84 results on '"Varkey, D"'
Search Results
2. Predicting subsurface stratigraphy using an improved Coupled Markov Chain method
- Author
-
Varkey, D. (author), van den Eijnden, A.P. (author), Hicks, M.A. (author), Varkey, D. (author), van den Eijnden, A.P. (author), and Hicks, M.A. (author)
- Abstract
Geological uncertainty can significantly influence the computed response of a geotechnical structure. For example, ignoring the presence of a weak soil layer embedded within a stronger layer and assuming a deterministic stratigraphic boundary can significantly underestimate the probability of failure. In this paper, the coupled Markov chain method has been used for modelling this form of uncertainty. A strategy for estimating the horizontal transition probability matrix with limited data has been proposed, which is one of the biggest challenges with using this method. In particular, different sampling intervals in the vertical and horizontal directions have been considered in estimating the matrix for simulating realistic field situations. The applicability of the proposed method has been demonstrated using a set of CPTs in the Netherlands. The results highlight a problem that arises due to the coupling algorithm used in this method., Geo-engineering
- Published
- 2023
3. Machine learning for prediction of undrained shear strength from cone penetration test data
- Author
-
Yu, Beiyang (author), Varkey, D. (author), van den Eijnden, A.P. (author), Rongier, G. (author), Hicks, M.A. (author), Yu, Beiyang (author), Varkey, D. (author), van den Eijnden, A.P. (author), Rongier, G. (author), and Hicks, M.A. (author)
- Abstract
This research focuses on investigating the relative performance of a range of machine learning algorithms, namely the artificial neural network, support vector machine, Gaussian process regression, random forest, and XGBoost, for predicting the undrained shear strength from cone penetration test data. This is to assess how machine learning could help us lower the need for laboratory test data. The training dataset compiles 526 data from 12 regions and the testing dataset consists of 20 data from a polder located close to Leiden in the Netherlands. In addition, k-fold and group k-fold cross-validation strategies are both applied to validate the models. The poor performance of the models during group k-fold cross-validation suggests that, while machine learning techniques can perform well when site-specific data are included during training, they struggle to generalize without site-specific data. This highlights the difficulty of capturing soil heterogeneity and suggests that either machine learning methods should be trained on specific sites for which some data are already available, or much larger training datasets are needed., Geo-engineering, Applied Geology
- Published
- 2023
4. Predicting subsurface classification in 2D from cone penetration test data
- Author
-
Varkey, D. (author), Hicks, M.A. (author), van den Eijnden, A.P. (author), Varkey, D. (author), Hicks, M.A. (author), and van den Eijnden, A.P. (author)
- Abstract
Uncertainty is inevitable in the characterisation of a geotechnical site, especially due to the inherently heterogeneous nature of the ground. In this paper, a method for characterising a subsurface with limited cone penetration test (CPT) data is proposed. The method is based on integrating predictions of CPT parameters with a probabilistic approach for subsoil classification at the CPTs. The predicted stratigraphy is able to capture the spatial variability of soil measured via CPTs and takes account of the uncertainties that arise from transforming CPT measurements into soil units as well as errors in the measurements themselves. The applicability of the proposed method is demonstrated for a site in the Netherlands. The results show that the proposed approach can identify the most likely classification in the domain with good accuracy. Furthermore, the significance of considering the uncertainties in predicting the most likely classification is illustrated via finite element stability analyses of a slope cut-out in the domain., Geo-engineering
- Published
- 2023
- Full Text
- View/download PDF
5. Reliability-Based Partial Factors Considering Spatial Variability of Strength Parameters
- Author
-
Varkey, D. (author), Hicks, M.A. (author), van den Eijnden, A.P. (author), Varkey, D. (author), Hicks, M.A. (author), and van den Eijnden, A.P. (author)
- Abstract
The stability of six regional dyke cross-sections in the Netherlands was re-assessed using the random finite element method (RFEM), which explicitly accounts for the spatial variability of strength parameters. The RFEM assessments of the cross-sections were shown to result in significantly narrower response distributions than those obtained by ignoring the spatial variability, and therefore would result in more economical designs. Given the complexity of RFEM for applications in daily engineering practice, the results obtained from the re-assessments of the six dyke cross-sections were used to propose partial factors that can be used in practice to achieve the desired reliability levels for regional dykes. When applied in a conventional semi-probabilistic assessment of a dyke cross-section, these partial factors would result in the same level of reliability as would have been obtained by carrying out an RFEM analysis of the same cross-section., Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public., Geo-engineering
- Published
- 2023
- Full Text
- View/download PDF
6. Periodic random fields to perform site response and liquefaction susceptibility analysis
- Author
-
Gonzalez Acosta, J.L. (author), Varkey, D. (author), van den Eijnden, A.P. (author), Hicks, M.A. (author), Gonzalez Acosta, J.L. (author), Varkey, D. (author), van den Eijnden, A.P. (author), and Hicks, M.A. (author)
- Abstract
Free-field site response analysis is a standard technique used to predict soil deposit dynamic response and liquefaction susceptibility. Such analyses are typically carried out by implementing periodic boundaries to guarantee the same speed of the dynamic waves travelling across them. However, when using random fields to consider the impact of soil spatial variability there is the possibility of an inconsistency with periodic boundaries. This is due to the generation of non-identical properties at the lateral boundaries on using traditional random fields. To overcome this inconsistency, this paper proposes periodic random fields to model spatial variability by matching the periodicity at the boundaries. To investigate the significance of using the proposed approach, a heterogeneous soil deposit subjected to earthquake loading is analysed using the random finite element method. The results show that, for certain values of the horizontal scale of fluctuation, ensuring consistency at the lateral boundaries could result in less conservative predictions of the extent of the liquefied areas., Geo-engineering
- Published
- 2023
- Full Text
- View/download PDF
7. 3D slope stability analysis with spatially variable and cross-correlated shear strength parameters
- Author
-
Varkey, D., primary, Hicks, M.A., additional, and Vardon, P.J., additional
- Published
- 2018
- Full Text
- View/download PDF
8. Data review for 3LN redfish in preparation for an updated management strategy evaluation
- Author
-
Perreault, A. (Andrea), Rogers, B. (Bob), González-Troncoso, D. (Diana), Rideout, R. (Rick), Simpson, M. (Mark), Dwyer, K. (Karen), Varkey, D. (Divya), and NAFO
- Subjects
fish ,radio ,NAFO ,data ,Centro Oceanográfico de Vigo ,fisheries ,Grand Banks of Newfoundland ,Pesquerías ,management ,Scientific survey - Abstract
Data review for 3LN redfish in preparation for an updated management strategy evaluation, SI
- Published
- 2022
9. Widespread oxyregulation in tropical corals under hypoxia
- Author
-
Hughes, DJ, Alexander, J, Cobbs, G, Kühl, M, Cooney, C, Pernice, M, Varkey, D, Voolstra, CR, Suggett, DJ, Hughes, DJ, Alexander, J, Cobbs, G, Kühl, M, Cooney, C, Pernice, M, Varkey, D, Voolstra, CR, and Suggett, DJ
- Published
- 2022
10. Effect of uncertainties in geometry, inter-layer boundary and shear strength properties on the probabilistic stability of a 3D embankment slope
- Author
-
Varkey, D. (author), Hicks, M.A. (author), Vardon, P.J. (author), Varkey, D. (author), Hicks, M.A. (author), and Vardon, P.J. (author)
- Abstract
This paper investigates the influence of three forms of uncertainty on the probabilistic stability of an idealised 3D embankment slope. These are: 1D spatial variability in the external geometry of the slope along its length, 2D spatial variability in the depth of the boundary between the embankment material and the foundation layer, and 3D spatial variability in the shear strength properties of the slope and foundation materials. The relative influence of each uncertainty has been investigated using the random finite element method, based on statistics consistent with a Dutch regional dyke. The results indicate that, for such a structure, the soil spatial variability has a much greater influence than uncertainties relating to embankment geometry and inter-layer boundary. In particular, it is demonstrated that the spatial correlation of material properties along the length of the embankment has a greater influence on the probabilistic characteristics of the embankment slope stability and failure consequence than the spatial correlation of properties perpendicular to it. A worst case scale of fluctuation for the material properties is identified., Geo-engineering
- Published
- 2022
- Full Text
- View/download PDF
11. Assessing the status of the cod (Gadus morhua) stock in NAFO Subdivision 3Ps in 2020.
- Author
-
Ings, D. W., Varkey, D. A., Regular, P. R., Kumar, R., Rideout, R. M., and Vigneau, J.
