cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8199035
title: Acute pulmonary and splenic response in an <i>in vivo</i> model of whole-body low-dose X-radiation exposure

description: <b>Purpose:</b> Diagnostic radiation is an important part of patient care in the Intensive Care Unit; however, there is little data on the acute effects of exposure to these doses. We investigated pulmonary and splenic response 30 minutes, 4 hours or 24 hours after exposure to 2 mGy, 20 mGy, 200 mGy or 4 Gy whole-body X-radiation in a Sprague Dawley rat model. <b>Materials and methods:</b> Lung injury was assessed via respiratory mechanics, pulmonary edema, cellular, and proteinaceous fluid infiltrate and protein expression of oxidative stress markers. The radiation effect on the spleen was determined via proliferation, apoptosis and protein expression of oxidative stress markers. <b>Results:</b> All measurements of the lung did not differ from sham animals except for an increase in catalase after high dose exposure. Stimulated splenocyte proliferation increased after sham and low dose exposure, did not change after 200 mGy exposure and was significantly lower after 4 Gy exposure. The number of apoptotic cells increased 4 hours after 4 Gy exposure. There were fewer apoptotic cells after low dose exposure compared to sham. Both catalase and MnSOD were increased after 4 Gy exposure. <b>Conclusion:</b> There was no measured effect on pulmonary function while there was an impact to the spleen after low and high dose exposure.
DOI: 10.6084/m9.figshare.8199035.v2
title: Acute pulmonary and splenic response in an <i>in vivo</i> model of whole-body low-dose X-radiation exposure

description: <b>Purpose:</b> Diagnostic radiation is an important part of patient care in the Intensive Care Unit; however, there is little data on the acute effects of exposure to these doses. We investigated pulmonary and splenic response 30 minutes, 4 hours or 24 hours after exposure to 2 mGy, 20 mGy, 200 mGy or 4 Gy whole-body X-radiation in a Sprague Dawley rat model. <b>Materials and methods:</b> Lung injury was assessed via respiratory mechanics, pulmonary edema, cellular, and proteinaceous fluid infiltrate and protein expression of oxidative stress markers. The radiation effect on the spleen was determined via proliferation, apoptosis and protein expression of oxidative stress markers. <b>Results:</b> All measurements of the lung did not differ from sham animals except for an increase in catalase after high dose exposure. Stimulated splenocyte proliferation increased after sham and low dose exposure, did not change after 200 mGy exposure and was significantly lower after 4 Gy exposure. The number of apoptotic cells increased 4 hours after 4 Gy exposure. There were fewer apoptotic cells after low dose exposure compared to sham. Both catalase and MnSOD were increased after 4 Gy exposure. <b>Conclusion:</b> There was no measured effect on pulmonary function while there was an impact to the spleen after low and high dose exposure.
DOI: 10.6084/m9.figshare.8199035.v1
title: Acute Pulmonary and Splenic Response in an <i>In Vivo</i> Model of Whole-Body Low-Dose X-Radiation Exposure

description: Purpose: Diagnostic radiation is an important part of patient care in the Intensive Care Unit; however, there is little data on the acute effects of exposure to these doses. We investigated pulmonary and splenic response 30 minutes, 4 hours or 24 hours after exposure to 2 mGy, 20 mGy, 200 mGy or 4 Gy whole-body X-radiation in a Sprague Dawley rat model. Materials and Methods: Lung injury was assessed via respiratory mechanics, pulmonary edema, cellular and proteinaceous fluid infiltrate and protein expression of oxidative stress markers. The radiation effect on the spleen was determined via proliferation, apoptosis and protein expression of oxidative stress markers. Results: All measurements of the lung did not differ from sham animals except for an increase in catalase after high dose exposure. Stimulated splenocyte proliferation increased after sham and low dose exposure, did not change after 200 mGy exposure and was significantly lower after 4 Gy exposure. The number of apoptotic cells increased 4 hours after 4 Gy exposure. There were fewer apoptotic cells after low dose exposure compared to sham. Both catalase and MnSOD were increased after 4 Gy exposure. Conclusion: There was no measured effect on pulmonary function while there was an impact to the spleen after low and high dose exposure.
DOI: 10.6084/m9.figshare.8198999
title: Data from "Optogenetic control of Bacillus subtilis gene expression"

description: Flow cytometry data used to produce the figures in "Optogenetic control of Bacillus subtilis gene expression"
DOI: 10.6084/m9.figshare.8199005
title: 7-grams number

