bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimising biodiversity protection through artificial intelligence
Authors: Silvestro Daniele , Goria Stefano , Sterner Thomas , Antonelli Alexandre 
Published: April 2021

AbstractOver a million species face extinction, carrying with them untold options for food, medicine, fibre, shelter, ecological resilience, aesthetic and cultural values. There is therefore an urgent need to design conservation policies that maximise the protection of biodiversity and its contributions to people, within the constraints of limited budgets. Here we present a novel framework for spatial conservation prioritisation that combines simulation models, reinforcement learning and ground validation to identify optimal policies. Our methodology, CAPTAIN (Conservation Area Prioritisation Through Artificial Intelligence Networks), quantifies the trade-off between the costs and benefits of area and biodiversity protection, allowing the exploration of multiple biodiversity metrics. Under a fixed budget, our model protects substantially more species from extinction than the random or naively targeted protection of areas. CAPTAIN also outperforms the most widely used software for spatial conservation prioritisation (Marxan) in 97% of cases and reduces species loss by an average of 40% under simulations, besides yielding prioritisation maps at substantially higher spatial resolution using empirical data. We find that regular biodiversity monitoring, even if simple and with a degree of inaccuracy – characteristic of citizen science surveys – substantially improves biodiversity outcomes. Given the complexity of people–nature interactions and wealth of associated data, artificial intelligence holds great promise for improving the conservation of biological and ecosystem values in a rapidly changing and resource-limited world.
Measuring the health of people in places: a scoping review of OECD member countries
Authors: Murray Emily T , Shelton Nicola , Norman Paul , Head Jenny 
Published: April 2021

ABSTRACTBackgroundDefining and measuring population health in places is fundamental for local and national planning and conducting within-country and cross-national health comparisons. Yet availability and comparability of place-level health data is unknown.MethodsA scoping review was performed to identify how Organisation for Economic Co-operation and Development (OECD) countries measure overall health for sub-national geographies within each country. The search was conducted across MEDLINE, Scopus and Google Scholar, supplemented by searching all 38 OECD countries statistical agency and public health institute websites.ResultsSixty publications were selected, plus extracted information from 37 of 38 OECD countries statistical agency and/or public health institute websites. Data sources varied by categorisation into mortality (n=7) or morbidity (n=5) health indicators: the former mostly from national statistical agencies and the latter from population-level surveys. Region was the most common geographic scale: eight indicators for 26 countries, two indicators for 24 countries and one indicator for 20 countries. Similar but slightly fewer indicators were available for urban areas (max countries per most frequent indicator = 24), followed by municipality (range of 1-14 countries per indicator). Other geographies, particularly those at smaller granularity, were infrequently available across health indicators and countries.ConclusionHealth indicator data at sub-national geographies are generally only available for a limited number of indicators at large administrative boundaries. Relative uniformity of health indicator question format allows cross-national comparisons. However, wider availability of health indicators at smaller, and non-administrative, geographies is needed to explore the best way to measure population health in local areas.
Underwater dual-magnification imaging for automated lake plankton monitoring
Authors: Merz Ewa , Kozakiewicz Thea , Reyes Marta , Ebi Christian , Isles Peter , Baity-Jesi Marco , Roberts Paul , Jaffe Jules S. , Dennis Stuart , Hardeman Thomas , Stevens Nelson , Lorimer Tom , Pomati Francesco 
Published: April 2021