- Subjects
- *
ATLANTIC cod , *CODFISH , *FISH mortality , *COVID-19 pandemic , *RESEARCH vessels , *FISHERIES , *BYCATCHES , *ESTIMATES - Abstract
The status of the cod stock in the Northwest Atlantic Fisheries Organization (NAFO) Subdivision (Subdiv.) 3Ps was assessed during a Fisheries and Oceans Canada (DFO) Regional Peer Review Process meeting held November 2-7, 2020. Total landings for the 2019-20 management year (April 1-March 31) were 3,499 t, or 59% of the Total Allowable Catch (TAC). This marks the tenth consecutive season that the entire TAC has not been taken. There was no DFO research vessel (RV) survey during spring 2020 due to the pandemic. Sentinel gillnet catch rates have been very low and stable since 1999. Sentinel line trawl catch rates were below average over 2011-18, but the 2019 catch rates were relatively high. An integrated state space model resulting from the 2019 3Ps Cod Framework meeting was used to assess the status of the stock and estimate fishing mortality. The Limit Reference Point (LRP) is 66,000 t of Spawning Stock Biomass (SSB). SSB at January 1, 2021, is estimated to be 25 kt (18 kt-35 kt). The stock is in the Critical Zone (38% of Blim [27-53%]) as defined by the DFO Precautionary Approach (PA) Framework. The probability of being below Blim is >99.9%. The estimated fishing mortality rate (ages 5-8) has generally declined, from 0.16 in 2015 to 0.11 in 2019. With an assumed catch of 2,702 t in 2020, fishing mortality (F) is projected to be 0.07 (0.05-0.09) in 2020. Natural mortality (ages 5-8) was estimated to be 0.43 (0.35-0.52) in 2019. Values of natural mortality (M) during the last four years are the among the highest in the time series. Recruitment (age 2) estimates have been below the long term average since the mid-1990s. Projection of the stock to 2023 was conducted assuming. [ABSTRACT FROM AUTHOR]
- Published
- 2023
12. TAXONOMIC VARIABILITY IN THE ELECTRON REQUIREMENT FOR CARBON FIXATION ACROSS MARINE PHYTOPLANKTON
- Author
-
Hughes DJ, Giannini FC, Ciotti AM, Doblin MA, Ralph PJ, Varkey D, Verma A, and Suggett DJ
- Subjects
0607 Plant Biology, 0704 Fisheries Sciences ,Marine Biology & Hydrobiology - Published
- 2021
13. Functional characterisation of substrate-binding proteins to address nutrient uptake in marine picocyanobacteria.
- Author
-
Ford, BA, Sullivan, GJ, Moore, L, Varkey, D, Zhu, H, Ostrowski, M, Mabbutt, BC, Paulsen, IT, Shah, BS, Ford, BA, Sullivan, GJ, Moore, L, Varkey, D, Zhu, H, Ostrowski, M, Mabbutt, BC, Paulsen, IT, and Shah, BS
- Abstract
Marine cyanobacteria are key primary producers, contributing significantly to the microbial food web and biogeochemical cycles by releasing and importing many essential nutrients cycled through the environment. A subgroup of these, the picocyanobacteria (Synechococcus and Prochlorococcus), have colonised almost all marine ecosystems, covering a range of distinct light and temperature conditions, and nutrient profiles. The intra-clade diversities displayed by this monophyletic branch of cyanobacteria is indicative of their success across a broad range of environments. Part of this diversity is due to nutrient acquisition mechanisms, such as the use of high-affinity ATP-binding cassette (ABC) transporters to competitively acquire nutrients, particularly in oligotrophic (nutrient scarce) marine environments. The specificity of nutrient uptake in ABC transporters is primarily determined by the peripheral substrate-binding protein (SBP), a receptor protein that mediates ligand recognition and initiates translocation into the cell. The recent availability of large numbers of sequenced picocyanobacterial genomes indicates both Synechococcus and Prochlorococcus apportion >50% of their transport capacity to ABC transport systems. However, the low degree of sequence homology among the SBP family limits the reliability of functional assignments using sequence annotation and prediction tools. This review highlights the use of known SBP structural representatives for the uptake of key nutrient classes by cyanobacteria to compare with predicted SBP functionalities within sequenced marine picocyanobacteria genomes. This review shows the broad range of conserved biochemical functions of picocyanobacteria and the range of novel and hypothetical ABC transport systems that require further functional characterisation.
- Published
- 2021
14. Geotechnical uncertainties and reliability-based assessments of dykes
- Author
-
Varkey, D., Hicks, M.A., Vardon, P.J., and Delft University of Technology
- Subjects
Statistical analysis ,Slope stability ,Hetereogeneity ,Reliability ,RFEM - Abstract
This thesis utilises the random finite element method (RFEM) to provide practical guidance and tools for geotechnical engineers to account for the influence of soil spatial variability. This has involved: (a) practical insight and guidance on the choice of characteristic soil property values and scales of fluctuation; (b) a robust approach to reliability assessment and design that obviates the need for explicit calculation of characteristic values; and (c) the benchmarking and improving of simpler analysis tools.
- Published
- 2020
15. Taxonomic variability in the electron requirement for carbon fixation across marine phytoplankton
- Author
-
Hughes, DJ, Giannini, FC, Ciotti, AM, Doblin, MA, Ralph, PJ, Varkey, D, Verma, A, and Suggett, DJ
- Subjects
0607 Plant Biology, 0704 Fisheries Sciences ,Marine Biology & Hydrobiology - Abstract
Fast Repetition Rate fluorometry (FRRf) has been increasingly used to measure marine primary productivity by oceanographers to understand how carbon (C) uptake patterns vary over space and time in the global oceans. As FRRf measures electron transport rates through photosystem II (ETRPSII ), a critical, but difficult-to-predict conversion factor termed the "electron requirement for carbon fixation" (Φe,C ) is needed to scale ETRPSII to C-fixation rates. Recent studies have generally focused on understanding environmental regulation of Φe,C , while taxonomic control has been explored by only a handful of laboratory studies encompassing a limited diversity of phytoplankton species. We therefore assessed Φe,C for a wide range of marine phytoplankton (n=17 strains) spanning multiple taxonomic and size-classes. Data mined from previous studies were further considered to determine whether Φe,C variability could be explained by taxonomy versus other phenotypic traits influencing growth and physiological performance (e.g., cell size). We found that Φe,C exhibited considerable variability (~4-10 mol e- · [mol C]-1 ), and was negatively correlated with growth rate (R2 = 0.7, p < 0.01). Diatoms exhibited a lower Φe,C compared to chlorophytes during steady-state, nutrient-replete growth. Inclusion of meta-analysis data did not find significant relationships between Φe,C and class, or growth rate, although confounding factors inherent to methodological inconsistencies between studies likely contributed to this. Knowledge of empirical relationships between Φe,C and growth rate coupled with recent improvements in quantifying phytoplankton growth rates in-situ, facilitate up-scaling of FRRf campaigns to routinely derive Φe,C needed to assess ocean C-cycling.
