cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5263225
title: Epidermal Growth Factor Receptor activation promotes ADA3 acetylation through the AKT-p300 pathway

description: The ADA3 (Alteration/Deficiency in Activation 3) protein is an essential adaptor component of several Lysine Acetyltransferase (KAT) complexes involved in chromatin modifications. Previously, we and others have demonstrated a crucial role of ADA3 in cell cycle progression and in maintenance of genomic stability. Recently, we have shown that acetylation of ADA3 is key to its role in cell cycle progression. Here, we demonstrate that AKT activation downstream of Epidermal Growth Factor Receptor (EGFR) family proteins stimulation leads to phosphorylation of p300, which in turn promotes the acetylation of ADA3. Inhibition of upstream receptor tyrosine kinases (RTKs), HER1 (EGFR)/HER2 by lapatinib and the accompanying reduction of phospho-AKT levels led to a decrease in p300 phosphorylation and ADA3 protein levels. The p300/PCAF inhibitor garcinol also destabilized the ADA3 protein in a proteasome-dependent manner and an ADA3 mutant with K→R mutations exhibited a marked increase in half-life, consistent with opposite role of acetylation and ubiquitination of ADA3 on shared lysine residues. <i>ADA3</i> knockdown led to cell cycle inhibitory effects, as well as apoptosis similar to those induced by lapatinib treatment of HER2+ breast cancer cells, as seen by accumulation of CDK inhibitor p27, reduction in mitotic marker pH3(S10), and a decrease in the S-phase marker PCNA, as well as the appearance of cleaved PARP. Taken together our results reveal a novel RTK-AKT-p300-ADA3 signaling pathway involved in growth factor-induced cell cycle progression.
DOI: 10.6084/m9.figshare.5263243.v1
title: Spatially Dependent Responses of a Large-River Fish Assemblage to Bank Stabilization and Side Channels

description: The alteration of rivers by anthropogenic bank stabilization to prevent the erosion of economically valuable lands and structures has become commonplace. However, such alteration has ambiguous consequences for fish assemblages, especially in large rivers. Because most large, temperate rivers have impoundments, it can be difficult to separate the influences of bank stabilization structures from those of main-stem impoundments, especially because both stabilization structures and impoundments can cause side-channel loss. Few large rivers are free flowing and retain extensive side channels, but the Yellowstone River (our study area) is one such river. We hypothesized that in this river (1) bank stabilization has changed fish assemblage structure by altering habitats, (2) side-channel availability has influenced fish assemblage structure by providing habitat heterogeneity, and (3) the influences of bank stabilization and side channels on fish assemblages were spatially scale dependent. We developed a spatially explicit framework to test these hypotheses. Fish assemblage structure varied with the extent of bank stabilization and the availability of side channels; however, not all assemblage subsets were influenced. Nevertheless, bank stabilization and side channels had different and sometimes opposite influences on the fish assemblage. The effects of side channels on fish were more consistent and widespread than those of bank stabilization; the catches of more fishes were positively correlated with side-channel availability than with the extent of bank stabilization. The influences of bank stabilization and side channels on the relative abundances of fish also varied, depending on species and river bend geomorphology. The variation in river morphology probably contributed to the assemblage differences between stabilized and reference river bends; stabilized alluvial pools were deeper than reference alluvial pools, but the depths of stabilized and reference bluff pools did not differ. The strengths of the relationships among fish assemblages, bank stabilization, and side channels were spatially scale dependent; optimum spatial scales ranged from less than 200 m to 3,200 m up- and downstream, suggesting that bank stabilization and side channels influenced fish assemblages across multiple spatial scales. Received October 7, 2016; accepted January 23, 2017 Published online July 31, 2017
DOI: 10.6084/m9.figshare.5263225.v2
title: Epidermal Growth Factor Receptor activation promotes ADA3 acetylation through the AKT-p300 pathway

