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  • 2014-2023
  • Natural Sciences and Engineering Re...
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Natalia B. Fernandez; Natalia B. Fernandez; Patrik Vuilleumier; Patrik Vuilleumier; +4 Authors

    Congenital amusia in its most common form is a disorder characterized by a musical pitch processing deficit. Although pitch is involved in conveying emotion in music, the implications for pitch deficits on musical emotion judgements is still under debate. Relatedly, both limited and spared musical emotion recognition was reported in amusia in conditions where emotion cues were not determined by musical mode or dissonance. Additionally, assumed links between musical abilities and visuo-spatial attention processes need further investigation in congenital amusics. Hence, we here test to what extent musical emotions can influence attentional performance. Fifteen congenital amusic adults and fifteen healthy controls matched for age and education were assessed in three attentional conditions: executive control (distractor inhibition), alerting, and orienting (spatial shift) while music expressing either joy, tenderness, sadness, or tension was presented. Visual target detection was in the normal range for both accuracy and response times in the amusic relative to the control participants. Moreover, in both groups, music exposure produced facilitating effects on selective attention that appeared to be driven by the arousal dimension of musical emotional content, with faster correct target detection during joyful compared to sad music. These findings corroborate the idea that pitch processing deficits related to congenital amusia do not impede other cognitive domains, particularly visual attention. Furthermore, our study uncovers an intact influence of music and its emotional content on the attentional abilities of amusic individuals. The results highlight the domain-selectivity of the pitch disorder in congenital amusia, which largely spares the development of visual attention and affective systems.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Frontiers in Human N...arrow_drop_down
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Frontiers in Human N...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      Article . 2021
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  • Authors: Kennedy, Dylan;

    Across Canada and around the world, damaged and aging infrastructure is a major issue facing civil engineers and infrastructure planners. Funding to replace these aging structures is unlikely to become available, therefore, economical repair techniques, which can return a structure to its original state are required. Several of those techniques are mortar adhered near surface mounted (NSM) fibre reinforced polymer (FRP) bars and fabric reinforced cementitious mortar (FRCM) wraps. These composites overcome financial and safety related concerns of previously used repair methods, while delivering similar levels of strengthening efficiency. This study was designed to investigate the effectiveness of these two composite strengthening systems on shear-damaged reinforced concrete (RC) beams with different levels of damage (1st shear crack and 70% of maximum theoretical load), adhesives (mortar and epoxy), wrapping patterns (continuous and intermittent), and different stirrup spacings (150mm or 200mm). Fifteen half-scale (200x265x2000 mm) RC beams (2 control, 6 strengthened without damage, and 7 strengthened after damage) were cast and tested under monotonic three-point bending conditions. Load, stiffness, mid-span displacement, pseudo-ductility, energy absorption, and failure mode were used as performance indicators. Results showed that most of the beams failed due to debonding failure between the strengthening material and the concrete substrate. The strengthening systems did not have a significant effect on the beams’ stiffness, however, all the strengthening systems were able to increase the load bearing capacity, the pseudo-ductility, and the energy absorption. Load bearing capacity was increased between 22% and 42%, depending on the strengthening system used. Recommendations on the maximum design strains in the different strengthening systems were also made.

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  • Authors: Rezajooei, Nazanin;

    Newly developed Neural Network Potentials (NNPs) like ANI are powerful tools to describe these systems with a high level of accuracy but with a modest computational cost. Because they use short-range cutoffs (e.g., 5 Å), interactions outside this range are not described correctly. Significantly, London dispersion is a fundamental intermolecular force that extends beyond 5 Å, so it is neglected by current NNPs. The dispersion interaction in a chemical system can be estimated as the sum of pairwise atomic interactions with 6th, 8th, and 10th order terms (i.e., C₆, C₈, and C₁₀). The exchange hole dipole moment (XDM) model provides an accurate ab initio method for calculating these coefficients. However, a computationally intensive Density-Functional Theory (DFT) calculation is required to calculate these coefficients, so they cannot be used practically with NNPs. In this thesis, we developed a neural network to calculate these dispersion coefficients of atoms without the DFT calculation, providing an NNP that describes dispersion rigorously while maintaining the computational efficiency of NNPs. This new NNP is trained to reproduce PBE0/aug-cc-pVTZ with an XDM dispersion correction. This method was validated by comparison to high-level ab initio calculations from the DES15K test set. This method predicted intermolecular interaction energies of neutral molecules with a mean absolute error of 1.1 kcal/mol and a coefficient of determination of 0.91, demonstrating that this method has comparable accuracy to the QM method with a dramatically reduced computational cost.