- Published
- 2020
16. Revealing changes in the microbiome of Symbiodiniaceae under thermal stress
- Author
-
Camp EF, Kahlke T, Nitschke MR, Varkey D, Fisher NL, Fujise L, Goyen S, Hughes DJ, Lawson CA, Ros M, Woodcock S, Xiao K, Leggat W, and Suggett DJ
- Subjects
Bacteria ,RNA, Ribosomal, 16S ,Microbiota ,Dinoflagellida ,Animals ,0603 Evolutionary Biology, 0605 Microbiology ,Microbiology ,Heat-Shock Response - Abstract
Symbiodiniaceae are a diverse family of marine dinoflagellates, well known as coral endosymbionts. Isolation and in vitro culture of Symbiodiniaceae strains for physiological studies is a widely adopted tool, especially in the context of understanding how environmental stress perturbs Symbiodiniaceae cell functioning. While the bacterial microbiomes of corals often correlate with coral health, the bacterial communities co-cultured with Symbiodiniaceae isolates have been largely overlooked, despite the potential of bacteria to significantly influence the emergent physiological properties of Symbiodiniaceae cultures. We examined the physiological response to heat stress by Symbiodiniaceae isolates (spanning three genera) with well-described thermal tolerances, and combined these observations with matched changes in bacterial composition and abundance through 16S rRNA metabarcoding. Under thermal stress, there were Symbiodiniaceae strain-specific changes in maximum quantum yield of photosystem II (proxy for health) and growth rates that were accompanied by changes in the relative abundance of multiple Symbiodiniaceae-specific bacteria. However, there were no Symbiodiniaceae-independent signatures of bacterial community reorganisation under heat stress. Notably, the thermally tolerant Durusdinium trenchii (ITS2 major profile D1a) had the most stable bacterial community under heat stress. Ultimately, this study highlights the complexity of Symbiodiniaceae-bacteria interactions and provides a first step towards uncoupling their relative contributions towards Symbiodiniaceae physiological functioning.
- Published
- 2020
17. On characteristic values for calculating factors of safety for dyke stability
- Author
-
Varkey, D. (author), Hicks, M.A. (author), van den Eijnden, A.P. (author), Vardon, P.J. (author), Varkey, D. (author), Hicks, M.A. (author), van den Eijnden, A.P. (author), and Vardon, P.J. (author)
- Abstract
Various simplified approaches are used to calculate the characteristic values of shear strength properties, which have then been used in deterministic stability analyses of a dyke cross-section. The calculated factors of safety are compared with the 5-percentile ‘system response’ of the dyke cross-section, calculated using the more exhaustive random finite-element method (RFEM), which is consistent with the requirements of Eurocode 7. The simplified methods accounting for variance reduction due to averaging of property values mostly give factors of safety within 10% of the RFEM solution, whereas the factor of safety based on the 5-percentile material properties is significantly over-conservative., Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public., Geo-engineering
- Published
- 2020
- Full Text
- View/download PDF
18. Geotechnical uncertainties and reliability-based assessments of dykes
- Author
-
Varkey, D. (author) and Varkey, D. (author)
- Abstract
This thesis utilises the random finite element method (RFEM) to provide practical guidance and tools for geotechnical engineers to account for the influence of soil spatial variability. This has involved: (a) practical insight and guidance on the choice of characteristic soil property values and scales of fluctuation; (b) a robust approach to reliability assessment and design that obviates the need for explicit calculation of characteristic values; and (c) the benchmarking and improving of simpler analysis tools., Geo-engineering
- Published
- 2020
19. On characteristic values for calculating factors of safety for dyke stability
- Author
-
Varkey, D., primary, Hicks, M. A., additional, van den Eijnden, A. P., additional, and Vardon, P. J., additional
- Published
- 2020
- Full Text
- View/download PDF
20. A state-space model for stock assessment of cod (Gadus morhua) stock in NAFO Subdivision 3Ps.
- Author
-
Varkey, D. A., Babyn, J., Regular, P., Ings, D. W., Kumar, R., Rogers, B., Champagnat, J., and Morgan, M. J.
- Subjects
- *
ATLANTIC cod , *FISHERIES , *RANDOM walks , *FISH mortality , *SUBDIVISION surfaces (Geometry) , *AKAIKE information criterion , *DEATH rate - Abstract
The paper describes the development of a state-space model (HYBRID) for the stock assessment of Northwest Atlantic Fisheries Organization (NAFO) Subdivision 3Ps cod stock. The HYBRID model fits to the DFO RV survey (1983-2005, 2007-19) as well as the following additional survey time series: the IFREMER (Institut Français de Recherche pour l'Exploitation de la Mer, English: French Research Institute for Exploitation of the Sea) ERHAPS (Evaluation des Ressources Halieutiques de la région 3PS) survey (1978-91), the Groundfish Enterprise Allocation Committee (GEAC) survey (1998-2005), and the sentinel gillnet and line-trawl surveys (1995-2018). The HYBRID model also fits to fisheries data with the expectation that the model can separate fishing mortality from natural mortality. Fisheries catch-at-age is fit using continuation ratio logits, and the fisheries landings are fit via censored likelihood. The use of censored likelihood for fitting landings allows the inclusion of expert opinion on reliability of landings throughout the model time series. The HYBRID model presented here starts in 1959, which is the first year for which landings data are available. The HYBRID model allows exploration of different forms for parameterization of time-varying fisheries selectivity, natural mortality, and approaches for estimation of catch-at-age data. The model formulations also differ depending on the survey series used in fitting the model. Seventeen model formulations are presented. Alternate formulations based on fishing mortality included: 1. a logistic flat topped or dome selectivity with time-blocks 2. SAM (State-space Assessment Model, Nielsen and Berg, 2014) style Multivariate Normal random walk 3. a separable age-year correlated process for fishing mortality rate (F) similar to NCAM (Cadigan 2016), and 4. option to break the processes for F in years where important events (like a moratorium) have impacted the fishery. Alternate formulation based on natural mortality included: 1. invariant natural mortality across age and years, and 2. time-varying natural mortality related to fish condition. The different model formulations are compared and evaluated on the basis of AIC (Akaike Information Criterion) values and their performance in retrospective analyses. The meeting concluded that time-varying natural mortality is an important consideration for modelling the dynamics of 3Ps cod and selecting a population model for this stock. Following the evaluations of the alternate model formulations, model formulations 11 which includes fit to sentinel data series, has F modelled using an MVN Random walk with year break for the moratorium, and has time-varying natural mortality rate (M) was considered to have utility as an assessment model for 3Ps cod stock assessment. [ABSTRACT FROM AUTHOR]
- Published
- 2022
21. Sediment bacterial communities associated with environmental factors in Intermittently Closed and Open Lakes and Lagoons (ICOLLs)
- Author
-
Filippini, G, Bugnot, AB, Johnston, EL, Ruszczyk, J, Potts, J, Scanes, P, Ferguson, A, Ostrowski, M, Varkey, D, and Dafforn, KA
- Subjects
RNA, Bacterial ,Geologic Sediments ,Lakes ,Bacteria ,Sequence Analysis, RNA ,RNA, Ribosomal, 16S ,Microbiota ,Cities ,New South Wales ,Environmental Sciences ,Environmental Monitoring - Abstract
© 2019 Elsevier B.V. Intermittently Closed and Open Lakes and Lagoons (ICOLLS) are important coastal systems that are periodically separated from the ocean by a sand barrier or a berm. In urban ICOLLs, continuous inputs of organic material and nutrients into coastal lagoons are contributing to eutrophic conditions that, together with natural environmental factors have implications for the resident sediment bacterial communities. We used molecular tools to investigate the ecological communities of four ICOLLs; Narrabeen, Dee Why, Curl Curl and Manly in Sydney, Australia, which have been subjected to increasing pressure from anthropogenic activities over the last century. We used targeted gene sequencing of the prokaryotic 16S ribosomal RNA gene to describe the bacterial diversity and community structure and discuss differences with respect to environmental factors at the ICOLL scale (e.g. size, shape, normalised N loading) and site scale (e.g. water and sediment quality) within each lagoon. Due to differences in hydrological patterns, we expected that sediment bacterial communities would be more heterogenous in displacement-dominated lagoons (Curl Curl and Manly) than the mixing-dominated lagoons (Narrabeen and Dee Why). Interestingly, we did not find strong relationships between the main bacterial groups and distance from the lagoon entrance (used as a proxy for salinity and silt) in the displacement-dominated lagoons. Moreover, we found that α diversity was highest in Narrabeen and Manly lagoons despite differences in lagoon size and shape. Furthermore, while bacterial community structure was similar in Curl Curl and Dee Why, communities in Manly and Narrabeen differed along temperature/TOC and salinity/silt gradients respectively. In Manly lagoon, we found relatively more anaerobic bacteria such as Epsilonbactereota which is involved in the oxidation and reduction of sulfur compounds. Moreover, we identified several bacterial taxa (including sulfur metabolising Chlorobiaceae) related to increasing TOC that could be investigated further as potential indicators of excess enrichment.