AbstractWe present an approach for automatedin-situmonitoring of phytoplankton and zooplankton communities based on a dual magnification dark-field imaging microscope/camera. We describe the Dual Scripps Plankton Camera (DSPC) system and associated image processing, and assess its capabilities in detecting and characterizing plankton species of different size and taxonomic categories, and in measuring their abundances in both laboratory and field applications. In the laboratory, body size and abundance estimates by the DSPC significantly and robustly scale with the same measurements derived by traditional microscopy. In the field, a DSPC installed permanently at 3 m depth in Lake Greifensee (Switzerland), delivered images of plankton individuals, colonies, and heterospecific aggregates without disrupting natural arrangements of interacting organisms, their microenvironment or their behavior at hourly timescales. The DSPC was able to track the dynamics of taxa in the size range between ∼10 μm to ∼ 1 cm, covering virtually all the components of the planktonic food web (including parasites and potentially toxic cyanobacteria). Comparing data from the field-deployed DSPC to traditional sampling and microscopy revealed a general overall agreement in estimates of plankton diversity and abundances, despite imaging limitations in detecting small phytoplankton species and rare and large zooplankton taxa (e.g. carnivorous zooplankton). The most significant disagreements between traditional methods and the DSPC resided in the measurements of community properties of zooplankton, organisms that are heterogeneously distributed spatially and temporally, and whose demography appeared to be better captured by automated imaging. Time series collected by the DSPC depicted ecological succession patterns, algal bloom dynamics and circadian fluctuations with a temporal frequency and morphological resolution that would have been impossible with traditional methods. We conclude that the DSPC approach is suitable for stable long-term deployments, and robust for both research and water quality monitoring. Access to high frequency, reproducible and real-time data of a large spectrum of the planktonic ecosystem might represent a breakthrough in both applied and fundamental plankton ecology.
Visual search for upright bigrams predicts reading fluency in children
Authors: Agrawal Aakash , Nag Sonali , Hari K.V.S. , Arun S. P. 
Published: April 2021

ABSTRACTFluent reading is an important milestone in education, but we lack a clear understanding of why children vary so widely in attaining this milestone. Language-related factors such as rapid automatized naming (RAN) and phonological awareness have been identified as important factors that influence reading fluency. Of theoretical interest is also, however, whether aspects of visual processing influence reading fluency. To investigate this issue, we tested primary school children (n = 68) on four tasks: two reading fluency tasks (word reading and passage reading), a RAN task to measure naming speed, and a visual search task using letters and bigrams to measure visual processing. As expected, the RAN score was strongly correlated with reading fluency. In addition, visual processing of bigrams was correlated with reading fluency. Importantly, this association was specific to upright but not inverted bigrams, and to bigrams with normal but not large letter spacing. Thus, reading fluency in children is accompanied by specialized changes in upright bigram processing. We propose that bigram processing during visual search could complement existing measures of language processing to understand individual differences in reading fluency.
Interacting phenotypes and the coevolutionary process: Interspecific indirect genetic effects alter coevolutionary dynamics
Authors: De Lisle Stephen P. , Bolnick Daniel I. , Brodie Edmund D. , Moore Allen J. , McGlothlin Joel W. 
Published: April 2021

AbstractCoevolution occurs when species interact to influence one another’s fitness, resulting in reciprocal evolutionary change. In many coevolving lineages, trait expression in one species is modified by the genotypes and phenotypes of the other, forming feedback loops reminiscent of models of intraspecific social evolution. Here, we adapt the theory of within-species social evolution, characterized by indirect genetic effects and social selection imposed by interacting individuals, to the case of interspecific interactions. In a trait-based model, we derive general expressions for multivariate evolutionary change in two species and the expected between-species covariance in evolutionary change when selection varies across space. We show that reciprocal interspecific indirect genetic effects can dominate the coevolutionary process and drive patterns of correlated evolution beyond what is expected from direct selection alone. In extreme cases, interspecific indirect genetic effects can lead to coevolution when selection does not covary between species or even when one species lacks genetic variance. Moreover, our model indicates that interspecific indirect genetic effects may interact in complex ways with cross-species selection to determine the course of coevolution. Importantly, our model makes empirically testable predictions for how different forms of reciprocal interactions contribute to the coevolutionary process.
Soft tissue deformations explain most of the mechanical work variations of human walking
Authors: van der Zee Tim J. , Kuo Arthur D. 
Published: April 2021

