Faculty Publications (BioMed Central & Faculty of Science)
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Articles from BioMed Central by University of Victoria, Faculty of Science authors. Also other journal articles by UVic Faculty of Science authors.
Click on this link to see Work published with BioMed Central, Chemistry Central and SpringerOpen by researchers at University of Victoria.
Click on this link to see Work published with BioMed Central, Chemistry Central and SpringerOpen by researchers at University of Victoria.
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Item The pseudoarc is a co-existentially closed continuum(Topology and Its Applications, 2016) Eagle, Christopher J.; Goldbring, Isaac; Vignati, AlessandroAnswering a question of P. Bankston, we show that the pseudoarc is a co-existentially closed continuum. We also show thatC (X), for X a nondegenerate continuum, can never have quantifier elimination, answering a question of the first and third named authors and Farah and Kirchberg.Item Molecular basis for differential activation of p101 and p84 complexes of PI3Kγ by Ras and GPCRs(Cell Reports, 2023) Rathinaswamy, Manoj K.; Jenkins, Meredith L.; Duewell, Benjamin R.; Zhang, Xuxiao; Harris, Noah J.; Evans, John T.; Stariha, Jordan T. B.; Dalwadi, Udit; Fleming, Kaelin D.; Ranga-Prasad, Harish; Yip, Calvin K.; Williams, Roger L.; Hansen, Scott D.; Burke, JohnClass IB phosphoinositide 3-kinase (PI3Kγ) is activated in immune cells and can form two distinct complexes (p110γ-p84 and p110γ-p101), which are differentially activated by G protein-coupled receptors (GPCRs) and Ras. Using a combination of X-ray crystallography, hydrogen deuterium exchange mass spectrometry (HDX-MS), electron microscopy, molecular modeling, single-molecule imaging, and activity assays, we identify molecular differences between p110γ-p84 and p110γ-p101 that explain their differential membrane recruitment and activation by Ras and GPCRs. The p110γ-p84 complex is dynamic compared with p110γ-p101. While p110γ-p101 is robustly recruited by Gβγ subunits, p110γ-p84 is weakly recruited to membranes by Gβγ subunits alone and requires recruitment by Ras to allow for Gβγ activation. We mapped two distinct Gβγ interfaces on p101 and the p110γ helical domain, with differences in the C-terminal domain of p84 and p101 conferring sensitivity of p110γ-p101 to Gβγ activation. Overall, our work provides key insight into the molecular basis for how PI3Kγ complexes are activated.Item Bycatch-threatened seabirds disproportionally contribute to community trait composition across the world(Global Ecology and Conservation, 2024) Richards, Cerren; Cooke, Rob; Bowler, Diana E.; Boerder, Kristina; Bates, AmandaHuman pressures in the ocean are restructuring biological communities, driving non-random extinctions, and disrupting marine ecosystem functioning. In particular, fisheries bycatch, the incidental mortality of non-target species, is a major threat to seabirds worldwide. Direct bycatch data are often scarce. Instead, leveraging trait-based analyses with fine-scale fisheries data could answer fundamental questions about spatial patterns of bycatch-threatened species and facilitate targeted conservation strategies. Here, we combine a dataset of species' traits and distribution ranges for 361 seabird and sea duck species with spatially resolved fishing effort data for gillnet, longline, trawl, and purse seine gears. First, we quantify geographic patterns of seabird community traits. Second, we describe how community traits could shift under local extinction scenarios in areas where bycatch-threatened seabirds spatially overlap with fishing activities. These objectives allow us to highlight the collective contribution of species currently threatened from bycatch to ecosystem functioning. We reveal distinct spatial variation in the community weighted mean of five seabird traits (body mass, generation length, clutch size, diet guild, and foraging guild) are evident. Moreover, our results show that fisheries bycatch is selectively removing a distinct suite of traits from the community within particular oceanic regions. Specifically, fisheries bycatch is threatening species with larger body masses, slower reproductive speeds (smaller clutch sizes and longer generation lengths), and specialised diet and foraging guilds. The spatial non-uniformity of the community trait shifts suggests that within specific marine regions, communities have limited redundancy and