cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5066/p9l2uxsi
title: Groundwater-withdrawal data from the Coastal Lowlands Aquifer System in parts of Texas, Louisiana, Mississippi, Alabama, and Florida, 1925-2018

description: This data release contains compiled historical groundwater-withdrawal data for the Coastal Lowlands Aquifer System in Texas, Louisiana, Mississippi, Alabama, and Florida from 1925 to 2018. Most groundwater-withdrawals were distributed to groundwater wells and separated into water-use categories of industrial, production wells, power generation, mining, domestic, irrigation, livestock or commercial. Groundwater-withdrawal data were obtained, where available, from existing database resources hosted by various State and Federal agencies. For Texas, data were obtained from the Texas Water Development Board (TWDB) from both existing Groundwater Availability Models (GAM), and from historical groundwater-withdrawal data. For Louisiana data were obtained from the U.S. Geological Survey Lower Mississippi-Gulf Water Science Center, Baton Rouge, Louisiana office. For Mississippi data were obtained from the Mississippi Department of Environmental Quality, and from the U.S. Geological Survey Lower Mississippi-Gulf Water Science Center, Jackson, Mississippi. For Alabama data were obtained from the Alabama Department of Economic and Community Affairs, Office of Water Resources, and from the U.S. Geological Survey Lower Mississippi-Gulf Water Science Center, Montgomery, Alabama office. For Florida data were obtained from the U.S. Geological Survey Caribbean-Florida Water Science Center, Lutz and Orlando Florida offices.
DOI: 10.6084/m9.figshare.15135140
title: Gene fusions in vascular tumors and their underlying molecular mechanisms

description: The group of vascular tumors contains many different entities, and is considered difficult by pathologists, as they often have overlapping histological characteristics. Chromosomal translocations have been identified in ~20% of mesenchymal tumors and are considered the drivers of tumor formation. Many translocations have been discovered over the past decade through next-generation sequencing. This technological advancement has also revealed several recurrent gene fusions in vascular tumors. This review will discuss the various vascular tumors for which recurrent gene fusions have been identified. The gene fusions and the presumed molecular mechanisms underlying tumorigenesis are shown, and potential implications for targeted therapies discussed. The identification of these gene fusions in vascular tumors has improved diagnostic accuracy, especially since several of these fusions can be easily detected using surrogate immunohistochemical markers. The identification of gene fusions in a subset of vascular tumors over the past decade has improved diagnostic accuracy, and has provided the pathologists with novel diagnostic tools to accurately diagnose these often difficult tumors. Moreover, the increased understanding of the underlying molecular mechanisms can guide the development of targeted therapeutic strategies.
DOI: 10.6084/m9.figshare.14912480
title: Prognostic value of baculoviral IAP repeat containing 5 expression as a new biomarker in lung adenocarcinoma: a meta-analysis

description: BIRC5 is associated with the prognosis of a variety of tumors. This meta-analysis aimed to identify whether BIRC5 is associated with the prognosis of lung adenocarcinoma (LUAD). We conducted an in-depth review of seven Chinese and English databases and two high-throughput sequencing databases according to inclusion and exclusion criteria to find relevant studies. The pooled standardized mean differences (SMDs) and 95% confidence intervals (CIs) for the associations between the BIRC5 expression level and clinicopathological characteristics were calculated, and the pooled hazard ratios (HRs) and 95% CIs were calculated to estimate associations between the BIRC5 expression level and survival outcomes. In total, 17 studies involving 2887 LUAD patients whose BIRC5 expression level was known were included in this meta-analysis. The BIRC5 expression level was higher in younger patients, males, and smokers and correlated with advanced AJCC, T and N stages but not M stage. A high BIRC5 expression level also correlated with poor overall survival (OS) and progression-free survival (PFS). There was no publication bias in this study. This meta-analysis indicates that BIRC5 is a significant biomarker for a poor prognosis and poor clinicopathological outcomes in patients with LUAD.
DOI: 10.6084/m9.figshare.15135140.v2
title: Gene fusions in vascular tumors and their underlying molecular mechanisms

