cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6662378
title: The <i>Enchytraeus crypticus</i> stress metabolome – CuO NM case study

description: The stress metabolome provides a thorough insight into the signals and hence mechanisms of response of organisms. This is an excellent tool to advance the understanding of interactions, especially for substances like nanomaterials (NMs), for which there is an urgent need for alternative methods for hazard assessment. The metabolome of <i>Enchytraeus crypticus</i> was studied for the first time. The case study, CuO NM (and CuCl<sub>2</sub>) covered exposure along a time frame [0–7–14 days (d)] and two reproduction effect concentrations (EC10 and EC50). High-performance liquid chromatography-mass spectrometry based method (HPLC-MS) was used, with reversed phase (RP) separation and mass spectrometric detection in positive and negative modes. Metabolite profiling of Cu materials yielded 155 and 382 metabolite features in positive and negative modes, respectively, showing an expression related with time, material, and ECx. The number of differentially expressed metabolites (DEMs) decreased with exposure time (14 d) for CuO NM, whereas for CuCl<sub>2</sub> EC50 it increased. Overall, almost all DEMs are down-regulated for CuO NM and up-regulated for CuCl<sub>2</sub> (both modes). Early effects were mainly related to amino acids and later to lysophospholipids (down-regulation). Furthermore, the underlying mechanisms of CuO NM toxicity (e.g. neurotransmission, nucleic acids generation, cellular energy, and immune defense) differ from CuCl<sub>2</sub>, where later metabolomic responses are mostly linked to the metabolism of lipids and fewer to amino acids. This study reports a large scale metabolome profiling for <i>E. crypticus</i> and identifies potential markers of Cu materials, which can help to align intelligent testing strategies and safer-by-design materials.
DOI: 10.6084/m9.figshare.6662378.v1
title: The <i>Enchytraeus crypticus</i> stress metabolome – CuO NM case study

description: The stress metabolome provides a thorough insight into the signals and hence mechanisms of response of organisms. This is an excellent tool to advance the understanding of interactions, especially for substances like nanomaterials (NMs), for which there is an urgent need for alternative methods for hazard assessment. The metabolome of <i>Enchytraeus crypticus</i> was studied for the first time. The case study, CuO NM (and CuCl<sub>2</sub>) covered exposure along a time frame [0–7–14 days (d)] and two reproduction effect concentrations (EC10 and EC50). High-performance liquid chromatography-mass spectrometry based method (HPLC-MS) was used, with reversed phase (RP) separation and mass spectrometric detection in positive and negative modes. Metabolite profiling of Cu materials yielded 155 and 382 metabolite features in positive and negative modes, respectively, showing an expression related with time, material, and ECx. The number of differentially expressed metabolites (DEMs) decreased with exposure time (14 d) for CuO NM, whereas for CuCl<sub>2</sub> EC50 it increased. Overall, almost all DEMs are down-regulated for CuO NM and up-regulated for CuCl<sub>2</sub> (both modes). Early effects were mainly related to amino acids and later to lysophospholipids (down-regulation). Furthermore, the underlying mechanisms of CuO NM toxicity (e.g. neurotransmission, nucleic acids generation, cellular energy, and immune defense) differ from CuCl<sub>2</sub>, where later metabolomic responses are mostly linked to the metabolism of lipids and fewer to amino acids. This study reports a large scale metabolome profiling for <i>E. crypticus</i> and identifies potential markers of Cu materials, which can help to align intelligent testing strategies and safer-by-design materials.
DOI: 10.6084/m9.figshare.6662159
title: Bonding in the metallic molecular solid <i>α</i>-Gallium

description: Solid, liquid and alloyed phases of gallium play a role in a variety of important technological applications. While many of the gallium phases involved in these applications are metallic, some have been proposed or are known to contain covalently bound Ga dimers. Thus, understanding the nature of bonding in Ga is crucial to the development of Ga-based materials. The solid phase of gallium at ambient conditions, <i>α</i>-Ga, is metallic and composed of molecular dimers, and can serve as a testing ground for studying gallium bonding with electronic structure calculations. We use density functional theory-based molecular dynamics simulations in conjunction with maximally localised Wannier functions to examine the nature of chemical bonding in <i>α</i>-Ga. We propose a geometric criterion for defining various bonding environments, which enables the quantification of covalent and weak bonds in solid gallium. We additionally connect the bonding structure of <i>α</i>-Ga to its phonon density of states and discuss similarities and differences with diatomic halogen crystals.
DOI: 10.6084/m9.figshare.6662159.v2
title: Bonding in the metallic molecular solid <i>α</i>-Gallium