therefore may have less insurance to buffer against declines in ecosystem functioning. Our extinction scenario warns that seabirds currently threatened from fisheries bycatch substantially contribute to community functional composition. Management actions that incorporate species’ traits and fine-scale fisheries datasets as tools for marine spatial planning will add an important dimension when evaluating the success of conservation initiatives.Item Seasonal and regional variability of model-based zooplankton biomass in the Salish Sea and evaluation against observations(Progress in Oceanography, 2023) Suchy, Karyn D.; Olson, Elise; Allen, Susan E.; Galbraith, Moira; Herrman, BethElLee; Keister, Julie E.; Perry, R. Ian; Sastri, Akash R.; Young, KellyWe used a three-dimensional coupled biophysical model to examine zooplankton dynamics in the Salish Sea, NE Pacific. First, we evaluated the two zooplankton classes of the SalishSeaCast model using a transboundary zooplankton dataset comprised of observation data from the Canadian and United States waters of the Salish Sea from 2015 to 2019. Model zooplankton classes correspond to micro- and meso-zooplankton whose biomass is tightly coupled to phytoplankton through modelled food web dynamics (Z1) and mesozooplankton with life cycle-based seasonal grazing impacts (Z2). Overall, the model effectively captured seasonal patterns in observed biomass, although with slightly higher biomass estimates for both Z1 and Z2 (Bias = 0.10 and 0.08 g C m−2, respectively). Model fit varied regionally, with a weaker model fit being observed in nearshore regions. In addition, an autumn peak in Z2 was observed in the model, but not in the observations, suggesting some seasonal variations in model fit. Following the model evaluation, we used the model to determine seasonal and regional patterns of zooplankton grazing. Seasonally, the main peak in modelled zooplankton biomass increased in April or May in most of the regions defined within the Salish Sea and was driven by grazing on diatoms. Regionally, depth-integrated zooplankton biomass was consistently highest in areas adjacent to regions of strong tidal mixing. In addition, model-based zooplankton grazing was highest in the tidally mixed regions where phytoplankton biomass was high due to advection into the region despite low primary productivity. Our model-based results provide an opportunity to examine bottom-up food web processes at spatio-temporal scales not achievable with in situ sampling and help to elucidate key drivers of lower trophic level dynamics within the Salish Sea.Item Assessing the effect of aquatic noise on fish behavior and physiology: a meta-analysis approach(Proceedings of Meetings on Acoustics, 2016) Cox, Kieran D.; Brennan, Lawrence P.; Dudas, Sarah E.; Juanes, FrancisDue to the extreme distance that sounds can travel through water, many marine species rely on the soundscape for auditory information regarding predator or prey locations, communication, and habitat selection. These species not only take advantage of the prevailing sounds but also contribute to the soundscape through their own vocalizations. Certain sounds have been shown to have negative effects on marine species, resulting in disrupted communication and unbalanced predator-prey interactions. Unfortunately, the vast majority of soundscape studies are biased towards marine mammals, and only recently has attention been directed towards the potential repercussions for fishes. In an attempt to determine the implications that changes to the soundscape may have on the fishes, a meta-analysis was conducted focusing primarily on the role that anthropogenic noises may play in altering fish behavior and physiology. The review identified 3,174 potentially relevant papers of which were 27 used. The analysis indicates that anthropogenic noise has an adverse effect on marine and freshwater fish behavior and physiology. These findings suggest that although certain species may be more susceptible to anthropogenic noise than others, the vast majority of fish have the potential to be negatively affected by noise pollution.Item Assessing the performance of group-based trajectory modeling method to discover different patterns of medication adherence(Pharmaceutical Statistics, 2024) Diop, Awa; Gupta, Alind; Mueller, Sabrina; Dron, Louis; Harari, Ofir; Berringer, Heather; Kalatharan, Vinusha; Park, Jay J.H.; MESIDOR, Miceline; Talbot, DenisIt is well known that medication adherence is critical