- Published
- 2019
22. Modified Semi-Analytical Method for 3D Slope Reliability
- Author
-
Varkey, D., Hicks, M.A., Vardon, P.J., Ching, Jianye, Li, Dian-Qing, and Zhang, Jie
- Subjects
slope stability ,random fields ,spatial variability ,finite element analysis ,Analytical ,three dimensional - Abstract
An improved method for the reliability analysis of 3D slopes has been proposed based on the semi-analytical method of Vanmarcke (1977). Comparing the predicted responses of an idealised 3D slope obtained by the more general, albeit computationally intensive, random finite element method (RFEM), and the original semi-analytical method showed that the latter gives unconservative estimates of the probability of failure. Three significant areas were identified as requiring improvement in the simpler method. These were corrected by: (i) a correction factor to reduce the overestimation of endresistance in 3D failures, i.e. reducing the impact of conservative geometric assumptions; (ii) a correction factor to correct for overestimating the average shear strength on the failure plane, which is found to be lower than the average shear strength for the entire slope; and (iii) an alternative relationship for the expected failure length for intermediate values of the spatial correlation length of the shear strength. The proposed modified semi-analytical method gives substantially improved results that are comparable to RFEM, while retaining the simplicity of the original method.
- Published
- 2019
23. Modified Semi-Analytical Method for 3D Slope Reliability
- Author
-
Varkey, D. (author), Hicks, M.A. (author), Vardon, P.J. (author), Varkey, D. (author), Hicks, M.A. (author), and Vardon, P.J. (author)
- Abstract
An improved method for the reliability analysis of 3D slopes has been proposed based on the semi-analytical method of Vanmarcke (1977). Comparing the predicted responses of an idealised 3D slope obtained by the more general, albeit computationally intensive, random finite element method (RFEM), and the original semi-analytical method showed that the latter gives unconservative estimates of the probability of failure. Three significant areas were identified as requiring improvement in the simpler method. These were corrected by: (i) a correction factor to reduce the overestimation of endresistance in 3D failures, i.e. reducing the impact of conservative geometric assumptions; (ii) a correction factor to correct for overestimating the average shear strength on the failure plane, which is found to be lower than the average shear strength for the entire slope; and (iii) an alternative relationship for the expected failure length for intermediate values of the spatial correlation length of the shear strength. The proposed modified semi-analytical method gives substantially improved results that are comparable to RFEM, while retaining the simplicity of the original method., Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public., Geo-engineering
- Published
- 2019
- Full Text
- View/download PDF
24. On characteristic values and the reliability-based assessment of dykes
- Author
-
Hicks, M.A. (author), Varkey, D. (author), van den Eijnden, A.P. (author), de Gast, T. (author), Vardon, P.J. (author), Hicks, M.A. (author), Varkey, D. (author), van den Eijnden, A.P. (author), de Gast, T. (author), and Vardon, P.J. (author)
- Abstract
A case study involving the assessment and re-design of an existing dyke, founded on a layered soil, has compared deterministic analysis based on 5-percentile property values and a reliability-based random finite element analysis consistent with the requirements of Eurocode 7. The results show that a consideration of the spatial nature of soil variability generally leads to higher computed factors of safety and, for those dyke sections requiring remedial action, to more economic designs. Back-figured characteristic values are shown to be considerably higher than the 5-percentile soil properties; hence, a reduction in over-conservatism is achieved., Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public., Geo-engineering
- Published
- 2019
- Full Text
- View/download PDF
25. An improved semi-analytical method for 3D slope reliability assessments
- Author
-
Varkey, D. (author), Hicks, M.A. (author), Vardon, P.J. (author), Varkey, D. (author), Hicks, M.A. (author), and Vardon, P.J. (author)
- Abstract
An improved semi-analytical method for calculating the reliability of 3D slopes with spatially varying shear strength parameters is proposed. The response of an existing semi-analytical method has been compared with that of the computationally more intensive, but more general, random finite element method (RFEM), demonstrating that the simpler method underestimates the failure probability. An alternative relationship for the expected failure length and two correction factors are proposed, which modify the original formulation of the simpler method. The proposed approach gives substantially improved results that compare favourably with those obtained by RFEM, and therefore provides a more accurate simplified solution., Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public., Geo-engineering
- Published
- 2019
- Full Text
- View/download PDF
26. The collapse and continued low productivity of a keystone forage fish species
- Author
-
Buren, AD, primary, Murphy, HM, additional, Adamack, AT, additional, Davoren, GK, additional, Koen-Alonso, M, additional, Montevecchi, WA, additional, Mowbray, FK, additional, Pepin, P, additional, Regular, PM, additional, Robert, D, additional, Rose, GA, additional, Stenson, GB, additional, and Varkey, D, additional
- Published
- 2019
- Full Text
- View/download PDF
27. 3D slope stability analysis with spatially variable and cross-correlated shear strength parameters
- Author
-
Varkey, D. (author), Hicks, M.A. (author), Vardon, P.J. (author), Varkey, D. (author), Hicks, M.A. (author), and Vardon, P.J. (author)
- Abstract
The paper investigates the stability of slopes with spatially variable and cross-correlated shear strength parameters in 3D. The influence of various cross-correlation coefficients between these parameters on the probability of 3D slope failure has been considered for different levels of anisotropy of the heterogeneity in the shear strength. Specifically, 3D random fields of cohesion and friction angle were generated using the Local Average Subdivision method, and these were correlated with each other by various degrees. The fields were then linked to finite element analyses within a Monte Carlo framework. The results indicate that a positive cross-correlation between the parameters reduces the slope reliability, whereas a negative cross-correlation between the parameters increases the reliability., Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public., Geo-engineering, Geoscience and Engineering
- Published
- 2018
28. Stormwater influences phytoplankton assemblages within the diverse, but impacted Sydney Harbour estuary
- Author
-
Varkey, D, Mazard, S, Jeffries, TC, Hughes, DJ, Seymour, J, Paulsen, IT, Ostrowski, M, Varkey, D, Mazard, S, Jeffries, TC, Hughes, DJ, Seymour, J, Paulsen, IT, and Ostrowski, M
- Abstract
© 2018 Varkey et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Sydney Harbour is subjected to persistent stress associated with anthropogenic activity and global climate change, but is particularly subjected to pulse stress events associated with stormwater input during episodic periods of high rainfall. Photosynthetic microbes underpin metazoan diversity within estuarine systems and are therefore important bioindicators of ecosystem health; yet how stormwater input affects their occurrence and distribution in Sydney Harbour remains poorly understood. We utilised molecular tools (16S/18S rRNA and petB genes) to examine how the phytoplankton community structure (both prokaryotes and eukaryotes) within Sydney Harbour varies between high and low rainfall periods. The relative proportion of phytoplankton sequences was more abundant during the high rainfall period, comprising mainly of diatoms, an important functional group supporting increased productivity within estuarine systems, together with cyanobacteria. Increased spatial variability in the phytoplankton community composition was observed, potentially driven by the steepened physico-chemical gradients associated with stormwater inflow. Conversely, during a low rainfall period, the proportion of planktonic photosynthetic microbes was significantly lower and the persistent phytoplankton were predominantly represented by chlorophyte and dinoflagellate sequences, with lower overall diversity. Differences in phytoplankton composition between the high and low rainfall periods were correlated with temperature, salinity, total nitrogen and silicate. These results suggest that increased frequency of high-rainfall events may change the composition, productivity and health of the estuary. Our study begins to populate the knowledge gap
- Published
- 2018
29. Impact of nitrogen availability upon the electron requirement for carbon fixation in Australian coastal phytoplankton communities
- Author
-
Hughes, DJ, Varkey, D, Doblin, MA, Ingleton, T, Mcinnes, A, Ralph, PJ, van Dongen-Vogels, V, Suggett, DJ, Hughes, DJ, Varkey, D, Doblin, MA, Ingleton, T, Mcinnes, A, Ralph, PJ, van Dongen-Vogels, V, and Suggett, DJ
- Abstract
© 2018 Association for the Sciences of Limnology and Oceanography Nitrogen (N) availability affects phytoplankton photosynthetic performance and regulates marine primary production (MPP) across the global coast and oceans. Bio-optical tools including Fast Repetition Rate fluorometry (FRRf) are particularly well suited to examine MPP variability in coastal regions subjected to dynamic spatio-temporal fluctuations in nutrient availability. FRRf determines photosynthesis as an electron transport rate through Photosystem II (ETRPSII), requiring knowledge of an additional parameter, the electron requirement for carbon fixation (KC), to retrieve rates of CO2-fixation. KC strongly depends upon environmental conditions regulating photosynthesis, yet the importance of N-availability to this parameter has not been examined. Here, we use nutrient bioassays to isolate how N (relative to other macronutrients P, Si) regulates KC of phytoplankton communities from the Australian coast during summer, when N-availability is often highly variable. KC consistently responded to N-amendment, exhibiting up to a threefold reduction and hence an apparent increase in the efficiency with which electrons were used to drive C-fixation. However, the process driving this consistent reduction was dependent upon initial conditions. When diatoms dominated assemblages and N was undetectable (e.g., post bloom), KC decreased predominantly via a physiological adjustment of the existing community to N-amendment. Conversely, for mixed assemblages, N-addition achieved a similar reduction in KC through a change in community structure toward diatom domination. We generate new understanding and parameterization of KC that is particularly critical to advance how FRRf can be applied to examine C-uptake throughout the global ocean where nitrogen availability is highly variable and thus frequently limits primary productivity.
