased, representing potential differential photoadaptation of <i>Corallina</i> across species ranges in the NE Atlantic. In contrast, highly conserved inter-specific patterns in photophysiological responses to irradiance were apparent. This study demonstrates the photophysiological mechanisms allowing <i>Corallina</i> to optimize use of the variable irradiance conditions apparent in rock pool environments, when and how they are employed, and their limitations.
DOI: 10.6084/m9.figshare.6282686
title: Data Set for the Research Article Effects of multi-stakeholder platforms on multi-stakeholder innovation networks: Implications for research for development interventions targeting innovations at scale

description: Multi-stakeholder platforms (MSPs) have been playing an increasing role in interventions aiming to generate and scale innovations in agricultural systems. However, the contribution of MSPs in achieving innovations and scaling has been varied, and many factors have been reported to be important for their performance. This paper aims to provide evidence on the contribution of MSPs to innovation and scaling by focusing on three developing country cases in Burundi, Democratic Republic of Congo, and Rwanda. Through social network analysis and logistic models, the paper studies the changes in the characteristics of multi-stakeholder innovation networks targeted by MSPs and identifies factors that play significant roles in triggering these changes. The results demonstrate that MSPs do not necessarily expand and decentralize innovation networks but can lead to contraction and centralization in the initial years of implementation. They show that some of the intended next users of interventions with MSPs – local-level actors – left the innovation networks, whereas the lead organization controlling resource allocation in the MSPs substantially increased its centrality. They also indicate that not all the factors of change in innovation networks are country specific. Initial conditions of innovation networks and funding provided by the MSPs are common factors explaining changes in innovation networks across countries and across different network functions. The study argues that investigating multi-stakeholder innovation network characteristics targeted by the MSP using a network approach in early implementation can contribute to better performance in generating and scaling innovations, and that funding can be an effective implementation tool in developing country contexts.<br>
DOI: 10.6084/m9.figshare.6282686.v2
title: Data Set for the Research Article Effects of multi-stakeholder platforms on multi-stakeholder innovation networks: Implications for research for development interventions targeting innovations at scale

description: Multi-stakeholder platforms (MSPs) have been playing an increasing role in interventions aiming to generate and scale innovations in agricultural systems. However, the contribution of MSPs in achieving innovations and scaling has been varied, and many factors have been reported to be important for their performance. This paper aims to provide evidence on the contribution of MSPs to innovation and scaling by focusing on three developing country cases in Burundi, Democratic Republic of Congo, and Rwanda. Through social network analysis and logistic models, the paper studies the changes in the characteristics of multi-stakeholder innovation networks targeted by MSPs and identifies factors that play significant roles in triggering these changes. The results demonstrate that MSPs do not necessarily expand and decentralize innovation networks but can lead to contraction and centralization in the initial years of implementation. They show that some of the intended next users of interventions with MSPs – local-level actors – left the innovation networks, whereas the lead organization controlling resource allocation in the MSPs substantially increased its centrality. They also indicate that not all the factors of change in innovation networks are country specific. Initial conditions of innovation networks and funding provided by the MSPs are common factors explaining changes in innovation networks across countries and across different network functions. The study argues that investigating multi-stakeholder innovation network characteristics targeted by the MSP using a network approach in early implementation can contribute to better performance in generating and scaling innovations, and that funding can be an effective implementation tool in developing country contexts.<br>
DOI: 10.6084/m9.figshare.6282686.v1
title: Data Set for the Research Article Effects of multi-stakeholder platforms on multi-stakeholder innovation networks: Implications for research for development interventions targeting innovations at scale

description: Multi-stakeholder platforms (MSPs) have been playing an increasing role in interventions aiming to generate and scale innovations in agricultural systems. However, the contribution of MSPs in achieving innovations and scaling has been varied, and many factors have been reported to be important for their performance. This paper aims to provide evidence on the contribution of MSPs to innovation and scaling by focusing on three developing country cases in Burundi, Democratic Republic of Congo, and Rwanda. Through social network analysis and logistic models, the paper studies the changes in the characteristics of multi-stakeholder innovation networks targeted by MSPs and identifies factors that play significant roles in triggering these changes. The results demonstrate that MSPs do not necessarily expand and decentralize innovation networks but can lead to contraction and centralization in the initial years of implementation. They show that some of the intended next users of interventions with MSPs – local-level actors – left the innovation networks, whereas the lead organization controlling resource allocation in the MSPs substantially increased its centrality. They also indicate that not all the factors of change in innovation networks are country specific. Initial conditions of innovation networks and funding provided by the MSPs are common factors explaining changes in innovation networks across countries and across different network functions. The study argues that investigating multi-stakeholder innovation network characteristics targeted by the MSP using a network approach in early implementation can contribute to better performance in generating and scaling innovations, and that funding can be an effective implementation tool in developing country contexts.<br>
DOI: 10.6084/m9.figshare.6282680
title: Supplementary Material for: A Novel ex vivo Mouse Mesometrium Culture Model for Investigating Angiogenesis in Microvascular Networks

