cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5281831.v1
title: Glutathione oxidation in response to intracellular H<sub>2</sub>O<sub>2</sub>: key but overlapping roles for dehydroascorbate reductases

description: Glutathione is a pivotal molecule in oxidative stress, during which it is potentially oxidized by several pathways linked to H<sub>2</sub>O<sub>2</sub> detoxification. We have investigated the response and functional importance of three potential routes for glutathione oxidation pathways mediated by glutathione S-transferases (GST), glutaredoxin-dependent peroxiredoxins (PRXII), and dehydroascorbate reductases (DHAR) in Arabidopsis during oxidative stress. Loss-of-function <i>gstU8, gstU24, gstF8, prxIIE</i> and <i>prxIIF</i> mutants as well as double <i>gstU8 gstU24, gstU8 gstF8, gstU24 gstF8, prxIIE prxIIF</i> mutants were obtained. No mutant lines showed marked changes in their phenotype and glutathione profiles in comparison to the wild-type plants in either optimal or oxidative stress triggered by catalase inhibition. By contrast, multiple loss of DHAR functions markedly decreased glutathione oxidation triggered by catalase deficiency. To assess whether this effect was mediated directly by loss of DHAR enzyme activity, or more indirectly by up-regulation of other enzymes involved in glutathione and ascorbate recycling, we measured expression of glutathione reductase (GR) and expression and activity of monodehydroascorbate reductases (MDHAR). No evidence was obtained that either GRs or MDHARs were up-regulated in plants lacking DHAR function. Hence, interplay between different DHARs appears to be necessary to couple ascorbate and glutathione pools and to allow glutathione-related signaling during enhanced H<sub>2</sub>O<sub>2</sub> metabolism.
DOI: 10.6084/m9.figshare.5281525.v1
title: Modified chemical coprecipitation of magnetic magnetite nanoparticles using linear–dendritic copolymers

description: In this investigation, magnetite nanoparticles (Fe<sub>3</sub>O<sub>4</sub> NPs) with a diameter of 5–10 nm were synthesized by coprecipitation from an alkaline solution of ferrous/ferric mixed salt-solution in the presence of copolymers. In this process, linear–dendritic copolymers containing a linear poly (ethylene glycol) core and dendritic poly (citric acid) arms were used as the stabilizer. The Fe<sub>3</sub>O<sub>4</sub> NPs were characterized by transmission electron microscopy, energy-dispersive spectra, X-ray powder diffraction, field emission scanning electron microscopy, Fourier transform infrared spectrometer, and vibrating sample magnetometer. Compared to classical coprecipitation, the results showed that uniform, ultrafine, nearly spherical, and high purity nano-magnetite particles with better magnetic properties could be prepared by this method.
DOI: 10.6084/m9.figshare.5281324
title: Capsaicin - Molecule of the Month April 2001 [Archived version]

description: This is the Molecule of the Month entry for April 2001 about capsaicin. It is a pdf archive version of the HTML webpage.
DOI: 10.6084/m9.figshare.5281327
title: Mvt_vis_10_Data

description: Data
DOI: 10.6084/m9.figshare.5281303
title: A checklist of the bryophytes of Andorra

description: A checklist of 137 liverwort and 445 moss species is established for Andorra based on a review of the literature and a long-term floristic survey. Five moss species, <i>Barbula amplexifolia</i>, <i>Ditrichum zonatum</i>, <i>Grimmia donniana</i>, <i>Pohlia bulbifera</i>, and <i>P. lutescens</i>, are new to the Iberian Peninsula. Another 7 liverwort and 156 moss species are new to Andorra. For each species, the distribution at the scale of 1 km<sup>2</sup> and altitudinal range are documented, resulting in an improved assessment of the frequency and distribution of 101 moss species previously reported from a single record. <i>Haplomitrium hookeri</i> and <i>Scapania verrucosa</i>, which are the two Regionally Extinct species of the Spanish Red List of liverworts, occur in Andorra, which hosts between 23 and 37% of the species listed as Critically Rare, Endangered, or Vulnerable in the Spanish Red List of bryophytes. Therefore, it appears that Andorra is a key area for the conservation of the high-altitude flora of the Iberian Peninsula.
DOI: 10.6084/m9.figshare.5281297
title: The oldest Asian hesperornithiform from the Upper Cretaceous of Japan, and the phylogenetic reassessment of Hesperornithiformes