description: The ADA3 (Alteration/Deficiency in Activation 3) protein is an essential adaptor component of several Lysine Acetyltransferase (KAT) complexes involved in chromatin modifications. Previously, we and others have demonstrated a crucial role of ADA3 in cell cycle progression and in maintenance of genomic stability. Recently, we have shown that acetylation of ADA3 is key to its role in cell cycle progression. Here, we demonstrate that AKT activation downstream of Epidermal Growth Factor Receptor (EGFR) family proteins stimulation leads to phosphorylation of p300, which in turn promotes the acetylation of ADA3. Inhibition of upstream receptor tyrosine kinases (RTKs), HER1 (EGFR)/HER2 by lapatinib and the accompanying reduction of phospho-AKT levels led to a decrease in p300 phosphorylation and ADA3 protein levels. The p300/PCAF inhibitor garcinol also destabilized the ADA3 protein in a proteasome-dependent manner and an ADA3 mutant with K→R mutations exhibited a marked increase in half-life, consistent with opposite role of acetylation and ubiquitination of ADA3 on shared lysine residues. <i>ADA3</i> knockdown led to cell cycle inhibitory effects, as well as apoptosis similar to those induced by lapatinib treatment of HER2+ breast cancer cells, as seen by accumulation of CDK inhibitor p27, reduction in mitotic marker pH3(S10), and a decrease in the S-phase marker PCNA, as well as the appearance of cleaved PARP. Taken together our results reveal a novel RTK-AKT-p300-ADA3 signaling pathway involved in growth factor-induced cell cycle progression.
DOI: 10.6084/m9.figshare.5263225.v1
title: Epidermal Growth Factor Receptor Activation Promotes ADA3 Acetylation through the AKT-p300 Pathway

description: The ADA3 (Alteration/Deficiency in Activation 3) protein is an essential adaptor component of several Lysine Acetyltransferase (KAT) complexes involved in chromatin modifications. Previously, we and others have demonstrated a crucial role of ADA3 in cell cycle progression and maintenance of genomic stability. Recently, we have shown that acetylation of ADA3 is key to its role in cell cycle progression. Here, we demonstrate that AKT activation downstream of Epidermal Growth Factor Receptor (EGFR) family proteins stimulation leads to phosphorylation of p300, which in turn promotes the acetylation of ADA3. Inhibition of upstream receptor tyrosine kinases (RTKs), HER1 (EGFR)/HER2 by lapatinib and the accompanying reduction of phospho-AKT levels led to a decrease in p300 phosphorylation and ADA3 protein levels. The p300/PCAF inhibitor garcinol also destabilized the ADA3 protein in a proteasome-dependent manner and an ADA3 mutant with K-&gt;R mutations exhibited a marked increase in half-life, consistent with opposite role of acetylation and ubiquitination of ADA3 on shared lysine residues. <i>ADA3</i> knockdown led to cell cycle inhibitory effects, as well as apoptosis similar to those induced by lapatinib treatment of HER2+ breast cancer cells, as seen by accumulation of CDK inhibitor p27, reduction in mitotic marker pH3(S10), and a decrease in the S-phase marker PCNA, as well as the appearance of cleaved PARP. Taken together our results reveal a novel RTK-AKT-p300-ADA3 signaling pathway involved in growth factor-induced cell cycle progression.
DOI: 10.6084/m9.figshare.5263120
title: Diversity and evolution of the flowering plants of the Caatinga Domain - Supplementary Data

description: These are supplementary files to the chapter "Diversity and evolution of the flowering plants of the Caatinga Domain" published in "Silva JMCS, Leal IR, Tabarelli M (eds) <b>Caatinga: The largest Tropical Dry Forest Region in South America</b>" by Springer. The data presented here describe in detail the methods and results of the meta-analysis we made on phylogenetic and diversification of evolution of plants in the semiarid Caatinga. The images here bring in full resolution the trees presented in the publication. To analyze biogeographical patterns of plant evolution in Caatinga we compiled published (and a few inedited) phylogenies of plant lineages from the Brazilian semiarid. Due to space limitation in the book chapter, the detailed methods and individual phylogenetic trees for each clade are presented here.
DOI: 10.6084/m9.figshare.5263093
title: Data for "Facilitative and competitive interaction components among New England salt marsh plants" (Bruno et al 2017, PeerJ)

description: Raw data and calculated species interaction strengths for the manuscript: Facilitative and competitive interaction components among New England salt marsh plants (Bruno et al 2017, PeerJ)<br>
DOI: 10.6084/m9.figshare.5263099
title: DATA_UNCOMPLICATED MALARIA.xlsx