description: <b><i>Background:</i></b> The development of models that incorporate intact microvascular networks enables the investigation of multicellular dynamics during angiogenesis. Our laboratory introduced the rat mesentery culture model as such a tool, which would be enhanced with mouse tissue. Since mouse mesentery is avascular, an alternative is mouse mesometrium, the connective tissue of uterine horns. The study’s objective was to demonstrate that mouse mesometrium contains microvascular networks that can be cultured to investigate multicellular dynamics during angiogenesis. <b><i>Methods:</i></b> Harvested mesometrium tissues from C57Bl/6 female mice were cultured in media with serum for up to 7 days. PECAM, NG2, αSMA, and LYVE-1 labeling identified endothelial cells, pericytes, smooth muscle cells, and lymphatic endothelial cells, respectively.<b><i> Results:</i></b> These cells comprised microvascular networks with arterioles, venules, and capillaries. Compared to day 0, capillary sprouts per vascular length were increased by 3 and 5 days in culture (day 0, 0.08 ± 0.01; day 3, 3.19 ± 0.78; day 5, 2.49 ± 0.05 sprouts/mm; <i>p</i> &lt; 0.05). Time-lapse imaging of cultured tissues from FlkEGFP mice showcases the use of the model for lineage studies. The impact is supported by the identification of endothelial cell jumping from one sprout to another. <b><i>Conclusion:</i></b> These results introduce a novel culture model for investigating multicellular dynamics during angiogenesis in real-time ex vivo microvascular networks.
DOI: 10.6084/m9.figshare.6282680.v1
title: Supplementary Material for: A Novel ex vivo Mouse Mesometrium Culture Model for Investigating Angiogenesis in Microvascular Networks

description: <b><i>Background:</i></b> The development of models that incorporate intact microvascular networks enables the investigation of multicellular dynamics during angiogenesis. Our laboratory introduced the rat mesentery culture model as such a tool, which would be enhanced with mouse tissue. Since mouse mesentery is avascular, an alternative is mouse mesometrium, the connective tissue of uterine horns. The study’s objective was to demonstrate that mouse mesometrium contains microvascular networks that can be cultured to investigate multicellular dynamics during angiogenesis. <b><i>Methods:</i></b> Harvested mesometrium tissues from C57Bl/6 female mice were cultured in media with serum for up to 7 days. PECAM, NG2, αSMA, and LYVE-1 labeling identified endothelial cells, pericytes, smooth muscle cells, and lymphatic endothelial cells, respectively.<b><i> Results:</i></b> These cells comprised microvascular networks with arterioles, venules, and capillaries. Compared to day 0, capillary sprouts per vascular length were increased by 3 and 5 days in culture (day 0, 0.08 ± 0.01; day 3, 3.19 ± 0.78; day 5, 2.49 ± 0.05 sprouts/mm; <i>p</i> &lt; 0.05). Time-lapse imaging of cultured tissues from FlkEGFP mice showcases the use of the model for lineage studies. The impact is supported by the identification of endothelial cell jumping from one sprout to another. <b><i>Conclusion:</i></b> These results introduce a novel culture model for investigating multicellular dynamics during angiogenesis in real-time ex vivo microvascular networks.
DOI: 10.6084/m9.figshare.6282671
title: Supplementary Material for: Association of Pre-End-Stage Renal Disease Hemoglobin with Early Dialysis Outcomes