to patient outcomes and can decrease patient mortality. The Pharmacy Quality Alliance (PQA) has recognized and identified medication adherence as an important indicator of medication-use quality. Hence, there is a need to use the right methods to assess medication adherence. The PQA has endorsed the proportion of days covered (PDC) as the primary method of measuring adherence. Although easy to calculate, the PDC has however several drawbacks as a method of measuring adherence. PDC is a deterministic approach that cannot capture the complexity of a dynamic phenomenon. Group-based trajectory modeling (GBTM) is increasingly proposed as an alternative to capture heterogeneity in medication adherence. The main goal of this paper is to demonstrate, through a simulation study, the ability of GBTM to capture treatment adherence when compared to its deterministic PDC analogue and to the nonparametric longitudinal K-means. A time-varying treatment was generated as a quadratic function of time, baseline, and time-varying covariates. Three trajectory models are considered combining a cat's cradle effect, and a rainbow effect. The performance of GBTM was compared to the PDC and longitudinal K-means using the absolute bias, the variance, the c-statistics, the relative bias, and the relative variance. For all explored scenarios, we find that GBTM performed better in capturing different patterns of medication adherence with lower relative bias and variance even under model misspecification than PDC and longitudinal K-means.Item Molecular basis for the recruitment of the Rab effector protein WDR44 by the GTPase Rab11(Journal of Biochemistry, 2023) Thibodeau, Matthew; Harris, Noah; Jenkins, Meredith; Parson, Matthew; Evans, John T.; Scott, Mackenzie K.; Shaw, Alexandria; Pokorný, Daniel; Leonard, Thomas; Burke, JohnThe formation of complexes between Rab11 and its effectors regulates multiple aspects of membrane trafficking, including recycling and ciliogenesis. WD repeat-containing protein 44 (WDR44) is a structurally uncharacterized Rab11 effector that regulates ciliogenesis by competing with prociliogenesis factors for Rab11 binding. Here, we present a detailed biochemical and biophysical characterization of the WDR44-Rab11 complex and define specific residues mediating binding. Using AlphaFold2 modeling and hydrogen/deuterium exchange mass spectrometry, we generated a molecular model of the Rab11-WDR44 complex. The Rab11-binding domain of WDR44 interacts with switch I, switch II, and the interswitch region of Rab11. Extensive mutagenesis of evolutionarily conserved residues in WDR44 at the interface identified numerous complex-disrupting mutations. Using hydrogen/deuterium exchange mass spectrometry, we found that the dynamics of the WDR44-Rab11 interface are distinct from the Rab11 effector FIP3, with WDR44 forming a more extensive interface with the switch II helix of Rab11 compared with FIP3. The WDR44 interaction was specific to Rab11 over evolutionarily similar Rabs, with mutations defining the molecular basis of Rab11 specificity. Finally, WDR44 can be phosphorylated by Sgk3, with this leading to reorganization of the Rab11-binding surface on WDR44. Overall, our results provide molecular detail on how WDR44 interacts with Rab11 and how Rab11 can form distinct effector complexes that regulate membrane trafficking events.Item Toxoplasma gondii mitochondrial association factor 1b interactome reveals novel binding partners including Ral GTPase accelerating protein α1(Journal of Biological Chemistry, 2024) Powell, Cameron; Jenkins, Meredith; Hill, Tara B.; Blank, Matthew L.; Cabo, Leah; Thompson, Lexie; Burke, John; Boyle, Jon P.; Boulanger, Martin J.The intracellular parasite, Toxoplasma gondii, has developed sophisticated molecular strategies to subvert host processes and promote growth and survival. During infection, T. gondii replicates in a parasitophorous vacuole (PV) and modulates host functions through a network of secreted proteins. Of these, Mitochondrial Association Factor 1b (MAF1b) recruits host mitochondria to the PV, a process that confers an in vivo growth advantage, though the precise mechanisms remain enigmatic. To address this knowledge gap, we mapped the MAF1b interactome in human fibroblasts using a commercial Yeast-2-hybrid (Y2H) screen, which revealed several previously unidentified binding partners including the GAP domain of Ral GTPase Accelerating Protein α1 (RalGAPα1(GAP)). Recombinantly produced MAF1b and RalGAPα1(GAP) formed