description: Data from allover DRC in a drug utilisation study about drug use in the management of uncomplicated malaria in public health facilities in DRCcross sectionnal studyEthical clearance obtained from the School of Public Health Ethic Committee.
DOI: 10.6084/m9.figshare.5263093.v1
title: Data for "Facilitative and competitive interaction components among New England salt marsh plants" (Bruno et al 2017, PeerJ)

description: Raw data and calculated species interaction strengths for the manuscript: Facilitative and competitive interaction components among New England salt marsh plants (Bruno et al 2017, PeerJ)<br>
DOI: 10.6084/m9.figshare.5260708
title: Aly_class_all.out

description: Ath/Aly/Cgr_metL.out<br>Methylation levels in the three species in gene bodies (from start to stop codons)<br>1st col: gene ID<br>2nd col: CG methylation levels<br>3rd: col: CHG<br>4th col: CHH<br><br>Ath/Aly/Cgr_class.out<br>gbM levels are categorized into three: BM, IM and UM.<br>Please see Takuno and Gaut (2012) MBE; Takuno and Gaut (2013) PNAS<br>Takuno et al. (2017) MBE.<br><br>1st col: gene ID<br>2nd col: CG<br><br>3rd: col: CHG<br>4th col: CHH<br><br>AthAlyCgra1.out<br>The three-way orthologs
DOI: 10.6084/m9.figshare.5260693
title: Απραξία της Ομιλίας Παιδιών και Ενηλίκων [Sprechapraxie im Kindes- und Erwachsenenalter]

description: Editing of the German Version: Sprechapraxie im Kindes- und Erwachsenenalter<br><br>Greek ISBN: 978-618-82798-0-3<br>
DOI: 10.6084/m9.figshare.5260708.v1
title: Aly_class_all.out

description: Ath/Aly/Cgr_metL.out<br>Methylation levels in the three species in gene bodies (from start to stop codons)<br>1st col: gene ID<br>2nd col: CG methylation levels<br>3rd: col: CHG<br>4th col: CHH<br><br>Ath/Aly/Cgr_class.out<br>gbM levels are categorized into three: BM, IM and UM.<br>Please see Takuno and Gaut (2012) MBE; Takuno and Gaut (2013) PNAS<br>Takuno et al. (2017) MBE.<br><br>1st col: gene ID<br>2nd col: CG<br><br>3rd: col: CHG<br>4th col: CHH<br><br>AthAlyCgra1.out<br>The three-way orthologs
DOI: 10.6084/m9.figshare.5260660
title: Simulated HN(CO)CACB peak lists

description: Simulated peak lists that were used for robustness testing of Spin System Creator program.
DOI: 10.6084/m9.figshare.5260678
title: Κλινική Διαχείριση των Διαταραχών Κατάποσης σε Παιδιά και Ενήλικες [Clinical Management of Swallowing Disorders]

description: Editing and Translation in Greek of the Book: Clinical Management of Swallowing Disorders<br><br>Greek ISBN: 978-960-9427-27-2
DOI: 10.6084/m9.figshare.5260678.v1
title: Κλινική Διαχείριση των Διαταραχών Κατάποσης σε Παιδιά και Ενήλικες [Clinical Management of Swallowing Disorders]

description: Editing and Translation in Greek of the Book: Clinical Management of Swallowing Disorders<br><br>Greek ISBN: 978-960-9427-27-2
DOI: 10.6084/m9.figshare.5260693.v1
title: Απραξία της Ομιλίας Παιδιών και Ενηλίκων [Sprechapraxie im Kindes- und Erwachsenenalter]

description: Editing of the German Version: Sprechapraxie im Kindes- und Erwachsenenalter<br><br>Greek ISBN: 978-618-82798-0-3<br>
DOI: 10.6084/m9.figshare.5260660.v2
title: Simulated HN(CO)CACB peak lists

description: Simulated peak lists that were used for robustness testing of Spin System Creator program.
DOI: 10.6084/m9.figshare.5260660.v1
title: Simulated HN(CO)CACB peak lists

description: Simulated peak lists that were used for robustness testing of Spin System Creator program.
DOI: 10.6084/m9.figshare.5260366
title: Unsteady non-premixed methane/oxygen flame structures at supercritical pressures

