55 Works

A critical literature review of spatio-temporal simulation methods for daylight glare assessment

Stephen Wasilewski, Lars Oliver Grobe, Jan Wienold & Marilyne Andersen

Monetary Commitment and the Level of Public Debt

Stefano Gnocchi & Luisa Lambertini
We analyze the interaction between committed monetary policy and discretionary fiscal policy in a model with public debt, endogenous government expenditures, distortive taxation and nominal rigidities. Fiscal decisions lack commitment but are Markov-perfect. Monetary commitment to an interest rate path leads to a unique level of debt. This level of debt is positive if the central bank adopts closed-loop strategies that raise the real interest rate when inflation is above target owing to fiscal deviations....

Both diversity and functional composition affect productivity and water use efficiency in experimental temperate grasslands

Charlotte Grossiord, Manuel Walde, Eric Allan, Seraina L. Cappelli, Margaux Didion‐Gency, Arthur Gessler, Marco M. Lehmann & Noémie A. Pichon
Many experiments have shown that biodiversity promotes ecosystem functioning and stability and that this relationship varies with resource availability. However, we still have a poor understanding of the underlying physiological and ecological mechanisms driving diversity effects and how they may interact with soil nutrient availability. We collected data in a grassland experiment factorially manipulating fertilization, species richness, functional composition (slow-growing vs. fast-growing species), and functional diversity in resource economic traits. We measured aboveground productivity, nitrogen...

Drainage Canals in Southeast Asian Peatland

Nathan Dadap, Alison M Hoyt, Alexander R Cobb, Doruk Oner, Mateusz Kozinski, Pascal V Fua, Krishna Rao, Charles F Harvey & Alexandra G Konings
These images depict drainage canals and roads in peatlands in Borneo, Sumatra, and Peninsular Malaysia at 5 meter resolution. These canals were detected from July-September 2017 Planet Basemaps satellite imagery using a convolutional neural network. Please contact Nathan Dadap (ndadap@stanford.edu) with any questions.

Data from: Very high resolution digital elevation models: are multi-scale derived variables ecologically relevant?

Kevin Leempoel, Christian Parisod, Céline Geiser, Lucas Daprà, Pascal Vittoz & Stéphane Joost
Digital Elevation Models (DEMs) are often used in landscape ecology to retrieve elevation or first derivative terrain attributes such as slope or aspect in the context of species distribution modelling. However, DEM-derived variables are scale-dependent and, given the increasing availability of very high resolution (VHR) DEMs, their ecological relevance must be assessed for different spatial resolutions. In a study area located in the Swiss Western Alps, we computed VHR DEMs-derived variables related to morphometry, hydrology...

Amoebocytes facilitate efficient carbon and nitrogen assimilation in the Cassiopea Symbiodiniaceae symbiosis

Niclas Heidelberg Lyndby, Nils Rädecker, Sandrine Bessette, Louise Jensen, Stéphane Escrig, Erik Trampe, Michael Kühl & Anders Meibom
The upside-down jellyfish Cassiopea engages in symbiosis with photosynthetic microalgae that facilitate uptake and recycling of inorganic nutrients. In contrast to most other symbiotic cnidarians, algal endosymbionts in Cassiopea are not restricted to the gastroderm but are found in amoebocyte cells within the mesoglea. While symbiont-bearing amoebocytes are highly abundant, their role in nutrient uptake and cycling in Cassiopea remains unknown. By combining isotopic labelling experiments with correlated SEM and NanoSIMS imaging, we quantified the...

Carabids data of Pterostichus flavofemoratus and Carabus depressus in the Gran Paradiso National Park (2006, 2007, 2012, 2013)

Jonathan Giezendanner, Damiano Pasetto, Javier Perez-Saez, Cristiana Cerrato, Ramona Viterbi, Silvia Terzago, Elisa Palazzi & Andrea Rinaldo
Understanding risks to biodiversity requires predictions of the spatial distribution of species adapting to changing ecosystems and, to that end, earth observations integrating field surveys prove essential as they provide key figures for assessing landscape-wide biodiversity scenarios. Here, we develop, and apply to a relevant case study, a method suited to merge earth/field observations with spatially explicit stochastic metapopulation models to study the near-term ecological dynamics of target species in complex terrains. Our framework incorporates...

