cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7376417.v1
title: DataYgueletalForestEcolManage2018.txt

description: This file contain the data published in the main text of the article "Beyond species richness and biomass: impact of selective logging and silvicultural treatments on the functional composition of a neotropical forest" by Yguel et al. published in Forest ecology and management. Description of the variables are also found in the method section of the article. The meanings of the variable measured in 1984 (before the forest exploitation) and 2013 (27 years after the forest exploitation) are: TRTMT: silvicultural treatment C is the control (T0 in the article) and T1 to T3 corresponds to the silvicultural treatments with increasing exploitation intensity. LvraiZoo: Community weighted mean of seed length of zoochorous species measured in cm and on data with species level identification WvraiZoo: Community weighted mean of seed width of zoochorous species measured in cm and on data with species level identification LvernZoo: Community weighted mean of seed length of zoochorous species measured in cm and on data with vernacular identification WvernZoo: Community weighted mean of seed width of zoochorous species measured in cm and on data with vernacular identification The seed measurments are also measured for all species without the extension “Zoo” at the end of the variables. Woodensvrai: Community weighted mean of wood density of all species measured on data with species level identification. Wood density is expressed in g/cm<sup>3</sup>. Woodensvern: Community weighted mean of wood density of all species measured on data with vernacular identification. Wood density is expressed in g/cm<sup>3</sup>. Heliovrai: Community weighted mean of heliophily (affinity to light) of all species measured on data with species level identification. The measure is in percentage of Cecropia species in the ten closest individuals. Heliovern: Community weighted mean of heliophily (affinity to light) of all species measured on data with vernacular identification. The measure is in percentage of Cecropia species in the ten closest individuals. bcRichgenre: Corrected genus richness (see the method section of the article for details on measurement. The measure is in number of genus for the same sample size. agb1984cam: Above ground biomass for all species measured in 1984 in ton per hectare agb1984_comcam: Above ground biomass for commercial species in 1984 in ton per hectare
DOI: 10.7284/129873
title: PTU (Pressure, Temperature, Humidity) data collected during research cruise OC1801A using a Vaisala PTU300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7376363.v1
title: A New Development of Non-local Image Denoising Using Fixed-Point Iteration For Non-Convex ‘ p Sparse Optimization

description: there is a .zip file containing commonly used standard digital images.
DOI: 10.7284/129876
title: Radiometer data collected during research cruise OC1801A using a RMR Co. PRP instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129877
title: Water Temperature data collected during research cruise OC1801A using a Sea-Bird SBE-38 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.17028/rd.lboro.7376333
title: Supplementary Information files for "Characterisation of particle-surface interactions via anharmonic acoustic transduction"

description: These are the SI files for the article "Characterisation of particle-surface interactions via anharmonic acoustic transduction".<br>Abstract:Most transduction methods for measuring particle-surface interactions are unable to differentiate the strength of interaction and largely reliant on extensive washing to reduce the ubiquitous non-specific background. Label-based methods, in particular, are limited in wide applicability due to their inherent operational complexity. On the other hand, label-free force-spectroscopic methods that can differentiate particle-surface interaction strength are skill-demanding and time-consuming. Here, we present a label-free anharmonic (nonlinear) acoustic transduction method employing the quartz crystal resonator that reads out ligand-receptor binding based on the interaction strength. We show that while stronger specific interactions are transduced more strongly, and in linear proportionality to the ligand concentration on microparticles, non-specific interactions are significantly attenuated. This allows ligand quantification with high specificity and sensitivity in realtime under flow without separate washing steps. Constructing an analytical model of a quartz resonator, we can relate the number and type (specific vs. non-specific) of ligand-receptor interactions with the change in characteristic nonlinearity coefficient of the resonator. The entirely-electronic and microfluidic-integrable transduction method could potentially allow a simple, fast and reliable way for characterising particle-surface interactions with economy of scale.
DOI: 10.6084/m9.figshare.7376243
title: "Citizen generated data" according to Google Search, 30th July 2018

description: Results for "citizen generated data" on Google Search, 30th July 2018. Drawing on the "search as research" approach [1], repurposing data from search engines in order to see how different perspectives on citizen generated data are organised and ordered. These results were extracted using a research browser [2].<br>[1] Rogers, R. (2013). <i>Digital Methods</i>. Cambridge, MA: MIT Press.[2] https://wiki.digitalmethods.net/Dmi/FirefoxToolBar
DOI: 10.17028/rd.lboro.7376333.v1
title: Supplementary Information files for "Characterisation of particle-surface interactions via anharmonic acoustic transduction"

