85 Works

Synthetic self-affine topography scanned with a virtual spherical probe

Tevis D. B. Jacobs, Till Junge & Lars Pastewka
This surface contains a self-affine topography that has been scanned with a spherical virtual probe of radius 40 nm. The probe was lowered normal to the surface on each point of the reference topography (that is also included here) and the center of the probe was taken as the "measured" value of the topography. The reference topography has a Hurst exponent of 0.8 and was generated with a Fourier-filtering algorithm. This surface was used to...

The combined impact of persistent infections and human genetic variation on C-reactive protein levels

Flavia Hodel, Olivier Naret, Clara Bonnet, Nicole Brenner, Noemi Bender, Tim Waterboer, Pedro Marques-Vidal, Peter Vollenweider & Jacques Fellay
Abstract Multiple human pathogens establish chronic, sometimes life-long infections. Even if they are often latent, these infections can trigger some degree of local or systemic immune response, resulting in chronic low-grade inflammation. There remains an incomplete understanding of the potential contribution of both persistent infections and human genetic variation on chronic low-grade inflammation. We searched for potential associations between seropositivity for 13 persistent pathogens and the plasma levels of the inflammatory biomarker C-reactive protein (CRP),...

Additional file 3 of The combined impact of persistent infections and human genetic variation on C-reactive protein levels

Flavia Hodel, Olivier Naret, Clara Bonnet, Nicole Brenner, Noemi Bender, Tim Waterboer, Pedro Marques-Vidal, Peter Vollenweider & Jacques Fellay
Additional file 3: Fig. S3. Principal component analysis (PCA) of combined genotyping data. A) PCA plot of the first ten PCs of the genotyping data. Samples are colored by cohort. B) Histogram explaining the variance of each PC component. In the histogram, the variance explained by each eigenvalue is labeled on top.

Additional file 3 of The combined impact of persistent infections and human genetic variation on C-reactive protein levels

Flavia Hodel, Olivier Naret, Clara Bonnet, Nicole Brenner, Noemi Bender, Tim Waterboer, Pedro Marques-Vidal, Peter Vollenweider & Jacques Fellay
Additional file 3: Fig. S3. Principal component analysis (PCA) of combined genotyping data. A) PCA plot of the first ten PCs of the genotyping data. Samples are colored by cohort. B) Histogram explaining the variance of each PC component. In the histogram, the variance explained by each eigenvalue is labeled on top.

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...

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

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

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...

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....

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.

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...

Self-affine synthetic surface

Tevis D. B. Jacobs, Till Junge & Lars Pastewka
This surface contains virtual measurements taken out of a large self-affine synthetic surface with Hurst exponent 0.8. The original surface had 50,000 x 50,000 data points and was created using a Fourier filtering algorithm. The surface was "measured" in block containing 500 x 500 data points with a variety of scan sizes ranging from almost the full surface with 100 μm width to 10 μm to 1 μm, with pixel sizes scaling accordingly. This surface...

Tetravalent uranium mobilization by complexation or oxidation and associated U isotope fractionation

Yvonne Roebbert , Chris Daniel Rosendahl , Ashley Brown , Axel Schippers , Rizlan Bernier-Latmani & Stefan Weyer
Uranium (U) isotopes are suggested to monitor the success of (bio)remediation relying on the reduction of soluble and mobile U(VI) to less soluble U(IV)1. However, the subsurface stability of U(IV), typically present as solid-phase non-crystalline U, may be affected by complexation or oxidation. Understanding these processes and their impact on U isotope fractionation is important to correctly interpret field U isotope signatures. We investigated U mobilization by complexation and oxidation and measured the associated U...

Additional file 2 of The combined impact of persistent infections and human genetic variation on C-reactive protein levels

Flavia Hodel, Olivier Naret, Clara Bonnet, Nicole Brenner, Noemi Bender, Tim Waterboer, Pedro Marques-Vidal, Peter Vollenweider & Jacques Fellay
Additional file 2: Fig. S2. Scatterplot and regression line (with 95% confidence intervals) to describe the relationship of hs-CRP with characteristics of study participants. Relationship between hs-CRP and A) age, B) sex, C) BMI and D) polygenic risk score (PRS). For linear regressions, linear regression equation, R-squared and P-value are shown.

Additional file 4 of The combined impact of persistent infections and human genetic variation on C-reactive protein levels

Flavia Hodel, Olivier Naret, Clara Bonnet, Nicole Brenner, Noemi Bender, Tim Waterboer, Pedro Marques-Vidal, Peter Vollenweider & Jacques Fellay
Additional file 4: Fig. S4. Distribution of polygenic risk score (PRS) values. Density distribution of standardized PRS values by subcohort (CoLaus|PsyCoLaus and UKB) and across all participants (combined).

Positive interactions between corals and damselfish increase coral resistance to temperature stress

Andrew Shantz, Mark Ladd, Leila Ezzat, Russell Schmitt, Sally Holbrook, Rebecca Vega Thurber, Deron Burkepile & Emily Schmeltzer
By the century’s end, many tropical seas will reach temperatures exceeding most coral species’ thermal tolerance on an annual basis. The persistence of corals in these regions will therefore depend on their abilities to tolerate recurrent thermal stress. Although ecologists have long recognized that positive interspecific interactions can ameliorate environmental stress to expand the realized niche of plants and animals, coral bleaching studies have largely overlooked how interactions with community members outside of the coral...