Automated flow control of a multi-lane swimming chamber for small fishes indicates species-specific sensitivity to experimental protocols

Björn Illing, Andrea Severati, Justin Hochen, Paul Boyd, Paulin Raison, Rachel Mather, Adam T. Downie, Jodie L. Rummer, Frederieke J. Kroon & Craig Humphrey
In fishes, swimming performance is considered an important metric to measure fitness, dispersal, and migratory abilities. Swimming performance of individual larval fishes is often integrated into models to make inferences on how environmental parameters affect population-level dynamics (e.g., connectivity). However, little information exists regarding how experimental protocols affect the swimming performance of marine fish larvae. In addition, the technical setups used to measure larval fish swimming performance often lack automation and accurate control of water...

Data from: Demographic stochasticity and resource autocorrelation control biological invasions in heterogeneous landscapes

Andrea Giometto, Florian Altermatt & Andrea Rinaldo
Mounting theoretical evidence suggests that demographic stochasticity, environmental heterogeneity and biased movement of organisms individually affect the dynamics of biological invasions and range expansions. Studies of species spread in heterogeneous landscapes have traditionally characterized invasion velocities as functions of the mean resource density throughout the landscape, thus neglecting higher-order moments of the spatial resource distribution. Here, we show theoretically that different spatial arrangements of resources lead to different spread velocities even if the mean resource...

Data from: Tracking individuals shows spatial fidelity is a key regulator of ant social organization

Danielle P. Mersch, Alessandro Crespi & Laurent Keller
Ants live in organized societies with a marked division of labor among workers, but little is known about how this is generated. We use a tracking system to continuously monitor individually-tagged workers in six colonies of the ant Camponotus fellah over 41 days. Network analyses of over 9 million interactions revealed three distinct groups that differ in behavioral repertoires. Each group represents a functional behavioral unit with workers moving from one group to the next...

Data from: Signatures of selection and environmental adaptation across the goat genome post-domestication

Licia Colli, Marco Milanesi, Andrea Talenti, Francesca Bertolini, Minhui Chen, Alessandra Crisà, Kevin Daly, Marcello Del Corvo, Bernt Guldbrandtsen, Johannes A. Lenstra, Ben D. Rosen, Elia Vajana, Gennaro Catillo, Stéphane Joost, Ezequiel Luis Nicolazzi, Estelle Rochat, Max F. Rothschild, Bertrand Servin, Tad S. Sonstegard, Roberto Steri, Curtis P. Van Tassel, Paolo Ajmone-Marsan, Paola Crepaldi, Alessandra Stella & AdaptMap Consortium
Background: Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in terms of phenotypic characteristics and are adapted to a wide range of climatic conditions. In this work, we...

Data from: Contrasting leaf trait responses of conifer and broadleaved seedlings to altered resource availability are linked to resource strategies

Barbara Moser, Yan-Li Zhang, Mai-He Li, Thomas Wohlgemuth, Jing-Pin Lei & Christoph Bachofen
(1) Understanding tree seedling responses to water, nutrient and light availability is crucial to precisely predict potential shifts in composition and structure of forest communities under future climatic conditions. (2) We exposed seedlings of widespread central European tree species with contrasting leaf habit, deciduous broadleaves (DB) and evergreen conifers (EC), to factorial combinations of manipulated precipitation (100% and 50% of ambient), shade (40% and 60% of full sunlight) and nutrient availability (low and high NPK),...

Seek and learn: automated identification of microevents in animal behaviour using envelopes of acceleration data and machine learning

Pritish Chakravarty, Gabriele Cozzi, Hooman Dejnabadi, Pierre-Alexandre Léziart, Marta Manser, Arpat Ozgul & Kamiar Aminian
1. Animal-borne accelerometers have been used across more than 120 species to infer biologically significant information such as energy expenditure and broad behavioural categories. While the accelerometer’s high sensitivity to movement and fast response times present the unprecedented opportunity to resolve fine-scale behaviour, leveraging this opportunity will require overcoming the challenge of developing general, automated methods to analyse the nonstationary signals generated by nonlinear processes governing erratic, impulsive movement characteristic of fine-scale behaviour. 2. We...