description: Solid, liquid and alloyed phases of gallium play a role in a variety of important technological applications. While many of the gallium phases involved in these applications are metallic, some have been proposed or are known to contain covalently bound Ga dimers. Thus, understanding the nature of bonding in Ga is crucial to the development of Ga-based materials. The solid phase of gallium at ambient conditions, <i>α</i>-Ga, is metallic and composed of molecular dimers, and can serve as a testing ground for studying gallium bonding with electronic structure calculations. We use density functional theory-based molecular dynamics simulations in conjunction with maximally localised Wannier functions to examine the nature of chemical bonding in <i>α</i>-Ga. We propose a geometric criterion for defining various bonding environments, which enables the quantification of covalent and weak bonds in solid gallium. We additionally connect the bonding structure of <i>α</i>-Ga to its phonon density of states and discuss similarities and differences with diatomic halogen crystals.
DOI: 10.6084/m9.figshare.6662159.v1
title: Bonding in the metallic molecular solid <i>α</i>-Gallium

description: Solid, liquid and alloyed phases of gallium play a role in a variety of important technological applications. While many of the gallium phases involved in these applications are metallic, some have been proposed or are known to contain covalently bound Ga dimers. Thus, understanding the nature of bonding in Ga is crucial to the development of Ga-based materials. The solid phase of gallium at ambient conditions, <i>α</i>-Ga, is metallic and composed of molecular dimers, and can serve as a testing ground for studying gallium bonding with electronic structure calculations. We use density functional theory-based molecular dynamics simulations in conjunction with maximally localised Wannier functions to examine the nature of chemical bonding in <i>α</i>-Ga. We propose a geometric criterion for defining various bonding environments, which enables the quantification of covalent and weak bonds in solid gallium. We additionally connect the bonding structure of <i>α</i>-Ga to its phonon density of states and discuss similarities and differences with diatomic halogen crystals.
DOI: 10.6084/m9.figshare.6662054
title: MOESM2 of Episomal HBV persistence within transcribed host nuclear chromatin compartments involves HBx

description: Additional file 2. RNA-seq derived gene expression results of HBV-negative and HBV-positive HepaRG cells as well as HepG2.2.15 and HepG2H1.3 cell lines (Excel spreadsheet).
DOI: 10.6084/m9.figshare.6662054.v1
title: MOESM2 of Episomal HBV persistence within transcribed host nuclear chromatin compartments involves HBx

description: Additional file 2. RNA-seq derived gene expression results of HBV-negative and HBV-positive HepaRG cells as well as HepG2.2.15 and HepG2H1.3 cell lines (Excel spreadsheet).
DOI: 10.6084/m9.figshare.6661871
title: Hypothesis Tests - All data versus All data without Undergraduates

description: This table shows our hypothesis tests results from a survey of 196 people all over the world. The hypothesis tested was if undergraduate students biased our results from other kind of people (professionals, professors and postgraduate students).<br>
DOI: 10.6084/m9.figshare.6661871.v2
title: Hypothesis Tests - All data versus All data without Undergraduates

description: This table shows our hypothesis tests results from a survey of 196 people all over the world. The hypothesis tested was if undergraduate students biased our results from other kind of people (professionals, professors and postgraduate students).<br>
DOI: 10.6084/m9.figshare.6661871.v1
title: Hypothesis Testes - All data versus All data without Undergraduates

description: This table shows our hypothesis tests results from a survey of 196 people all over the world. The hypothesis tested was if undergraduate students biased our results from other kind of people (professionals, professors and postgraduat students).<br>
DOI: 10.6084/m9.figshare.6661862.v1
title: Measured data of disturbances of reaction wheels