description: The group of vascular tumors contains many different entities, and is considered difficult by pathologists, as they often have overlapping histological characteristics. Chromosomal translocations have been identified in ~20% of mesenchymal tumors and are considered the drivers of tumor formation. Many translocations have been discovered over the past decade through next-generation sequencing. This technological advancement has also revealed several recurrent gene fusions in vascular tumors. This review will discuss the various vascular tumors for which recurrent gene fusions have been identified. The gene fusions and the presumed molecular mechanisms underlying tumorigenesis are shown, and potential implications for targeted therapies discussed. The identification of these gene fusions in vascular tumors has improved diagnostic accuracy, especially since several of these fusions can be easily detected using surrogate immunohistochemical markers. The identification of gene fusions in a subset of vascular tumors over the past decade has improved diagnostic accuracy, and has provided the pathologists with novel diagnostic tools to accurately diagnose these often difficult tumors. Moreover, the increased understanding of the underlying molecular mechanisms can guide the development of targeted therapeutic strategies.
DOI: 10.6084/m9.figshare.14912480.v2
title: Prognostic value of baculoviral IAP repeat containing 5 expression as a new biomarker in lung adenocarcinoma: a meta-analysis

description: BIRC5 is associated with the prognosis of a variety of tumors. This meta-analysis aimed to identify whether BIRC5 is associated with the prognosis of lung adenocarcinoma (LUAD). We conducted an in-depth review of seven Chinese and English databases and two high-throughput sequencing databases according to inclusion and exclusion criteria to find relevant studies. The pooled standardized mean differences (SMDs) and 95% confidence intervals (CIs) for the associations between the BIRC5 expression level and clinicopathological characteristics were calculated, and the pooled hazard ratios (HRs) and 95% CIs were calculated to estimate associations between the BIRC5 expression level and survival outcomes. In total, 17 studies involving 2887 LUAD patients whose BIRC5 expression level was known were included in this meta-analysis. The BIRC5 expression level was higher in younger patients, males, and smokers and correlated with advanced AJCC, T and N stages but not M stage. A high BIRC5 expression level also correlated with poor overall survival (OS) and progression-free survival (PFS). There was no publication bias in this study. This meta-analysis indicates that BIRC5 is a significant biomarker for a poor prognosis and poor clinicopathological outcomes in patients with LUAD.
DOI: 10.6084/m9.figshare.15135140.v1
title: Gene fusions in vascular tumors and their underlying molecular mechanisms

description: The group of vascular tumors contains many different entities, and is considered difficult by pathologists, as they often have overlapping histological characteristics. Chromosomal translocations have been identified in ~20% of mesenchymal tumors and are considered the drivers of tumor formation. Many translocations have been discovered over the past decade through next-generation sequencing. This technological advancement has also revealed several recurrent gene fusions in vascular tumors. This review will discuss the various vascular tumors for which recurrent gene fusions have been identified. The gene fusions and the presumed molecular mechanisms underlying tumorigenesis are shown, and potential implications for targeted therapies discussed. The identification of these gene fusions in vascular tumors has improved diagnostic accuracy, especially since several of these fusions can be easily detected using surrogate immunohistochemical markers. The identification of gene fusions in a subset of vascular tumors over the past decade has improved diagnostic accuracy, and has provided the pathologists with novel diagnostic tools to accurately diagnose these often difficult tumors. Moreover, the increased understanding of the underlying molecular mechanisms can guide the development of targeted therapeutic strategies.
DOI: 10.6084/m9.figshare.14912480.v1
title: Prognostic value of baculoviral IAP repeat containing 5 expression as a new biomarker in lung adenocarcinoma: a meta-analysis