description: These are the SI files for the article "Characterisation of particle-surface interactions via anharmonic acoustic transduction".<br>Abstract:Most transduction methods for measuring particle-surface interactions are unable to differentiate the strength of interaction and largely reliant on extensive washing to reduce the ubiquitous non-specific background. Label-based methods, in particular, are limited in wide applicability due to their inherent operational complexity. On the other hand, label-free force-spectroscopic methods that can differentiate particle-surface interaction strength are skill-demanding and time-consuming. Here, we present a label-free anharmonic (nonlinear) acoustic transduction method employing the quartz crystal resonator that reads out ligand-receptor binding based on the interaction strength. We show that while stronger specific interactions are transduced more strongly, and in linear proportionality to the ligand concentration on microparticles, non-specific interactions are significantly attenuated. This allows ligand quantification with high specificity and sensitivity in realtime under flow without separate washing steps. Constructing an analytical model of a quartz resonator, we can relate the number and type (specific vs. non-specific) of ligand-receptor interactions with the change in characteristic nonlinearity coefficient of the resonator. The entirely-electronic and microfluidic-integrable transduction method could potentially allow a simple, fast and reliable way for characterising particle-surface interactions with economy of scale.
DOI: 10.6084/m9.figshare.7376228
title: 24 days of Christmassy hot drinks

description: This deposit contains festive hot drinks marketed in the UK each year from 2018 onwards.<br>Hot drinks are selected from nationwide cafe/lunch venues, the list is deliberately limited to 24 drinks each year.
DOI: 10.6084/m9.figshare.7376243.v2
title: "Citizen generated data" according to Google Search, 30th July 2018

description: Results for "citizen generated data" on Google Search, 30th July 2018. Drawing on the "search as research" approach [1], repurposing data from search engines in order to see how different perspectives on citizen generated data are organised and ordered. These results were extracted using a research browser [2].<br>[1] Rogers, R. (2013). <i>Digital Methods</i>. Cambridge, MA: MIT Press.[2] https://wiki.digitalmethods.net/Dmi/FirefoxToolBar
DOI: 10.7284/129883
title: Water Temperature data collected during research cruise OC1801A using a Sea-Bird SBE-48 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7376243.v1
title: "Citizen generated data" according to Google Search, 30th July 2018

description: Results for "citizen generated data" on Google Search, 30th July 2018. Drawing on the "search as research" approach [1], repurposing data from search engines in order to see how different perspectives on citizen generated data are organised and ordered. These results were extracted using a research browser [2].<br>[1] Rogers, R. (2013). <i>Digital Methods</i>. Cambridge, MA: MIT Press.[2] https://wiki.digitalmethods.net/Dmi/FirefoxToolBar
DOI: 10.6084/m9.figshare.7376228.v1
title: 24 days of Christmassy hot drinks

description: This deposit contains festive hot drinks marketed in the UK each year from 2018 onwards.<br>Hot drinks are selected from nationwide cafe/lunch venues, the list is deliberately limited to 24 drinks each year.
DOI: 10.7284/129882
title: Timeserver data collected during research cruise OC1801A using a Microsemi SyncServer S350 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7376228.v3
title: 24 days of Christmassy hot drinks

description: This deposit contains festive hot drinks marketed in the UK each year from 2018 onwards.<br>Hot drinks are selected from nationwide cafe/lunch venues, the list is deliberately limited to 24 drinks each year.
DOI: 10.6084/m9.figshare.7376228.v2
title: 24 days of Christmassy hot drinks

description: This deposit contains festive hot drinks marketed in the UK each year from 2018 onwards.<br>Hot drinks are selected from nationwide cafe/lunch venues, the list is deliberately limited to 24 drinks each year.
DOI: 10.7284/129884
title: TSG (Thermosalinograph) data collected during research cruise OC1801A using a Sea-Bird SBE-45 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129889
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise OC1802A using a Hawaii UHDAS instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129892
title: Anemometer data collected during research cruise OC1802A using a Gill WindObserver II instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129888
title: Fluorometer data collected during research cruise OC1802A using a WET Labs WETStar instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129893
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1802A using a Furuno GP-90 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129899
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1802A using a Ashtech ADU5 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129886
title: Gyrocompass data collected during research cruise OC1802A using a Sperry MK-37 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129887
title: PTU (Pressure, Temperature, Humidity) data collected during research cruise OC1802A using a Vaisala PTU300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129890
title: Radiometer data collected during research cruise OC1802A using a RMR Co. PRP instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129891
title: Water Temperature data collected during research cruise OC1802A using a Sea-Bird SBE-38 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129897
title: Water Temperature data collected during research cruise OC1802A using a Sea-Bird SBE-48 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129896
title: Timeserver data collected during research cruise OC1802A using a Microsemi SyncServer S350 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129906
title: Anemometer data collected during research cruise OC1802B using a Gill WindObserver II instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129902
title: Fluorometer data collected during research cruise OC1802B using a WET Labs WETStar instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7376114
title: Supplementary Material for: Predictors of Renal Outcomes in Sclerotic Class Anti-Neutrophil Cytoplasmic Antibody Glomerulonephritis