- Published
- 2018
30. Influence of Spatial Variability of Shear Strength Parameters on 3D Slope Reliability and Comparison of Analysis Methods
- Author
-
Varkey, D., Hicks, M.A., and Vardon, P.J.
- Abstract
A 3D slope stability problem with spatially varying shear strength parameters has been analysed using the 3D random finite element method. This method links random fields of the random variables, in this case, cohesion and friction angle, with the finite element method within a Monte Carlo framework. The influence of spatial variability on calculated factors of safety and failure consequence has been investigated, and the results compared with a simpler 3D solution proposed by Vanmarcke. The simpler approach predicted a lower probability of failure under certain conditions, although, at high levels of anisotropy of the heterogeneity, the solutions converged. The reasons for the different solutions have been evaluated
- Published
- 2017
31. Influence of Spatial Variability of Shear Strength Parameters on 3D Slope Reliability and Comparison of Analysis Methods
- Author
-
Varkey, D. (author), Hicks, M.A. (author), Vardon, P.J. (author), Varkey, D. (author), Hicks, M.A. (author), and Vardon, P.J. (author)
- Abstract
A 3D slope stability problem with spatially varying shear strength parameters has been analysed using the 3D random finite element method. This method links random fields of the random variables, in this case, cohesion and friction angle, with the finite element method within a Monte Carlo framework. The influence of spatial variability on calculated factors of safety and failure consequence has been investigated, and the results compared with a simpler 3D solution proposed by Vanmarcke. The simpler approach predicted a lower probability of failure under certain conditions, although, at high levels of anisotropy of the heterogeneity, the solutions converged. The reasons for the different solutions have been evaluated, Geo-engineering
- Published
- 2017
32. Characterization and Vaccine Potential of Membrane Vesicles Produced by Francisella noatunensis subsp orientalis in an Adult Zebrafish Model
- Author
-
Lagos, L, Tandberg, JI, Repnik, U, Boysen, P, Ropstad, E, Varkey, D, Paulsen, IT, Winther-Larsen, HC, Lagos, L, Tandberg, JI, Repnik, U, Boysen, P, Ropstad, E, Varkey, D, Paulsen, IT, and Winther-Larsen, HC
- Published
- 2017
33. Effects of low temperature on tropical and temperate isolates of marine Synechococcus
- Author
-
Varkey, D, Mazard, S, Ostrowski, M, Tetu, SG, Haynes, P, Paulsen, IT, Varkey, D, Mazard, S, Ostrowski, M, Tetu, SG, Haynes, P, and Paulsen, IT
- Abstract
© 2016 International Society for Microbial Ecology All rights reserved. Temperature is an important factor influencing the distribution of marine picocyanobacteria. However, molecular responses contributing to temperature preferences are poorly understood in these important primary producers. We compared the temperature acclimation of a tropical Synechococcus strain WH8102 with temperate strain BL107 at 18 °C relative to 22 °C and examined their global protein expression, growth patterns, photosynthetic efficiency and lipid composition. Global protein expression profiles demonstrate the partitioning of the proteome into major categories: photosynthesis (>40%), translation (10-15%) and membrane transport (2-8%) with distinct differences between and within strains grown at different temperatures. At low temperature, growth and photosynthesis of strain WH8102 was significantly decreased, while BL107 was largely unaffected. There was an increased abundance of proteins involved in protein biosynthesis at 18 °C for BL107. Each strain showed distinct differences in lipid composition with higher unsaturation in strain BL107. We hypothesize that differences in membrane fluidity, abundance of protein biosynthesis machinery and the maintenance of photosynthesis efficiency contribute to the acclimation of strain BL107 to low temperature. Additional proteins unique to BL107 may also contribute to this strain's improved fitness at low temperature. Such adaptive capacities are likely important factors favoring growth of temperate strains over tropical strains in high latitude niches.
- Published
- 2016
34. Comparative Analysis of Membrane Vesicles from Three Piscirickettsia salmonis Isolates Reveals Differences in Vesicle Characteristics
- Author
-
Tandberg, JI, Lagos, LX, Langlete, P, Berger, E, Rishovd, A-L, Roos, N, Varkey, D, Paulsen, IT, Winther-Larsen, HC, Tandberg, JI, Lagos, LX, Langlete, P, Berger, E, Rishovd, A-L, Roos, N, Varkey, D, Paulsen, IT, and Winther-Larsen, HC
- Published
- 2016
35. Impact of DNA damaging agents on genome-wide transcriptional profiles in two marine Synechococcus species
- Author
-
Tetu, SG, Johnson, DA, Varkey, D, Phillippy, K, Stuart, RK, Dupont, CL, Hassan, KA, Palenik, B, Paulsen, IT, Tetu, SG, Johnson, DA, Varkey, D, Phillippy, K, Stuart, RK, Dupont, CL, Hassan, KA, Palenik, B, and Paulsen, IT
- Published
- 2013
36. Practice-Based Research Network Partnership with CDC to Acquire Clinical Specimens to Study the Etiology of Southern Tick-Associated Rash Illness (STARI)
- Author
-
Vaughn, M. F., primary, Sloane, P. D., additional, Knierim, K., additional, Varkey, D., additional, Pilgard, M. A., additional, and Johnson, B. J. B., additional
- Published
- 2010
- Full Text
- View/download PDF
37. Antimicrobial activity and in-silico analysis of 3, 5, 6-trichloro-2-pyridinol
- Author
-
Varkey, D. R., Danie Kingsley, and Abraham, J.