description: BIRC5 is associated with the prognosis of a variety of tumors. This meta-analysis aimed to identify whether BIRC5 is associated with the prognosis of lung adenocarcinoma (LUAD). We conducted an in-depth review of seven Chinese and English databases and two high-throughput sequencing databases according to inclusion and exclusion criteria to find relevant studies. The pooled standardized mean differences (SMDs) and 95% confidence intervals (CIs) for the associations between the BIRC5 expression level and clinicopathological characteristics were calculated, and the pooled hazard ratios (HRs) and 95% CIs were calculated to estimate associations between the BIRC5 expression level and survival outcomes. In total, 17 studies involving 2887 LUAD patients whose BIRC5 expression level was known were included in this meta-analysis. The BIRC5 expression level was higher in younger patients, males, and smokers and correlated with advanced AJCC, T and N stages but not M stage. A high BIRC5 expression level also correlated with poor overall survival (OS) and progression-free survival (PFS). There was no publication bias in this study. This meta-analysis indicates that BIRC5 is a significant biomarker for a poor prognosis and poor clinicopathological outcomes in patients with LUAD.
DOI: 10.6084/m9.figshare.14380834.v1
title: Is the oral health-related quality of life associated with quality of life among pregnant Finnish families: a cross-sectional study

description: The objectives of this study was to find out if oral health-related quality of life and its dimensions (OHRQoL) are associated with overall quality of life (QoL) among mothers and fathers during pregnancy and whether these two constructs were associated within the family sharing the same living environment. The data (mothers <i>n</i> = 2580, fathers <i>n</i> = 1467) for this cross-sectional data study were collected from the FinnBrain Birth Cohort study during 2011–2015. OHRQoL was measured using a 14-item Oral Health Impact Profile (OHIP-14) questionnaire and QoL by using the WHOQoL-Bref questionnaire. Spearman correlation coefficients were used to assess the statistical significance of the associations. OHRQoL was weakly associated at the individual level with the overall QoL (mothers <i>r</i> = 0.21, fathers <i>r</i> = 0.22, <i>p</i> Our findings suggest that overall QoL is a different construct than OHRQoL though slightly overlapping.
DOI: 10.6084/m9.figshare.14825352.v1
title: Aldosterone and corticosterone of a larval amphibian exposed to increased salinity

description: We exposed larval leopard frogs to increased salinity and RU486 (a glucocorticoid receptor antagonist) and tested their influence on waterborne corticosterone (baseline and stress-induced) and aldosterone.
DOI: 10.6073/pasta/6dffebb3fdfdf461866cc98aa970f046
title: Chemistry of stream water from the Luquillo Mountains

description: Stream water is collected weekly at the Luquillo Mountain sites listed below. These data sets begin as early as 1983; LTER sampling began in 1988. Stream water samples are grab samples taken from the water/air interface at stream channel center on the sampling day (usually Tuesdays). A continuous record of stream stage (height) is recorded by a datalogger at all ongoing stream sampling sites. Average daily streamflows are available from the USGS and at other locations (Hydrology and Meteorology) on this site. All samples are measured for pH and conductivity, and then filtered (pre-combusted Whatman GF/F glass fiber filter) prior to further analysis. From 1983-1994 samples were cooled and returned to the San Juan chemistry laboratory for analysis. During those years, samples for NH4 and NO3 analyses were refrigerated continuously until analysis. Subsamples for NH4 analysis were also preserved with 1 molar H2SO4. From 1994 on, samples for NH4 and NO3were frozen until analysis, were not acidified, and all analyses were conducted at the University of New Hampshire. Stream water Sampling SitesDescriptions of LTER LUQ stream water weekly sample chemistry data from 1988 onwards. Chemical concentrations are recorded as mg/L or mg/L as appropriate. Values below detection limits are recorded as 1/2 the detection limit. Site Abbreviation Description Comments Quebrada Sonadora QS El Verde stream. Quebrada Toronja QT = QT1 El Verde stream. Rio Espiritu Santo RES4 LEF North Stream LEF= Luquillo Experimental Forest Quebrada Prieta A QPA El Verde stream Quebrada Prieta B QPB El Verde stream Quebrada Prieta QP El Verde stream Puente Roto Mameyes MPR Bisley stream Previously "PRM" Quebrada uno-Bisley Q1 . Bisley stream Quebrada dos-Bisley Q2 Bisley stream Quebrada tres-Bisley Q3 . Bisley stream Rio Mameyes Gage MG Bisley stream Rio Icacos RI LEF South stream Rio Sabana RS LEF West stream Quebrada Guaba QG Icacois stream
DOI: 10.5281/zenodo.5537134
title: Forest carbon removal factor variance by climate domain