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    Authors: Klappstein, N.J.; Potts, J.R.; Michelot, T.; Börger, L.; +3 Authors

    1. The energetic gains from foraging and costs of movement are expected to be key drivers of animal decision-making, as their balance is a large determinant of body condition and survival. This fundamental perspective is often missing from habitat selection studies, which mainly describe correlations between space use and environmental features, rather than the mechanisms behind these correlations.\ud \ud \ud \ud 2. To address this gap, we present a novel parameterisation of step selection functions (SSFs), that we term the energy selection function (ESF). In this model, the likelihood of an animal selecting a movement step depends directly on the corresponding energetic gains and costs, and we can therefore assess how moving animals choose habitat based on energetic considerations.\ud \ud \ud \ud 3. The ESF retains the mathematical convenience and practicality of other SSFs and can be quickly fitted using standard software. In this article, we outline a workflow, from data gathering to statistical analysis, and use a case study of polar bears Ursus maritimus to demonstrate application of the model.\ud \ud \ud \ud 4. We explain how defining gains and costs at the scale of the movement step allows us to include information about resource distribution, landscape resistance and movement patterns. We further demonstrate this process with a case study of polar bears and show how the parameters can be interpreted in terms of selection for energetic gains and against energetic costs.\ud \ud \ud \ud 5. The ESF is a flexible framework that combines the energetic consequences of both movement and resource selection, thus incorporating a key mechanism into habitat selection analysis. Further, because it is based on familiar habitat selection models, the ESF is widely applicable to any study system where energetic gains and costs can be derived, and has immense potential for methodological extensions.

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    Authors: Vinoth Balasubramani; Małgorzata Kujawińska; Cédric Allier; Vijayakumar Anand; +13 Authors

    Quantitative Phase Imaging (QPI) provides unique means for the imaging of biological or technical microstructures, merging beneficial features identified with microscopy, interferometry, holography, and numerical computations. This roadmap article reviews several digital holography-based QPI approaches developed by prominent research groups. It also briefly discusses the present and future perspectives of 2D and 3D QPI research based on digital holographic microscopy, holographic tomography, and their applications.

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  • Authors: Kim, Jihyun;

    Climate change is resulting in ongoing temperature warming and increased frequencies of heatwaves. In aquatic ecosystems, temperature not only affects the distribution and abundance of phytoplankton, but warming may also be reducing the quantities of key nutrients produced by these important primary producers. However, thus far most research in this field has examined the effects of warming temperatures on nutrient production in individual species of phytoplankton. To characterize how warming affects phytoplankton-based nutrients at the community scale, we subjected naturally occurring phytoplankton assemblages to three temperature treatments (ambient, warming, heat wave) in a seven-week laboratory experiment. We used community-wide fatty acid composition and stoichiometric indicators (C:N, C:P and N:P ratios) as our measures of phytoplankton nutritional quality. By the end of the experiment, there was no effect of temperature on phytoplankton community composition. Phytoplankton communities from the heatwave treatment had decreased concentrations of C, N and P, but neither the heatwave nor warming affected community-wide C:N, C:P and N:P ratios. Both warming and the heatwave reduced phytoplankton polyunsaturated fatty acid (PUFA) content, but as the heatwave subsided, PUFA quantities in this treatment approached those found in the ambient temperature treatment. We then fed warmed phytoplankton communities to naturally-collected zooplankton assemblages and found that the PUFA composition of the zooplankton communities closely reflected that of their food source. Our results suggest that 1) temperature warming has negative effects on phytoplankton community nutritional quality, 2) these responses are not caused by broad-scale shifts in phytoplankton taxonomy, and 3) phytoplankton PUFA levels appear to closely track water temperature. Furthermore, we provide evidence that zooplankton communities experience indirect effects of temperature warming through nutritional shifts in their phytoplankton resource. Overall, this study improves our understanding of the types of phytoplankton nutrients that are affected by warming, how quickly these nutrients can respond to temperature change, and the down-stream effects of phytoplankton-based nutrients on zooplankton consumers.