description: <b><i>Background:</i></b> The prognostic value of the anti-neutrophil cytoplasmic antibody (ANCA) associated glomerulonephritis (GN) classification has been demonstrated in several cohorts with sclerotic class having the worst renal outcome. Relevant published data on factors predicting outcomes in sclerotic ANCA GN is limited. <b><i>Methods:</i></b> Sclerotic ANCA GN patients were recruited from 5 centers worldwide for this retrospective cohort study. We describe the clinical characteristics of this cohort and evaluate predictors of 1-year glomerular filtration rate (GFR) and end-stage renal disease (ESRD). Kidney function at 12 months as measured by Modification of Diet in Renal Disease estimated GFR (eGFR) was modeled by simple and multiple linear regression analyses. We used Cox proportional hazards regression modeling to evaluate ESRD-free survival. <b><i>Results:</i></b> Of the 50 patients, 92% were Caucasian and 60% male with a mean age of 61 years. While 72% had renal limited disease, 82% were MPO ANCA positive. Kidney biopsies contained a median of 20 (interquartile range [IQR] 15–34) glomeruli with 96% showing moderate to severe interstitial fibrosis. Overall, 96% of patients received immunosuppressive drug therapy and 16% received plasmapheresis. Treatment response was achieved in all but 1 patient. The median (IQR) eGFR at entry was 14.5 (9–19) mL/min/1.73 m<sup>2</sup>. Over a median (IQR) follow-up of 33.5 (17–82) months, 26 patients reached ESRD. Ten patients died with 6 of the deaths occurring within the first year of diagnosis. The hazard of progression to ESRD was significantly higher in those with lower GFR at study entry (<i>p</i> = 0.003) and with higher degree of tubular atrophy (<i>p</i> = 0.043). <b><i>Conclusions:</i></b> Renal recovery is rare among sclerotic ANCA GN patients requiring dialysis at entry and 12% of patients died in the first year. Entry GFR and tubular atrophy were significant predictors of GFR at 12 months and renal survival in patients with sclerotic class ANCA GN.
DOI: 10.6084/m9.figshare.7376120
title: Supplementary Material for: Trends in the Causes of Death among Kidney Transplant Recipients in the United States (1996–2014)

description: <b><i>Background:</i></b> Death with graft function remains an important cause of graft loss among kidney transplant recipients (KTRs). Little is known about the trend of specific causes of death in KTRs in recent years. <b><i>Methods:</i></b> We analyzed United States Renal Data System data (1996–2014) to determine 1- and 10-year all-cause and cause-specific mortality in adult KTRs who died with a functioning allograft. We also studied 1- and 10-year trends in the various causes of mortality. <b><i>Results:</i></b> Of 210,327 KTRs who received their first kidney transplant from 1996 to 2014, 3.2% died within 1 year after transplant. Cardiovascular deaths constituted the majority (24.7%), followed by infectious (15.2%) and malignant (2.9%) causes; 40.1% of deaths had no reported cause. Using 1996 as the referent year, all-cause as well as cardiovascular mortality declined, whereas mortality due to malignancy did not. For analyses of 10-year mortality, we studied 94,384 patients who received a first kidney transplant from 1996 to 2005. Of those, 22.1% died over 10 years and the causative patterns of their causes of death were similar to those associated with 1-year mortality. <b><i>Conclusions:</i></b> Despite the downtrend in mortality over the last 2 decades, a significant percentage of KTRs die in 10-years with a functioning graft, and cardiovascular mortality remains the leading cause of death. These data also highlight the need for diligent collection of mortality data in KTRs.
DOI: 10.6084/m9.figshare.7376108
title: Transfer function-based 2D/3D interactive spatiotemporal visualizations of mesoscale eddies

description: In this paper, we present a transfer function-based approach to developing an interactive visualization algorithm for ocean mesoscale eddies. Spatiotemporal coherence and viewport coherence are achieved. Evenly spaced streamlines are only integrated for visible portions of the datasets that maintain a relatively stable visual pattern resolution. The interactive transfer function is introduced to extract 2D and 3D eddy features, such as the Okubo-Weiss parameter, from background ocean currents, and a highly efficient GPU-based framework with an output-sensitive performance is utilized. Using the high-resolution 2D/3D ocean current datasets Maps of Sea Level Anomalies (MSLA) and Hybrid Coordinate Ocean Model (HYCOM), the feasibility and efficiency of our framework are demonstrated.
DOI: 10.6084/m9.figshare.7376114.v1
title: Supplementary Material for: Predictors of Renal Outcomes in Sclerotic Class Anti-Neutrophil Cytoplasmic Antibody Glomerulonephritis