description: Uncertainty (variance) in removal factor (annual sequestration rate) for forest carbon in new and existing forests by climate domain (tropical, subtropical, temperate, boreal). Uncertainty analysis is from Harris et al. 2021 Nature Climate Change. Units are aboveground carbon Mg^2/ha^2/year^2. New and existing forest are distinguished by the presence or absence of Hansen et al. 2013 tree cover gain pixels. Note: Uncertainty for existing temperate forest removal factors is so high because the IPCC national greenhouse gas inventory guidelines have a very high uncertainty for these forests (2019 refinement of guidelines). Note: Uncertainty analysis is for published version of the model (v1.2.0). https://github.com/wri/carbon-budget
description: {"references": ["Harris et al. 2021. Nature Climate Change. https://www.nature.com/articles/s41558-020-00976-6"]}
DOI: 10.5281/zenodo.5537133
title: Forest carbon removal factor variance by climate domain

description: Uncertainty (variance) in removal factor (annual sequestration rate) for forest carbon in new and existing forests by climate domain (tropical, subtropical, temperate, boreal). Uncertainty analysis is from Harris et al. 2021 Nature Climate Change. Units are aboveground carbon Mg^2/ha^2/year^2. New and existing forest are distinguished by the presence or absence of Hansen et al. 2013 tree cover gain pixels. Note: Uncertainty for existing temperate forest removal factors is so high because the IPCC national greenhouse gas inventory guidelines have a very high uncertainty for these forests (2019 refinement of guidelines). Note: Uncertainty analysis is for published version of the model (v1.2.0). https://github.com/wri/carbon-budget
description: {"references": ["Harris et al. 2021. Nature Climate Change. https://www.nature.com/articles/s41558-020-00976-6"]}
DOI: 10.17632/5xdw5ysk5y.1
title: Stream food webs and cumulative forestry effects

description: The River Continuum Concept (RCC) predicts a downstream shift in the reliance of aquatic consumers from terrestrial to aquatic carbon sources, but this concept has rarely been assessed with longitudinal studies. Similarly, there are no studies addressing how forestry related disturbances to the structure of headwater food webs manifest (accumulate/dissipate) downstream and/or whether forest management alters natural longitudinal trends predicted by the RCC. Using stable isotopes of carbon, nitrogen and hydrogen, we investigated how: 1) autochthony in macroinvertebrates and fish change from small streams to larger downstream sites within a basin with minimal forest management (New Brunswick, Canada); 2) longitudinal trends in autochthony and food web length compare among three basins with different forest management intensity [intensive (harvest and replanting), extensive (harvest only), minimal] to detect potential cumulative/dissipative effects; and 3) forest management intensity and other catchment variables are influencing food web dynamics. 

Attached are the 1) carbon, nitrogen and hydrogen stable isotope data for benthic macroinvertebrates, sculpin and food sources in 18 streams, and 2) the algal contribution to consumer diet calculated based on MixSIAR mixing models (see published article for details). 


The research resulting from this data is reported in:
Erdozain, M., Kidd, K.A., Emilson, E.J.S., Capell, S.S., Kreutzweiser, D.P., Gray, M.A. (in press). Elevated allochthony in stream food webs as a result of longitudinal cumulative effects of forest management. Ecosystems.
DOI: 10.6084/m9.figshare.16699615
title: Title

description: Description
DOI: 10.6084/m9.figshare.16699615.v1
title: Title

description: Description
DOI: 10.17632/79t4psrhwj.2
title: Dataset on microclimate and drone-based thermal patterns within an oil palm agroforestry system

description: We share here:
- microclimate data (as .txt files) containing air temperature, soil temperature and relative humidity data 
- Land surface temperature metrics and other climatic data (as .csv file)
DOI: 10.6084/m9.figshare.12118575.v2
title: Doubly Robust Estimation of Optimal Dosing Strategies