description: Unsteady non-premixed flame structures of methane/oxygen mixtures are investigated at supercritical pressures, representative of liquid rocket engines combustion chamber operating conditions. A general-fluid formulation of the flamelet equations is used and deviations from ideality of the thermodynamic properties are taken into account by means of a computationally efficient cubic equation of state written in a general three-parameter fashion. The effects of pressure and scalar dissipation rate are investigated in the context of prototypical unsteady laminar flame configurations, such as autoignition and re-ignition/quenching. In auto-igniting flamelets, real gas effects are observed to influence different flame regions depending on the thermodynamic pressure. Moreover the mixture ensuing from methane oxidation is never observed to reach a saturated (two-phase) thermodynamic region. Re-ignition and quenching phenomena are analyzed using a time dependent forcing function for the scalar dissipation rate, in order to investigate the response of the real gas flame structures to typical turbulent perturbations. The role of pressure on the critical strain values that a real gas laminar flame can sustain without quenching is investigated and compared to its ideal gas counterpart.
DOI: 10.6084/m9.figshare.5260375
title: Zap70 and downstream <i>RanBP2</i> are required for the exact timing of the meiotic cell cycle in oocytes

description: In previous studies, we observed that Zeta-chain-associated protein kinase 70 (Zap70) regulates spindle assembly and chromosome alignment in mouse oocyte and that Ran binding protein 2 (RanBP2) is a highly associated gene with Zap70 based on a microarray analysis. Because RanBP2 is related to nuclear envelope breakdown (NEBD) during mitosis, the aim of the present study was to elucidate the molecular mechanism of Zap70 with respect to RanBP2 in the germinal vesicle breakdown (GVBD) of oocytes. Results indicated that RanBP2 expression was regulated by Zap70 and that depletion of RanBP2 using <i>RanBP2</i> RNAi manifested comparable phenotypes to those observed in <i>Zap70</i> RNAi-treated oocytes, which presented faster processing of GVBD. Additionally, <i>Zap70</i> RNAi-treated oocytes showed faster meiotic resumption with premature activation of maturation-promoting factor (MPF), premature division of chromosomes at approximately 6–8 h and more rapid degradation of securin. In conclusion, we report that Zap70 is a crucial factor for controlling the exact timing of meiotic progression in mouse oocytes.
DOI: 10.6084/m9.figshare.5260375.v1
title: Zap70 and downstream <i>RanBP2</i> are required for the exact timing of the meiotic cell cycle in oocytes

description: In previous studies, we observed that Zeta-chain-associated protein kinase 70 (Zap70) regulates spindle assembly and chromosome alignment in mouse oocyte and that Ran binding protein 2 (RanBP2) is a highly associated gene with Zap70 based on a microarray analysis. Because RanBP2 is related to nuclear envelope breakdown (NEBD) during mitosis, the aim of the present study was to elucidate the molecular mechanism of Zap70 with respect to RanBP2 in the germinal vesicle breakdown (GVBD) of oocytes. Results indicated that RanBP2 expression was regulated by Zap70 and that depletion of RanBP2 using <i>RanBP2</i> RNAi manifested comparable phenotypes to those observed in <i>Zap70</i> RNAi-treated oocytes, which presented faster processing of GVBD. Additionally, <i>Zap70</i> RNAi-treated oocytes showed faster meiotic resumption with premature activation of maturation-promoting factor (MPF), premature division of chromosomes at approximately 6–8 h and more rapid degradation of securin. In conclusion, we report that Zap70 is a crucial factor for controlling the exact timing of meiotic progression in mouse oocytes.
DOI: 10.6084/m9.figshare.5260366.v1
title: Unsteady non-premixed methane/oxygen flame structures at supercritical pressures

description: Unsteady non-premixed flame structures of methane/oxygen mixtures are investigated at supercritical pressures, representative of liquid rocket engines combustion chamber operating conditions. A general-fluid formulation of the flamelet equations is used and deviations from ideality of the thermodynamic properties are taken into account by means of a computationally efficient cubic equation of state written in a general three-parameter fashion. The effects of pressure and scalar dissipation rate are investigated in the context of prototypical unsteady laminar flame configurations, such as autoignition and re-ignition/quenching. In auto-igniting flamelets, real gas effects are observed to influence different flame regions depending on the thermodynamic pressure. Moreover the mixture ensuing from methane oxidation is never observed to reach a saturated (two-phase) thermodynamic region. Re-ignition and quenching phenomena are analyzed using a time dependent forcing function for the scalar dissipation rate, in order to investigate the response of the real gas flame structures to typical turbulent perturbations. The role of pressure on the critical strain values that a real gas laminar flame can sustain without quenching is investigated and compared to its ideal gas counterpart.
DOI: 10.6084/m9.figshare.5260285
title: Second trimester extracellular microRNAs in maternal blood and fetal growth: An exploratory study

