cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8277512.v2
title: <i>Diaphorocetus poucheti</i> (Cetacea, Odontoceti, Physeteroidea) from Patagonia, Argentina: one of the earliest sperm whales

description: Sperm whales (Physeteroidea) are the basal-most surviving lineage of odontocetes, represented today by just three highly specialized, deep-diving suction feeders. By contrast, extinct sperm whales were relatively diverse, reflecting a major Miocene diversification into various suction feeding and macroraptorial forms. The beginnings of this diversification, however, remain poorly understood. The Atlantic coast of South America provides a crucial window into early physeteroid evolution and has yielded some of the oldest species known from cranial material, <i>Idiorophus patagonicus</i> and <i>Diaphorocetus poucheti</i> – both of which are in need of re-description and phylogenetic reappraisal. Here, we re-examine <i>Diaphorocetus</i> in detail and, in light of its complex taxonomic history, declare it a <i>nomen protectum</i>. Phylogenetically, the species forms part of a polytomy including ‘<i>Aulophyseter</i>’ <i>rionegresis</i> and the two crown lineages (Physeteridae and Kogiidae) and demonstrates that facial asymmetry and a clearly defined supracranial basin have characterized this lineage for at least 20 Ma. With a total body length of 3.5–4 m, <i>Diaphorocetus</i> is one of the smallest physeteroids yet known. Its cranial morphology hints at an intermediate raptorial/suction feeding strategy and it has a moderately developed spermaceti organ and junk.
DOI: 10.6084/m9.figshare.8277623.v2
title: Whole-genome sequencing metadata of Leptospira strains isolated from cattle in Uruguay

description: Metadata associated to 40 pathogenic Leptospira strains isolated from naturally infected cattle in Uruguay. These strains have been whole-genome sequenced.<br>
DOI: 10.6084/m9.figshare.8277461
title: Rodriguez_et_al_2019_Fractionation.xlsx

description: Database used in the manuscript "Forest die-off reduces soil organic C and N stocks and the less stable forms in a Mediterranean woodland.
DOI: 10.6084/m9.figshare.8277497
title: Trends in bicycle-related injuries, hospital admissions, and deaths in the USA 1997–2013

description: <b>Objective:</b> Cycling is associated with numerous health benefits but also the risk of traumatic injury. Recent data demonstrate an increase in overall cycling injuries as well as hospital admissions from 1997 to 2013 in the United States. We seek to better understand the causes of the increase in cycling injuries and hospital admissions. <b>Methods:</b> Data regarding cycling-related injuries and hospital admissions were obtained from the National Electronic Injury Surveillance System (NEISS). Participation data were derived from the <i>National Sporting Goods Association Sports Participation Survey</i>, and fatality data were collected from the Fatality Analysis Reporting System (FARS). Population estimates were obtained using a complex survey design. Linear regression was used to evaluate univariate relationships between cycling injuries, hospital admissions, deaths, and participation. To evaluate factors associated with hospital admission, we developed a multivariable logistic regression model that included year, age, gender, body part injured, and injury type (i.e., contusion, fracture, or laceration). <b>Results:</b> The number of individuals who cycle did not change significantly over time, but there was a substantial increase in cycling-related injuries, leading to an increase in per participant injuries from 701/100,000 in 1997 to 1,164/100,000 in 2013. When the injuries were evaluated by age group, younger cyclists have an increased risk for injury, whereas the rise in injuries among older cyclists stemmed from an increase in ridership rather than a unique susceptibility to injury. Trends in hospital admissions and fatalities appeared to be driven by increases in the older age groups. In the multivariable model evaluating factors related to hospital admission, the odds of hospital admission increased for each decade after age 25, as well as male gender and body part injured. <b>Conclusion:</b> On a per participant basis, the rate of cycling-related injuries and hospital admissions increased between 1997 and 2013. This trend likely reflects a combination of shifting demographics among cyclists with an increase in older cyclists who are at increased risk of severe injury.
DOI: 10.6084/m9.figshare.8277512.v1
title: <i>Diaphorocetus poucheti</i> (Cetacea, Odontoceti, Physeteroidea) from Patagonia, Argentina: one of the earliest sperm whales