description: Asian hesperornithiforms are extremely rare in contrast to the much more abundant record from North America. In Asia, these fossil birds are only known from fragmentary materials from Mongolia. Here we describe the skeletal remains of a new hesperornithiform <i>Chupkaornis keraorum</i> gen. et sp. nov. from the Upper Cretaceous Kashima Formation (Coniacian to Santonian) of the Yezo Group in Mikasa City, Hokkaido, Japan. This is the best-preserved hesperornithiform material from Asia and it is the first report of hesperornithiforms from the eastern margin of the Eurasian continent. <i>Chupkaornis</i> has a unique combination of characters: finger-like projected tibiofibular crest of femur, deep, emarginated lateral excavation with a sharply defined edge of the ventral margin of the thoracic vertebrae, and the heterocoelous articular surface of the thoracic vertebrae. Our new phylogenetic analysis revises the phylogenetic relationships of Hesperornithiformes. In contrast to previous studies, <i>Enaliornis</i> is assigned as the most basal taxon and <i>Baptornis</i> is positioned as more derived than <i>Brodavis</i>. <i>Chupkaornis</i> is a sister taxon to the clade of <i>Brodavis</i> and higher taxa. <i>Parahesperornis</i> and <i>Hesperornis</i> are positioned within Hesperornithidae, the derived Hesperornithiformes. Many of the skeletal character changes are concentrated at the base of Hesperornithidae (<i>Parahesperornis</i> and more derived taxa), and involve the modification of the pelvic girdle and hind limb morphology (e.g. dorsal directed antitrochanter of pelvis, short and sprawled femur, including probable lobe-toed feet suggested by the specialized distal articular surface of first digit of fourth toe, and predominantly robust digit IV phalanges). These skeletal modifications are likely adaptations for foot-propelled diving behaviour. http://zoobank.org/urn:lsid:zoobank.org:pub:FB783237-E565-4B74-9386-EADF8E12DFD4
DOI: 10.6084/m9.figshare.5281300
title: Gene structure and cDNA sequence of 2-Cys peroxiredoxin in the harmful algal bloom species <i>Chattonella marina</i> and its gene transcription under different light intensities

description: We investigated the gene structure and predicted amino acid sequence of the antioxidant enzyme 2-Cys peroxiredoxin (2-Cys Prx) in the raphidophyte <i>Chattonella marina</i>, which is a harmful algal bloom (HAB) species. The open reading frame of 2-Cys Prx was 585 bp long and encoded a protein consisting of 195 amino acids. The putative amino acid sequence contained two cysteine residues located at the 49th and 170th amino acid positions from the N-terminal methionine residue. The sequence also possessed 2-Cys Prx characteristic motifs, F (FFYPLDFTFVCPTEI) and EVCP. The position of the 2-Cys Prx gene relative to several others (<i>ycf</i>59 <i>– 2-CysPrx – rpl</i>35 <i>– rpl</i>20) was the same as that found in the chloroplast genome in the raphidophyte <i>Heterosigma akashiwo</i>. Upstream of the 2-Cys Prx gene, possible TATA and GGA motifs recognized by nuclear-encoded plastid RNA polymerase (NEP), and a possible -10 box and -35 box recognized by plastid-encoded plastid RNA polymerase (PEP) were observed. We measured the transcript levels of 2-Cys Prx in <i>C. marina</i> cells grown under three different light intensities (0, 100, 1000 µmol photons m<sup>–2</sup> s<sup>–1</sup>, 14-h light/8-h dark photoperiod) by quantitative PCR. The 2-Cys Prx transcript level in cells grown under the highest light intensity on day 3 was threefold that on day 0 but two lower light intensities resulted in relatively stable transcription levels. The 2-Cys Prx transcript level was significantly positively related to the H<sub>2</sub>O<sub>2</sub> concentration per cell and the H<sub>2</sub>O<sub>2</sub> scavenging activity per cell. These results suggest that <i>C. marina</i> 2-Cys Prx functions in the chloroplast and its transcription could be regulated by both NEP and PEP. Moreover, the 2-Cys Prx transcript level might increase to remove excessive H<sub>2</sub>O<sub>2</sub> produced under strong light conditions in order to maintain cell proliferation activity.
DOI: 10.6084/m9.figshare.5281303.v1
title: A checklist of the bryophytes of Andorra