description: Healthy feto-maternal communication is critical during pregnancy and is orchestrated by the placenta. Dysfunction of the placenta leads to fetal growth complications; however, the underlying biological mechanisms have yet to be fully elucidated. Circulating extracellular microRNAs (exmiRNAs) in the blood have been implicated in cell-to-cell communication. Therefore, exmiRNAs may provide useful biological information about communication between the mother, the fetus, and the placenta during pregnancy. We used logistic regression to determine the association of exmiRNAs with abnormal fetal growth by comparing mothers of infants classified as small-for-gestational age (SGA) (n = 36) and large-for-gestational age (LGA) (n = 13) to appropriate-for-gestational age (AGA), matched by gestational age at delivery and infant sex. In addition, we used linear regression to determine associations between exmiRNAs and birth weight-for-gestational age (BWGA) z-score (n = 100), adjusting for maternal age, body mass index, and parity. We found that higher levels of miR-20b-5p, miR-942-5p, miR-324-3p, miR-223-5p, and miR-127-3p in maternal serum were associated with lower odds for having a SGA vs. AGA infant, and higher levels of miR-661, miR-212-3p, and miR-197-3p were associated with higher odds for having a LGA vs. AGA infant. We also found associations between miR-483-5p, miR-10a-5p, miR-204-5p, miR-202-3p, miR-345-5p, miR-885-5p, miR-127-3p, miR-148b-3p, miR-324-3p, miR-1290, miR-597-5p, miR-139-5p, miR-215-5p, and miR-99b-5p and BWGA z-score. We also found sex-specific associations with exmiRNAs and fetal growth. Our findings suggest that exmiRNAs circulating in maternal blood at second trimester are associated with fetal growth. Validation of our findings may lead to the development of minimally-invasive biomarkers of fetal growth during pregnancy.
DOI: 10.6084/m9.figshare.5260282
title: Using medico-legal data to investigate fatal older road user crash circumstances and risk factors

description: <b>Objective</b>: This study used medico-legal data to investigate fatal older road user (ORU, aged 65 years and older) crash circumstances and risk factors relating to 4 key components of the Safe System approach (e.g., roads and roadsides, vehicles, road users, and speeds) to identify areas of priority for targeted prevention activity. <b>Method</b>: The Coroners' Court of Victoria's (CCOV) Surveillance Database was searched to identify and describe the frequency and rate per 100,000 population of fatal ORU crashes in the Australian state of Victoria for 2013–2014. Information relating to the deceased ORU, crash characteristics and circumstances, and risk factors was extracted and analyzed. <b>Results</b>: One hundred and thirty-eight unintentional fatal ORU crashes were identified in the CCOV Surveillance Database. Of these fatal ORU crashes, most involved older drivers (44%), followed by older pedestrians (32%), older passengers (17%), older pedal cyclists (4%), older motorcyclists (1%), and older mobility scooter users (1%). The average annual rate of fatal ORU crashes per 100,000 population was 8.1 (95% confidence interval [CI], 6.0–10.2). In terms of the crash characteristics and circumstances, most fatal ORU crashes involved a counterpart (98%), of which the majority were passenger cars (50%) or fixed/stationary objects (25%), including trees (46%) or embankments (23%). In addition, most fatal ORU crashes occurred close to home (73%), on-road (87%), on roads that were paved (94%), on roads with light traffic volume (37%), and during low-risk conditions: between 12 p.m. and 6 p.m. (44%), on weekdays (80%), during daylight (75%), and under dry/clear conditions (81%). Road user (RU) error was identified by the police and/or the coroner for the majority of fatal crashes (55%), with a significant proportion of deceased ORUs deemed to have failed to yield (54%) or misjudged (41%). <b>Conclusions</b>: RU error was the most significant factor identified in fatal ORU crashes, which suggests that there is a limited capacity of the road system to fully accommodate RU errors. Initiatives related to safer roads and roadsides, vehicles, speed zones, as well as behavioral approaches are key areas of priority for targeted activity to prevent fatal ORU crashes in the future.