cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1586773.v9
title: The Geoscience Paper of the Future: OntoSoft Training

description: This presentation was developed to train scientists on best practices for digital scholarship, reproducibility, and data and software sharing. It was developed as part of the NSF EarthCube Initiative and funded under the OntoSoft project. More details about the project can be found at http://www.ontosoft.org/gpf. A powerpoint version of the slides is available upon request from ontosoft@gmail.com. These OntoSoft GPF training materials were developed and edited by Yolanda Gil (USC), with contributions from the OntoSoft team including Chris Duffy (PSU), Chris Mattmann (JPL), Scott Pechkam (CU), Ji-Hyun Oh (USC), Varun Ratnakar (USC), Erin Robinson (ESIP). They were significantly improved through input from GPF pioneers Cedric David (JPL), Ibrahim Demir (UI), Bakinam Essawy (UV), Robinson W. Fulweiler (BU), Jon Goodall (UV), Leif Karlstrom (UO), Kyo Lee (JPL), Heath Mills (UH), Suzanne Pierce (UT), Allen Pope (CU), Mimi Tzeng (DISL), Karan Venayagamoorthy (CSU), Sandra Villamizar (UC), and Xuan Yu (UD). Others contributed with feedback on best practices, including Ruth Duerr (NSIDC), James Howison (UT), Matt Jones (UCSB), Lisa Kempler (Matworks), Kerstin Lehnert (LDEO), Matt Meyernick (NCAR), and Greg Wilson (Software Carpentry). These materials were also improved thanks to the many scientists and colleagues that have taken the training and asked hard questions about GPFs.
DOI: 10.6084/m9.figshare.1585880.v1
title: Biofidelity Assessment of the 6-Year-Old ATDs in Lateral Impact

description: ABSTRACTObjectives: The objective of this study was to assess and compare the current lateral impact biofidelity of the shoulder, thorax, abdomen, and pelvis of the Q6, Q6s, and Hybrid III (HIII) 6-year-old anthropometric test devices (ATDs) through lateral impact testing. Methods: A series of lateral impact pendulum tests, vertical drop tests, and Wayne State University (WSU) sled tests were performed, based on the procedures detailed in ISO/TR 9790 (1999) and scaling to the 6-year-old using Irwin et al. (2002). The HIII used in this study was tested with the Ford-designed abdomen described in Rouhana (2006) and Elhagediab et al. (2006). The data collected from the three different ATDs was filtered using SAE J211 (SAE J211–1 2003), aligned using the methodology described by Donnelly and Moorhouse (2012), and compared for each body region tested (shoulder, thorax, abdomen, and pelvis). The biofidelity performance in lateral impact for the three ATDs was assessed against the scaled biofidelity targets published in Irwin et al. (2002), the abdominal biofidelity target suggested in van Ratingen et al. (1997), and the biofidelity targets published in Rhule et al. (2013). Regional and overall biofidelity rankings for each of the three ATDs were performed using both the ISO 9790 Biofidelity Rating System (ISO/TR 9790 1999) and the National Highway Traffic Safety Administration's (NHTSA) External Biofidelity Ranking System (BRS) (Rhule et al. 2013).Results: All three 6-year-old ATD's pelves were rated as least biofidelic of the four body regions tested, based on both the ISO and BRS biofidelity rating systems, followed by the shoulder, and abdomen, respectively. The thorax of all three ATDs was rated as the most biofidelic body region using the aforementioned biofidelity rating systems. The HIII 6-year-old ATD was rated last in overall biofidelity of the three tested ATDs, based on both rating systems. The Q6s ATD was rated as having the best overall biofidelity using both rating systems. Conclusions: All three ATDs are more biofidelic in the thorax and abdomen than the shoulder and pelvis, with the pelvis being the least biofidelic of all four tested body regions. None of the three tested 6-year-old ATDs had an overall ranking of 2.0 or less, based on the BRS ranking. Therefore, it is expected that none of the three ATDs would mechanically respond like a Post Mortem Human Subject (PMHS) in a lateral impact crash test based on this ranking system. With respect to the ISO biofidelity rating, the HIII dummy would be considered unsuitable, and the Q-series dummies would be considered marginal, for assessing side impact occupant protection.
DOI: 10.6084/m9.figshare.1585875.v2
title: SGO1C is a non-functional isoform of Shugoshin and can disrupt sister chromatid cohesion by interacting with PP2A–B56