as a stable binary complex as shown by size exclusion chromatography with a Kd of 334 nM as measured by isothermal titration calorimetry (ITC). Notably, no binding was detected between RalGAPα1(GAP) and the structurally conserved MAF1b homolog, MAF1a, which does not recruit host mitochondria. Next, we used hydrogen deuterium exchange mass spectrometry (HDX-MS) to map the RalGAPα1(GAP)-MAF1b interface, which led to identification of the “GAP-binding loop” on MAF1b that was confirmed by mutagenesis and ITC to be necessary for complex formation. A high-confidence Alphafold model predicts the GAP-binding loop to lie at the RalGAPα1(GAP)-MAF1b interface further supporting the HDX-MS data. Mechanistic implications of a RalGAPα1(GAP)-MAF1b complex are discussed in the context of T. gondii infection and indicates that MAF1b may have evolved multiple independent functions to increase T. gondii fitness.Item Toward increased reliability, transparency, and accessibility in cross-linking mass spectrometry(Structure, 2020) Leitner, Alexander; Bonvin, Alexandre M. J. J.; Borchers, Christoph H.; Chalkley, Robert J.; Chamot-Rooke, Julia; Combe, Colin W.; Cox, Jürgen; Dong, Meng-Qiu; Fischer, Lutz; Götze, Michael; Gozzo, Fabio C.; Heck, Albert J. R.; Hoopmann, Michael R.; Huang, Lan; Ishihama, Yasushi; Jones, Andrew R.; Kalisman, Nir; Kohlbacher, Oliver; Mechtler, Karl; Moritz, Robert L.; Netz, Eugen; Novak, Petr; Petrotchenko, Evgeniy; Sali, Andrej; Scheltema, Richard A.; Schmidt, Carla; Schriemer, David; Sinz, Andrea; Sobott, Frank; Stengel, Florian; Thalassinos, Konstantinos; Urlaub, Henning; Viner, Rosa; Vizcaíno, Juan A.; Wilkins, Marc R.; Rappsilber, JuriCross-linking mass spectrometry (MS) has substantially matured as a method over the past 2 decades through parallel development in multiple labs, demonstrating its applicability to protein structure determination, conformation analysis, and mapping protein interactions in complex mixtures. Cross-linking MS has become a much-appreciated and routinely applied tool, especially in structural biology. Therefore, it is timely that the community commits to the development of methodological and reporting standards. This white paper builds on an open process comprising a number of events at community conferences since 2015 and identifies aspects of Cross-linking MS for which guidelines should be developed as part of a Cross-linking MS standards initiative.Item The potential of video imagery from worldwide cabled observatory networks to provide information supporting fish-stock and biodiversity assessment(ICES Journal of Marine Science, 2020) Aguzzi, Jacopo; CHATZIEVANGELOU, DAMIANOS; Company, J. B.; Thomsen, L.; Marini, S.; Bonofiglio, F.; Juanes, F.; Rountree, Rodney; Berry, A.; Chumbinho, Rogerio; Lordan, Colm; Doyle, J.; del Rio, J.; Navarro, J.; De Leo, F. C.; Bahamon, N.; Garcia, J. A.; Danovaro, P. R.; Francescangeli, M.; Lopez-Vazquez, V.; Gaughan, P.Seafloor multiparametric fibre-optic-cabled video observatories are emerging tools for standardized monitoring programmes, dedicated to the production of real-time fishery-independent stock assessment data. Here, we propose that a network of cabled cameras can be set up and optimized to ensure representative long-term monitoring of target commercial species and their surrounding habitats. We highlight the importance of adding the spatial dimension to fixed-point-cabled monitoring networks, and the need for close integration with Artificial Intelligence pipelines, that are necessary for fast and reliable biological data processing. We then describe two pilot studies, exemplary of using video imagery and environmental monitoring to derive robust data as a foundation for future ecosystem-based fish-stock and biodiversity management. The first example is from the NE Pacific Ocean where the deep-water sablefish (Anoplopoma fimbria) has been monitored since 2010 by the NEPTUNE cabled observatory operated by Ocean Networks Canada. The second example is from the NE Atlantic Ocean where the Norway lobster (Nephrops norvegicus) is being monitored using the SmartBay observatory developed for the European Multidisciplinary Seafloor and water column Observatories. Drawing from these two examples, we provide insights into the technological challenges and future steps required to develop full-scale fishery-independent stock assessments.Item A cleavable crosslinking strategy for commodity polymer functionalization and generation of reprocessable