description: 7-grams
DOI: 10.6084/m9.figshare.8198990
title: 7-grams

description: 7-grams
DOI: 10.6084/m9.figshare.8199005.v1
title: 7-grams number

description: 7-grams
DOI: 10.6084/m9.figshare.8198990.v1
title: 7-grams

description: 7-grams
DOI: 10.6084/m9.figshare.8198969
title: 6-grams number

description: 6-grams<br>
DOI: 10.6084/m9.figshare.8198948
title: 6-grams

description: 6-grams<br>
DOI: 10.6084/m9.figshare.8198969.v1
title: 6-grams number

description: 6-grams<br>
DOI: 10.6084/m9.figshare.8198876
title: Volume Data

description: <b>Data supporting the paper: </b>Association between regional brain volumes and BMI z-score change over one year in children<br><b><br></b><b>Abstract:</b><b>Purpose: </b>Associations between brain region volume and weight status have been observed in children cross-sectionally. However, it is unclear if differences in brain region volume precede weight gain. <b>Methods: </b> Two high-quality structural brain images were obtained approximately one year apart in 65 children aged 9-12 years old. Children’s height and weight were also measured at each scan. Structural images were processed using the FreeSurfer software-package providing volume measures for regions of interest including the entorhinal cortex, nucleus accumbens, and hippocampus. Age- and sex-adjusted BMI z-scores (BMIz) were calculated at both timepoints. The association between brain region volume and BMIz was examined cross-sectionally using linear regression and longitudinally using structural equation modeling. All models were adjusted by estimated cranial volume to account for individual variation in head size and were corrected for multiple comparisons (pFDR&lt;0.05). <b>Results</b>: The sample of children was primarily healthy weight at baseline (79.78%). Cross-sectionally at the one-year follow-up, a positive relationship was observed between right hippocampal volume and BMIz ( ). Longitudinally a negative relationship was observed between left entorhinal volume at baseline and BMIz at the one-year follow-up ( ). <b>Conclusion</b>: These results suggest that measured volumes from certain regions of the brain that have been associated with BMI in adults are associated with both concurrent BMIz and BMIz change over one-year in a primarily healthy weight sample of children. As the entorhinal cortex integrates signals from both reward and control regions, this region may be particularly important to weight management during child development.<b><br></b>
DOI: 10.6084/m9.figshare.8198948.v1
title: 6-grams

description: 6-grams<br>
DOI: 10.6084/m9.figshare.8198876.v1
title: Volume Data

description: <b>Data supporting the paper: </b>Association between regional brain volumes and BMI z-score change over one year in children<br><b><br></b><b>Abstract:</b><b>Purpose: </b>Associations between brain region volume and weight status have been observed in children cross-sectionally. However, it is unclear if differences in brain region volume precede weight gain. <b>Methods: </b> Two high-quality structural brain images were obtained approximately one year apart in 65 children aged 9-12 years old. Children’s height and weight were also measured at each scan. Structural images were processed using the FreeSurfer software-package providing volume measures for regions of interest including the entorhinal cortex, nucleus accumbens, and hippocampus. Age- and sex-adjusted BMI z-scores (BMIz) were calculated at both timepoints. The association between brain region volume and BMIz was examined cross-sectionally using linear regression and longitudinally using structural equation modeling. All models were adjusted by estimated cranial volume to account for individual variation in head size and were corrected for multiple comparisons (pFDR&lt;0.05). <b>Results</b>: The sample of children was primarily healthy weight at baseline (79.78%). Cross-sectionally at the one-year follow-up, a positive relationship was observed between right hippocampal volume and BMIz ( ). Longitudinally a negative relationship was observed between left entorhinal volume at baseline and BMIz at the one-year follow-up ( ). <b>Conclusion</b>: These results suggest that measured volumes from certain regions of the brain that have been associated with BMI in adults are associated with both concurrent BMIz and BMIz change over one-year in a primarily healthy weight sample of children. As the entorhinal cortex integrates signals from both reward and control regions, this region may be particularly important to weight management during child development.<b><br></b>
DOI: 10.6084/m9.figshare.8198801
title: 3D visualisation of the forest biomass and fuel wood harvest under the influence of discount rate, marginal rate of substitution and cultural & social values.xlsx