description: This dataset includes the measured data of reaction wheels:The two word documents named ‘Disturbances of reaction wheels over 0~500Hz’ and ‘Disturbances of reaction wheels over 35~300Hz’ summarize the waterfall plots of measured disturbing forces and torques of each reaction wheel together to give a more direct comprehension on the differences between the disturbances of different reaction wheels. The measured data are shown at 0~500Hz and 35~300Hz separately since the disturbances caused by radial rocking (&gt;350Hz), radial translation (&gt;350Hz) and the basic harmonic (&lt;33Hz) of the reaction wheels are so large that they cover the details of harmonics over 50~300Hz.
DOI: 10.6084/m9.figshare.6661856
title: Optimum sampling algorithm for the prediction of soil properties from the infrared spectra

description: Spectroscopy data from three datasets were included in this study. These datasets have different coverages: a European national dataset (LUCAS, <i>n</i> = 5639), a regional dataset from Australia (Geeves, <i>n</i> = 379), and a local dataset from New South Wales, Australia (Hillston, <i>n</i> = 384).<br>Three sampling algorithms: Kennard-Stone (KS), conditioned Latin Hypercube (cLHS) and k-means clustering (KM) were compared against random sampling on the prediction of up to five different soil properties (sand, clay, carbon content, cation exchange capacity and pH) on three datasets. The sampling algorithms were used to select various calibration sample sizes ranging from 50 to 3000 for the continental dataset; and from 50 to 200 samples for the regional and local datasets.<br>All calculations were conducted in R statistical language on High Performance Computing Services provided by the University of Sydney.
DOI: 10.6084/m9.figshare.6661856.v2
title: Optimum sampling algorithm for the prediction of soil properties from the infrared spectra

description: Spectroscopy data from three datasets were included in this study. These datasets have different coverages: a European national dataset (LUCAS, <i>n</i> = 5639), a regional dataset from Australia (Geeves, <i>n</i> = 379), and a local dataset from New South Wales, Australia (Hillston, <i>n</i> = 384).<br>Three sampling algorithms: Kennard-Stone (KS), conditioned Latin Hypercube (cLHS) and k-means clustering (KM) were compared against random sampling on the prediction of up to five different soil properties (sand, clay, carbon content, cation exchange capacity and pH) on three datasets. The sampling algorithms were used to select various calibration sample sizes ranging from 50 to 3000 for the continental dataset; and from 50 to 200 samples for the regional and local datasets.<br>All calculations were conducted in R statistical language on High Performance Computing Services provided by the University of Sydney.
DOI: 10.6084/m9.figshare.6661856.v1
title: Optimum sampling algorithm for the prediction of soil properties from the infrared spectra

description: Spectroscopy data from three datasets were included in this study. These datasets have different coverages: a European national dataset (LUCAS, <i>n</i> = 5639), a regional dataset from Australia (Geeves, <i>n</i> = 379), and a local dataset from New South Wales, Australia (Hillston, <i>n</i> = 384).<br>Three sampling algorithms: Kennard-Stone (KS), conditioned Latin Hypercube (cLHS) and k-means clustering (KM) were compared against random sampling on the prediction of up to five different soil properties (sand, clay, carbon content, cation exchange capacity and pH) on three datasets. The sampling algorithms were used to select various calibration sample sizes ranging from 50 to 3000 for the continental dataset; and from 50 to 200 samples for the regional and local datasets.<br>All calculations were conducted in R statistical language on High Performance Computing Services provided by the University of Sydney.
DOI: 10.6084/m9.figshare.6661847
title: Data_YT.xlsx

description: Data Set: "Relationship between sympathoadrenal and pituitary-adrenal response during colorectal distention in the presence of corticotropin-releasing hormone in patients with irritable bowel syndrome and healthy controls" (PLOS ONE)<br>
DOI: 10.6084/m9.figshare.6661847.v1
title: Data_YT.xlsx

description: Data Set: "Relationship between sympathoadrenal and pituitary-adrenal response during colorectal distention in the presence of corticotropin-releasing hormone in patients with irritable bowel syndrome and healthy controls" (PLOS ONE)<br>
DOI: 10.6084/m9.figshare.6661799
title: Theoretical ribosomal protein mass fingerprint of Providencia rettgeri

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Providencia rettgeri.</i><br><br>
DOI: 10.6084/m9.figshare.6661799.v1
title: Theoretical ribosomal protein mass fingerprint of Providencia rettgeri