description: <b><i>Background:</i></b> Incident hemodialysis patients have a high mortality risk within the first months after dialysis initiation. Pre-end-stage renal disease (ESRD) factors like anemia management may impact early post-ESRD outcomes. Therefore, we evaluated the impact of pre-ESRD hemoglobin (Hgb) and pre-ESRD Hgb slope on post-ESRD mortality and hospitalization outcomes. <b><i>Methods:</i></b> The study included 31,472 veterans transitioning to ESRD. Using Cox and negative binomial regression models, we evaluated the association of pre-ESRD Hgb and Hgb slope with 12-month post-ESRD all-cause and cardiovascular mortality and hospitalization rates using 4 levels of hierarchical multivariable adjustment, including erythropoietin use and kidney decline in slope models. <b><i>Results:</i></b> The cohort was 2% female, 30% African-American, and on average 68 ± 11 years old. Compared to Hgb 10–&lt; 11 g/dL, both low (&lt; 10 g/dL) and high (≥12 g/dL) levels were associated with higher all-cause mortality after full adjustment (HR 1.25 [95% CI 1.15–1.35] and 1.09 [95% CI 1.02–1.18], respectively). Similarly, Hgb exhibited a U-shaped association with CV mortality, while only lower Hgb was associated with a higher hospitalization rate. Neither an annual pre-ESRD decline in Hgb nor increase was associated with higher post-ESRD mortality risk after adjustment for kidney decline. However, we observed a modest J-shaped association between pre-ESRD Hgb slope and post-ESRD hospitalization rate. <b><i>Conclusions:</i></b> Lower and higher pre-ESRD Hgb levels are associated with a higher risk of early post-ESRD mortality, while there was no association between the pre-ESRD slope and mortality. An increase in pre-ESRD Hgb slope was associated with higher risk of post-ESRD hospitalization. Additional studies aimed at anemia management prior to ESRD transition are warranted.
DOI: 10.6084/m9.figshare.6282671.v1
title: Supplementary Material for: Association of Pre-End-Stage Renal Disease Hemoglobin with Early Dialysis Outcomes

description: <b><i>Background:</i></b> Incident hemodialysis patients have a high mortality risk within the first months after dialysis initiation. Pre-end-stage renal disease (ESRD) factors like anemia management may impact early post-ESRD outcomes. Therefore, we evaluated the impact of pre-ESRD hemoglobin (Hgb) and pre-ESRD Hgb slope on post-ESRD mortality and hospitalization outcomes. <b><i>Methods:</i></b> The study included 31,472 veterans transitioning to ESRD. Using Cox and negative binomial regression models, we evaluated the association of pre-ESRD Hgb and Hgb slope with 12-month post-ESRD all-cause and cardiovascular mortality and hospitalization rates using 4 levels of hierarchical multivariable adjustment, including erythropoietin use and kidney decline in slope models. <b><i>Results:</i></b> The cohort was 2% female, 30% African-American, and on average 68 ± 11 years old. Compared to Hgb 10–&lt; 11 g/dL, both low (&lt; 10 g/dL) and high (≥12 g/dL) levels were associated with higher all-cause mortality after full adjustment (HR 1.25 [95% CI 1.15–1.35] and 1.09 [95% CI 1.02–1.18], respectively). Similarly, Hgb exhibited a U-shaped association with CV mortality, while only lower Hgb was associated with a higher hospitalization rate. Neither an annual pre-ESRD decline in Hgb nor increase was associated with higher post-ESRD mortality risk after adjustment for kidney decline. However, we observed a modest J-shaped association between pre-ESRD Hgb slope and post-ESRD hospitalization rate. <b><i>Conclusions:</i></b> Lower and higher pre-ESRD Hgb levels are associated with a higher risk of early post-ESRD mortality, while there was no association between the pre-ESRD slope and mortality. An increase in pre-ESRD Hgb slope was associated with higher risk of post-ESRD hospitalization. Additional studies aimed at anemia management prior to ESRD transition are warranted.
DOI: 10.6084/m9.figshare.6282668
title: Postoperative examination results from 75 patients undergoing a novel procedure to correct pterygium

description: These data consist of demographic and postoperative examination results from 75 patients that underwent an experimental surgery to correct pteyrgium, a condition affecting the conjunctive and cornea.<br>Data are provided in Excel format and consist of the following:<br><b>name </b>- An anonymous identifier.<b>age </b>- Age of the patient in years.<b>gender </b>- Gender of the patient.<b>date of surgery</b> - date that the experimental procedure was performed.<b>R/L</b> - Left or right eye affected.<b>final visit</b> - Data of postoperative examination.<b>grade</b> - A scale of 1 - 4 grading the recurrence of pterygia following the procedure: <i>grade 1</i> - A normal appearance of the operative site. <i>grade 2</i> - Indicates the presence of some fine episcleral vessels extending up to but not beyond the limbus, but without any fibrous tissue. <i>grade 3</i> - Indicates the presence of additional fibrous tissues in the area without invading the cornea. <i>grade 4 </i>- Represents a true recurrence with a fibrovascular tissue invading the cornea across the limbus.<b>follow up</b> - Days elapsed between date of surgery and final visit.<b>pinguecula</b> - Presence of pinguecula at final visit (1 = yes, 0 = no).<b>POV </b>- Presence of palisades of Vogt at final visit (1 = yes, 0 = no).<b>loop</b> - Presence of vascular loop at final visit (1 = yes, 0 = no).<br><br>
DOI: 10.6084/m9.figshare.6282668.v1
title: Postoperative examination results from 75 patients undergoing a novel procedure to correct pterygium