AbstractHumans perform mechanical work during walking, some by leg joints actuated by muscles, and some by passive, dissipative soft tissues. Dissipative losses must be restored by active muscle work, potentially in amounts sufficient to cost substantial metabolic energy. The most dissipative, and therefore costly, walking conditions might be predictable from the pendulum-like dynamics of the legs. If pendulum behavior is systematic, it may also predict the work distribution between active joints and passive soft tissues. We therefore tested whether the overall negative work of walking, and the fraction due to soft tissue dissipation, are both predictable by a pendulum model across a wide range of conditions. The model predicts whole-body negative work from the leading leg’s impact with ground (termed the Collision), to increase with the squared product of walking speed and step length. We experimentally tested this in humans (N = 9) walking in 26 different combinations of speed (0.7 – 2.0 m·s-1) and step length (0.5 – 1.1 m), with recorded motions and ground reaction forces. Whole-body negative Collision work increased as predicted (R2= 0.73), with a consistent fraction of about 63% (R2= 0.88) due to soft tissues. Soft tissue dissipation consistently accounted for about 56% of the variation in total whole-body negative work. During typical walking, active work to restore dissipative losses could account for 31% of the net metabolic cost. Soft tissue dissipation, not included in most biomechanical studies, explains most of the variation in negative work of walking, and could account for a substantial fraction of the metabolic cost.Summary statementSoft tissue deformations dissipate substantial energy during human walking, as predicted by a simple walking model.
Coma-corrected rapid single-particle cryo-EM data collection on the CRYO ARM 300
Authors: Efremov Rouslan G. , Stroobants Annelore 
Published: April 2021

Single-particle cryogenic electron microscopy has recently become a major method for determining the structures of proteins and protein complexes. This has markedly increased the demand for throughput of high-resolution electron microscopes, which are required to produce high-resolution images at high rates. An increase in data-collection throughput can be achieved by using large beam-image shifts combined with off-axis coma correction, enabling the acquisition of multiple images from a large area of the EM grid without moving the microscope stage. Here, the optical properties of the JEOL CRYO ARM 300 electron microscope equipped with a K3 camera were characterized under off-axis illumination conditions. It is shown that efficient coma correction can be achieved for beam-image shifts with an amplitude of at least 10 µm, enabling a routine throughput for data collection of between 6000 and 9000 images per day. Use of the benchmark for the rapid data-collection procedure (with beam-image shifts of up to 7 µm) on apoferritin resulted in a reconstruction at a resolution of 1.7 Å. This demonstrates that the rapid automated acquisition of high-resolution micrographs is possible using a CRYO ARM 300.
Contribution of opioid and neurotensin receptors in the anti‐inflammatory activity of PK20 hybrid compound in murine airways
Authors: Russjan Ewelina , Zając Dominika , Sulejczak Dorota , Kleczkowska Patrycja , Kaczyńska Katarzyna 
Published: April 2021

AbstractPK20 is an anti‐inflammatory hybrid compound, composed of an endomorphin‐2‐like and neurotensin‐like fragments. The aim of the present study is to assess the contribution of particular pharmacophores to the activity of the hybrid tested. For this purpose, airway hyperresponsiveness, accumulation of inflammatory cells in bronchoalveolar lavage fluid (BALF), concentration of mouse mast cell protease, malondialdehyde and secretory phospholipase 2 activity in lung tissue, as well as production of pro‐inflammatory cytokines in BALF and lung were determined by using murine model of non‐atopic asthma. Blocking either neurotensin receptors or mu opioid receptors did not alter the potential of PK20 in reducing airway hyperresponsiveness. In studies of inflammatory cells, the beneficial effect of the entire peptide occurs to be mediated by the stimulation of neurotensin receptors. However, regarding cytokine and biochemical assays, pretreatment with both receptor antagonists resulted in a different effect on its activity depending on the parameter studied. To conclude, the activation of both the opioid and neurotensin receptors seems to be necessary to induce the full anti‐inflammatory activity of the hybrid compound.
A simple, switchable pili‐labelling method by plasmid‐based replacement of pilin
Authors: Zhang Jingchao , Li Shubin , Sun Tao , Zong Yiwu , Zhang Weiwen , Zhao Kun 
Published: April 2021