description: Shugoshin (SGO1) plays a pivotal role in sister chromatid cohesion during mitosis by protecting the centromeric cohesin from mitotic kinases and WAPL. Mammalian cells contain at least 6 alternatively spliced isoforms of SGO1. The relationship between the canonical SGO1A with shorter isoforms including SGO1C remains obscure. Here we show that SGO1C was unable to replace the loss of SGO1A. Instead, expression of SGO1C alone induced aberrant mitosis similar to depletion of SGO1A, promoting premature sister chromatid separation, activation of the spindle-assembly checkpoint, and mitotic arrest. In disagreement with previously published data, we found that SGO1C localized to kinetochores. However, the ability to induce aberrant mitosis did not correlate with its kinetochore localization. SGO1C mutants that abolished binding to kinetochores still triggered premature sister chromatid separation. We provide evidence that SGO1C-mediated mitotic arrest involved the sequestering of PP2A–B56 pool. Accordingly, SGO1C mutants that abolished binding to PP2A localized to kinetochores but did not induce aberrant mitosis. These studies imply that the expression of SGO1C should be tightly regulated to prevent dominant-negative effects on SGO1A and genome instability.
DOI: 10.6084/m9.figshare.1585875.v1
title: SGO1C is a non-functional isoform of Shugoshin and can disrupts sister chromatid cohesion by interacting with PP2A–B56

description: ABSTRACTShugoshin (SGO1) plays a pivotal role in sister chromatid cohesion during mitosis by protecting the centromeric cohesin from mitotic kinases and WAPL. Mammalian cells contain at least six alternatively spliced isoforms of SGO1. The relationship between the canonical SGO1A with shorter isoforms including SGO1C remains obscure. Here we show that SGO1C was unable to replace the loss of SGO1A. Instead, expression of SGO1C alone induced aberrant mitosis similar to depletion of SGO1A, promoting premature sister chromatid separation, activation of the spindle-assembly checkpoint, and mitotic arrest. In disagreement with previously published data, we found that SGO1C was localized to kinetochores. However, the ability to induce aberrant mitosis did not correlate with its kinetochore localization. SGO1C mutants that abolished binding to kinetochores still triggered premature sister chromatid separation. We provide evidence that SGO1C-mediated mitotic arrest involved the sequestering of PP2A–B56 pool. Accordingly, SGO1C mutants that abolished binding to PP2A localized to kinetochores but did not induce aberrant mitosis. These studies imply that the expression of SGO1C should be tightly regulated to prevent dominant-negative effects on SGO1A and induce genome instability.
DOI: 10.6084/m9.figshare.1585871
title: p21<sup>WAF1</sup> modulates drug-induced apoptosis and cell cycle arrest in B-cell precursor acute lymphoblastic leukemia

description: p21<sup>WAF1</sup> is a well-characterized mediator of cell cycle arrest and may also modulate chemotherapy-induced cell death. The role of p21<sup>WAF1</sup> in drug-induced cell cycle arrest and apoptosis of acute lymphoblastic leukemia (ALL) cells was investigated using p53-functional patient-derived xenografts (PDXs), in which p21<sup>WAF1</sup> was epigenetically silenced in T-cell ALL (T-ALL), but not in B-cell precursor (BCP)-ALL PDXs. Upon exposure to diverse cytotoxic drugs, T-ALL PDX cells exhibited markedly increased caspase-3/7 activity and phosphatidylserine (PS) externalization on the plasma membrane compared with BCP-ALL cells. Despite dramatic differences in apoptotic characteristics between T-ALL and BCP-ALL PDXs, both ALL subtypes exhibited similar cell death kinetics and were equally sensitive to p53-inducing drugs <i>in vitro</i>, although T-ALL PDXs were significantly more sensitive to the histone deacetylase inhibitor vorinostat. Transient siRNA suppression of p21<sup>WAF1</sup> in the BCP-ALL 697 cell line resulted in a moderate depletion of the cell fraction in G1 phase and marked increase in PS externalization following exposure to etoposide. Furthermore, stable lentiviral p21<sup>WAF1</sup> silencing in the BCP-ALL Nalm-6 cell line accelerated PS externalization and cell death following exposure to etoposide and vorinostat, supporting previous findings. Finally, the Sp1 inhibitor, terameprocol, inhibited p21<sup>WAF1</sup> expression in Nalm-6 cells exposed to vorinostat and also partially augmented vorinostat-induced cell death. Taken together, these findings demonstrate that p21<sup>WAF1</sup> regulates the early stages of drug-induced apoptosis in ALL cells and significantly modulates their sensitivity to vorinostat.
DOI: 10.6084/m9.figshare.1585871.v2
title: p21<sup>WAF1</sup> modulates drug-induced apoptosis and cell cycle arrest in B-cell precursor acute lymphoblastic leukemia