Quantification of Bone Marrow Compartments in Histological Sections

Josefine Tratwal & Olaia Naveiras
Away from the Mouse H&E quantification, the current version of MarrowQuant was tested on a small set of H&E bone marrow biopsies from anonymised patients. The tool performs in a comparable way as compared to the gold standard (Pathologists’ scorings), but it needs many optimisations before validating at the level of the human bone marrow biopsies quantifications and in clinical context.

Diversity, equity, and inclusion in engineering education: an exploration of European higher education institutions’ strategic frameworks, resources, and initiatives

I. Direito, Shannon Chance, L. Clemmensen, S. Craps, S.B. Economides, S.R. Isaac, A.M. Jolly, F.R. Truscott & N. Wint

The Fairness and Generalizability Assessment Framework

Eliane Röösli, Selen Bozkurt & Tina Hernandez-Boussard
As artificial intelligence makes continuous progress to improve quality of care for some patients by leveraging ever increasing amounts of digital health data, others are left behind. Empirical evaluation studies are required to keep biased AI models from reinforcing systemic health disparities faced by minority populations through dangerous feedback loops. We developed a broadly applicable fairness and generalizability assessment framework and used it to perform a case study on a MIMIC-trained benchmarking model. While open-science...

Data from: Male competition and the evolution of mating and life history traits in experimental populations of Aedes aegypti

Alima Qureshi, Andrew Aldersley, Brian Hollis, Alongkot Ponlawat & Lauren J. Cator
Aedes aegypti is an important disease vector and a major target of reproductive control efforts. We manipulated the opportunity for sexual selection in populations of Ae. aegypti by controlling the number of males competing for a single female. Populations exposed to higher levels of male competition rapidly evolved higher male competitive mating success relative to populations evolved in the absence of competition, with an evolutionary response visible after only five generations. We also detected correlated...

Data from: Intraneural stimulation elicits discrimination of textural features by artificial fingertip in intact and amputee humans

Calogero Maria Oddo, Stanisa Raspopovic, Fiorenzo Artoni, Alberto Mazzoni, Giacomo Spigler, Francesco Petrini, Giambattistelli Federica, Vecchio Fabrizio, Miraglia Francesca, Zollo Loredana, Giovanni Di Pino, Domenico Camboni, Maria Chiara Carrozza, Eugenio Guglielmelli, Paolo Maria Rossini, Ugo Faraguna & Silvestro Micera
Restoration of touch after hand amputation is a desirable feature of ideal prostheses. Here, we show that texture discrimination can be artificially provided in human subjects by implementing a neuromorphic real-time mechano-neuro-transduction (MNT), which emulates to some extent the firing dynamics of SA1 cutaneous afferents. The MNT process was used to modulate the temporal pattern of electrical spikes delivered to the human median nerve via percutaneous microstimulation in four intact subjects and via implanted intrafascicular...

Data from: Mitotic chromosome binding predicts transcription factor properties in interphase

Mahé Raccaud, Elias T. Friman, Andrea B. Alber, Harsha Agarwal, Cédric Deluz, Timo Kuhn, J. Christof M. Gebhardt & David M. Suter
Mammalian transcription factors (TFs) differ broadly in their nuclear mobility and sequence-specific/non-specific DNA binding. How these properties affect their ability to occupy specific genomic sites and modify the epigenetic landscape is unclear. The association of TFs with mitotic chromosomes observed by fluorescence microscopy is largely mediated by non-specific DNA interactions and differs broadly between TFs. Here we combine quantitative measurements of mitotic chromosome binding (MCB) of 501 TFs, TF mobility measurements by fluorescence recovery after...

