cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1232119.v3
title: Modeling and forecasting persistent financial durations

description: This article introduces the Markov-Switching Multifractal Duration (MSMD) model by adapting the MSM stochastic volatility model of Calvet and Fisher (2004) to the duration setting. Although the MSMD process is exponential β-mixing as we show in the article, it is capable of generating highly persistent autocorrelation. We study, analytically and by simulation, how this feature of durations generated by the MSMD process propagates to counts and realized volatility. We employ a quasi-maximum likelihood estimator of the MSMD parameters based on the Whittle approximation and establish its strong consistency and asymptotic normality for general MSMD specifications. We show that the Whittle estimation is a computationally simple and fast alternative to maximum likelihood. Finally, we compare the performance of the MSMD model with competing short- and long-memory duration models in an out-of-sample forecasting exercise based on price durations of three major foreign exchange futures contracts. The results of the comparison show that the MSMD and the Long Memory Stochastic Duration model perform similarly and are superior to the short-memory Autoregressive Conditional Duration models.
DOI: 10.6084/m9.figshare.1232114
title: Structure and molecular characterization of barley nudix hydrolase genes

description: Putative nudix hydrolase (NUDX) genes, which encode amino acid sequences showing homology with those of Arabidopsis NUDXs and conserve nudix motif, were identified from barley. The 14 deduced barley NUDXs (HvNUDX1-14) were classified into established subfamilies, except for 8-oxo-deoxyguanosine 5′-triphosphate (8-oxo-dGTP) pyrophosphohydrolase and mRNA decapping enzyme subfamilies, and three substrate-unknown subfamilies. Drought and UV-C stresses, respectively, up-regulated 7 and 4 HvNUDX genes, but some homologs of Arabidopsis NUDXs showed different responses to abiotic stress. HvNUDX12 gene, belonging to diadenosine tetraphosphates (Ap<sub>4</sub>A) pyrophosphohydrolase subfamily gene and up-regulated by UV-C, was expressed in <i>Escherichia coli</i> cells. The recombinant protein showed 8-oxo-dGTP, Ap<sub>4</sub>A, and guanosine-3′,5′-tetraphosphate (ppGpp) pyrophosphohydrolase activities, and the suppression of the <i>lacZ</i> amber mutation in a <i>mutT</i>-deficient <i>E. coli</i> cells caused by the incorporation of 8-oxo-GTP into mRNA was prevented to a significant degree. These results suggest that barley NUDXs have unique constitution and response of NUDX to abiotic stress.
DOI: 10.6084/m9.figshare.1232116.v2
title: Rules relating hepatotoxicity with structural attributes of drugs

description: The relationship between molecular structures of drugs and their hepatotoxicity was studied by characterizing their structure in a new way and using formal concept analysis, a mathematical technique to condense knowledge into particular rules, which does not imply linearly assumptions as many conventional statistical techniques. The structural characterization was based on molecular descriptors and molecular frameworks, further decomposed into structural elements, rings, and bridges. The methodology was applied to drugs in the liver toxicity knowledge base database with the potential to cause drug-induced liver injury. Numbers of atoms and bonds along with the aromatic ratio were suitable descriptors for such drugs. The higher the number of rings and asymmetric structural elements in their terminal ring systems, the higher is the probability of hepatotoxicity. Rules were found which may help to design drugs which are unlikely to be hepatotoxic.
DOI: 10.6084/m9.figshare.1232119.v2
title: Modeling and Forecasting Persistent Financial Durations

description: This article introduces the Markov-Switching Multifractal Duration (MSMD) model by adapting the MSM stochastic volatility model of Calvet and Fisher (2004) to the duration setting. Although the MSMD process is exponential β-mixing as we show in the article, it is capable of generating highly persistent autocorrelation. We study, analytically and by simulation, how this feature of durations generated by the MSMD process propagates to counts and realized volatility. We employ a quasi-maximum likelihood estimator of the MSMD parameters based on the Whittle approximation and establish its strong consistency and asymptotic normality for general MSMD specifications. We show that the Whittle estimation is a computationally simple and fast alternative to maximum likelihood. Finally, we compare the performance of the MSMD model with competing short- and long-memory duration models in an out-of-sample forecasting exercise based on price durations of three major foreign exchange futures contracts. The results of the comparison show that the MSMD and the Long Memory Stochastic Duration model perform similarly and are superior to the short-memory Autoregressive Conditional Duration models.
DOI: 10.6084/m9.figshare.1232112
title: the effect of power lines on plant growth data/metadata