description: The data provides simulation of Southeast Asian Tropical forest growth (Kallio et al., 1987) under the influence of varied discount rate (delta), marginal rate of substitution of fuelwood by its substitute (alpha/beta) and Cultural & Spiritual Value (CSV) (phi). <br>Kallio, M., Dykstra, D. & Binkley, C. Z. E. The global forest
sector: an analytical perspective. <i>Glob. For. Sect. Anal. Perspect.</i>
(1987).<br>
DOI: 10.6084/m9.figshare.8198816
title: Data(180818)_arthritis.sav

description: The sample consists of 226 Korean adults, who are aged 65 years or older, with self-reported arthritis (n=103) and without arthritis (n=123). The variables are general characteristics, social networks (Lubben social network scale), health-promoting lifestyle profile(Waler et al., 1995), and health-related quality of life (EQ-5D-5L).
DOI: 10.6084/m9.figshare.8198681
title: Residual solvent or intrinsically formed during production: analysing volatile compounds in unrefined vegetable oils using headspace gas chromatography coupled with mass spectrometry

description: Vegetable oils are an essential part of a healthy and balanced diet and have major economic significance. The type of production, whether performed by extraction with solvents, or by mechanical techniques, significantly influences the quality of the oil and its potential field of use. Occasionally, volatile organic substances, which are considered indicative for an oil that has been produced by solvent extraction, are detected in unrefined vegetable oils. This can have a negative impact on high-quality oil mills and their reputation. The goal of the study was to analyse unrefined oils of different raw materials for such compounds. A previously developed and validated method using headspace gas chromatography coupled with a mass spectrometry was used for this task. Another aim was to determine the origin of any solvent residues in the vegetable oils and to find ways to avoid them. Complementary measurements by solid phase micro extraction gas chromatography were conducted to compare the results of the measurements to an orthogonal methodology. Multivariate data analysis was used to find correlations between the spectrum of substances in the oil and other parameters like the producer of the oil or the pattern of fatty acids.
DOI: 10.6084/m9.figshare.8198687
title: A new tool to assess ecosystem health in large subtropical reservoirs: Development and validation of a Planktonic Index of Biotic Integrity

description: We developed and validated a Planktonic Index of Biotic Integrity for subtropical reservoirs to assess their ecosystem health. For this purpose, we analyzed the phytoplankton and zooplankton communities and determined reservoir trophic status in the Paranapanema River system (Southeast Brazil). Eleven dams were constructed in the main course of this river to supply hydropower plants. Three of the reservoirs are accumulation systems (i.e. with high water retention times), whereas the others are run-of-the-river systems. For the study the three larger reservoirs (Jurumirim, Chavantes and Capivara) were selected. Physical, chemical, and biological (phytoplankton and zooplankton) data were obtained in two sampling campaigns carried out in March (wet season) and October (dry season) of 2011. For each reservoir we sampled six stations, arranged on a gradient established between the lotic (Paranapanema River entrance) and lentic (dam) areas. According to the Trophic State Index for tropical/subtropical reservoirs, the sampling stations were categorized between ultraoligotrophic and mesotrophic. Four metrics achieved significant discrimination (out of a set of 20 candidate metrics). The individual metric scores were summed to provide a Planktonic Index of Biotic Integrity score, which ranged as Mesotrophic (4-9), Oligotrophic (10-14) and Ultraoligotrophic (15-20), corresponding to the classification of fair, good and excellent, respectively. Following the longitudinal sequence, Jurumirim was classified as Oligotophic (Good) and both Chavantes and Capivara as Ultraoligotrophic (Excellent). This study demonstrated that the Planktonic Index of Biotic Integrity is a potential tool for monitoring large subtropical reservoirs, as planktonic organisms are sensitive to environmental changes and this index integrates distinct temporal and spatial scales.
DOI: 10.6084/m9.figshare.8198591
title: 5-grams number

description: 5-grams
DOI: 10.6084/m9.figshare.8198591.v1
title: 5-grams number

description: 5-grams
DOI: 10.6084/m9.figshare.8198585
title: 5-grams

description: 5-grams<br>
DOI: 10.6084/m9.figshare.8198585.v1
title: 5-grams

description: 5-grams<br>
DOI: 10.6084/m9.figshare.8198561
title: Appendix Tables S1-S5 from When spring ephemerals fail to meet pollinators: mechanism of phenological mismatch and its impact on plant reproduction