description: p21<sup>WAF1</sup> is a well-characterized mediator of cell cycle arrest and may also modulate chemotherapy-induced cell death. The role of p21<sup>WAF1</sup> in drug-induced cell cycle arrest and apoptosis of acute lymphoblastic leukemia (ALL) cells was investigated using p53-functional patient-derived xenografts (PDXs), in which p21<sup>WAF1</sup> was epigenetically silenced in T-cell ALL (T-ALL), but not in B-cell precursor (BCP)-ALL PDXs. Upon exposure to diverse cytotoxic drugs, T-ALL PDX cells exhibited markedly increased caspase-3/7 activity and phosphatidylserine (PS) externalization on the plasma membrane compared with BCP-ALL cells. Despite dramatic differences in apoptotic characteristics between T-ALL and BCP-ALL PDXs, both ALL subtypes exhibited similar cell death kinetics and were equally sensitive to p53-inducing drugs <i>in vitro</i>, although T-ALL PDXs were significantly more sensitive to the histone deacetylase inhibitor vorinostat. Transient siRNA suppression of p21<sup>WAF1</sup> in the BCP-ALL 697 cell line resulted in a moderate depletion of the cell fraction in G1 phase and marked increase in PS externalization following exposure to etoposide. Furthermore, stable lentiviral p21<sup>WAF1</sup> silencing in the BCP-ALL Nalm-6 cell line accelerated PS externalization and cell death following exposure to etoposide and vorinostat, supporting previous findings. Finally, the Sp1 inhibitor, terameprocol, inhibited p21<sup>WAF1</sup> expression in Nalm-6 cells exposed to vorinostat and also partially augmented vorinostat-induced cell death. Taken together, these findings demonstrate that p21<sup>WAF1</sup> regulates the early stages of drug-induced apoptosis in ALL cells and significantly modulates their sensitivity to vorinostat.
DOI: 10.6084/m9.figshare.1585871.v1
title: p21<sup>WAF1</sup> modulates drug-induced apoptosis and cell cycle arrest in B-cell precursor acute lymphoblastic leukemia

description: p21<sup>WAF1</sup> is a well-characterized mediator of cell cycle arrest and may also modulate chemotherapy-induced cell death. The role of p21<sup>WAF1</sup> in drug-induced cell cycle arrest and apoptosis of acute lymphoblastic leukemia (ALL) cells was investigated using p53-functional patient-derived xenografts (PDXs), in which p21<sup>WAF1</sup> was epigenetically silenced in T-cell ALL (T-ALL), but not in B-cell precursor (BCP)-ALL PDXs. Upon exposure to diverse cytotoxic drugs, T-ALL PDX cells exhibited markedly increased caspase-3/7 activity and phosphatidylserine (PS) externalization on the plasma membrane compared with BCP-ALL cells. Despite dramatic differences in apoptotic characteristics between T-ALL and BCP-ALL PDXs, both ALL subtypes exhibited similar cell death kinetics and were equally sensitive to p53-inducing drugs <i>in vitro</i>, although T-ALL PDXs were significantly more sensitive to the histone deacetylase inhibitor vorinostat. Transient siRNA suppression of p21<sup>WAF1</sup> in the BCP-ALL 697 cell line resulted in a moderate depletion of the cell fraction in G1 phase and marked increase in PS externalization following exposure to etoposide. Furthermore, stable lentiviral p21<sup>WAF1</sup> silencing in the BCP-ALL Nalm-6 cell line accelerated PS externalization and cell death following exposure to etoposide and vorinostat, supporting previous findings. Finally, the Sp1 inhibitor, terameprocol, inhibited p21<sup>WAF1</sup> expression in Nalm-6 cells exposed to vorinostat and also partially augmented vorinostat-induced cell death. Taken together, these findings demonstrate that p21<sup>WAF1</sup> regulates the early stages of drug-induced apoptosis in ALL cells and significantly modulates their sensitivity to vorinostat.
DOI: 10.6084/m9.figshare.1585858
title: Association between genetic variants of serotonergic and glutamatergic pathways and the concentration of neurometabolites of the anterior cingulate cortex in paediatric patients with obsessive–compulsive disorder