description: A checklist of 137 liverwort and 445 moss species is established for Andorra based on a review of the literature and a long-term floristic survey. Five moss species, <i>Barbula amplexifolia</i>, <i>Ditrichum zonatum</i>, <i>Grimmia donniana</i>, <i>Pohlia bulbifera</i>, and <i>P. lutescens</i>, are new to the Iberian Peninsula. Another 7 liverwort and 156 moss species are new to Andorra. For each species, the distribution at the scale of 1 km<sup>2</sup> and altitudinal range are documented, resulting in an improved assessment of the frequency and distribution of 101 moss species previously reported from a single record. <i>Haplomitrium hookeri</i> and <i>Scapania verrucosa</i>, which are the two Regionally Extinct species of the Spanish Red List of liverworts, occur in Andorra, which hosts between 23 and 37% of the species listed as Critically Rare, Endangered, or Vulnerable in the Spanish Red List of bryophytes. Therefore, it appears that Andorra is a key area for the conservation of the high-altitude flora of the Iberian Peninsula.
DOI: 10.6084/m9.figshare.5281327.v1
title: Mvt_vis_10_Data

description: Data
DOI: 10.6084/m9.figshare.5281300.v1
title: Gene structure and cDNA sequence of 2-Cys peroxiredoxin in the harmful algal bloom species <i>Chattonella marina</i> and its gene transcription under different light intensities

description: We investigated the gene structure and predicted amino acid sequence of the antioxidant enzyme 2-Cys peroxiredoxin (2-Cys Prx) in the raphidophyte <i>Chattonella marina</i>, which is a harmful algal bloom (HAB) species. The open reading frame of 2-Cys Prx was 585 bp long and encoded a protein consisting of 195 amino acids. The putative amino acid sequence contained two cysteine residues located at the 49th and 170th amino acid positions from the N-terminal methionine residue. The sequence also possessed 2-Cys Prx characteristic motifs, F (FFYPLDFTFVCPTEI) and EVCP. The position of the 2-Cys Prx gene relative to several others (<i>ycf</i>59 <i>– 2-CysPrx – rpl</i>35 <i>– rpl</i>20) was the same as that found in the chloroplast genome in the raphidophyte <i>Heterosigma akashiwo</i>. Upstream of the 2-Cys Prx gene, possible TATA and GGA motifs recognized by nuclear-encoded plastid RNA polymerase (NEP), and a possible -10 box and -35 box recognized by plastid-encoded plastid RNA polymerase (PEP) were observed. We measured the transcript levels of 2-Cys Prx in <i>C. marina</i> cells grown under three different light intensities (0, 100, 1000 µmol photons m<sup>–2</sup> s<sup>–1</sup>, 14-h light/8-h dark photoperiod) by quantitative PCR. The 2-Cys Prx transcript level in cells grown under the highest light intensity on day 3 was threefold that on day 0 but two lower light intensities resulted in relatively stable transcription levels. The 2-Cys Prx transcript level was significantly positively related to the H<sub>2</sub>O<sub>2</sub> concentration per cell and the H<sub>2</sub>O<sub>2</sub> scavenging activity per cell. These results suggest that <i>C. marina</i> 2-Cys Prx functions in the chloroplast and its transcription could be regulated by both NEP and PEP. Moreover, the 2-Cys Prx transcript level might increase to remove excessive H<sub>2</sub>O<sub>2</sub> produced under strong light conditions in order to maintain cell proliferation activity.
DOI: 10.6084/m9.figshare.5281282
title: Neuroimaging_clinical_data_dystonia.xlsx

description: Data set - neuroimaging statistics, clinical data. Craniocervical dystonia.
DOI: 10.6084/m9.figshare.5281273
title: What mediates tree mortality during drought in the southern Sierra Nevada?