thermosets(Angewandte Chemie, 2023) Bi, Liting; Godwin, Benjamin; Baran, Miranda; Nazir, Rashid; Wulff, JeremyCovalently crosslinked polymeric materials, known as thermosets, possess enhanced mechanical strength and thermal stability relative to the corresponding uncrosslinked thermoplastics. However, the presence of covalent inter-chain crosslinks that makes thermosets so attractive is precisely what makes them so difficult to reprocess and recycle. Here, we demonstrate the introduction of chemically cleavable groups into a bis-diazirine crosslinker. Application of this cleavable crosslinker reagent to commercial low-functionality polyolefins (or to a small-molecule model) results in the rapid, efficient introduction of molecular crosslinks that can be uncoupled by specific chemical inputs. These proof-of-concept findings provide one potential strategy for circularization of the thermoplastic/thermoset plastics economy, and may allow crosslinked polyolefins to be manufactured, used, reprocessed, and re-used without losing value. As an added benefit, the method allows the ready introduction of functionality into non-functionalized commodity polymers.Item CVX based algorithms for constructing various optimal regression designs(Canadian Journal of Statistics, 2019) Wong, Weng Kee; Zhou, JulieCVX-based numerical algorithms are widely and freely available for solving convex optimization problems but their applications to solve optimal design problems are limited. Using the CVX programs in MATLAB, we demonstrate their utility and flexibility over traditional algorithms in statistics for finding different types of optimal approximate designs under a convex criterion for nonlinear models. They are generally fast and easy to implement for any model and any convex optimality criterion. We derive theoretical properties of the algorithms and use them to generate new A-, c-, D- and E-optimal designs for various nonlinear models, including multi-stage and multi-objective optimal designs. We report properties of the optimal designs and provide sample CVX program codes for some of our examples that users can amend to find tailored optimal designs for their problems. The Canadian Journal of Statistics 47: 374–391; 2019 © 2019 Statistical Society of CanadaItem Complex 3-D surface deformation in the 1971 San Fernando, California earthquake reveals static and dynamic controls on off-fault deformation(Journal of Geophysical Research: Solid Earth, 2023) Gaudreau, É.; Hollingsworth, J.; Nissen, E.; Funning, G. J.The shallow 1971 MW 6.6 San Fernando, California earthquake involved a complex rupture process on an immature thrust fault with a non-planar geometry, and is notable for having a higher component of left-lateral surface slip than expected from seismic source models. We extract its 3-D coseismic surface displacement field from aerial stereo photographs and document the amount and width of the vertical and fault trace-parallel components of distributed deformation along strike. The results confirm the significant left-lateral surface offsets, suggesting a slip vector rotation at shallow depths. Comparing our offsets against field measurements of fault slip, we observe that most of the offset was accommodated in the damage zone, with off-fault deformation averaging 69% in both the fault trace-parallel and vertical components. However, the magnitude and width of off-fault deformation behave differently between the vertical and fault trace-parallel components, which, along with the rotation in rake near the surface, can be explained by dynamic rupture effects.Item Identification of fish sounds in the wild using a set of portable audio-video arrays(Methods in Ecology and Evolution, 2023) Mouy, Xavier; Black, Morgan J.; Cox, Kieran D.; Qualley, Jessica; Dosso, Stan; Juanes, Francis1. Associating fish sounds to specific species and behaviours is important for making passive acoustics a viable tool for monitoring fish. While recording fish sounds in tanks can sometimes be performed, many fish do not produce sounds in captivity. Consequently, there is a need to identify fish sounds in situ and characterise these sounds under a wide variety of behaviours and habitats. 