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    Authors: Krens, S. F. Gabriel; Veldhuis, Jim H.; Barone, Vanessa; Čapek, Daniel; +3 Authors

    The segregation of different cell types into distinct tissues is a fundamental process in metazoan development. Differences in cell adhesion and cortex tension are commonly thought to drive cell sorting by regulating tissue surface tension (TST). However, the role that differential TST plays in cell segregation within the developing embryo is as yet unclear. Here, we have analyzed the role of differential TST for germ layer progenitor cell segregation during zebrafish gastrulation. Contrary to previous observations that differential TST drives germ layer progenitor cell segregation in vitro, we show that germ layers display indistinguishable TST within the gastrulating embryo, arguing against differential TST driving germ layer progenitor cell segregation in vivo. We further show that the osmolarity of the interstitial fluid (IF) is an important factor that influences germ layer TST in vivo, and that lower osmolarity of the IF compared with standard cell culture medium can explain why germ layers display differential TST in culture but not in vivo. Finally, we show that directed migration of mesendoderm progenitors is required for germ layer progenitor cell segregation and germ layer formation. Highlighted Article: Segregation of the germ layer progenitors in the zebrafish gastrula is driven by directed cell migration, rather than differential tissue surface tension.

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  • Authors: Fleming, Kathleen;

    On the Avalon Peninsula of Newfoundland, fairies are no longer feared and avoided (Reiti, 1991; Narvaez, 1991), but are something people have commodified and are marketing and selling. This thesis includes some of these examples: Tina White’s guided tours the Fairy Door Tours and Fairy Lore Walkabout, the Faerie Garden and Fairy Nights at the Cupids Legacy Centre, described by Claudine Garland and Peter Laracy, and the written representation by local writers Dennis Flynn and Dale Jarvis, and local publisher Marnie Parsons who owns and operates the Running the Goat: Books and Broadsides publishing company in Tors Cove. Applying the theoretical concepts of play (Masters, 2008; Eicher-Catt, 2016; Lambrow, 2020), assemblage (Santino, 1986), enchantment/re-enchantment (Magliocco, 2018; Saler, 2003, 2004), and escapism (Heilman, 1975; Young, 1976; Usherwood and Toyne, 2002), to the theoretical framework of commodification, I show how locals are adapting “our” fairy traditions and using the interest sparked by the popular culture representation of fairies to teach audiences about different aspects of Newfoundland culture, such as storytelling traditions, as well as Newfoundland values, like respect for nature and for other people. I also show how the visual representation of fairies has been more sanitized than the written form. Finally, I show how locals, both proprietors and consumers, are using these examples to create and foster a sense of local identity.

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    Authors: Dubois, Emmanuel; Doummar, Joanna; Pistre, Séverin; Larocque, Marie;

    Flow in complex karst aquifers is challenging to conceptualize and model, especially in poorly investigated areas, in semiarid climates, and under changing climatic conditions; however, it is necessary in order to implement long-term sustainable water management practices. Thus, the objectives of this work were to propose a calibration approach based on time series analyses for a karst aquifer and to assess the impact of climate change on spring discharge. Based on more than 3 years of high-resolution continuous monitoring, a semi-distributed lumped model was calibrated and validated for the Qachqouch karst spring, north of Beirut (Lebanon). Time series analyses and decomposition of spring hydrographs revealed that the system has a high regulatory function, with considerable storage capacity providing stable flow (minimum flow of 0.2 m3 s−1) during the dry season and with flow rates exceeding 10 m3 s−1 during the wet season, which is similar to other karst aquifers in the region. Based on this detailed understanding of the hydrodynamics of the system, the model geometry and parameters were validated. Three linear reservoirs were implemented to reproduce the combined contribution of the different flow components of the system. A satisfactory simulation (Nash–Sutcliffe efficiency coefficient, NSE, of 0.72) of the measured spring flow rates was obtained after calibration. Climate change conditions (+1 to +3 ∘C warming, −10 % to −30 % less precipitation annually, and the intensification of rain events) were added to a baseline climatic year to produce scenarios of expected spring flow responses. Results show that the Qachqouch karst aquifer is sensitive to decreasing rainfall, which is associated with more pronounced recessions, with flow rates decreasing by 34 % and 1-month longer dry periods. Because of the limited influence of snow on the spring flow rate, a warming climate has less impact on spring flow conditions than a reduction in precipitation. Although the model shows that increasing rainfall intensity induces larger floods, recessions, and shorter low-flow periods, the real impact of high-intensity precipitation events remains uncertain, as the model does not account for complex unsaturated and epikarstic processes. This work shows that calibrating a semi-distributed lumped model using time series analyses can be an efficient approach to improve simulations of complex karst aquifers, thereby providing useful models for long-term sustainable water management.