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Providencia rettgeri.</i><br><br>
DOI: 10.6084/m9.figshare.6661796
title: Theoretical ribosomal protein mass fingerprint of Proteus vulgaris

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Proteus vulgaris.</i><br><br>
DOI: 10.6084/m9.figshare.6661796.v1
title: Theoretical ribosomal protein mass fingerprint of Proteus vulgaris

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Proteus vulgaris.</i><br><br>
DOI: 10.6084/m9.figshare.6661793
title: Theoretical ribosomal protein mass fingerprint of Proteus penneri

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Proteus penneri</i>.<br><br>
DOI: 10.6084/m9.figshare.6661793.v1
title: Theoretical ribosomal protein mass fingerprint of Proteus penneri

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Proteus penneri</i>.<br><br>
DOI: 10.6084/m9.figshare.6657992
title: AdviceRCT_1.sav

description: Database with different diabetes markers warranting an advice to intensify or deintensify treatment setting and reasons for not following advice.
DOI: 10.6084/m9.figshare.6656405
title: Supplemental Files for Goff et al. (2009)

description: Additional files related to published work.<br>
DOI: 10.6084/m9.figshare.6656405.v1
title: Supplemental Files for Goff et al. (2009)

description: Additional files related to published work.<br>
DOI: 10.6084/m9.figshare.6656234
title: dbcAMP Microarray Methods and Raw Data

description: Supplemental methods and results from Hannila et al. (2013) Secretory Leukocyte Protease Inhibitor Reverses Inhibition by CNS Myelin, Promotes Regeneration in the Optic Nerve, and Suppresses Expression of the Transforming Growth Factor-β Signaling Protein Smad2, Journal of Neuroscience 20 March 2013, 33 (12) 5138-5151
DOI: 10.6084/m9.figshare.6656234.v1
title: dbcAMP Microarray Methods and Raw Data

description: Supplemental methods and results from Hannila et al. (2013) Secretory Leukocyte Protease Inhibitor Reverses Inhibition by CNS Myelin, Promotes Regeneration in the Optic Nerve, and Suppresses Expression of the Transforming Growth Factor-β Signaling Protein Smad2, Journal of Neuroscience 20 March 2013, 33 (12) 5138-5151
DOI: 10.6084/m9.figshare.6656090
title: Removed entry

description: Empty<br>
DOI: 10.6084/m9.figshare.6656090.v2
title: CAMP_raw_array_results.xls

description: Raw microarray data from Hannila et al. (2013). cAMP treated samples.<br>
DOI: 10.6084/m9.figshare.6656090.v1
title: CAMP_raw_array_results.xls

description: Raw microarray data from Hannila et al. (2013).<br>
DOI: 10.6084/m9.figshare.6655478
title: Infant cortisol stress–response is associated with thymic function and vaccine response

description: Stress can impair T cell-mediated immunity. To determine if infants with high stress responses had deficits in T-cell mediated immunity, we examined the association of pain-induced cortisol responsiveness with thymic function and vaccine responses in infants. This study was performed among 306 (male = 153 and female = 153) participants of a randomized, controlled trial examining the effect of neonatal vitamin A supplementation on immune function in Bangladesh (NCT01583972). Salivary cortisol was measured before and 20 min after a needle stick (vaccination) at 6 weeks of age. The thymic index (TI) was determined by ultrasonography at 1, 6, 10 and 15 weeks. T-cell receptor excision circle and blood T-cell concentrations were measured at 6 and 15 weeks. Responses to Bacillus Calmette–Guérin (BCG), tetanus toxoid, hepatitis B virus and oral poliovirus vaccination were assayed at 6 and 15 weeks. Cortisol responsiveness was negatively associated with TI at all ages (<i>p</i> p = .0035) and 15 weeks (<i>p</i> = .0083), and was negatively associated with the delayed-type hypersensitivity (DTH) skin test response to BCG vaccination at 15 weeks (<i>p</i> = .034) in both sexes. Infants with a higher cortisol response to pain have differences in the T-cell compartment and a lower DTH response to vaccination. Sex differences in the immune system were seen as early as 6 weeks of age in these healthy infants.
DOI: 10.6084/m9.figshare.6655478.v2
title: Infant cortisol stress–response is associated with thymic function and vaccine response