description: Sperm whales (Physeteroidea) are the basal-most surviving lineage of odontocetes, represented today by just three highly specialized, deep-diving suction feeders. By contrast, extinct sperm whales were relatively diverse, reflecting a major Miocene diversification into various suction feeding and macroraptorial forms. The beginnings of this diversification, however, remain poorly understood. The Atlantic coast of South America provides a crucial window into early physeteroid evolution and has yielded some of the oldest species known from cranial material, <i>Idiorophus patagonicus</i> and <i>Diaphorocetus poucheti</i> – both of which are in need of re-description and phylogenetic reappraisal. Here, we re-examine <i>Diaphorocetus</i> in detail and, in light of its complex taxonomic history, declare it a <i>nomen protectum</i>. Phylogenetically, the species forms part of a polytomy including ‘<i>Aulophyseter</i>’ <i>rionegresis</i> and the two crown lineages (Physeteridae and Kogiidae) and demonstrates that facial asymmetry and a clearly defined supracranial basin have characterized this lineage for at least 20 Ma. With a total body length of 3.5–4 m, <i>Diaphorocetus</i> is one of the smallest physeteroids yet known. Its cranial morphology hints at an intermediate raptorial/suction feeding strategy and it has a moderately developed spermaceti organ and junk.
DOI: 10.6084/m9.figshare.8277506.v2
title: Vaccination with FAdV-8a induces protection against inclusion body hepatitis caused by homologous and heterologous strains

description: Fowl aviadenoviruses (FAdV) are important avian pathogens, responsible for several poultry diseases prevalent worldwide, including inclusion body hepatitis (IBH). FAdV intraspecies cross-protection has been clearly demonstrated, but there is little evidence that any interspecies cross-protection exists. The present study aimed to assess the inter- and intraspecies protection between three FAdV field isolates (FAdV-8a, FAdV-8b, FAdV-11) identified in association with severe IBH outbreaks. Inocula prepared using inactivated plaque-purified virus with adjuvant Montanide™ ISA 71VG, were injected intramuscularly into 3-week-old SPF chickens. At 6-weeks of age, the birds were challenged with 10<sup>6</sup> TCID<sub>50</sub> of homologous or heterologous virus intraperitoneally, and full <i>post mortem</i> examination performed at 4 days post-challenge. Various tissues were examined for gross and histological lesions and assessed for the presence of virus by PCR-HRM. All homologous-type vaccine/challenge groups exhibited protection against IBH lesions with no virus detected in the tissues. Unvaccinated groups challenged with virus showed evidence of FAdV-induced lesions; however, FAdV-8a demonstrated lower pathogenicity compared with FAdV-8b and FAdV-11. In the heterologous-type vaccine/challenge groups, FAdV-8a vaccine was shown to protect against challenge with both FAdV-8b and FAdV-11. FAdV-8a and 8b belong to species E and were therefore anticipated to cross-protect. However, FAdV-11 belongs to species D and therefore cross-protection by FAdV-8a was an uncharacteristic and unique finding of this study. Further research is required to disseminate the molecular basis for the interspecies cross-protection between FAdV-8a and FAdV-11. Nonetheless, the FAdV-8a isolate was shown to have substantial potential as a vaccine candidate in countries where FAdV-8a, 8b or 11 are prevalent.
DOI: 10.6084/m9.figshare.8277461.v1
title: Rodriguez_et_al_2019_Fractionation.xlsx

description: Database used in the manuscript "Forest die-off reduces soil organic C and N stocks and the less stable forms in a Mediterranean woodland.
DOI: 10.6084/m9.figshare.8277497.v1
title: Trends in bicycle-related injuries, hospital admissions, and deaths in the USA 1997–2013

description: <b>Objective:</b> Cycling is associated with numerous health benefits but also the risk of traumatic injury. Recent data demonstrate an increase in overall cycling injuries as well as hospital admissions from 1997 to 2013 in the United States. We seek to better understand the causes of the increase in cycling injuries and hospital admissions. <b>Methods:</b> Data regarding cycling-related injuries and hospital admissions were obtained from the National Electronic Injury Surveillance System (NEISS). Participation data were derived from the <i>National Sporting Goods Association Sports Participation Survey</i>, and fatality data were collected from the Fatality Analysis Reporting System (FARS). Population estimates were obtained using a complex survey design. Linear regression was used to evaluate univariate relationships between cycling injuries, hospital admissions, deaths, and participation. To evaluate factors associated with hospital admission, we developed a multivariable logistic regression model that included year, age, gender, body part injured, and injury type (i.e., contusion, fracture, or laceration). <b>Results:</b> The number of individuals who cycle did not change significantly over time, but there was a substantial increase in cycling-related injuries, leading to an increase in per participant injuries from 701/100,000 in 1997 to 1,164/100,000 in 2013. When the injuries were evaluated by age group, younger cyclists have an increased risk for injury, whereas the rise in injuries among older cyclists stemmed from an increase in ridership rather than a unique susceptibility to injury. Trends in hospital admissions and fatalities appeared to be driven by increases in the older age groups. In the multivariable model evaluating factors related to hospital admission, the odds of hospital admission increased for each decade after age 25, as well as male gender and body part injured. <b>Conclusion:</b> On a per participant basis, the rate of cycling-related injuries and hospital admissions increased between 1997 and 2013. This trend likely reflects a combination of shifting demographics among cyclists with an increase in older cyclists who are at increased risk of severe injury.
DOI: 10.6084/m9.figshare.8277506.v1
title: Vaccination with FAdV-8a induces protection against inclusion body hepatitis caused by homologous and heterologous strains