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    Authors: Naccache, Rafik; Mazhorova, Anna; Clerici, Matteo; Piccoli, Riccardo; +5 Authors

    The accurate and non-invasive determination of multiple physical parameters, with well-defined spatial resolution, is crucial for applications in manufacturing, chemistry, medicine and biology. Specifically, the ability to simultaneously measure both temperature and spectral signatures is still experimentally unavailable. To this end, we propose a mapping technique for biological systems, which exploits a linear correlation between terahertz wave reflectivity and temperature, and allows to spatially and spectrally resolve thermal distributions. This method is applied to a model biological system in two relevant cases where in one example, nanoplasmonic-induced photothermal effects are imaged gaining new insights into collective heating phenomena. In the second example, we demonstrate a joint thermal-hyperspectral imaging approach to chemically map the presence of a model drug formulation and simultaneously investigate its thermal stability in our biological system. This concept can be easily extended and widely applied to all materials that demonstrate a measurable change in their dielectric properties.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Natalia B. Fernandez; Natalia B. Fernandez; Patrik Vuilleumier; Patrik Vuilleumier; +4 Authors

    Congenital amusia in its most common form is a disorder characterized by a musical pitch processing deficit. Although pitch is involved in conveying emotion in music, the implications for pitch deficits on musical emotion judgements is still under debate. Relatedly, both limited and spared musical emotion recognition was reported in amusia in conditions where emotion cues were not determined by musical mode or dissonance. Additionally, assumed links between musical abilities and visuo-spatial attention processes need further investigation in congenital amusics. Hence, we here test to what extent musical emotions can influence attentional performance. Fifteen congenital amusic adults and fifteen healthy controls matched for age and education were assessed in three attentional conditions: executive control (distractor inhibition), alerting, and orienting (spatial shift) while music expressing either joy, tenderness, sadness, or tension was presented. Visual target detection was in the normal range for both accuracy and response times in the amusic relative to the control participants. Moreover, in both groups, music exposure produced facilitating effects on selective attention that appeared to be driven by the arousal dimension of musical emotional content, with faster correct target detection during joyful compared to sad music. These findings corroborate the idea that pitch processing deficits related to congenital amusia do not impede other cognitive domains, particularly visual attention. Furthermore, our study uncovers an intact influence of music and its emotional content on the attentional abilities of amusic individuals. The results highlight the domain-selectivity of the pitch disorder in congenital amusia, which largely spares the development of visual attention and affective systems.

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  • Authors: Kennedy, Dylan;

    Across Canada and around the world, damaged and aging infrastructure is a major issue facing civil engineers and infrastructure planners. Funding to replace these aging structures is unlikely to become available, therefore, economical repair techniques, which can return a structure to its original state are required. Several of those techniques are mortar adhered near surface mounted (NSM) fibre reinforced polymer (FRP) bars and fabric reinforced cementitious mortar (FRCM) wraps. These composites overcome financial and safety related concerns of previously used repair methods, while delivering similar levels of strengthening efficiency. This study was designed to investigate the effectiveness of these two composite strengthening systems on shear-damaged reinforced concrete (RC) beams with different levels of damage (1st shear crack and 70% of maximum theoretical load), adhesives (mortar and epoxy), wrapping patterns (continuous and intermittent), and different stirrup spacings (150mm or 200mm). Fifteen half-scale (200x265x2000 mm) RC beams (2 control, 6 strengthened without damage, and 7 strengthened after damage) were cast and tested under monotonic three-point bending conditions. Load, stiffness, mid-span displacement, pseudo-ductility, energy absorption, and failure mode were used as performance indicators. Results showed that most of the beams failed due to debonding failure between the strengthening material and the concrete substrate. The strengthening systems did not have a significant effect on the beams’ stiffness, however, all the strengthening systems were able to increase the load bearing capacity, the pseudo-ductility, and the energy absorption. Load bearing capacity was increased between 22% and 42%, depending on the strengthening system used. Recommendations on the maximum design strains in the different strengthening systems were also made.

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  • Authors: Rezajooei, Nazanin;

    Newly developed Neural Network Potentials (NNPs) like ANI are powerful tools to describe these systems with a high level of accuracy but with a modest computational cost. Because they use short-range cutoffs (e.g., 5 Å), interactions outside this range are not described correctly. Significantly, London dispersion is a fundamental intermolecular force that extends beyond 5 Å, so it is neglected by current NNPs. The dispersion interaction in a chemical system can be estimated as the sum of pairwise atomic interactions with 6th, 8th, and 10th order terms (i.e., C₆, C₈, and C₁₀). The exchange hole dipole moment (XDM) model provides an accurate ab initio method for calculating these coefficients. However, a computationally intensive Density-Functional Theory (DFT) calculation is required to calculate these coefficients, so they cannot be used practically with NNPs. In this thesis, we developed a neural network to calculate these dispersion coefficients of atoms without the DFT calculation, providing an NNP that describes dispersion rigorously while maintaining the computational efficiency of NNPs. This new NNP is trained to reproduce PBE0/aug-cc-pVTZ with an XDM dispersion correction. This method was validated by comparison to high-level ab initio calculations from the DES15K test set. This method predicted intermolecular interaction energies of neutral molecules with a mean absolute error of 1.1 kcal/mol and a coefficient of determination of 0.91, demonstrating that this method has comparable accuracy to the QM method with a dramatically reduced computational cost.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Klappstein, N.J.; Potts, J.R.; Michelot, T.; Börger, L.; +3 Authors