description: The goal of precision medicine is to tailor treatment strategies on an individual patient level. Although several estimation techniques have been developed for determining optimal treatment rules, the majority of methods focus on the case of a dichotomous treatment, an example being the dynamic weighted ordinary least squares regression approach of Wallace and Moodie. We propose an extension to the aforementioned framework to allow for a continuous treatment with the ultimate goal of estimating optimal dosing strategies. The proposed method is shown to be doubly robust against model misspecification whenever the implemented weights satisfy a particular balancing condition. A broad class of weight functions can be derived from the balancing condition, providing a flexible regression based estimation method in the context of adaptive treatment strategies for continuous valued treatments. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.12071430.v2
title: A Hierarchical Max-Infinitely Divisible Spatial Model for Extreme Precipitation

description: Understanding the spatial extent of extreme precipitation is necessary for determining flood risk and adequately designing infrastructure (e.g., stormwater pipes) to withstand such hazards. While environmental phenomena typically exhibit weakening spatial dependence at increasingly extreme levels, limiting max-stable process models for block maxima have a rigid dependence structure that does not capture this type of behavior. We propose a flexible Bayesian model from a broader family of (conditionally) max-infinitely divisible processes that allows for weakening spatial dependence at increasingly extreme levels, and due to a hierarchical representation of the likelihood in terms of random effects, our inference approach scales to large datasets. Therefore, our model not only has a flexible dependence structure, but it also allows for fast, fully Bayesian inference, prediction and conditional simulation in high dimensions. The proposed model is constructed using flexible random basis functions that are estimated from the data, allowing for straightforward inspection of the predominant spatial patterns of extremes. In addition, the described process possesses (conditional) max-stability as a special case, making inference on the tail dependence class possible. We apply our model to extreme precipitation in North-Eastern America, and show that the proposed model adequately captures the extremal behavior of the data. Interestingly, we find that the principal modes of spatial variation estimated from our model resemble observed patterns in extreme precipitation events occurring along the coast (e.g., with localized tropical cyclones and convective storms) and mountain range borders. Our model, which can easily be adapted to other types of environmental datasets, is therefore useful to identify extreme weather patterns and regions at risk. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.12312242.v2
title: Brain Regions Identified as Being Associated With Verbal Reasoning Through the Use of Imaging Regression via Internal Variation

description: <b><i>Abstract–</i>Brain-imaging data have been increasingly used to understand intellectual disabilities. Despite significant progress in biomedical research, the mechanisms for most of the intellectual disabilities remain unknown. Finding the underlying neurological mechanisms has proved difficult, especially in children due to the rapid development of their brains. We investigate verbal reasoning, which is a reliable measure of an individual’s general intellectual abilities, and develop a class of high-order imaging regression models to identify brain subregions which might be associated with this specific intellectual ability. A key novelty of our method is to take advantage of spatial brain structures, and specifically the piecewise smooth nature of most imaging coefficients in the form of high-order tensors. Our approach provides an effective and urgently needed method for identifying brain subregions potentially underlying certain intellectual disabilities. The idea behind our approach is a carefully constructed concept called internal variation (IV). The IV employs tensor decomposition and provides a computationally feasible substitution for total variation, which has been considered suitable to deal with similar problems but may not be scalable to high-order tensor regression. Before applying our method to analyze the real data, we conduct comprehensive simulation studies to demonstrate the validity of our method in imaging signal identification. Next, we present our results from the analysis of a dataset based on the Philadelphia Neurodevelopmental Cohort for which we preprocessed the data including reorienting, bias-field correcting, extracting, normalizing, and registering the magnetic resonance images from 978 individuals. Our analysis identified a subregion across the cingulate cortex and the corpus callosum as being associated with individuals’ verbal reasoning ability, which, to the best of our knowledge, is a novel region that has not been reported in the literature. This finding is useful in further investigation of functional mechanisms for verbal reasoning. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.</b>