description: We used high-fidelity imaging spectroscopy (HiFIS) and light detection and ranging (LiDAR) from the Carnegie Airborne Observatory (CAO) to estimate the effect of forest dieback on species composition in response to drought stress in Sequoia National Park. Our aims were: (1) to quantify site-specific conditions that mediate tree mortality along an elevation gradient in the southern Sierra Nevada Mountains; (2) to assess where mortality events have a greater probability of occurring; and (3) to estimate which tree species have a greater likelihood of mortality along the elevation gradient. The data-set include dead trees and highly stressed trees that were identified in 2015 in the forests of Sequoia National Park (SNP), along an elevation gradient in California’s southern Sierra. <br><br><br>
DOI: 10.6084/m9.figshare.5281276
title: Reporting guidelines identified by authors for manuscripts submitted before and after intervention using Penelope EQUATOR wizard

description: Anonymised manuscript list for articles submitted to four BioMed Central journals, and the EQUATOR reporting guideline identified as relevant by the authors during submission. This includes data for both before and after introduction of the Penelope EQUATOR wizard decision-tree tool to support authors in identification of the relevant reporting guideline, and analysis.
DOI: 10.6084/m9.figshare.5281276.v1
title: Reporting guidelines identified by authors for manuscripts submitted before and after intervention using Penelope Research

description: Anonymised manuscript list for articles submitted to four BioMed Central journals, and the EQUATOR reporting guideline identified as relevant by the authors during submission. This includes data for both before and after introduction of the Penelope EQUATOR wizard decision-tree tool to support authors in identification of the relevant reporting guideline, and analysis.
DOI: 10.6084/m9.figshare.5281276.v2
title: Reporting guidelines identified by authors for manuscripts submitted before and after intervention using Penelope EQUATOR wizard

description: Anonymised manuscript list for articles submitted to four BioMed Central journals, and the EQUATOR reporting guideline identified as relevant by the authors during submission. This includes data for both before and after introduction of the Penelope EQUATOR wizard decision-tree tool to support authors in identification of the relevant reporting guideline, and analysis.
DOI: 10.6084/m9.figshare.5281276.v3
title: Reporting guidelines identified by authors for manuscripts submitted before and after intervention using Penelope EQUATOR wizard

description: Anonymised manuscript list for articles submitted to four BioMed Central journals, and the EQUATOR reporting guideline identified as relevant by the authors during submission. This includes data for both before and after introduction of the Penelope EQUATOR wizard decision-tree tool to support authors in identification of the relevant reporting guideline, and analysis.
DOI: 10.6084/m9.figshare.5281132
title: Ecotoxicological modelling of cosmetics for aquatic organisms: A QSTR approach

description: In this study, externally validated quantitative structure–toxicity relationship (QSTR) models were developed for toxicity of cosmetic ingredients on three different ecotoxicologically relevant organisms, namely <i>Pseudokirchneriella subcapitata</i>, <i>Daphnia magna</i> and <i>Pimephales promelas</i> following the OECD guidelines. The final models were developed by partial least squares (PLS) regression technique, which is more robust than multiple linear regression. The obtained model for <i>P. subcapitata</i> shows that molecular size and complexity have significant impacts on the toxicity of cosmetics. In case of <i>P. promelas</i> and <i>D. magna</i>, we found that the largest contribution to the toxicity was shown by hydrophobicity and van der Waals surface area, respectively. All models were validated using both internal and test compounds employing multiple strategies. For each QSTR model, applicability domain studies were also performed using the “Distance to Model in X-space” method. A comparison was made with the ECOSAR predictions in order to prove the good predictive performances of our developed models. Finally, individual models were applied to predict toxicity for an external set of 596 personal care products having no experimental data for at least one of the endpoints, and the compounds were ranked based on a decreasing order of toxicity using a scaling approach.
DOI: 10.6084/m9.figshare.5281090
title: Results from a clinical trial evaluating the efficacy of real-time body surface visual feedback in reducing patient motion during lung cancer radiotherapy