    1. The energetic gains from foraging and costs of movement are expected to be key drivers of animal decision-making, as their balance is a large determinant of body condition and survival. This fundamental perspective is often missing from habitat selection studies, which mainly describe correlations between space use and environmental features, rather than the mechanisms behind these correlations.\ud \ud \ud \ud 2. To address this gap, we present a novel parameterisation of step selection functions (SSFs), that we term the energy selection function (ESF). In this model, the likelihood of an animal selecting a movement step depends directly on the corresponding energetic gains and costs, and we can therefore assess how moving animals choose habitat based on energetic considerations.\ud \ud \ud \ud 3. The ESF retains the mathematical convenience and practicality of other SSFs and can be quickly fitted using standard software. In this article, we outline a workflow, from data gathering to statistical analysis, and use a case study of polar bears Ursus maritimus to demonstrate application of the model.\ud \ud \ud \ud 4. We explain how defining gains and costs at the scale of the movement step allows us to include information about resource distribution, landscape resistance and movement patterns. We further demonstrate this process with a case study of polar bears and show how the parameters can be interpreted in terms of selection for energetic gains and against energetic costs.\ud \ud \ud \ud 5. The ESF is a flexible framework that combines the energetic consequences of both movement and resource selection, thus incorporating a key mechanism into habitat selection analysis. Further, because it is based on familiar habitat selection models, the ESF is widely applicable to any study system where energetic gains and costs can be derived, and has immense potential for methodological extensions.

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    Authors: Vinoth Balasubramani; Małgorzata Kujawińska; Cédric Allier; Vijayakumar Anand; +13 Authors

    Quantitative Phase Imaging (QPI) provides unique means for the imaging of biological or technical microstructures, merging beneficial features identified with microscopy, interferometry, holography, and numerical computations. This roadmap article reviews several digital holography-based QPI approaches developed by prominent research groups. It also briefly discusses the present and future perspectives of 2D and 3D QPI research based on digital holographic microscopy, holographic tomography, and their applications.

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  • Authors: Kim, Jihyun;

    Climate change is resulting in ongoing temperature warming and increased frequencies of heatwaves. In aquatic ecosystems, temperature not only affects the distribution and abundance of phytoplankton, but warming may also be reducing the quantities of key nutrients produced by these important primary producers. However, thus far most research in this field has examined the effects of warming temperatures on nutrient production in individual species of phytoplankton. To characterize how warming affects phytoplankton-based nutrients at the community scale, we subjected naturally occurring phytoplankton assemblages to three temperature treatments (ambient, warming, heat wave) in a seven-week laboratory experiment. We used community-wide fatty acid composition and stoichiometric indicators (C:N, C:P and N:P ratios) as our measures of phytoplankton nutritional quality. By the end of the experiment, there was no effect of temperature on phytoplankton community composition. Phytoplankton communities from the heatwave treatment had decreased concentrations of C, N and P, but neither the heatwave nor warming affected community-wide C:N, C:P and N:P ratios. Both warming and the heatwave reduced phytoplankton polyunsaturated fatty acid (PUFA) content, but as the heatwave subsided, PUFA quantities in this treatment approached those found in the ambient temperature treatment. We then fed warmed phytoplankton communities to naturally-collected zooplankton assemblages and found that the PUFA composition of the zooplankton communities closely reflected that of their food source. Our results suggest that 1) temperature warming has negative effects on phytoplankton community nutritional quality, 2) these responses are not caused by broad-scale shifts in phytoplankton taxonomy, and 3) phytoplankton PUFA levels appear to closely track water temperature. Furthermore, we provide evidence that zooplankton communities experience indirect effects of temperature warming through nutritional shifts in their phytoplankton resource. Overall, this study improves our understanding of the types of phytoplankton nutrients that are affected by warming, how quickly these nutrients can respond to temperature change, and the down-stream effects of phytoplankton-based nutrients on zooplankton consumers.

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