description: Fowl aviadenoviruses (FAdV) are important avian pathogens, responsible for several poultry diseases prevalent worldwide, including inclusion body hepatitis (IBH). FAdV intraspecies cross-protection has been clearly demonstrated, but there is little evidence that any interspecies cross-protection exists. The present study aimed to assess the inter- and intraspecies protection between three FAdV field isolates (FAdV-8a, FAdV-8b, FAdV-11) identified in association with severe IBH outbreaks. Inocula prepared using inactivated plaque-purified virus with adjuvant Montanide™ ISA 71VG, were injected intramuscularly into 3-week-old SPF chickens. At 6-weeks of age, the birds were challenged with 10<sup>6</sup> TCID<sub>50</sub> of homologous or heterologous virus intraperitoneally, and full <i>post mortem</i> examination performed at 4 days post-challenge. Various tissues were examined for gross and histological lesions and assessed for the presence of virus by PCR-HRM. All homologous-type vaccine/challenge groups exhibited protection against IBH lesions with no virus detected in the tissues. Unvaccinated groups challenged with virus showed evidence of FAdV-induced lesions; however, FAdV-8a demonstrated lower pathogenicity compared with FAdV-8b and FAdV-11. In the heterologous-type vaccine/challenge groups, FAdV-8a vaccine was shown to protect against challenge with both FAdV-8b and FAdV-11. FAdV-8a and 8b belong to species E and were therefore anticipated to cross-protect. However, FAdV-11 belongs to species D and therefore cross-protection by FAdV-8a was an uncharacteristic and unique finding of this study. Further research is required to disseminate the molecular basis for the interspecies cross-protection between FAdV-8a and FAdV-11. Nonetheless, the FAdV-8a isolate was shown to have substantial potential as a vaccine candidate in countries where FAdV-8a, 8b or 11 are prevalent.
DOI: 10.6084/m9.figshare.8277362
title: 2 n consort 2010 t.doc

description: complete consort checklist<br>
DOI: 10.6084/m9.figshare.8277371
title: Cropped substrate-binding sites of T.thermophilus AlaRS and D-aminoacyl-tRNA-deacylase from molecular dynamics simulations studies

description: Supplement data to the article "Stereospecificity control in aminoacyl-tRNA synthetases: new evidence of D-amino acids activation and editing"<br>
DOI: 10.6084/m9.figshare.8277362.v1
title: 2 n consort 2010 t.doc

description: complete consort checklist<br>
DOI: 10.6084/m9.figshare.8277311
title: Protein array data

description: Protein array results using the NCI-60 cell lines from the Cancer Research Technology Program at NCI-Frederick.
DOI: 10.6084/m9.figshare.8277341
title: Tissue immunohistochemistry data

description: Tissue microarray IHC results using ovarian, colon, lung, and breast tissue cores.
DOI: 10.6084/m9.figshare.8277371.v2
title: Cropped substrate-binding sites of T.thermophilus AlaRS and D-aminoacyl-tRNA-deacylase from molecular dynamics simulations studies

description: Supplement data to the article "Stereospecificity control in aminoacyl-tRNA synthetases: new evidence of D-amino acids activation and editing"<br>
DOI: 10.6084/m9.figshare.8277263
title: Data Availability Statement

description: Raw data of antioxidant activity, sperm lipid peroxidation, sperm motility, sperm plasma membrane, acrosome, mitochondria, and healthy spermResults of statistical analysis<br>
DOI: 10.6084/m9.figshare.8277371.v1
title: Cropped substrate-binding sites of T.thermophilus AlaRS and D-aminoacyl-tRNA-deacylase from molecular dynamics simulations studies

description: Supplement data to the article "Stereospecificity control in aminoacyl-tRNA synthetases: new evidence of D-amino acids activation and editing"<br>
DOI: 10.6084/m9.figshare.8277311.v1
title: Protein array data