description: <b>Introduction:</b> Optical surface measurement devices are a maturing technology in radiotherapy. The challenge for such devices is to demonstrate how they can improve clinical care. We present results from a phase 1 clinical trial designed to test the hypothesis that if presented with live data from a novel optical measurement device, showing their deviation from an ideal radiotherapy treatment position, patients will be able to better control their motion and increase their geometrical conformance. <b>Method and materials:</b> Fourteen lung cancer patients were enrolled in a prospective clinical study and asked to use a variety of visual feedback schema from a novel in-house developed optical surface measurement device. The magnitude and regularity of their body surface motion using the different schema was compared to that when free-breathing at three time-points throughout their radiotherapy treatment schedule. Additionally, 4D Cone Beam CT data, acquired simultaneously with the optical measurements, was used to test if improvements in external motion are reflected in changes in internal tumor motion. <b>Results:</b> The primary endpoint of the trial, device tolerability assessed by the fraction of participants completing all study sessions, was 86%. Secondary endpoints showed that use of the visual feedback device was found to statistically significantly decrease body surface motion magnitude by an average of 17% over the study cohort, although not universally. Similarly body surface motion variability was decreased by 18% on average. Internal tumor motion magnitude was also found to be statistically significantly decreased by an average of 14% when using the feedback device. Reduction in external motion was predictive of reduced internal motion but no evidence of a simple correlation between changes in internal and external motion magnitude was found. <b>Conclusions:</b> Visual feedback of live motion is well tolerated by lung cancer patients and can reduce both body surface and tumor motion.
DOI: 10.6084/m9.figshare.5281132.v1
title: Ecotoxicological modelling of cosmetics for aquatic organisms: A QSTR approach

description: In this study, externally validated quantitative structure–toxicity relationship (QSTR) models were developed for toxicity of cosmetic ingredients on three different ecotoxicologically relevant organisms, namely <i>Pseudokirchneriella subcapitata</i>, <i>Daphnia magna</i> and <i>Pimephales promelas</i> following the OECD guidelines. The final models were developed by partial least squares (PLS) regression technique, which is more robust than multiple linear regression. The obtained model for <i>P. subcapitata</i> shows that molecular size and complexity have significant impacts on the toxicity of cosmetics. In case of <i>P. promelas</i> and <i>D. magna</i>, we found that the largest contribution to the toxicity was shown by hydrophobicity and van der Waals surface area, respectively. All models were validated using both internal and test compounds employing multiple strategies. For each QSTR model, applicability domain studies were also performed using the “Distance to Model in X-space” method. A comparison was made with the ECOSAR predictions in order to prove the good predictive performances of our developed models. Finally, individual models were applied to predict toxicity for an external set of 596 personal care products having no experimental data for at least one of the endpoints, and the compounds were ranked based on a decreasing order of toxicity using a scaling approach.
DOI: 10.6084/m9.figshare.5281090.v1
title: Results from a clinical trial evaluating the efficacy of real-time body surface visual feedback in reducing patient motion during lung cancer radiotherapy

description: <b>Introduction:</b> Optical surface measurement devices are a maturing technology in radiotherapy. The challenge for such devices is to demonstrate how they can improve clinical care. We present results from a phase 1 clinical trial designed to test the hypothesis that if presented with live data from a novel optical measurement device, showing their deviation from an ideal radiotherapy treatment position, patients will be able to better control their motion and increase their geometrical conformance. <b>Method and materials:</b> Fourteen lung cancer patients were enrolled in a prospective clinical study and asked to use a variety of visual feedback schema from a novel in-house developed optical surface measurement device. The magnitude and regularity of their body surface motion using the different schema was compared to that when free-breathing at three time-points throughout their radiotherapy treatment schedule. Additionally, 4D Cone Beam CT data, acquired simultaneously with the optical measurements, was used to test if improvements in external motion are reflected in changes in internal tumor motion. <b>Results:</b> The primary endpoint of the trial, device tolerability assessed by the fraction of participants completing all study sessions, was 86%. Secondary endpoints showed that use of the visual feedback device was found to statistically significantly decrease body surface motion magnitude by an average of 17% over the study cohort, although not universally. Similarly body surface motion variability was decreased by 18% on average. Internal tumor motion magnitude was also found to be statistically significantly decreased by an average of 14% when using the feedback device. Reduction in external motion was predictive of reduced internal motion but no evidence of a simple correlation between changes in internal and external motion magnitude was found. <b>Conclusions:</b> Visual feedback of live motion is well tolerated by lung cancer patients and can reduce both body surface and tumor motion.