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1. Closing the gap between in vivo and in vitro omics: using QA/QC to strengthen ex vivo NMR metabolomics

   https://doi.org/10.1002/nbm.4594  

   Maroli, Amith_Sadananda; Powers, Robert (August 2021, NMR in Biomedicine)

   Metabolomics aims to achieve a global quantitation of the pool of metabolites within a biological system. Importantly, metabolite concentrations serve as a sensitive marker of both genomic and phenotypic changes in response to both internal and external stimuli. NMR spectroscopy greatly aids in the understanding of both in vitro and in vivo physiological systems and in the identification of diagnostic and therapeutic biomarkers. Accordingly, NMR is widely utilized in metabolomics and fluxomics studies due to its limited requirements for sample preparation and chromatography, its non‐destructive and quantitative nature, its utility in the structural elucidation of unknown compounds, and, importantly, its versatility in the analysis of in vitro, in vivo, and ex vivo samples. This review provides an overview of the strengths and limitations of in vitro and in vivo experiments for translational research and discusses how ex vivo studies may overcome these weaknesses to facilitate the extrapolation of in vitro insights to an in vivo system. The application of NMR‐based metabolomics to ex vivo samples, tissues, and biofluids can provide essential information that is close to a living system (in vivo) with sensitivity and resolution comparable to those of in vitro studies. The success of this extrapolation process is critically dependent on high‐quality and reproducible data. Thus, the incorporation of robust quality assurance and quality control checks into the experimental design and execution of NMR‐based metabolomics experiments will ensure the successful extrapolation of ex vivo studies to benefit translational medicine. 

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2. Evapotranspiration Seasonality over Tropical Ecosystems in Mato Grosso, Brazil

   https://doi.org/10.3390/rs14102482  

   Biudes, Marcelo Sacardi; Geli, Hatim M.; Vourlitis, George Louis; Machado, Nadja Gomes; Pavão, Vagner Marques; dos Santos, Luiz Octávio; Querino, Carlos Alexandre (May 2022, Remote Sensing)

   Brazilian tropical ecosystems in the state of Mato Grosso have experienced significant land use and cover changes during the past few decades due to deforestation and wildfire. These changes can directly affect the mass and energy exchange near the surface and, consequently, evapotranspiration (ET). Characterization of the seasonal patterns of ET can help in understanding how these tropical ecosystems function with a changing climate. The goal of this study was to characterize temporal (seasonal-to-decadal) and spatial patterns in ET over Mato Grosso using remotely sensed products. Ecosystems over areas with limited to no flux towers can be performed using remote sensing products such as NASA’s MOD16A2 ET (MOD16 ET). As the accuracy of this product in tropical ecosystems is unknown, a secondary objective of this study was to evaluate the ability of the MOD16 ET (ETMODIS) to appropriately represent the spatial and seasonal ET patterns in Mato Grosso, Brazil. Actual ET was measured (ETMeasured) using eight flux towers, three in the Amazon, three in the Cerrado, and two in the Pantanal of Mato Grosso. In general, the ETMODIS of all sites had no significant difference from ETMeasured during all analyzed periods, and ETMODIS had a significant moderate to strong correlation with the ETMeasured. The spatial variation of ET had some similarity to the climatology of Mato Grosso, with higher ET in the mid to southern parts of Mato Grosso (Cerrado and Pantanal) during the wet period compared to the dry period. The ET in the Amazon had three seasonal patterns, a higher and lower ET in the wet season compared to the dry season, and minimal to insignificant variation in ET during the wet and dry seasons. The wet season ET in Amazon decreased from the first and second decades, but the ET during the wet and dry season increased in Cerrado and Pantanal in the same period. This study highlights the importance of deepening the study of ET in the state of Mato Grosso due to the land cover and climate change. 

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3. Topology in soft and biological matter

   https://doi.org/10.1016/j.physrep.2024.04.002  

   Tubiana, Luca; Alexander, Gareth P; Barbensi, Agnese; Buck, Dorothy; Cartwright, Julyan HE; Chwastyk, Mateusz; Cieplak, Marek; Coluzza, Ivan; Čopar, Simon; Craik, David J; et al (July 2024, Physics Reports)

   The last years have witnessed remarkable advances in our understanding of the emergence and consequences of topological constraints in biological and soft matter. Examples are abundant in relation to (bio)polymeric systems and range from the characterization of knots in single polymers and proteins to that of whole chromosomes and polymer melts. At the same time, considerable advances have been made in the description of the interplay between topological and physical properties in complex fluids, with the development of techniques that now allow researchers to control the formation of and interaction between defects in diverse classes of liquid crystals. Thanks to technological progress and the integration of experiments with increasingly sophisticated numerical simulations, topological biological and soft matter is a vibrant area of research attracting scientists from a broad range of disciplines. However, owing to the high degree of specialization of modern science, many results have remained confined to their own particular fields, with different jargon making it difficult for researchers to share ideas and work together towards a comprehensive view of the diverse phenomena at play. Compelled by these motivations, here we present a comprehensive overview of topological effects in systems ranging from DNA and genome organization to entangled proteins, polymeric materials, liquid crystals, and theoretical physics, with the intention of reducing the barriers between different fields of soft matter and biophysics. Particular care has been taken in providing a coherent formal introduction to the topological properties of polymers and of continuum materials and in highlighting the underlying common aspects concerning the emergence, characterization, and effects of topological objects in different systems. The second half of the review is dedicated to the presentation of the latest results in selected problems, specifically, the effects of topological constraints on the viscoelastic properties of polymeric materials; their relation with genome organization; a discussion on the emergence and possible effects of knots and other entanglements in proteins; the emergence and effects of topological defects and solitons in complex fluids. This review is dedicated to the memory of Marek Cieplak. 