description: <i>Objectives</i>: The present study aimed to assess the relationship between variability in genes related to the pathophysiology of obsessive–compulsive disorder (OCD) and the concentration of different neurometabolites in the anterior cingulate cortex (ACC). <i>Methods</i>: We concomitantly assessed neurometabolite concentrations using 3-T <sup>1</sup>H-MRS and 262 single nucleotide polymorphism (SNPs) in 35 genes in 41 paediatric OCD patients. <i>Results</i>: There were significant associations, after Bonferroni correction, between the concentration of inositol, glutamate and glutamine, and total choline and five polymorphisms located in genes related to serotonin and glutamate (i.e., the vesicular monoamine transporter 1 gene, <i>SLC18A1</i> [rs6586896]; the serotonin receptor 1B gene, <i>HTR1B</i> [rs6296 and rs6298]; and the glutamate receptor, ionotropic, AMPA1 gene, <i>GRIA1</i> [rs707176 and rs2963944]). <i>Conclusions</i>: The association observed between these polymorphisms and the neurometabolite concentrations could indicate the presence of a biological interaction between the serotonin and the glutamate pathways that could be involved in the pathophysiology of OCD. More studies with this methodology could increase our understanding of the aetiology and pathophysiology of OCD in children.
DOI: 10.6084/m9.figshare.1585853
title: Origin and phylogeny of the Cretaceous thoracican cirripede family Stramentidae

description: A cladistic analysis of basal scalpellomorph cirripedes was undertaken in order to identify the phylogenetic position of the Stramentidae. This yielded a well-supported tree, in which the family is positioned crownwards of <i>Archaeolepas</i>, but basal to the families Scalpellidae and Zeugmatolepadidae. A new genus, <i>Loriolepas</i>, is described to accommodate some species previously referred to <i>Archaeolepas.</i> Basal scalpellomorphs display a remarkable change in shell mineralogy from calcium phosphate to calcium carbonate (<i>Eolepas</i> to <i>Archaeolepas</i>); the latter group is identified as a monophyletic clade, the Thoracicalcarea nov. A revised taxonomy of the predominantly Late Cretaceous cirripede family Stramentidae is presented. Stramentidae are subdivided into two subfamilies, Loriculinae subfam. nov., and Stramentinae, based on characters of tergum, carinolatus and peduncular plates. The former subfamily includes <i>Loriculina</i> Dames, 1885, <i>Metaloriculina</i> gen. nov. and, doubtfully, <i>Blastolepas</i> Drushchits & Zevina, 1969, and three new species are described, <i>Loriculina ifrimae</i> sp. nov<i>.</i>, <i>Metaloriculina stramentioides</i> sp. nov and <i>Metaloriculina norvicensis</i> sp. nov. The Stramentinae include <i>Leweslepas</i> gen. nov., <i>Stramentum</i> Logan, 1897 and <i>Parastramentum</i> gen. nov. New species are <i>Leweslepas hattini</i> sp. nov, <i>L. hauschkei</i> sp. nov, <i>L. wrightorum</i> sp. nov, <i>Parastramentum albertaensis</i> sp. nov, <i>P. brydonei</i> sp. nov, <i>P. peakei</i> sp. nov, <i>Stramentum alekseevi</i> sp. nov and <i>S. praecursor</i> sp. nov<i>.</i> Cladistic analysis of the Stramentidae, based on 25 characters, supports the monophyly of the family, but relationships between subfamilies and genera are poorly resolved. However, in north-west Europe there is an evolutionary morphocline, stratigraphically calibrated, from the early Cenomanian <i>Leweslepas hauschkei</i> gen. et sp. nov. through the middle Cenomanian <i>Stramentum praecursor</i> sp. nov. to the late Cenomanian–Turonian <i>S. pulchellum</i>. A split from this lineage is found in the Western Interior Basin of North America, and the early Turonian <i>S. canadensis</i> gave rise to the middle Turonian <i>S. elegans</i>, which lived epibenthically. <i>Stramentum elegans</i> gave rise to <i>Parastramentum</i> gen. nov. http://zoobank.org/urn:lsid:zoobank.org:pub:E01B7F39-6C1B-4AF3-B79A-E2D5972D3E28
DOI: 10.6084/m9.figshare.1585853.v1
title: Origin and phylogeny of the Cretaceous thoracican cirripede family Stramentidae