38. Association Of Emotional Intelligence With Pharmacy Students' Leadership And Academic Performance.
- Author
-
Shamsi A, Varisco T, De La Cruz A, El-Desoky R, Wanat M, Coyle E, and Varkey D
- Abstract
Objective: To examine the association between emotional intelligence, leadership involvement, and academic performance among student pharmacists., Methods: This was a retrospective, observational study that included all second-year student pharmacists in the 2022-23 and 2023-24 academic years. Emotional intelligence was assessed using the Emotional Quotient Inventory, version 2.0 (EQ-i 2.0), with results reported for 15 skills of EQ. Leadership involvement was collected from student organizations as the number of officer positions held by each student throughout the PharmD curriculum. Academic performance was reported as the cumulative grade point average (GPA). The primary endpoint was the mean EQ-i 2.0 skill results compared between students with <2 and ≥2 leadership positions. The secondary endpoint was mean EQ-i 2.0 skill results of students with GPA<3.5 and GPA≥3.5. Bivariate logistic regression was used to analyze each outcome., Results: All 214 second-year students in both cohorts completed the assessment. Students who held ≥2 leadership positions on average had a higher social responsibility score than students with <2 positions. Students with GPA≥3.5 had an assertiveness score lower than students with GPA<3.5., Conclusion: The results indicated that students with higher social responsibility as an EQ skill were reported to have increased leadership involvement. Students with lower assertiveness as an EQ skill were reported to have GPA≥3.5. These findings demonstrate the importance of emphasizing social responsibility in the pharmacy curriculum., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 American Association of Colleges of Pharmacy. Published by Elsevier Inc. All rights reserved.)
- Published
- 2024
- Full Text
- View/download PDF
39. The influence of bioturbator activity on sediment bacterial structure and function is moderated by environment.
- Author
-
Palmer J, Bugnot AB, Filippini G, Gribben PE, Varkey D, Erickson K, and Dafforn KA
- Subjects
- Australia, Ecosystem, Environmental Monitoring, Estuaries, Nitrogen analysis, Nitrogen Cycle, Biodiversity, Geologic Sediments microbiology, Geologic Sediments chemistry, Bacteria classification, Bacteria genetics
- Abstract
Bioturbation in coastal sediments plays a crucial role in biogeochemical cycling. However, a key knowledge gap is the extent to which bioturbation influences bacterial community diversity and ecosystem processes, such as nitrogen cycling. This study paired bacterial diversity, bioturbation activity and in situ flux measurements of oxygen and nitrogen from bioturbated sediments at six estuaries along the East coast of Australia. Bacterial community diversity, composition and predicted functional profiles were similar across burrow and surface sediments but were significantly influenced by bioturbator activity (measured as number of burrows) at sites with higher fine grain content. Sediment oxygen demand increased with bioturbator activity but changes in nitrogen cycling (as measured by fluxes and predicted bacterial functional gene analysis) were more spatially variable and were unrelated to bioturbator activity and bacterial community shifts. This study highlights how bioturbator activity influences bacterial community structure and functioning and what implications this has for biogeochemical cycles in estuarine sediments., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Ana Bugnot, Paul Gribben, Katherine Dafforn reports financial support was provided by Australian Research Council. Julia Palmer reports financial support was provided by Macquarie University. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)
- Published
- 2024
- Full Text
- View/download PDF
40. Substrate specificity and ecological significance of PstS homologs in phosphorus uptake in marine Synechococcus sp. WH8102.
- Author
-
Ranjit P, Varkey D, Shah BS, and Paulsen IT
- Subjects
- Phosphorus metabolism, Substrate Specificity, Ecosystem, Phosphates metabolism, Phosphate-Binding Proteins metabolism, Synechococcus
- Abstract
Phosphorus, a vital macronutrient, often limits primary productivity in marine environments. Marine Synechococcus strains, including WH8102, rely on high-affinity phosphate-binding proteins (PstS) to scavenge inorganic phosphate in oligotrophic oceans. However, WH8102 possesses three distinct PstS homologs whose substrate specificity and ecological roles are unclear. The three PstS homologs were heterologously expressed and purified to investigate their substrate specificity and binding kinetics. Our study revealed that all three PstS homologs exhibited a high degree of specificity for phosphate but differed in phosphate binding affinities. Notably, PstS1b displayed nearly 10-fold higher binding affinity ( K
D = 0.44 µM) compared to PstS1a ( KD = 3.3 μM) and PstS2 ( KD = 4.3 μM). Structural modeling suggested a single amino acid variation in the binding pocket of PstS1b (threonine instead of serine in PstS1a and PstS2) likely contributed to its higher Pi affinity. Genome context data, together with the protein biophysical data, suggest distinct ecological roles for the three PstS homologs. We propose that PstS1b may be involved in scavenging inorganic phosphorus in oligotrophic conditions and that PstS1a may be involved in transporting recycled phosphate derived from organic phosphate cleavage. The role of PstS2 is less clear, but it may be involved in phosphate uptake when environmental phosphate concentrations are transiently higher. The conservation of three distinct PstS homologs in Synechococcus clade III strains likely reflects distinct adaptations for P acquisition under varying oligotrophic conditions. IMPORTANCE Phosphorus is an essential macronutrient that plays a key role in marine primary productivity and biogeochemistry. However, intense competition for bioavailable phosphorus in the marine environment limits growth and productivity of ecologically important cyanobacteria. In oligotrophic oceans, marine Synechococcus strains, like WH8102, utilize high-affinity phosphate-binding proteins (PstS) to scavenge inorganic phosphate. However, WH8102 possesses three distinct PstS homologs, with unclear substrate specificity and ecological roles, creating a knowledge gap in understanding phosphorus acquisition mechanisms in picocyanobacteria. Through genomic, functional, biophysical, and structural analysis, our study unravels the ecological functions of these homologs. Our findings enhance our understanding of cyanobacterial nutritional uptake strategies and shed light on the crucial role of these conserved nutrient uptake systems in adaptation to specific niches, which ultimately underpins the success of marine Synechococcus across a diverse array of marine ecosystems., Competing Interests: The authors declare no conflict of interest.- Published
- 2024
- Full Text
- View/download PDF
41. Marine picocyanobacterial PhnD1 shows specificity for various phosphorus sources but likely represents a constitutive inorganic phosphate transporter.
- Author
-
Shah BS, Ford BA, Varkey D, Mikolajek H, Orr C, Mykhaylyk V, Owens RJ, and Paulsen IT
- Subjects
- Phosphorus metabolism, Phosphate Transport Proteins, Phosphates metabolism, Membrane Transport Proteins, Phosphites metabolism, Synechococcus metabolism, Organophosphonates
- Abstract
Despite being fundamental to multiple biological processes, phosphorus (P) availability in marine environments is often growth-limiting, with generally low surface concentrations. Picocyanobacteria strains encode a putative ABC-type phosphite/phosphate/phosphonate transporter, phnDCE, thought to provide access to an alternative phosphorus pool. This, however, is paradoxical given most picocyanobacterial strains lack known phosphite degradation or carbon-phosphate lyase pathway to utilise alternate phosphorus pools. To understand the function of the PhnDCE transport system and its ecological consequences, we characterised the PhnD1 binding proteins from four distinct marine Synechococcus isolates (CC9311, CC9605, MITS9220, and WH8102). We show the Synechococcus PhnD1 proteins selectively bind phosphorus compounds with a stronger affinity for phosphite than for phosphate or methyl phosphonate. However, based on our comprehensive ligand screening and growth experiments showing Synechococcus strains WH8102 and MITS9220 cannot utilise phosphite or methylphosphonate as a sole phosphorus source, we hypothesise that the picocyanobacterial PhnDCE transporter is a constitutively expressed, medium-affinity phosphate transporter, and the measured affinity of PhnD1 to phosphite or methyl phosphonate is fortuitous. Our MITS9220_PhnD1 structure explains the comparatively lower affinity of picocyanobacterial PhnD1 for phosphate, resulting from a more limited H-bond network. We propose two possible physiological roles for PhnD1. First, it could function in phospholipid recycling, working together with the predicted phospholipase, TesA, and alkaline phosphatase. Second, by having multiple transporters for P (PhnDCE and Pst), picocyanobacteria could balance the need for rapid transport during transient episodes of higher P availability in the environment, with the need for efficient P utilisation in typical phosphate-deplete conditions., (© 2023. The Author(s).)