description: The research topic explores the effects of power lines on the growth of plants. Height (m), density, and diversity of plants were the variables used to indirectly measure/represent plant growth. Each variable was measured within 1metrex1metre quadrats, at 2m intervals from the power line (0m,2m,4m,6m). The purpose of this reseach was to gain knowlege about the direct (electric transmission) or indirect (soil toxicity, human impact, environmental pollution) effects of power lines on the growth of plants (Goldenrod, White Aster, Purple Aster, Queen Anne's Lace)- whether there is an effect or not, and how that can be measured. Once a week for 3 hours, for 3 weeks, data was collected in a power line field in the York Region of the GTA, across from York University. 1mx1m quadrats were placed at 0m from a power line and within the quadrat, height of 10 of each different type of plant (Goldenrod, White Aster, Purple Aster, Queen Anne's Lace) (m), different types of plants (diversity), and number of each different type of plant (density), was measured and recorded. 10 plants of each species was randomly selected to measure. All the different types of plants, well as how many there were of each were simply counted. This was repeated 2m, 4m, and 6m on the North and south sides of the power line, and then again 20m east/west, to have roughly 16 quadrats measured per 3 hour period.
DOI: 10.6084/m9.figshare.1232116.v1
title: Rules relating hepatotoxicity with structural attributes of drugs

description: The relationship between molecular structures of drugs and their hepatotoxicity was studied by characterizing their structure in a new way and using formal concept analysis, a mathematical technique to condense knowledge into particular rules, which does not imply linearly assumptions as many conventional statistical techniques. The structural characterization was based on molecular descriptors and molecular frameworks, further decomposed into structural elements, rings, and bridges. The methodology was applied to drugs in the liver toxicity knowledge base database with the potential to cause drug-induced liver injury. Numbers of atoms and bonds along with the aromatic ratio were suitable descriptors for such drugs. The higher the number of rings and asymmetric structural elements in their terminal ring systems, the higher is the probability of hepatotoxicity. Rules were found which may help to design drugs which are unlikely to be hepatotoxic.
DOI: 10.6084/m9.figshare.1232104
title: Defense suppression benefits herbivores that have a monopoly on their feeding site but can backfire within natural communities

description: Raw data including popution densities, mite fecundity, plant gene expression, phytohormone and bacterial growth data. November 2014.
DOI: 10.6084/m9.figshare.1232110
title: Week 7: Pantrap Dataset

description: The experiment was done at York University on October 24, 2014. The experiment was conducted at grassland next to Danby Wood lot from 3:00 pm to 5:00 pm. The temperature recorded during trial 1 was 16ºC and 14ºC during trial 2. The sun was higher during the first trial from 3:00pm to 4:00pm and was lower during trial 2 from 4:00 pm to 5:00 pm. The Beauford Scale recorded was 3 for both the trials. The data was recorded with two other lab partners, Elron and Carmella. The purpose of the experiment was to determine and observe the diversity and number of arthropods collected, based on plant species, colour of pan traps and the distance from plant species. 15 bowls of three colours (white, yellow and blue) were used for each plant species. These pan traps were placed at a distance of 0ft, 1ft, 2ft, 3ft, and 4ft from plant species. 15 bowls were used for the rest of the three plant species. Plant A species was a Pollinator Plant and Plant B species was tall grass, both located in shared areas. Plant C specie was a purple flowering pollinator whereas Plant D specie was Red leave shrub, both located in sunny areas. The bowls were then filled with soapy water, starting from species A. The bowls were then left with soapy water for 60 minutes in order to collect the insects. After one hour the taxonomic units and the number of arthropods for each pan trap was recorded.
DOI: 10.6084/m9.figshare.1232112.v2
title: the effect of power lines on plant growth data/metadata