SummaryLabelling of Type IV pili (TFP) can greatly improve our understanding of the pivotal roles of TFP in a variety of bacterial activities including motility, surface sensing and DNA‐uptake etc. Here we show a simple and switchable pili‐labelling method by plasmid‐based inducible replacement of PilA without genetic modification in bacterial genome employed by complicated methods. Using this method, we characterized pili morphology and twitching motility of Pseudomonas aeruginosa in details. More importantly, we demonstrate its application in studying the replenishment dynamics of pilin pool of P. aeruginosa.
Sapwood and heartwood affect differentially bacterial and fungal community structure and successional dynamics duringQuercus petraeadecomposition
Authors: Viotti Chloé , Bach Cyrille , Maillard François , Ziegler‐Devin Isabelle , Mieszkin Sophie , Buée Marc 
Published: April 2021

SummaryIn forests, bacteria and fungi are key players in wood degradation. Still, studies focusing on bacterial and fungal successions during the decomposition process depending on the wood types (i.e. sapwood and heartwood) remain scarce. This study aimed to understand the effect of wood type on the dynamics of microbial ecological guilds in wood decomposition. Using Illumina metabarcoding, bacterial and fungal communities were monitored every 3 months for 3 years fromQuercus petraeawood discs placed on forest soil. Wood density and microbial enzymes involved in biopolymer degradation were measured. We observed rapid changes in the bacterial and fungal communities and microbial ecological guilds associated with wood decomposition throughout the experiment. Bacterial and fungal succession dynamics were very contrasted between sapwood and heartwood. The initial microbial communities were quickly replaced by new bacterial and fungal assemblages in the sapwood. Conversely, some initial functional guilds (i.e. endophytes and yeasts) persisted all along the experiment in heartwood and finally became dominant, possibly limiting the development of saprotrophic fungi. Our data also suggested a significant role of bacteria in nitrogen cycle during wood decomposition.
Fifteen Years of a PBRFS in New Zealand: Incentives and Outcomes
Authors: Buckle Robert A. , Creedy John , Ball Ashley 
Published: April 2021

AbstractThis article examines the transformation of New Zealand universities following the introduction in 2003 of a performance‐based research fund system. The analysis, based on a social accounting framework, utilises longitudinal researcher data available from three full assessment rounds, in 2003, 2012 and 2018. This enables identification of the entry, exit and quality transformation of researchers and their contribution to changes in university and discipline research quality. Changes in the discipline composition of universities made a negligible contribution compared to improvements in the quality of researchers. The dynamics are closely related to the new incentives created by the system.
A changing sense of place: Geography and COVID‐19
Authors: Bissell David 
Published: April 2021

AbstractIn this essay, I explain how geography offers important ideas to better understand what is happening to our sense of place during the COVID‐19 crisis, complementing the scientific understandings provided by epidemiologists and public health experts. I explain how geographical ideas relating to place and mobility can help us make sense of our current situation and consider what we might be feeling. These geographical ideas also provide us with important political tools to identify the new forms of inequality and hardship that are unfolding, prompting questions about how we should collectively respond to shape the future of place.
Place‐based collaborative governance: The potential influence of governments
Authors: Greenway John 
Published: April 2021