- Published
- 2023
- Full Text
- View/download PDF
42. Evaluation of student emotional intelligence at various points in a pharmacy curriculum.
- Author
-
Biju A, Wanat MA, El-Desoky R, Vu C, and Varkey D
- Subjects
- Humans, Cross-Sectional Studies, Emotional Intelligence, Curriculum, Pharmacy, Students, Pharmacy psychology
- Abstract
Introduction: The purpose of this study is to evaluate emotional intelligence in doctor of pharmacy (PharmD) students at various points in the curriculum., Methods: This was a cross-sectional, single site, observational study that included first- through fourth-year PharmD students, conducted from December 2021 to April 2022. The study used the Emotional Quotient Inventory, version 2.0 (EQ-i 2.0) to obtain student emotional intelligence scores. A survey in Qualtrics
SM (SAP) was used to obtain baseline characteristics. The primary endpoint was the mean total EQ-i 2.0 scores comparing professional years. Secondary endpoints included mean EQ-i 2.0 scores in the composite scales of self-perception, self-expression, interpersonal, decision-making and stress-management. Change in EQ-i 2.0 scores was evaluated using descriptive statistics and analysis of variance. Multivariable regression analysis identified associations between baseline characteristics and EQ-i 2.0 scores., Results: A total of 137 (137/485, 28.2%) students completed the EQ-i 2.0 assessment. The mean (SD) total EQ-i 2.0 scores were 98.1 (15.5), 92.2 (15.9), 92.4 (12.9), and 103.5 (13.1), for first-, second- (P2), third- (P3), and fourth-year (P4) students, respectively. A statistically significant increase in total EQ-i 2.0 scores was noted in P4 students compared to P2 and P3 students. Work experience and leadership roles within student organizations may be associated with an increase in total EQ-i 2.0 scores., Conclusions: Emotional intelligence varied among students in different years of the pharmacy curriculum. P4 students were found to have the highest average emotional intelligence. The effect of curricular and co-curricular components on emotional intelligence development warrants further exploration., Competing Interests: Declaration of Competing Interest None., (Copyright © 2023 Elsevier Inc. All rights reserved.)- Published
- 2023
- Full Text
- View/download PDF
43. Identifying predictors of generalized anxiety among student pharmacists in response to the COVID-19 pandemic.
- Author
-
El-Desoky R, De La Cruz A, Thornton JD, Wanat MA, and Varkey D
- Subjects
- Humans, Pharmacists, Pandemics, Cross-Sectional Studies, Anxiety diagnosis, Anxiety epidemiology, Students psychology, COVID-19 epidemiology
- Abstract
Introduction: To explore the prevalence of generalized anxiety (GA) among doctor of pharmacy (PharmD) students at an academic institution during the COVID-19 pandemic and use Alderfer's existence, relatedness, and growth (ERG) theory to elucidate which unsatisfied needs are predictive of higher levels of GA symptoms., Methods: This was a cross-sectional, single-site survey administered to first- through fourth-year PharmD students from October 2020 to January 2021. The survey tool included demographic information, the validated Counseling Center Assessment of Psychological Symptoms-62 tool, and nine additional questions developed to assess Alderfer's ERG theory of needs. Predictors of GA symptoms were evaluated using descriptive statistics, multiple linear regression, correlation analysis, and multivariable analysis., Results: A total of 214 of 513 students completed the survey (42%) . Among students, 49.01% had no-clinical, 31.31% had low-clinical, and 19.63% had high-clinical GA symptoms. The relatedness needs, which included feeling disliked, socially disconnected, and misunderstood had the strongest correlation (65%) to GA symptoms and was most associated with GA symptoms (β = 0.56, P < .001). Students who did not exercise experienced more symptoms of GA (P = .008)., Conclusions: Over 50% of PharmD students met clinical cut-offs for GA symptoms and the relatedness need was most predictive of GA symptoms among students. Future student-centered interventions should aim to create opportunities that increase social connections, build resilience, and provide psychosocial support., (Copyright © 2023 Elsevier Inc. All rights reserved.)
- Published
- 2023
- Full Text
- View/download PDF
44. Widespread oxyregulation in tropical corals under hypoxia.
- Author
-
Hughes DJ, Alexander J, Cobbs G, Kühl M, Cooney C, Pernice M, Varkey D, Voolstra CR, and Suggett DJ
- Subjects
- Animals, Coral Reefs, Environmental Pollution, Hypoxia, Oxygen, Anthozoa physiology
- Abstract
Hypoxia (low oxygen stress) is increasingly reported on coral reefs, caused by ocean deoxygenation linked to coastal nutrient pollution and ocean warming. While the ability to regulate respiration is a key driver of hypoxia tolerance in many other aquatic taxa, corals' oxyregulatory capabilities remain virtually unexplored. Here, we examine O
2 -consumption patterns across 17 coral species under declining O2 partial pressure (pO2 ). All corals showed ability to oxyregulate, but total positive regulation (Tpos ) varied between species, ranging from 0.41 (Pocillopora damicornis) to 2.42 (P. acuta). On average, corals performed maximum regulation effort (Pcmax ) at low pO2 (30% air saturation, corresponding to lower O2 levels measured on natural reef systems), and exhibited detectable regulation down to as low as <10% air saturation. Our study shows that corals are not oxyconformers as previously thought, suggesting oxyregulation is likely important for survival in dynamic O2 environments of shallow coral reefs subjected to hypoxic events., (Copyright © 2022 Elsevier Ltd. All rights reserved.)- Published
- 2022
- Full Text
- View/download PDF
45. Functional characterisation of substrate-binding proteins to address nutrient uptake in marine picocyanobacteria.
- Author
-
Ford BA, Sullivan GJ, Moore L, Varkey D, Zhu H, Ostrowski M, Mabbutt BC, Paulsen IT, and Shah BS
- Subjects
- Carrier Proteins chemistry, Metals metabolism, Nitrogen metabolism, Phosphorus metabolism, Protein Conformation, Trace Elements metabolism, Carrier Proteins metabolism, Cyanobacteria metabolism, Nutrients metabolism, Seawater microbiology
- Abstract
Marine cyanobacteria are key primary producers, contributing significantly to the microbial food web and biogeochemical cycles by releasing and importing many essential nutrients cycled through the environment. A subgroup of these, the picocyanobacteria (Synechococcus and Prochlorococcus), have colonised almost all marine ecosystems, covering a range of distinct light and temperature conditions, and nutrient profiles. The intra-clade diversities displayed by this monophyletic branch of cyanobacteria is indicative of their success across a broad range of environments. Part of this diversity is due to nutrient acquisition mechanisms, such as the use of high-affinity ATP-binding cassette (ABC) transporters to competitively acquire nutrients, particularly in oligotrophic (nutrient scarce) marine environments. The specificity of nutrient uptake in ABC transporters is primarily determined by the peripheral substrate-binding protein (SBP), a receptor protein that mediates ligand recognition and initiates translocation into the cell. The recent availability of large numbers of sequenced picocyanobacterial genomes indicates both Synechococcus and Prochlorococcus apportion >50% of their transport capacity to ABC transport systems. However, the low degree of sequence homology among the SBP family limits the reliability of functional assignments using sequence annotation and prediction tools. This review highlights the use of known SBP structural representatives for the uptake of key nutrient classes by cyanobacteria to compare with predicted SBP functionalities within sequenced marine picocyanobacteria genomes. This review shows the broad range of conserved biochemical functions of picocyanobacteria and the range of novel and hypothetical ABC transport systems that require further functional characterisation., (© 2021 The Author(s).)