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4. Implications of Gamification in Learning Environments on Computer Sci-ence Students: A Comprehensive Study

   Zahedi, L. Ross (June 2019, 126th Annual Conference and Exposition of American Society for Engineering Education)

   Computers are used in almost all the fields in our daily life –they are used in various occupations and do the tasks with greater precision and as a result, made the life more comfortable. As such, more than 500,000 computing jobs remain unfulfilled in the US (Reported by app association), and many nations need more computer scientist. Therefore, this urge the need for engineering education community and researchers to focus more on underrepresentation of women in CS due to the fact that women currently comprise only 15.7% of computing degrees awarded ; Computer Science has one of the most considerable gender disparities in science, technology, and engineering and the number of female students choosing computer science as their major remains underrepresented regardless of recent improvements; and the reason behind this statistic is the challenges that lessen students’ motivation in CS majors; Programming courses have always had a negative image among students and usually need more practice. In order to increase the number of female students in CS and ensure the health of the community, there is a need to better understand and discover a mechanism that can improve women’s participation in computer science which leads to attracting more female students in computer science. Researchers have explored various engagements strategies in the fields of computer science. One of the strategies that have seen an increase and garnered attention in the last two decades is the use of video game elements or gamification in different fields such as education. Gamification -which usually refers to using video game mechanics in activities not related to video games - aims to increase participants’ engagement and enjoyment. This notion has been increasing popularity over time especially among especially education researchers because game elements -which provide challenges to the players and motivate them to set goals- can be used in learning environments appropriately to enhance the motivation of learners. While there is a strong body of literature around the implications of gamification on student learning, there are inconsistent results in the literature with regards to the interests or attitudes of women. This review aims to provide a critical evaluation of the use of gamification in the application in the existing literature in 1) education 2) computer science and 3) women in computer science to provide a basis for more targeted learning engagement strategies to motivate and retain more women in computing fields and build on the literature on gamification and gender. 

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5. The interactive effects of stratospheric ozone depletion, UV radiation, and climate change on aquatic ecosystems

   https://doi.org/10.1039/c8pp90062k  

   Williamson, Craig E.; Neale, Patrick J.; Hylander, Samuel; Rose, Kevin C.; Figueroa, Félix L.; Robinson, Sharon A.; Häder, Donat-P.; Wängberg, Sten-Åke; Worrest, Robert C. (March 2019, Photochemical & Photobiological Sciences)

   This assessment summarises the current state of knowledge on the interactive effects of ozone depletion and climate change on aquatic ecosystems, focusing on how these affect exposures to UV radiation in both inland and oceanic waters. The ways in which stratospheric ozone depletion is directly altering climate in the southern hemisphere and the consequent extensive effects on aquatic ecosystems are also addressed. The primary objective is to synthesise novel findings over the past four years in the context of the existing understanding of ecosystem response to UV radiation and the interactive effects of climate change. If it were not for the Montreal Protocol, stratospheric ozone depletion would have led to high levels of exposure to solar UV radiation with much stronger negative effects on all trophic levels in aquatic ecosystems than currently experienced in both inland and oceanic waters. This “world avoided” scenario that has curtailed ozone depletion, means that climate change and other environmental variables will play the primary role in regulating the exposure of aquatic organisms to solar UV radiation. Reductions in the thickness and duration of snow and ice cover are increasing the levels of exposure of aquatic organisms to UV radiation. Climate change was also expected to increase exposure by causing shallow mixed layers, but new data show deepening in some regions and shoaling in others. In contrast, climate-change related increases in heavy precipitation and melting of glaciers and permafrost are increasing the concentration and colour of UV-absorbing dissolved organic matter (DOM) and particulates. This is leading to the “browning” of many inland and coastal waters, with consequent loss of the valuable ecosystem service in which solar UV radiation disinfects surface waters of parasites and pathogens. Many organisms can reduce damage due to exposure to UV radiation through behavioural avoidance, photoprotection, and photoenzymatic repair, but meta-analyses continue to confirm negative effects of UV radiation across all trophic levels. Modeling studies estimating photoinhibition of primary production in parts of the Pacific Ocean have demonstrated that the UV radiation component of sunlight leads to a 20% decrease in estimates of primary productivity. Exposure to UV radiation can also lead to positive effects on some organisms by damaging less UV-tolerant predators, competitors, and pathogens. UV radiation also contributes to the formation of microplastic pollutants and interacts with artificial sunscreens and other pollutants with adverse effects on aquatic ecosystems. Exposure to UV-B radiation can decrease the toxicity of some pollutants such as methyl mercury (due to its role in demethylation) but increase the toxicity of other pollutants such as some pesticides and polycyclic aromatic hydrocarbons. Feeding on microplastics by zooplankton can lead to bioaccumulation in fish. Microplastics are found in up to 20% of fish marketed for human consumption, potentially threatening food security. Depletion of stratospheric ozone has altered climate in the southern hemisphere in ways that have increased oceanic productivity and consequently the growth, survival and reproduction of many sea birds and mammals. In contrast, warmer sea surface temperatures related to these climate shifts are also correlated with declines in both kelp beds in Tasmania and corals in Brazil. This assessment demonstrates that knowledge of the interactive effects of ozone depletion, UV radiation, and climate change factors on aquatic ecosystems has advanced considerably over the past four years and confirms the importance of considering synergies between environmental factors. 

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