description: The research topic explores the effects of power lines on the growth of plants. Height (m), density, and diversity of plants were the variables used to indirectly measure/represent plant growth. Each variable was measured within 1metrex1metre quadrats, at 2m intervals from the power line (0m,2m,4m,6m). The purpose of this reseach was to gain knowlege about the direct (electric transmission) or indirect (soil toxicity, human impact, environmental pollution) effects of power lines on the growth of plants (Goldenrod, White Aster, Purple Aster, Queen Anne's Lace)- whether there is an effect or not, and how that can be measured. Once a week for 3 hours, for 3 weeks, data was collected in a power line field in the York Region of the GTA, across from York University. 1mx1m quadrats were placed at 0m from a power line and within the quadrat, height of 10 of each different type of plant (Goldenrod, White Aster, Purple Aster, Queen Anne's Lace) (m), different types of plants (diversity), and number of each different type of plant (density), was measured and recorded. 10 plants of each species was randomly selected to measure. All the different types of plants, well as how many there were of each were simply counted. This was repeated 2m, 4m, and 6m on the North and south sides of the power line, and then again 20m east/west, to have roughly 16 quadrats measured per 3 hour period.
DOI: 10.6084/m9.figshare.1232114.v1
title: Structure and molecular characterization of barley nudix hydrolase genes

description: Putative nudix hydrolase (NUDX) genes, which encode amino acid sequences showing homology with those of Arabidopsis NUDXs and conserve nudix motif, were identified from barley. The 14 deduced barley NUDXs (HvNUDX1-14) were classified into established subfamilies, except for 8-oxo-deoxyguanosine 5′-triphosphate (8-oxo-dGTP) pyrophosphohydrolase and mRNA decapping enzyme subfamilies, and three substrate-unknown subfamilies. Drought and UV-C stresses, respectively, up-regulated 7 and 4 HvNUDX genes, but some homologs of Arabidopsis NUDXs showed different responses to abiotic stress. HvNUDX12 gene, belonging to diadenosine tetraphosphates (Ap<sub>4</sub>A) pyrophosphohydrolase subfamily gene and up-regulated by UV-C, was expressed in <i>Escherichia coli</i> cells. The recombinant protein showed 8-oxo-dGTP, Ap<sub>4</sub>A, and guanosine-3′,5′-tetraphosphate (ppGpp) pyrophosphohydrolase activities, and the suppression of the <i>lacZ</i> amber mutation in a <i>mutT</i>-deficient <i>E. coli</i> cells caused by the incorporation of 8-oxo-GTP into mRNA was prevented to a significant degree. These results suggest that barley NUDXs have unique constitution and response of NUDX to abiotic stress.
DOI: 10.6084/m9.figshare.1232104.v1
title: Defense suppression benefits herbivores that have a monopoly on their feeding site but can backfire within natural communities

description: Raw data including popution densities, mite fecundity, plant gene expression, phytohormone and bacterial growth data. November 2014.
DOI: 10.6084/m9.figshare.1232112.v1
title: the effect of power lines on plant growth data/metadata

description: The research topic explores the effects of power lines of the growth of plants. Height (m), density, and diversity of plants were the variables used to indirectly measure/represent plant growth. Each variable was measured within 1metrex1metre quadrats, at 2m intervals from the power line (0m,2m,4m,6m). The purpose of this reseach was to gain knowlege about the direct (electric transmission) or indirect (soil toxicity, human impact, environmental pollution) effects of power lines on the growth of plants (Goldenrod, White Aster, Purple Aster, Queen Anne's Lace)- whether there is an effect or not, and how that can be measured. once a week for 3 hours, for 3 weeks, data was collected in a power line field in the York Region of the GTA, across from York University. 1mx1m quadrats were placed at 0m from a power line and within the quadrat, height of 10 of each different type of plant (Goldenrod, White Aster, Purple Aster, Queen Anne's Lace) (m), different types of plants (diversity), and number of each different type of plant (density), was measured and recorded. We randomly selected 10 plants of each species to measure, and we simply counted all the different types of plants and well as how many there were of each. This was repeated 2m, 4m, and 6m on the North and south sides of the power line, and then again 20m east/west, to have roughly 16 quadrats measured per 3 hour period.
DOI: 10.6084/m9.figshare.1232092
title: Cyclin A/Cdk2 regulates Cdh1 and claspin during late S/G2 phase of the cell cycle