AbstractGovernments seeking to implement state/territory‐wide or national agendas and policies can impose (un)intended impacts and consequences on self‐managed community‐led collaborative governance initiatives by which people attempt to solve place‐based environmental and resource problems. The impacts of government actions and changes to policy, funding targets and criteria, and local government reform on emergent place‐based and self‐managed community collaborative governance initiatives can be significant in relation to longevity and ongoing achievement of beneficial environmental outcomes. Such outcomes are irrespective of whether place‐based initiatives are considered to emerge in the shadow of government or independent of central government. This article establishes that place‐based self‐managed community‐led collaborative governance initiatives are not immune to the influences and consequences of state/territorial and/or federal government decisions and actions, be those through the development of environmental regulations and policies that direct actions and/or set targets for policy outcomes; the provision of funding to be administered according to set criteria; or, at state/territory government levels, forced local government amalgamations. Discussion about these issues is positioned in relation to a successful place‐based community‐led collaborative water governance initiative known as the Clarence Floodplain Project (CFP) in northern New South Wales, Australia. The experience of the CFP suggests that state/territory and/or federal government decisions and actions may result in (un)intended negative as well as positive impacts on place‐based community‐led collaborative governance initiatives. Although the CFP was impacted by government actions, its success also highlights the importance of place‐based approaches to natural resource management and governance.
Nonparametric analysis of inter‐individual relations using an attention‐based neural network
Authors: Morita Takashi , Toyoda Aru , Aisu Seitaro , Kaneko Akihisa , Suda‐Hashimoto Naoko , Adachi Ikuma , Matsuda Ikki , Koda Hiroki 
Published: April 2021

Abstract

Social network analysis, which has been widely adopted in animal studies over the past decade, enables the revelation of global characteristic patterns of animal social systems from pairwise inter‐individual relations. Animal social networks are typically drawn based on the geometric proximity and/or frequency of social behaviours (e.g. grooming), but the appropriate metric for inter‐individual relationship is not clear, especially when prior knowledge on the species/data is limited.

In this study, researchers explored a nonparametric analysis of inter‐individual relations using a neural network with the attention mechanism, which plays a central role in natural language processing. The high interpretability of the attention mechanism and flexibility of the entire neural network allow for automatic detection of inter‐individual relations included in the raw data, without requiring prior knowledge/assumptions about what modes/types of relations are included in the data. For these case studies, three‐dimensional location data collected from simulated agents and real Japanese macaques were analysed.

The proposed method successfully recovered the latent relations behind the simulated data and discovered female‐oriented relations in the real data, which are in accordance with the previous generalizations about the macaque social structure.

The proposed method does not exploit any behavioural patterns that are particular to Japanese macaques, and researchers can use it for location data of other animals. The flexibility of the neural network would also allow for its application to a wide variety of data with interacting components, such as vocal communication.

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The response of citrus plants to the broad mitePolyphagotarsonemus latus(Banks) (Acari: Tarsonemidae)
Authors: Cabedo‐López Marc , Cruz‐Miralles Joaquín , Peris David , Ibáñez‐Gual M. Victoria , Flors Víctor , Jaques Josep A. 
Published: April 2021

Polyphagotarsonemus latus(Banks) (Acari: Tarsonemidae) is a common polyphagous mite in tropical and subtropical areas and is considered as an important citrus pest.To understand the response of citrus toP. latusinfestation, we have characterized the volatile profile and the molecular defence mechanisms of two citrus genotypes, namely sour orange (Citrus aurantium) and Cleopatra mandarin (Citrus reshni), toP. latusinfestation. These two species are important rootstocks for the citrus industry and display differential resistance toTetranychus urticaeKoch (Acari: Tetranychidae), with sour orange showing elevated levels of constitutive and induced resistance associated with the jasmonic acid (JA) pathway compared with Cleopatra mandarin.P. latusinfestation activated both the JA‐ and the salicylic acid‐dependent pathways in sour orange but not in Cleopatra mandarin. However, this differential activation resulted in the production of similar volatile blends (a mixture of green leaf volatiles and aromatic compounds).Contrary toT. urticaeinfestation, sour orange supported larger densities ofP. latusthan Cleopatra mandarin with similar injury levels.Therefore, sour orange may be more tolerant toP. latusthan Cleopatra mandarin.