description: Stress can impair T cell-mediated immunity. To determine if infants with high stress responses had deficits in T-cell mediated immunity, we examined the association of pain-induced cortisol responsiveness with thymic function and vaccine responses in infants. This study was performed among 306 (male = 153 and female = 153) participants of a randomized, controlled trial examining the effect of neonatal vitamin A supplementation on immune function in Bangladesh (NCT01583972). Salivary cortisol was measured before and 20 min after a needle stick (vaccination) at 6 weeks of age. The thymic index (TI) was determined by ultrasonography at 1, 6, 10 and 15 weeks. T-cell receptor excision circle and blood T-cell concentrations were measured at 6 and 15 weeks. Responses to Bacillus Calmette–Guérin (BCG), tetanus toxoid, hepatitis B virus and oral poliovirus vaccination were assayed at 6 and 15 weeks. Cortisol responsiveness was negatively associated with TI at all ages (<i>p</i> p = .0035) and 15 weeks (<i>p</i> = .0083), and was negatively associated with the delayed-type hypersensitivity (DTH) skin test response to BCG vaccination at 15 weeks (<i>p</i> = .034) in both sexes. Infants with a higher cortisol response to pain have differences in the T-cell compartment and a lower DTH response to vaccination. Sex differences in the immune system were seen as early as 6 weeks of age in these healthy infants.
DOI: 10.6084/m9.figshare.6655478.v1
title: Infant cortisol stress–response is associated with thymic function and vaccine response

description: Stress can impair T cell-mediated immunity. To determine if infants with high stress responses had deficits in T-cell mediated immunity, we examined the association of pain-induced cortisol responsiveness with thymic function and vaccine responses in infants. This study was performed among 306 (male = 153 and female = 153) participants of a randomized, controlled trial examining the effect of neonatal vitamin A supplementation on immune function in Bangladesh (NCT01583972). Salivary cortisol was measured before and 20 min after a needle stick (vaccination) at 6 weeks of age. The thymic index (TI) was determined by ultrasonography at 1, 6, 10 and 15 weeks. T-cell receptor excision circle and blood T-cell concentrations were measured at 6 and 15 weeks. Responses to Bacillus Calmette–Guérin (BCG), tetanus toxoid, hepatitis B virus and oral poliovirus vaccination were assayed at 6 and 15 weeks. Cortisol responsiveness was negatively associated with TI at all ages (<i>p</i> p = .0035) and 15 weeks (<i>p</i> = .0083), and was negatively associated with the delayed-type hypersensitivity (DTH) skin test response to BCG vaccination at 15 weeks (<i>p</i> = .034) in both sexes. Infants with a higher cortisol response to pain have differences in the T-cell compartment and a lower DTH response to vaccination. Sex differences in the immune system were seen as early as 6 weeks of age in these healthy infants.
DOI: 10.6084/m9.figshare.6655223
title: The effect of volanesorsen treatment on the burden associated with familial chylomicronemia syndrome: the results of the ReFOCUS study

description: <b>Background</b>: Volanesorsen, an investigational inhibitor of apoC-III synthesis, significantly reduced triglyceride levels in clinical trials in patients with familial chylomicronemia syndrome (FCS), a rare genetic disorder characterized by marked chylomicronemia leading to a spectrum of symptoms, including recurrent abdominal pain and episodes of potentially fatal acute pancreatitis (AP). <b>Objective</b>: To determine the effect of volanesorsen on burden of disease on patients with FCS <b>Methods</b>: ReFOCUS was a retrospective global web-based survey open to patients with FCS who received volanesorsen for ≥3 months in an open-label extension study. The survey included questions about patients’ experiences before and after volanesorsen treatment. <b>Results</b>: Twenty-two respondents had received volanesorsen for a median of 222 days. Volanesorsen significantly reduced the number of symptoms per patient across physical, emotional, and cognitive domains. Significant reductions from baseline were reported for steatorrhea, pancreatic pain, and constant worry about an attack of pain/AP. Respondents reported that volanesorsen improved overall management of symptoms and reduced interference of FCS with work/school responsibilities. Reductions in the negative impact of FCS on personal, social, and professional life were also reported. <b>Conclusions</b>: Treatment with volanesorsen has the potential to reduce disease burden in patients with FCS through modulation of multiple symptom domains.