description: Table S1. Snowmelt days and flowering onset days in the control and snow removal plots during the experimental period (2014–2017). Table S2. Results of GLMMs for the snow removal experiment (2014–2017). Table S3. Results of GLMMs for seed-set rates under hand pollination (HP) and natural pollination (control) during three years (2014–2016). Table S4. Snowmelt day, flowering onset day, pre-flowering period from snowmelt to onset (PFP), accumulated degree-days for flowering onset (DD-Flower), and daily mean surface temperature during the pre-flowering period in each plot across years. Table S5. First observation day of bumble bees, day number (DoY) on which daily mean soil temperature attained at the threshold value of 5, 6, and 7ºC (TMT), and accumulated degree-days of 2ºC threshold until bee emergence (DD-Bee).
DOI: 10.21227/hn32-8p87
title: VCN

description: Program folder contains all the programs used in the paper. The program is based on tensorflow 2.2.The data folder contains manually generated data and bearing data.
DOI: 10.6084/m9.figshare.8198408
title: Transcriptomic response to aquaculture intensification in Nile tilapia

description: Phenotypic and Gene expression data for Nile tilapia reared at low and high densities
DOI: 10.6084/m9.figshare.8198408.v1
title: Transcriptomic response to aquaculture intensification in Nile tilapia

description: Phenotypic and Gene expression data for Nile tilapia reared at low and high densities
DOI: 10.6084/m9.figshare.8198318
title: 4-grams

description: 4-grams
DOI: 10.6084/m9.figshare.8198318.v1
title: 4-grams

description: 4-grams
DOI: 10.6084/m9.figshare.8198357
title: 4-grams number

description: 4-grams
DOI: 10.6084/m9.figshare.8198357.v1
title: 4-grams number

description: 4-grams
DOI: 10.6084/m9.figshare.8198285
title: Effects of noise and reverberation on speech recognition with variants of a multichannel adaptive dynamic range compression scheme

description: <b>Objective:</b> Adaptive compression methods in hearing aids have been developed to maximise audibility while preserving temporal envelope modulations. Increasing the number of channels may improve listening comfort for loud sounds. However, the effects of this on speech recognition in different environmental conditions are unknown. This study evaluated the effects of different channel architectures and adaptive compression properties on speech recognition in noise and reverberation. <b>Design:</b> Sentences were mixed with steady or modulated noise at three signal-to-noise ratios (SNRs). These were processed with and without reverberation and amplified with four proprietary adaptive compression methods or linear amplification. <b>Study sample:</b> 36 listeners with mild to moderately-severe hearing loss. <b>Results:</b> Adaptive compression improved speech recognition over linear amplification to a small extent, with no significant differences among methods using 4 or 24 channels or a combination thereof. These effects remained across the different background noise and reverberation conditions. <b>Conclusions:</b> Increasing the number of channels does not negatively affect speech recognition in noise and reverberation when adaptive compression is used. If future research shows that increasing the number of channels improves listening comfort for loud sounds, these results indicate that adaptive compression methods with as many as 24 channels are viable options for hearing aids.
DOI: 10.6084/m9.figshare.8198012
title: Title

description: Description
DOI: 10.6084/m9.figshare.8198012.v1
title: Title

description: Description
DOI: 10.6084/m9.figshare.8197889
title: Supplementary Material for: Systemic Treatment Options in Hepatocellular Carcinoma

description: <b><i>Background:</i></b> Patients with advanced hepatocellular carcinoma (HCC) typically have poor survival outcomes. Until recently, sorafenib was the only systemic therapy option available and no agents were approved after sorafenib failure. However, rapid changes are beginning to emerge in the treatment landscape of advanced HCC, with approvals of regorafenib, nivolu­mab, lenvatinib, pembrolizumab, and cabozantinib and positive phase II/III clinical trial results with other agents. <b><i>Summary:</i></b> Here, we provide a comprehensive overview of the clinical trial data of systemic agents that are currently approved for advanced HCC (sorafenib, regorafenib, and nivolumab), including agents recently approved in 2018 (lenvatinib, pembrolizumab, and cabozantinib) and those with recent positive phase II/III results (ramucirumab). Key features of the clinical trial design, including patient selection criteria, the use of biomarkers in HCC, and criteria for efficacy assessment, and their implications in real-world practice are discussed. Important ongoing and planned trials in advanced HCC are summarized to provide a glimpse into the future of advanced HCC treatment. From a physician’s viewpoint, the treatment algorithms for advanced HCC are undergoing significant changes, as additional and imminent approvals impact the choices of first- and second-line treatment and decisions regarding the timing of therapy initiation. With these additional choices at hand, treatment sequencing remains a complex task and should take patient selection and tolerance profiles into account. <b><i>Key Messages:</i></b> The treatment of advanced HCC remains challenging and complex. The rapid developments in systemic therapy for advanced HCC should be considered when determining the best choice and sequence of treatment for patients with advanced HCC.
DOI: 10.6084/m9.figshare.8197889.v1
title: Supplementary Material for: Systemic Treatment Options in Hepatocellular Carcinoma