description: <b><i>Background:</i></b> The prognostic value of the anti-neutrophil cytoplasmic antibody (ANCA) associated glomerulonephritis (GN) classification has been demonstrated in several cohorts with sclerotic class having the worst renal outcome. Relevant published data on factors predicting outcomes in sclerotic ANCA GN is limited. <b><i>Methods:</i></b> Sclerotic ANCA GN patients were recruited from 5 centers worldwide for this retrospective cohort study. We describe the clinical characteristics of this cohort and evaluate predictors of 1-year glomerular filtration rate (GFR) and end-stage renal disease (ESRD). Kidney function at 12 months as measured by Modification of Diet in Renal Disease estimated GFR (eGFR) was modeled by simple and multiple linear regression analyses. We used Cox proportional hazards regression modeling to evaluate ESRD-free survival. <b><i>Results:</i></b> Of the 50 patients, 92% were Caucasian and 60% male with a mean age of 61 years. While 72% had renal limited disease, 82% were MPO ANCA positive. Kidney biopsies contained a median of 20 (interquartile range [IQR] 15–34) glomeruli with 96% showing moderate to severe interstitial fibrosis. Overall, 96% of patients received immunosuppressive drug therapy and 16% received plasmapheresis. Treatment response was achieved in all but 1 patient. The median (IQR) eGFR at entry was 14.5 (9–19) mL/min/1.73 m<sup>2</sup>. Over a median (IQR) follow-up of 33.5 (17–82) months, 26 patients reached ESRD. Ten patients died with 6 of the deaths occurring within the first year of diagnosis. The hazard of progression to ESRD was significantly higher in those with lower GFR at study entry (<i>p</i> = 0.003) and with higher degree of tubular atrophy (<i>p</i> = 0.043). <b><i>Conclusions:</i></b> Renal recovery is rare among sclerotic ANCA GN patients requiring dialysis at entry and 12% of patients died in the first year. Entry GFR and tubular atrophy were significant predictors of GFR at 12 months and renal survival in patients with sclerotic class ANCA GN.
DOI: 10.6084/m9.figshare.7376120.v1
title: Supplementary Material for: Trends in the Causes of Death among Kidney Transplant Recipients in the United States (1996–2014)

description: <b><i>Background:</i></b> Death with graft function remains an important cause of graft loss among kidney transplant recipients (KTRs). Little is known about the trend of specific causes of death in KTRs in recent years. <b><i>Methods:</i></b> We analyzed United States Renal Data System data (1996–2014) to determine 1- and 10-year all-cause and cause-specific mortality in adult KTRs who died with a functioning allograft. We also studied 1- and 10-year trends in the various causes of mortality. <b><i>Results:</i></b> Of 210,327 KTRs who received their first kidney transplant from 1996 to 2014, 3.2% died within 1 year after transplant. Cardiovascular deaths constituted the majority (24.7%), followed by infectious (15.2%) and malignant (2.9%) causes; 40.1% of deaths had no reported cause. Using 1996 as the referent year, all-cause as well as cardiovascular mortality declined, whereas mortality due to malignancy did not. For analyses of 10-year mortality, we studied 94,384 patients who received a first kidney transplant from 1996 to 2005. Of those, 22.1% died over 10 years and the causative patterns of their causes of death were similar to those associated with 1-year mortality. <b><i>Conclusions:</i></b> Despite the downtrend in mortality over the last 2 decades, a significant percentage of KTRs die in 10-years with a functioning graft, and cardiovascular mortality remains the leading cause of death. These data also highlight the need for diligent collection of mortality data in KTRs.
DOI: 10.7284/129907
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1802B using a Furuno GP-90 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7376108.v1
title: Transfer function-based 2D/3D interactive spatiotemporal visualizations of mesoscale eddies

description: In this paper, we present a transfer function-based approach to developing an interactive visualization algorithm for ocean mesoscale eddies. Spatiotemporal coherence and viewport coherence are achieved. Evenly spaced streamlines are only integrated for visible portions of the datasets that maintain a relatively stable visual pattern resolution. The interactive transfer function is introduced to extract 2D and 3D eddy features, such as the Okubo-Weiss parameter, from background ocean currents, and a highly efficient GPU-based framework with an output-sensitive performance is utilized. Using the high-resolution 2D/3D ocean current datasets Maps of Sea Level Anomalies (MSLA) and Hybrid Coordinate Ocean Model (HYCOM), the feasibility and efficiency of our framework are demonstrated.