description: Protein array results using the NCI-60 cell lines from the Cancer Research Technology Program at NCI-Frederick.
DOI: 10.6084/m9.figshare.8277341.v1
title: Tissue immunohistochemistry data

description: Tissue microarray IHC results using ovarian, colon, lung, and breast tissue cores.
DOI: 10.6084/m9.figshare.8277263.v1
title: Data Availability Statement

description: Raw data of antioxidant activity, sperm lipid peroxidation, sperm motility, sperm plasma membrane, acrosome, mitochondria, and healthy spermResults of statistical analysis<br>
DOI: 10.6084/m9.figshare.8277212
title: Results Summary Tables and Data Tables

description: The Results Summary Tables and Data Tables list monoclonal antibodies that enable detection of RAS signaling network proteins using Western blotting, immunoprecipitation, protein array, immunohistochemistry, and peptide immunoaffinity enrichment and mass spectrometry (immuno-MRM) assays. The proteins and peptide targets that are captured by the antibodies are given in the tables as well.
DOI: 10.6084/m9.figshare.8277248
title: Jerash Northwest Quarter magnetic data

description: This data was collected during the 2011 campaign of the Danish-German Jerash Northwest Quarter Project (Universities of Aarhus and Münster)<br>Geophysical prospections were undertaken by Eastern Atlas, Berlin<br><br>All data is converted into the Palestine1923 (EPSG:28192)<br>MAG data:<br>* 1x full dynamic range tiff (user has to set the dynamic to look at in the GIS program)<br>* GEOtiff with TWF files --&gt; capable for GIS-programs, BUT also for ACAD (!)<br>Available in 5 dynamics (5nT, 10nT,20nT,100nT)<br>
DOI: 10.6084/m9.figshare.8277236
title: Western blot data

description: Images of Western blots from screening the monoclonal antibodies (mAbs) using recombinant proteins and cell line lysates.
DOI: 10.6084/m9.figshare.8277212.v1
title: Results Summary Tables and Data Tables

description: The Results Summary Tables and Data Tables list monoclonal antibodies that enable detection of RAS signaling network proteins using Western blotting, immunoprecipitation, protein array, immunohistochemistry, and peptide immunoaffinity enrichment and mass spectrometry (immuno-MRM) assays. The proteins and peptide targets that are captured by the antibodies are given in the tables as well.
DOI: 10.6084/m9.figshare.8277236.v1
title: Western blot data

description: Images of Western blots from screening the monoclonal antibodies (mAbs) using recombinant proteins and cell line lysates.
DOI: 10.6084/m9.figshare.8277122
title: Data for"Circannual patterns and mechanisms of phosphorus mobility in estuarine sediments: evidence from in situ monthly sampling and indoor experiments"

description: Internal phosphorus (P) mobility is crucially important to overlying water ecosystems, while its spatiotemporal variations and mechanisms remain to be studied, especially in dynamic estuarine sediments. In this study, <i>in situ</i> monthly field sampling and indoor experiments were combined to measure the soluble reactive P (SRP), soluble Fe and diffusive gradients in thin films (DGT)-labile P/S in the overlying water, sediment and porewater in the Jiuxi River Estuary by employing high-resolution dialysis (HR-Peeper), the DGT technique and a MicroRhizon sampler.
DOI: 10.6084/m9.figshare.8277122.v1
title: Data for"Circannual patterns and mechanisms of phosphorus mobility in estuarine sediments: evidence from in situ monthly sampling and indoor experiments"

description: Internal phosphorus (P) mobility is crucially important to overlying water ecosystems, while its spatiotemporal variations and mechanisms remain to be studied, especially in dynamic estuarine sediments. In this study, <i>in situ</i> monthly field sampling and indoor experiments were combined to measure the soluble reactive P (SRP), soluble Fe and diffusive gradients in thin films (DGT)-labile P/S in the overlying water, sediment and porewater in the Jiuxi River Estuary by employing high-resolution dialysis (HR-Peeper), the DGT technique and a MicroRhizon sampler.
DOI: 10.6084/m9.figshare.8276885
title: Antioxidant activity

description: Antioxidant activity of Ocimum gratissimum essential oil and vitamin E<br>
DOI: 10.6084/m9.figshare.12058860.v1
title: Prohydrojasmon prevents spindly growth and induces the expression of an abiotic and biotic stress marker gene, <i>PBZ1p::sGFP</i>, in rice