Additional file 1 of Prominent astrocytic alpha-synuclein pathology with unique post-translational modification signatures unveiled across Lewy body disorders

Melek Firat Altay, Alan King Lun Liu, Janice L. Holton, Laura Parkkinen & Hilal A. Lashuel
Additional file 1: Table S1. The primary and secondary antibodies included in this study. AC = autoclave; agg-aSyn = aggregated alpha-synuclein; aSyn = alpha-synuclein; FA = formic acid; GFAP = glial fibrillary acidic protein; Iba1 = ionized calcium binding adaptor protein 1; IF = immunofluorescence; IHC = immunohistochemistry; MBP = myelin basic protein; mc = monoclonal; mus = mouse; na = not applicable; NF = neurofilament; pc = polyclonal; rab = rabbit; SB = slot...

Two simple movement mechanisms for spatial division of labour in social insects

Thomas Richardson, Nathalie Stroeymeyt, Alessandro Crespi & Laurent Keller
Many animal species divide space into a patchwork of home ranges, yet there is little consensus on the mechanisms individuals use to maintain fidelity to particular locations. Theory suggests that animal movement could be based upon simple behavioural rules that use local information such as olfactory deposits, or global strategies, such as long-range biases toward landmarks. However, empirical studies have rarely attempted to distinguish between these mechanisms. Here, we perform individual tracking experiments on four...

Data from: Shifting fitness landscapes in response to altered environments

Ryan T. Hietpas, Claudia Bank, Jeffrey D. Jensen & Daniel N. A. Bolon
The role of adaptation in molecular evolution has been contentious for decades. Here, we shed light on the adaptive potential in Saccharomyces cerevisiae by presenting systematic fitness measurements for all possible point mutations in a region of Hsp90 under four environmental conditions. Under elevated salinity, we observe numerous beneficial mutations with growth advantages up to 7% relative to the wild type. All of these beneficial mutations were observed to be associated with high costs of...

Data from: Identification of ZEB1 as a central component of the adipogenic gene regulatory network

Carine Gubelmann, Petra C. Schwalie, Sunil K. Raghav, Eva Röder, Delessa Tenagne, Elke Kiehlmann, Sebastian M. Waszak, Andrea Corsinotti, Gilles Udin, Wiebke Holcombe, Gottfried Rudowsky, Didier Trono, Christian Wolfrum & Bart Deplancke
Adipose tissue is a key determinant of whole body metabolism and energy homeostasis. Unraveling the regulatory mechanisms underlying adipogenesis is therefore highly relevant from a biomedical perspective. Our current understanding of fat cell differentiation is centered on the transcriptional cascades driven by the C/EBP protein family and the master regulator PPARγ. To elucidate further components of the adipogenic gene regulatory network, we performed a large-scale transcription factor (TF) screen overexpressing 734 TFs in mouse pre-adipocytes...

Data from: Diffantom: whole-brain diffusion MRI phantoms derived from real datasets of the Human Connectome Project

Oscar Esteban, Emmanuel Caruyer, Alessandro Daducci, Meritxell Bach-Cuadra, María J. Ledesma-Carbayo & Andres Santos
Diffantom is a whole-brain diffusion MRI (dMRI) phantom publicly available through the Dryad Digital Repository (doi:10.5061/dryad.4p080). The dataset contains two single-shell dMRI images, along with the corresponding gradient information, packed following the BIDS standard (Brain Imaging Data Structure, Gorgolewski et al., 2015). The released dataset is designed for the evaluation of the impact of susceptibility distortions and benchmarking existing correction methods. In this Data Report we also release the software instruments involved in generating diffantoms,...

Data from: Cell proliferation and migration during early development of a symbiotic scleractinian coral

Agathe Lecointe, Isabelle Domart-Coulon, Paris Alain & Anders Meibom
In scleractinian reef-building corals, patterns of cell self-renewal, migration and death remain virtually unknown, limiting our understanding of cellular mechanisms underlying initiation of calcification, and ontogenesis of the endosymbiotic dinoflagellate relationship. In this study we pulse-labeled the coral Stylophora pistillata for 24 h with BrdU at four life stages (planula, early metamorphosis, primary polyp, and adult colony) to investigate coral and endosymbiont cell proliferation during development, while simultaneously recording TUNEL-positive, i.e. apoptotic, nuclei. In the...

Data from: Experimental evolution of slowed cognitive aging in Drosophila melanogaster

Martyna K. Zwoinska, Alexei A. Maklakov, Tadeusz J. Kawecki & Brian Hollis
Reproductive output and cognitive performance decline in parallel during aging, but it is unknown whether this reflects a shared genetic architecture or merely the declining force of natural selection acting independently on both traits. We used experimental evolution in Drosophila melanogaster to test for the presence of genetic variation for slowed cognitive aging, and assess its independence from that responsible for other traits’ decline with age. Replicate experimental populations experienced either joint selection on learning...

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