description: A cladistic analysis of basal scalpellomorph cirripedes was undertaken in order to identify the phylogenetic position of the Stramentidae. This yielded a well-supported tree, in which the family is positioned crownwards of <i>Archaeolepas</i>, but basal to the families Scalpellidae and Zeugmatolepadidae. A new genus, <i>Loriolepas</i>, is described to accommodate some species previously referred to <i>Archaeolepas.</i> Basal scalpellomorphs display a remarkable change in shell mineralogy from calcium phosphate to calcium carbonate (<i>Eolepas</i> to <i>Archaeolepas</i>); the latter group is identified as a monophyletic clade, the Thoracicalcarea nov. A revised taxonomy of the predominantly Late Cretaceous cirripede family Stramentidae is presented. Stramentidae are subdivided into two subfamilies, Loriculinae subfam. nov., and Stramentinae, based on characters of tergum, carinolatus and peduncular plates. The former subfamily includes <i>Loriculina</i> Dames, 1885, <i>Metaloriculina</i> gen. nov. and, doubtfully, <i>Blastolepas</i> Drushchits & Zevina, 1969, and three new species are described, <i>Loriculina ifrimae</i> sp. nov<i>.</i>, <i>Metaloriculina stramentioides</i> sp. nov and <i>Metaloriculina norvicensis</i> sp. nov. The Stramentinae include <i>Leweslepas</i> gen. nov., <i>Stramentum</i> Logan, 1897 and <i>Parastramentum</i> gen. nov. New species are <i>Leweslepas hattini</i> sp. nov, <i>L. hauschkei</i> sp. nov, <i>L. wrightorum</i> sp. nov, <i>Parastramentum albertaensis</i> sp. nov, <i>P. brydonei</i> sp. nov, <i>P. peakei</i> sp. nov, <i>Stramentum alekseevi</i> sp. nov and <i>S. praecursor</i> sp. nov<i>.</i> Cladistic analysis of the Stramentidae, based on 25 characters, supports the monophyly of the family, but relationships between subfamilies and genera are poorly resolved. However, in north-west Europe there is an evolutionary morphocline, stratigraphically calibrated, from the early Cenomanian <i>Leweslepas hauschkei</i> gen. et sp. nov. through the middle Cenomanian <i>Stramentum praecursor</i> sp. nov. to the late Cenomanian–Turonian <i>S. pulchellum</i>. A split from this lineage is found in the Western Interior Basin of North America, and the early Turonian <i>S. canadensis</i> gave rise to the middle Turonian <i>S. elegans</i>, which lived epibenthically. <i>Stramentum elegans</i> gave rise to <i>Parastramentum</i> gen. nov. http://zoobank.org/urn:lsid:zoobank.org:pub:E01B7F39-6C1B-4AF3-B79A-E2D5972D3E28
DOI: 10.6084/m9.figshare.1585851
title: Oikos meta-analyses until 2015: bibliometric summary

description: A brief output of analytics from the Web of Science for Oikos meta-analyses (terms: meta-anal* in any field, source title 'Oikos').
DOI: 10.6084/m9.figshare.1585843
title: A computational study on molecular structure, multiple interactions, chemical reactivity and molecular docking studies on 6[D (−) α-amino-phenyl-acetamido] penicillanic acid (ampicillin)

description: Ampicillin 6[D (−) α-amino-phenyl-acetamido] penicillanic acid (AMP) is a β-lactam antibiotic that is active against both gram-positive and gram-negative. Due to industrial and biological importance of β-lactam antibiotics, an extensive quantum chemical study on AMP was carried out. The theoretical ground-state geometry and electronic structure of AMP are optimised by the DFT/B3LYP/6-311++G(d,p) method and compared with those of the crystal data. Four conformers have been found by potential energy surface scan. Among them, the geometry of the conformer-IV matches well with the experimental value, so we proceed with it. Natural bond orbital analysis has been used to analyse the stability of the molecule arising from hyperconjugative interactions and charge delocalisation. HOMO and LUMO have been plotted and analysed in order to describe the chemical reactivity of the molecule. MEP for these conformers shows that the negative potential is visualised over the O41 atom of C=O group of the molecule. Molecular docking studies show that the title molecule exhibits an antibacterial activity. The interpretation of diverse aspects of chemical bonding has been done by computing global and local reactivity descriptors. The variation of thermodynamic properties (such as C<sup>°</sup><sub>p, m</sub>, S<sup>°</sup><sub>m</sub>, H<sup>°</sup><sub>m</sub>) with temperature has been studied theoretically. The present work will be helpful to systematically understand the structures and the electronic properties of AMP for studying the structure–activity relationship and to develop new drugs and their analytical methods.
DOI: 10.6084/m9.figshare.1585851.v1
title: Oikos meta-analyses until 2015: bibliometric summary

description: A brief output of analytics from the Web of Science for Oikos meta-analyses (terms: meta-anal* in any field, source title 'Oikos').
DOI: 10.6084/m9.figshare.1585839
title: Modeling of Solar Intensity via Markov Chains with Applications in Solar Energy Harvesting

description: Here, we propose a solar intensity model based on Markov chain. This model provides more accurate results for instantaneous solar intensity vector. We show that by increasing the order of Markov chain, we can achieve finer results in terms of maximum likelihood of the model matching the instantaneous data. Applying this model on the data collected from Rochester in upstate New York shows the effectiveness of our approach.