description: These data consist of demographic and postoperative examination results from 75 patients that underwent an experimental surgery to correct pteyrgium, a condition affecting the conjunctive and cornea.<br>Data are provided in Excel format and consist of the following:<br><b>name </b>- An anonymous identifier.<b>age </b>- Age of the patient in years.<b>gender </b>- Gender of the patient.<b>date of surgery</b> - date that the experimental procedure was performed.<b>R/L</b> - Left or right eye affected.<b>final visit</b> - Data of postoperative examination.<b>grade</b> - A scale of 1 - 4 grading the recurrence of pterygia following the procedure: <i>grade 1</i> - A normal appearance of the operative site. <i>grade 2</i> - Indicates the presence of some fine episcleral vessels extending up to but not beyond the limbus, but without any fibrous tissue. <i>grade 3</i> - Indicates the presence of additional fibrous tissues in the area without invading the cornea. <i>grade 4 </i>- Represents a true recurrence with a fibrovascular tissue invading the cornea across the limbus.<b>follow up</b> - Days elapsed between date of surgery and final visit.<b>pinguecula</b> - Presence of pinguecula at final visit (1 = yes, 0 = no).<b>POV </b>- Presence of palisades of Vogt at final visit (1 = yes, 0 = no).<b>loop</b> - Presence of vascular loop at final visit (1 = yes, 0 = no).<br><br>
DOI: 10.6084/m9.figshare.6282665
title: Supplementary Material for: Uromodulin mRNA from Urinary Extracellular Vesicles Correlate to Kidney Function Decline in Type 2 Diabetes Mellitus

description: <b><i>Background:</i></b> Extracellular vesicles (EVs) enclose mRNA derived from their cell of origin and are considered a source of potential biomarkers. We examined urinary EV mRNA from individuals with diabetic kidney disease (DKD), chronic kidney disease, type 2 diabetes (T2DM), and obese and healthy controls to determine if such biomarkers had the potential to classify kidney disease and predict patients at higher risk of renal function decline. <b><i>Methods:</i></b> A total of 242 participants enrolled in this study. Urinary EV mRNA from all subjects were isolated by a filter-based platform, and the expression of 8 target genes were determined by quantitative polymerase chain reaction (qPCR). Changes in estimated glomerular filtration rate (eGFR) in 161 T2DM patients were evaluated for 2 consecutive years and compared with EV RNA profiles at baseline. <b><i>Results:</i></b> We observe that mild and severe DKD groups show a significant 3.2- and ­4.4-fold increase in UMOD compared to healthy controls and expression increases linearly from healthy, diabetic, and DKD subjects. UMOD expression is significantly correlated to albumin creatinine ratio (ACR), eGFR, and HbA1c. Using linear discriminant analyses with mRNA from severe DKD and T2DM as training data, a multi-gene signature classified DKD and ­non-DKD with a sensitivity of 93% and specificity of 73% with area under the receiver operating characteristic (ROC) curve (AUC) = 0.90. Although 6% of T2DM were determined to have a &gt; 80% posterior probability of developing DKD based on this mRNA profile, eGFR changes observed within the 2-year follow-up did not reveal a decline in kidney function. <b><i>Conclusion:</i></b> Urinary EV UMOD mRNA levels are progressively elevated from T2DM to DKD groups and correlate with widely used eGFR and ACR diagnostic criteria. An EV mRNA signature could identify DKD with greater than 90% sensitivity and 70% specificity.
DOI: 10.6084/m9.figshare.6281567
title: The sequence and de novo assembly of hog deer (Axis porcinus) genome (Supplementary Tables and Figures.docx)

description: Supplementary Tables and Figures
DOI: 10.6084/m9.figshare.6281567.v1
title: The sequence and de novo assembly of hog deer (Axis porcinus) genome (Supplementary Tables and Figures.docx)

description: Supplementary Tables and Figures
DOI: 10.6084/m9.figshare.6281543
title: Stegastes diencaeus 5'-COI DNA barcode sequences

description: 347 5'-COI DNA barcode sequences for Longfin damselfish (Stegastes diencaeus) used by Phillips et al. (2015).