description: Prohydrojasmon (PDJ) is a synthetic derivative of the plant hormone jasmonic acid (JA), which is used in apples, grapes, and mandarin oranges as a plant growth regulator. Here, we show that irrigation of PDJ could prevent spindly growth of rice seedlings in both indica and japonica cultivars. PDJ also inhibited root elongation in hydroponically growing seedlings in various cultivars. The higher dry root weight following PDJ application than the controls was observed in two japonica cultivars. Furthermore, its reduction was slight in comparison with the inhibition of root elongation. Starch degradation in the endosperm of seedlings grown in PDJ solution was slower than those grown in the control. The inhibition of root elongation could be mediated by the combined application of PDJ and appropriate concentrations of a synthetic auxin, NAA (1-Naphthaleneacetic acid). Additionally, we generated transgenic rice carrying sGFP driven by the <i>PBZ1</i> promoter, a marker gene for abiotic and biotic stress responses. The expression of <i>PBZ1p::sGFP</i> was induced by PDJ treatment in the roots and seeds. PDJ could be used as a plant growth regulator to prevent spindly growth and to induce stress responses in rice seedlings.
DOI: 10.6084/m9.figshare.8276981
title: The effect of triple antibiotic paste as an intracanal medication with an anti-inflammatory drug on post-operative pain of asymptomatic uniradicular necrotic teeth: a double blind randomized clinical trial.

description: These files include the consort checklist and consort flow diagram of my RCT study, also it includes the postoperative pain scores for each patient participated in this clinical trial and the visual analogue scale chart provided for the patient to record their postoperative pain as well as diagnostic charts used to collect medical and dental history .
DOI: 10.6084/m9.figshare.11993403
title: Detection and characterization of quantitative trait loci for coleoptile elongation under anaerobic conditions in rice

description: Low oxygen concentrations in flooded paddy fields cause poor seedling establishment in wet direct seeded rice. We aimed to identify novel genomic regions associated with coleoptile elongation under anaerobic conditions in order to improve seedling establishment. Chromosome segment substitution lines (CSSLs), substituted with Koshihikari (Japonica-type) in the IR 64 genetic background (Indica-type) were evaluated. These lines were imbibed with a hydroponic solution containing Oxyrase to create a stable anaerobic condition and coleoptile lengths were measured six days after incubation at 30°C. Among the CSSLs, only SL2111 had a significantly longer coleoptile (23.9 mm) than that of IR 64 (14.3 mm). From genotype and phenotype analyses, a novel QTL, referred to as <i>qACE3.1</i>, for coleoptile elongation under anaerobic conditions was detected on chromosome 3. To explore the molecular mechanism of <i>qACE3.1</i>, the expression levels of genes encoding enzymes involved in starch degradation and fermentation were assessed. In SL2111 coleoptiles, the expression levels of pyruvate decarboxylase were significantly higher than in IR 64 coleoptiles whereas those of alcohol dehydrogenase were lower. In contrast, no differences were observed in the expression levels of genes associated with starch degradation. These results imply that <i>qACE3.1</i> may specifically affect fermentative metabolism. In addition, we evaluated the impact of <i>qACE3.1</i> on seedling establishment under flooded conditions in a paddy field.
DOI: 10.6084/m9.figshare.12058860
title: Prohydrojasmon prevents spindly growth and induces the expression of an abiotic and biotic stress marker gene, <i>PBZ1p::sGFP</i>, in rice

description: Prohydrojasmon (PDJ) is a synthetic derivative of the plant hormone jasmonic acid (JA), which is used in apples, grapes, and mandarin oranges as a plant growth regulator. Here, we show that irrigation of PDJ could prevent spindly growth of rice seedlings in both indica and japonica cultivars. PDJ also inhibited root elongation in hydroponically growing seedlings in various cultivars. The higher dry root weight following PDJ application than the controls was observed in two japonica cultivars. Furthermore, its reduction was slight in comparison with the inhibition of root elongation. Starch degradation in the endosperm of seedlings grown in PDJ solution was slower than those grown in the control. The inhibition of root elongation could be mediated by the combined application of PDJ and appropriate concentrations of a synthetic auxin, NAA (1-Naphthaleneacetic acid). Additionally, we generated transgenic rice carrying sGFP driven by the <i>PBZ1</i> promoter, a marker gene for abiotic and biotic stress responses. The expression of <i>PBZ1p::sGFP</i> was induced by PDJ treatment in the roots and seeds. PDJ could be used as a plant growth regulator to prevent spindly growth and to induce stress responses in rice seedlings.