description: Whereas many components regulating the progression from S phase through G2 phase into mitosis have been identified, the mechanism by which these components control this critical cell cycle progression is still not fully elucidated. Cyclin A/Cdk2 has been shown to regulate the timing of Cyclin B/Cdk1 activation and progression into mitosis although the mechanism by which this occurs is only poorly understood. Here we show that depletion of Cyclin A or inhibition of Cdk2 during late S/early G2 phase maintains the G2 phase arrest by reducing Cdh1 transcript and protein levels, thereby stabilizing Claspin and maintaining elevated levels of activated Chk1 which contributes to the G2 phase observed. Interestingly, the Cyclin A/Cdk2 regulated APC/C<sup>Cdh1</sup> activity is selective for only a subset of Cdh1 targets including Claspin. Thus, a normal role for Cyclin A/Cdk2 during early G2 phase is to increase the level of Cdh1 which destabilises Claspin which in turn down regulates Chk1 activation to allow progression into mitosis. This mechanism links S phase exit with G2 phase transit into mitosis, provides a novel insight into the roles of Cyclin A/Cdk2 in G2 phase progression, and identifies a novel role for APC/C<sup>Cdh1</sup> in late S/G2 phase cell cycle progression.
DOI: 10.6084/m9.figshare.1232114.v3
title: Structure and molecular characterization of barley nudix hydrolase genes

description: Putative nudix hydrolase (NUDX) genes, which encode amino acid sequences showing homology with those of Arabidopsis NUDXs and conserve nudix motif, were identified from barley. The 14 deduced barley NUDXs (HvNUDX1-14) were classified into established subfamilies, except for 8-oxo-deoxyguanosine 5′-triphosphate (8-oxo-dGTP) pyrophosphohydrolase and mRNA decapping enzyme subfamilies, and three substrate-unknown subfamilies. Drought and UV-C stresses, respectively, up-regulated 7 and 4 HvNUDX genes, but some homologs of Arabidopsis NUDXs showed different responses to abiotic stress. HvNUDX12 gene, belonging to diadenosine tetraphosphates (Ap<sub>4</sub>A) pyrophosphohydrolase subfamily gene and up-regulated by UV-C, was expressed in <i>Escherichia coli</i> cells. The recombinant protein showed 8-oxo-dGTP, Ap<sub>4</sub>A, and guanosine-3′,5′-tetraphosphate (ppGpp) pyrophosphohydrolase activities, and the suppression of the <i>lacZ</i> amber mutation in a <i>mutT</i>-deficient <i>E. coli</i> cells caused by the incorporation of 8-oxo-GTP into mRNA was prevented to a significant degree. These results suggest that barley NUDXs have unique constitution and response of NUDX to abiotic stress.
DOI: 10.6084/m9.figshare.1232091
title: Loss of circadian clock gene expression is associated with tumor progression in breast cancer

description: Several studies suggest a link between circadian rhythm disturbances and tumorigenesis. However, the association between circadian clock genes and prognosis in breast cancer has not been systematically studied. Therefore, we examined the expression of 17 clock components in tumors from 766 node-negative breast cancer patients that were untreated in both neoadjuvant and adjuvant settings. In addition, their association with metastasis-free survival (MFS) and correlation to clinicopathological parameters were investigated. Aiming to estimate functionality of the clockwork, we studied clock gene expression relationships by correlation analysis. Higher expression of several clock genes (e.g., <i>CLOCK</i>, <i>PER1</i>, <i>PER2</i>, <i>PER3</i>, <i>CRY2</i>, <i>NPAS2</i> and <i>RORC</i>) was found to be associated with longer MFS in univariate Cox regression analyses (HR&lt;1 and FDR-adjusted <i>P</i> &lt; 0.05). Stratification according to molecular subtype revealed prognostic relevance for <i>PER1</i>, <i>PER3</i>, <i>CRY2</i> and <i>NFIL3</i> in the ER+/HER2- subgroup, <i>CLOCK</i> and <i>NPAS2</i> in the ER-/HER2- subtype, and <i>ARNTL2</i> in HER2+ breast cancer. In the multivariate Cox model, only <i>PER3</i> (HR = 0.66; P = 0.016) and <i>RORC</i> (HR = 0.42; P = 0.003) were found to be associated with survival outcome independent of established clinicopathological parameters. Pairwise correlations between functionally-related clock genes (e.g., PER2-PER3 and CRY2-PER3) were stronger in ER+, HER2- and low-grade carcinomas; whereas, weaker correlation coefficients were observed in ER- and HER2+ tumors, high-grade tumors and tumors that progressed to metastatic disease. In conclusion, loss of clock genes is associated with worse prognosis in breast cancer. Coordinated co-expression of clock genes, indicative of a functional circadian clock, is maintained in ER+, HER2-, low grade and non-metastasizing tumors but is compromised in more aggressive carcinomas.
DOI: 10.6084/m9.figshare.1232114.v2
title: Structure and molecular characterization of barley nudix hydrolase genes