2. We designed three portable audio-video platforms capable of identifying species-specific fish sounds in the wild: a large array, a mini array and a mobile array. The large and mini arrays are static autonomous platforms than can be deployed on the seafloor and record audio and video for one to two weeks. They use multichannel acoustic recorders and low-cost video cameras mounted on PVC frames. The mobile array also uses a multichannel acoustic recorder, but mounted on a remotely operated vehicle with built-in video, which allows remote control and real-time positioning in response to observed fish presence. For all arrays, fish sounds were localised in three dimensions and matched to the fish positions in the video data. We deployed these three platforms at four locations off British Columbia, Canada. 3. The large array provided the best localisation accuracy and, with its larger footprint, was well suited to habitats with a flat seafloor. The mini and mobile arrays had lower localisation accuracy but were easier to deploy, and well suited to rough/uneven seafloors. Using these arrays, we identified, for the first time, sounds from quillback rockfish Sebastes maliger, copper rockfish Sebastes caurinus and lingcod Ophiodon elongatus. In addition to measuring temporal and spectral characteristics of sounds for each species, we estimated mean source levels for lingcod and quillback rockfish sounds (115.4 and 113.5 dB re 1 μPa, respectively) and maximum detection ranges at two sites (between 10.5 and 33 m). 4. All proposed array designs successfully identified fish sounds in the wild and were adapted to various budget, logistical and habitat constraints. We include here building instructions and processing scripts to help users replicate this methodology, identify more fish sounds around the world and make passive acoustics a more viable way to monitor fish.Item Cataloging fish sounds in the wild using combined acoustic and video recordings(The Journal of the Acoustical Society of America, 2018) Mouy, Xavier; Rountree, Rodney; Juanes, Francis; Dosso, Stan E.Although many fish are soniferous, few of their sounds have been identified, making passive acoustic monitoring (PAM) ineffective. To start addressing this issue, a portable 6-hydrophone array combined with a video camera was assembled to catalog fish sounds in the wild. Sounds are detected automatically in the acoustic recordings and localized in three dimensions using time-difference of arrivals and linearized inversion. Localizations are then combined with the video to identify the species producing the sounds. Uncertainty analyses show that fish are localized near the array with uncertainties < 50 cm. The proposed system was deployed off Cape Cod, MA and used to identify sounds produced by tautog (Tautoga onitis), demonstrating that the methodology can be used to build up a catalog of fish sounds that could be used for PAM and fisheries management.Item Polyphosphinoborane block copolymer synthesis using catalytic reversible chain-transfer dehydropolymerization(Angewandte Chemie International Edition, 2023) Race, James J.; Heyam, Alex; Wiebe, Matthew A.; Hernandez, J. Diego-Garcia; Ellis, Charlotte E.; Lei, Shixing; Manners, Ian; Weller, Andrew S.An amphiphilic block copolymer of polyphosphinoborane has been prepared by a mechanism-led strategy of the sequential catalytic dehydropolymerization of precursor monomers, H₃B ⋅ PRH₂ (R=Ph, n-hexyl), using the simple pre-catalyst [Rh(Ph₂PCH₂CH₂PPh₂)₂]Cl. Speciation, mechanism and polymer chain growth studies support a step-growth process where reversible chain transfer occurs, i.e. H₃B ⋅ PRH₂/oligomer/polymer can all coordinate with, and be activated by, the catalyst. Block copolymer [H₂BPPhH]₁₁₀-𝑏-[H₂BP(n-hexyl)H]₁₁ can be synthesized and self-assembles in solution to form either rod-like micelles or vesicles depending on solvent polarity.Item New numerical results on existence of Volterra-Fredholm integral equation of nonlinear boundary integro-differential type(Symmetry, 2023) HamaRashid, Hawsar; Srivastava, Hari Mohan; Hama, Mudhafar; Mohammed, Pshtiwan Othman; Al-Sarairah, Eman; Almusawa, Musawa YahyaSymmetry is presented in many works involving differential and integral equations. Whenever a human is involved in the design of an integral equation, they naturally tend to opt for symmetric features. The most common examples are the Green functions and linguistic kernels that are often designed symmetrically and regularly distributed over the universe of discourse. In the current study, the authors report a study on boundary value problem (BVP) for a nonlinear integro Volterra–Fredholm integral equation with variable coefficients and show the existence of solution by applying some fixed-point theorems. The authors employ various