description: <b><i>Background:</i></b> Patients with advanced hepatocellular carcinoma (HCC) typically have poor survival outcomes. Until recently, sorafenib was the only systemic therapy option available and no agents were approved after sorafenib failure. However, rapid changes are beginning to emerge in the treatment landscape of advanced HCC, with approvals of regorafenib, nivolu­mab, lenvatinib, pembrolizumab, and cabozantinib and positive phase II/III clinical trial results with other agents. <b><i>Summary:</i></b> Here, we provide a comprehensive overview of the clinical trial data of systemic agents that are currently approved for advanced HCC (sorafenib, regorafenib, and nivolumab), including agents recently approved in 2018 (lenvatinib, pembrolizumab, and cabozantinib) and those with recent positive phase II/III results (ramucirumab). Key features of the clinical trial design, including patient selection criteria, the use of biomarkers in HCC, and criteria for efficacy assessment, and their implications in real-world practice are discussed. Important ongoing and planned trials in advanced HCC are summarized to provide a glimpse into the future of advanced HCC treatment. From a physician’s viewpoint, the treatment algorithms for advanced HCC are undergoing significant changes, as additional and imminent approvals impact the choices of first- and second-line treatment and decisions regarding the timing of therapy initiation. With these additional choices at hand, treatment sequencing remains a complex task and should take patient selection and tolerance profiles into account. <b><i>Key Messages:</i></b> The treatment of advanced HCC remains challenging and complex. The rapid developments in systemic therapy for advanced HCC should be considered when determining the best choice and sequence of treatment for patients with advanced HCC.
DOI: 10.6084/m9.figshare.8197865
title: Supplementary Material for: Prostaglandin E<sub>2</sub> Regulates Activation of Mouse Peritoneal Macrophages by <b><i>Staphylococcus aureus</i></b> through Toll-Like Receptor 2, Toll-Like Receptor 4, and NLRP3 Inflammasome Signaling

description: Prostaglandin E<sub>2</sub> (PGE<sub>2</sub>), an essential endogenous lipid mediator for normal physiological functions, can also act as an inflammatory mediator in pathological conditions. We determined whether <i>Staphylococcus aureus</i> lipoproteins are essential for inducing PGE<sub>2</sub> secretion by immune cells and whether pattern recognition receptors mediate this process. PGE<sub>2</sub> levels secreted by mouse peritoneal macrophages infected with the <i>S. aureus</i> isogenic mutant, <i>lgt</i>::ermB (Δ<i>lgt</i>; deficient in lipoprotein maturation), decreased compared with those from macrophages infected with wild-type (WT) <i>S. aureus</i>. Experiments using toll-like receptors 2 (TLR2)-deficient, TLR4-deficient, and NLRP3-deficient mice indicated that these 3 proteins are involved in macrophage PGE<sub>2</sub> secretion in response to <i>S. aureus</i>, and lipoproteins were essential for <i>S. aureus</i> invasion and survival within macrophages. Inhibition of endogenous PGE<sub>2</sub> synthesis had no effect on bacterial invasion. Exogenous PGE<sub>2</sub> inhibited phagocytosis in the WT <i>S. aureus</i> and its isogenic mutant but increased intracellular killing accompanied by enhanced IL-1β secretion. Our data demonstrate that <i>S. aureus</i> can induce macrophage TLR/mitogen-activated protein kinase/NF-κB signaling and that PGE<sub>2</sub> treatment upregulates NLRP3/caspase-1 signaling activation. Thus, macrophage PGE<sub>2</sub> secretion after <i>S. aureus</i> infection depends on bacterial lipoprotein maturation and macrophage receptors TLR2, TLR4, and NLRP3. Moreover, exogenous PGE<sub>2</sub> regulates <i>S. aureus</i>-induced macrophage activation through TLRs and NLRP3 inflammasome signaling.