description: Putative nudix hydrolase (NUDX) genes, which encode amino acid sequences showing homology with those of Arabidopsis NUDXs and conserve nudix motif, were identified from barley. The 14 deduced barley NUDXs (HvNUDX1-14) were classified into established subfamilies, except for 8-oxo-deoxyguanosine 5′-triphosphate (8-oxo-dGTP) pyrophosphohydrolase and mRNA decapping enzyme subfamilies, and three substrate-unknown subfamilies. Drought and UV-C stresses, respectively, up-regulated 7 and 4 HvNUDX genes, but some homologs of Arabidopsis NUDXs showed different responses to abiotic stress. HvNUDX12 gene, belonging to diadenosine tetraphosphates (Ap<sub>4</sub>A) pyrophosphohydrolase subfamily gene and up-regulated by UV-C, was expressed in <i>Escherichia coli</i> cells. The recombinant protein showed 8-oxo-dGTP, Ap<sub>4</sub>A, and guanosine-3′,5′-tetraphosphate (ppGpp) pyrophosphohydrolase activities, and the suppression of the <i>lacZ</i> amber mutation in a <i>mutT</i>-deficient <i>E. coli</i> cells caused by the incorporation of 8-oxo-GTP into mRNA was prevented to a significant degree. These results suggest that barley NUDXs have unique constitution and response of NUDX to abiotic stress.
DOI: 10.6084/m9.figshare.1232088
title: Eribulin disrupts EB1-microtubule plus-tip complex formation

description: Eribulin mesylate is a synthetic analog of halichondrin B known to bind tubulin and microtubules, specifically at their protein rich plus-ends, thereby dampening microtubule (MT) dynamics, arresting cells in mitosis, and inducing apoptosis. The proteins which bind to the MT plus-end are known as microtubule plus-end tracking proteins (+TIPs) and have been shown to promote MT growth and stabilization. Eribulin's plus-end binding suggests it may compete for binding sites with known +TIP proteins such as End-binding 1 (EB1). To better understand the impact of eribulin plus-end binding in regard to the proteins which normally bind there, cells expressing GFP-EB1 were treated with various concentrations of eribulin. In a concentration dependent manner, GFP-EB1 became dissociated from the MT plus-ends following drug addition. Similar results were found with immuno-stained fixed cells. Cells treated with low concentrations of eribulin also showed decreased ability to migrate, suggesting the decrease in MT dynamics may have a downstream effect. Extended exposure of eribulin to cells leads to total depolymerization of the MT array. Taken together, these data show eribulin effectively disrupts EB1 +TIP complex formation, providing mechanistic insights into the impact of eribulin on MT dynamics.
DOI: 10.6084/m9.figshare.1232092.v1
title: Cyclin A/Cdk2 regulates Cdh1 and claspin during late S/G2 phase of the cell cycle

description: Whereas many components regulating the progression from S phase through G2 phase into mitosis have been identified, the mechanism by which these components control this critical cell cycle progression is still not fully elucidated. Cyclin A/Cdk2 has been shown to regulate the timing of Cyclin B/Cdk1 activation and progression into mitosis although the mechanism by which this occurs is only poorly understood. Here we show that depletion of Cyclin A or inhibition of Cdk2 during late S/early G2 phase maintains the G2 phase arrest by reducing Cdh1 transcript and protein levels, thereby stabilizing Claspin and maintaining elevated levels of activated Chk1 which contributes to the G2 phase observed. Interestingly, the Cyclin A/Cdk2 regulated APC/C<sup>Cdh1</sup> activity is selective for only a subset of Cdh1 targets including Claspin. Thus, a normal role for Cyclin A/Cdk2 during early G2 phase is to increase the level of Cdh1 which destabilises Claspin which in turn down regulates Chk1 activation to allow progression into mitosis. This mechanism links S phase exit with G2 phase transit into mitosis, provides a novel insight into the roles of Cyclin A/Cdk2 in G2 phase progression, and identifies a novel role for APC/C<sup>Cdh1</sup> in late S/G2 phase cell cycle progression.