Data from: Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers

George H. Perry, Matthieu Foll, Jean-Christophe Grenier, Etienne Patin, Yohann Nédélec, Alain Pacis, Maxime Barakatt, Simon Gravel, Xiang Zhou, Sam L. Nsobya, Laurent Excoffier, Lluis Quintana-Murci, Nathaniel J. Dominy & Luis B. Barreiro
The evolutionary history of the human pygmy phenotype (small body size), a characteristic of African and Southeast Asian rainforest hunter-gatherers, is largely unknown. Here we use a genome-wide admixture mapping analysis to identify 16 genomic regions that are significantly associated with the pygmy phenotype in the Batwa, a rainforest hunter-gatherer population from Uganda (east central Africa). The identified genomic regions have multiple attributes that provide supporting evidence of genuine association with the pygmy phenotype, including...

Data from: Light availability impacts structure and function of phototrophic stream biofilms across domains and trophic levels

Mia M. Bengtsson, Karoline Wagner, Clarissa Schwab, Tim Urich & Tom J. Battin
Phototrophic biofilms are ubiquitous in freshwater and marine environments where they are critical for biogeochemical cycling, food webs and in industrial applications. In streams, phototrophic biofilms dominate benthic microbial life and harbor an immense prokaryotic and eukaryotic microbial biodiversity with biotic interactions across domains and trophic levels. Here, we examine how community structure and function of these biofilms respond to varying light availability, as the crucial energy source for phototrophic biofilms. Using metatranscriptomics, we found...

Data from: Computer assisted detection of axonal bouton structural plasticity in in vivo time-lapse images

Rohan Gala, Daniel Lebrecht, Daniela A. Sahlender, Anne Jorstad, Graham Knott, Anthony Holtmaat & Armen Stepanyants
The ability to measure minute structural changes in neural circuits is essential for long-term in vivo imaging studies. Here, we propose a methodology for detection and measurement of structural changes in axonal boutons imaged with time-lapse two-photon laser scanning microscopy (2PLSM). Correlative 2PLSM and 3D electron microscopy (EM) analysis, performed in mouse barrel cortex, showed that the proposed method has low fractions of false positive/negative bouton detections (2/0 out of 18), and that 2PLSM-based bouton...

Data from: The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards

Stefan Laurent, Susanne P. Pfeifer, Matthew Settles, Samuel S. Hunter, Kayla M. Hardwick, Louise Ormond, Vitor C. Sousa, Jeffrey D. Jensen, Erica Bree Rosenblum & Matthew L. Settles
Understanding the process of adaptation during rapid environmental change remains one of the central focal points of evolutionary biology. The recently formed White Sands system of southern New Mexico offers an outstanding example of rapid adaptation, with a variety of species having rapidly evolved blanched forms on the dunes that contrast with their close relatives in the surrounding dark soil habitat. In this study, we focus on two of the White Sands lizard species, Sceloporus...

Data from: Sexual selection shapes development and maturation rates in Drosophila

Brian Hollis, Laurent Keller & Tadeusz J. Kawecki
Explanations for the evolution of delayed maturity usually invoke trade-offs mediated by growth, but processes of reproductive maturation often continue long after growth has ceased. Here, we tested whether sexual selection shapes the rate of post-eclosion maturation in the fruit fly Drosophila melanogaster. We found that populations maintained for more than 100 generations under a short generation time and polygamous mating system evolved faster post-eclosion maturation and faster egg-to-adult development of males, when compared to...

Comparative analysis of time-based and quadrat sampling in seasonal population dynamics of intermediate hosts of human schistosomes

Francisco Javier Perez-Saez, Theophile Mande, Dramane Zongo & Andrea Rinaldo
Background Despite their importance for designing and evaluating schistosomiasis control trials, little attention in the literature has been dedicated to sampling protocols for the parasite's snail intermediate hosts since their first development. We propose a comparative analysis of time-based and quadrat sampling protocols to quantify the seasonal variations in the abundance of these aquatic snail species of medical importance. Methodology/Principal Findings Snail populations were monitored during 42 consecutive months in three types of habitats (ephemeral...

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