- Published
- 2021
- Full Text
- View/download PDF
46. Systemization of a pharmacy technician career ladder in a multi-hospital system.
- Author
-
Deyhim N, Bhakta SB, Varkey AC, Metzen DL, Varkey D, Martinez RJ, and Garey KW
- Abstract
Purpose: Hospital consolidation into larger, systemized health systems has enabled system-wide standardization of promotion processes, including pharmacy technician career ladders. However, whether system standardization affects the job satisfaction or outcomes of pharmacy technicians is unknown. The purpose of this project was to assess pharmacy technician perceptions and outcomes after systemization of a pharmacy technician career ladder., Methods: Pharmacy technician satisfaction scores and outcomes (promotion and turnover rates) were assessed in an eight-hospital health system before and after systemization of a pharmacy technician career ladder., Results: Two hundred and forty-nine pharmacy technicians were employed during the pre-intervention ( n = 104) and post-intervention ( n = 145) time periods. One hundred and twenty-three of 145 (84.83%) pharmacy technicians completed a job satisfaction survey after implementation of the system-wide technician career ladder. Overall satisfaction for the career ladder averaged 3.8 ± 0.61 or between neutral to positive satisfaction. There was no difference in total satisfaction regardless of teaching (3.8 ± 0.59) or community hospital (3.8 ± 0.63) location ( p = 0.53) or stratifying by Pharmacy Technician status. A total of 50 pharmacy technicians were hired during the study period, either during the pre-implementation ( n = 36) or post-implementation ( n = 14) time periods. Time to the first promotion averaged 1.73 ± 1.00 years in the pre-implementation period and 1.36 ± 0.55 years in the post-implementation period ( p = 0.20). Technician voluntary turnover was similar between the time periods., Conclusion: In conclusion, the standardization of a systems-level pharmacy technician promotion ladder from a single hospital to a systems-level was associated with positive job satisfaction and similar promotions and turnover rates as the historic, single hospital-based promotion ladder., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2021 The Authors.)
- Published
- 2021
- Full Text
- View/download PDF
47. Correction: Herring supports Northeast Pacific predators and fisheries: Insights from ecosystem modelling and management strategy evaluation.
- Author
-
Surma S, Pitcher TJ, Kumar R, Varkey D, Pakhomov EA, and Lam ME
- Abstract
[This corrects the article DOI: 10.1371/journal.pone.0196307.].
- Published
- 2020
- Full Text
- View/download PDF
48. Program development of a preceptor bootcamp for operational pharmacy preceptors.
- Author
-
Smith DV, Gautreaux S, Gulbis AM, Bruno JJ, Garey K, Roux RK, and Varkey D
- Subjects
- Academic Medical Centers, Curriculum, Humans, Pharmaceutical Services organization & administration, Pilot Projects, Program Evaluation, Surveys and Questionnaires, Pharmacists organization & administration, Pharmacy Residencies organization & administration, Preceptorship standards, Program Development methods
- Abstract
Purpose: To describe the development, design, and implementation of a pilot preceptor development bootcamp and feedback related to its feasibility and impact on operational pharmacy preceptors., Summary: The University of Texas MD Anderson Cancer Center designed and implemented a pilot preceptor development bootcamp for operational staff pharmacists serving as residency preceptors for longitudinal weekend staffing experiences. A systematic, multipronged approach was taken to identify preceptor development gaps and design a full-day bootcamp curriculum. The resultant curriculum was comprised of content in major functional areas including using the 4 preceptor roles, documenting performance, giving and receiving feedback, and dealing with difficult situations or learners. The impact of the pilot preceptor development bootcamp was assessed using survey methodology and qualitative feedback from debrief discussions., Conclusion: Implementation of a pilot preceptor bootcamp program addressing major areas of precepting skill was well received, resulted in positive feedback from operational pharmacy preceptors, and was feasible to implement at a large academic medical center., (© American Society of Health-System Pharmacists 2020. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2020
- Full Text
- View/download PDF
49. Sediment bacterial communities associated with environmental factors in Intermittently Closed and Open Lakes and Lagoons (ICOLLs).
- Author
-
Filippini G, Bugnot AB, Johnston EL, Ruszczyk J, Potts J, Scanes P, Ferguson A, Ostrowski M, Varkey D, and Dafforn KA
- Subjects
- Cities, Environmental Monitoring, New South Wales, RNA, Bacterial analysis, RNA, Ribosomal, 16S analysis, Sequence Analysis, RNA, Bacteria classification, Geologic Sediments microbiology, Lakes microbiology, Microbiota
- Abstract
Intermittently Closed and Open Lakes and Lagoons (ICOLLS) are important coastal systems that are periodically separated from the ocean by a sand barrier or a berm. In urban ICOLLs, continuous inputs of organic material and nutrients into coastal lagoons are contributing to eutrophic conditions that, together with natural environmental factors have implications for the resident sediment bacterial communities. We used molecular tools to investigate the ecological communities of four ICOLLs; Narrabeen, Dee Why, Curl Curl and Manly in Sydney, Australia, which have been subjected to increasing pressure from anthropogenic activities over the last century. We used targeted gene sequencing of the prokaryotic 16S ribosomal RNA gene to describe the bacterial diversity and community structure and discuss differences with respect to environmental factors at the ICOLL scale (e.g. size, shape, normalised N loading) and site scale (e.g. water and sediment quality) within each lagoon. Due to differences in hydrological patterns, we expected that sediment bacterial communities would be more heterogenous in displacement-dominated lagoons (Curl Curl and Manly) than the mixing-dominated lagoons (Narrabeen and Dee Why). Interestingly, we did not find strong relationships between the main bacterial groups and distance from the lagoon entrance (used as a proxy for salinity and silt) in the displacement-dominated lagoons. Moreover, we found that α diversity was highest in Narrabeen and Manly lagoons despite differences in lagoon size and shape. Furthermore, while bacterial community structure was similar in Curl Curl and Dee Why, communities in Manly and Narrabeen differed along temperature/TOC and salinity/silt gradients respectively. In Manly lagoon, we found relatively more anaerobic bacteria such as Epsilonbactereota which is involved in the oxidation and reduction of sulfur compounds. Moreover, we identified several bacterial taxa (including sulfur metabolising Chlorobiaceae) related to increasing TOC that could be investigated further as potential indicators of excess enrichment., (Copyright © 2019 Elsevier B.V. All rights reserved.)
- Published
- 2019
- Full Text
- View/download PDF
50. A systematic approach to optimize electronic health record medication alerts in a health system.
- Author
-
Bhakta SB, Colavecchia AC, Haines L, Varkey D, and Garey KW
- Subjects
- Drug Interactions, Health Plan Implementation, Humans, Interrupted Time Series Analysis, Pharmacists organization & administration, Program Evaluation, Decision Support Systems, Clinical organization & administration, Electronic Health Records organization & administration, Medical Order Entry Systems organization & administration, Medication Errors prevention & control
- Abstract
Purpose: The effectiveness of a systematic, streamlined approach to optimize drug-drug interaction alerts in an electronic health record for a health system was studied., Methods: An 81-week quasi-experimental study was conducted to evaluate interventions made to medication-related clinical decision-support (CDS) alerts. Medication-related CDS alerts were systematically reduced using a multi disciplinary healthcare committee. The primary endpoint was weekly overall, modification, and acknowledgement rates of medication alerts after drug-drug interaction reclassification. Secondary endpoints included sub analysis of types of medication alerts (drug-drug interaction and duplicate therapy alerts) and alert use by providers (pharmacist and prescribers). Data was analyzed using interrupted time series regression analysis., Results: After implementation of the new alert system, total number of weekly inpatient alerts decreased from 68,900 (66,300-70,900) and 50,300 (48,600-53,600) in the postintervention period (p < 0.001). The perentage of alerts acknowledged weekly increased from 11.8% (IQR, 11.4-12.1%) in the preintervention period to 13.7% (IQR, 13.3-14.0%) in the postintervention period (p < 0.001). The percentage of alerts that were modified also increased from 5.0% (IQR, 4.9-5.3%) in the preintervention period to 7.3% (IQR, 7.0-7.6%) in the postintervention period (p < 0.001). Both increases were primarily seen with pharmacists versus other healthcare professionals (p < 0.001)., Conclusion: A committee-led systematic approach to optimizing drug-drug interactions facilitated a significant decrease in the overall number of alerts and an increase in both medication alert acknowledgement and modification rates., (© American Society of Health-System Pharmacists 2019. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2019
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.