numerical common approaches as the homotopy analysis methodology established by Liao and the modified Adomain decomposition technique to produce a numerical approximate solution, then graphical depiction reveals that both methods are most effective and convenient. In this regard, the authors address the requirements that ensure the existence and uniqueness of the solution for various variations of nonlinearity power. The authors also show numerical examples of how to apply our primary theorems and test the convergence and validity of our suggested approach.Item A direct immunoassay based on surface-enhanced spectroscopy using AuNP/PS-b-P2VP nanocomposites(Sensors, 2023) Vieira, Moyra F.; de Carvalho Bovolato, Ana Livia; da Fonseca, Bruno G.; M. S. Izumi, Celly; Brolo, Alexandre G.A biosensor was developed for directly detecting human immunoglobulin G (IgG) and adenosine triphosphate (ATP) based on stable and reproducible gold nanoparticles/polystyrene-b-poly(2-vinylpyridine) (AuNP/PS-b-P2VP) nanocomposites. The substrates were functionalized with carboxylic acid groups for the covalent binding of anti-IgG and anti-ATP and the detection of IgG and ATP (1 to 150 μg/mL). SEM images of the nanocomposite show 17 ± 2 nm AuNP clusters adsorbed over a continuous porous PS-b-P2VP thin film. UV–VIS and SERS were used to characterize each step of the substrate functionalization and the specific interaction between anti-IgG and the targeted IgG analyte. The UV–VIS results show a redshift of the LSPR band as the AuNP surface was functionalized and SERS measurements showed consistent changes in the spectral features. Principal component analysis (PCA) was used to discriminate between samples before and after the affinity tests. Moreover, the designed biosensor proved to be sensitive to different concentrations of IgG with a limit-of-detection (LOD) down to 1 μg/mL. Moreover, the selectivity to IgG was confirmed using standard solutions of IgM as a control. Finally, ATP direct immunoassay (LOD = 1 μg/mL) has demonstrated that this nanocomposite platform can be used to detect different types of biomolecules after proper functionalization.Item Starlikeness associated with the Van der Pol numbers(Mathematics, 2023) Raza, Mohsan; Srivastava, Hari Mohan; Xin, Qin; Tchier, Fairouz; Nawaz Malik, Sarfraz; Arif, MuhammadIn this paper, we define a subclass of starlike functions associated with the Van der Pol numbers. For this class, we derive structural formula, radius of starlikeness of order a, strong starlikeness, and some inclusion results. We also study radii problems for various classes of analytic functions. Furthermore, we investigate some coefficient-related problems which include the sharp initial coefficient bounds and sharp bounds on Hankel determinants of order two and three.Item In vivo HIV dynamics, modeling the interaction of HIV and immune system via non-linear derivatives(Fractal and Fractional, 2023) Jan, Asif; Srivastava, Hari Mohan; Khan, Amin; Mohammed, Pshtiwan Othman; Jan, Rashid; Hamed, Y. S.The economic burden of HIV extends beyond the individual level and affects communities and countries. HIV can lead to decreased economic growth due to lost productivity and increased healthcare costs. In some countries, the HIV epidemic has led to a reduction in life expectancy, which can impact the overall quality of life and economic prosperity. Therefore, it is significant to investigate the intricate dynamics of this viral infection to know how the virus interacts with the immune system. In the current research, we will formulate the dynamics of HIV infection in the host body to conceptualize the interaction of T-cells and the immune system. The recommended model of HIV infection is presented with the help of fractional calculus for more precious outcomes. We introduce numerical methods to demonstrate how the input parameters affect the output of the system. The dynamical behavior and chaotic nature of the system are visualized with the variation of different input factors. The system’s tracking path has been numerically depicted and the impact of the viruses on T-cells has been demonstrated. In addition to this, the key factors of the system has been predicted through numerical findings. Our results predict that the strong non-linearity of the system is responsible for the chaos and oscillation, which are so closely related. The chaotic parameters of the system are highlighted and are recommended for the control of the chaos of the system.