93 Works

Milk production and environmental conditions of mountain-pastured Braunvieh cows between 2000 and 2015

Solange Duruz & Christine Flury
This dataset is a subset of the dataset used in the associated article, linking environmental data to milk records of mountain-pastured cows between 2000 and 2015. In particular it contains information on the cow and lactation cycle (lactation number, date of calving, date of first record in the alp, average quantity of milk over 3 milk records taken in the alp) and environmental condition (temperature humidity index, cold stress index, averaged over 3 and 30...

Additional file 6 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 6: Fig. S6. Seroprevalence of tested antigens in the CoLaus|PsyCoLaus. List of the 27 antigens available from the CoLaus|PsyCoLaus study that are shared with the UK Biobank. The percentages indicate the seroprevalence of antibodies against infectious disease antigens tested using Multiplex Serology platform. The grey boxes indicate the pathogen on which the antigen protein is found, and the family to which the pathogen belongs.

Data from: Organic functional group and organic matter concentrations from FT-IR measurements of particulate matter samples in the Southeastern Aerosol Research and Characterization (SEARCH) network from 2009-2016

Ann M. Dillner, Alexandra J. Boris, Satoshi Takahama, Andrew T. Weakley, Bruno Debus, Carley D. Frederickson, Martin Esparza-Sanchez, Charlotte Burke, Matteo Reggente, Stephanie L. Shaw & Eric S. Edgerton
This dataset contains organic functional group, organic matter (OM), organic carbon (OC) concentration measurements at five sites in the SEARCH network from 2009-2016. Spectra from each sample are included, in the format used in these papers. The sampling sites are urban Birmingham (BHM) and rural Centreville (CTR) in Alabama, urban Jefferson Street, Atlanta (JST) and rural Yorkville (YRK) in Georgia, and rural Outlying Landing Field (OLF) near Pensacola in Florida as well as a co-located...

Data from: Sampling strategy optimization to increase statistical power in landscape genomics: a simulation-based approach

Oliver Selmoni, Elia Vajana, Annie Guillaume, Estelle Rochat & Stéphane Joost
An increasing number of studies are using landscape genomics to investigate local adaptation in wild and domestic populations. The implementation of this approach requires the sampling phase to consider the complexity of environmental settings and the burden of logistic constraints. These important aspects are often underestimated in the literature dedicated to sampling strategies. In this study, we computed simulated genomic datasets to run against actual environmental data in order to trial landscape genomics experiments under...

Data from: One-shot learning and behavioral eligibility traces in sequential decision making

Marco P. Lehmann, He A. Xu, Vasiliki Liakoni, Michael H. Herzog, Wulfram Gerstner & Kerstin Preuschoff
In many daily tasks we make multiple decisions before reaching a goal. In order to learn such sequences of decisions, a mechanism to link earlier actions to later reward is necessary. Reinforcement learning theory suggests two classes of algorithms solving this credit assignment problem: In classic temporal-difference learning, earlier actions receive reward information only after multiple repetitions of the task, whereas models with eligibility traces reinforce entire sequences of actions from a single experience (one-shot)....

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...

Data from: Seascape genomics as a new tool to empower coral reef conservation strategies: an example on north-western Pacific Acropora digitifera

Oliver Selmoni, Estelle Rochat, Gael Lecellier, Véronique Berteaux-Lecellier & Stephane Joost
Coral reefs are suffering a major decline due to the environmental constraints imposed by climate change. Over the last 20 years, three major coral bleaching events occurred in concomitance with anomalous heat waves, provoking a severe loss of coral cover worldwide. The conservation strategies for preserving reefs, as they are implemented now, cannot cope with global climatic shifts. Consequently, researchers are advocating for preservation networks to be set-up to reinforce coral adaptive potential. However, the...

Data from: The fitness landscape of the codon space across environments

Inês Fragata, Sebastian Matuszweski, Mark A. Schmitz, Thomas Bataillon, Jeffrey D. Jensen & Claudia Bank
Fitness landscapes map the relationship between genotypes and fitness. However, most fitness landscape studies ignore the genetic architecture imposed by the codon table and thereby neglect the potential role of synonymous mutations. To quantify the fitness effects of synonymous mutations and their potential impact on adaptation on a fitness landscape, we use a new software based on Bayesian Monte Carlo Markov Chain methods and re-estimate selection coefficients of all possible codon mutations across 9 amino-acid...

Data from: The effects of aging on neuropil structure in mouse somatosensory cortex—A 3D electron microscopy analysis of layer 1

Corrado Cali, Marta Wawrzyniak, Carlos Becker, Bohumil Maco, Marco Cantoni, Anne Jorstad, Biagio Nigro, Federico Grillo, Vincenzo De Paola, Pascal Fua & Graham William Knott
This study has used dense reconstructions from serial EM images to compare the neuropil ultrastructure and connectivity of aged and adult mice. The analysis used models of axons, dendrites, and their synaptic connections, reconstructed from volumes of neuropil imaged in layer 1 of the somatosensory cortex. This shows the changes to neuropil structure that accompany a general loss of synapses in a well-defined brain region. The loss of excitatory synapses was balanced by an increase...

Physically asymmetric division of the C. elegans zygote ensures invariably successful embryogenesis

Radek Jankele, Pierre Gönczy & Rob Jelier
Asymmetric divisions that yield daughter cells of different sizes are frequent during early embryogenesis, but the importance of such a physical difference for successful development remains poorly understood. Here, we investigated this question using the first division of C. elegans embryos, which yields a large AB cell and a small P1 cell. We equalized AB and P1 sizes using acute genetic inactivation or optogenetic manipulation of the spindle positioning protein LIN-5. We uncovered that only...

Ant behavioral maturation is mediated by a stochastic transition between two fundamental states

Thomas Richardson, Tomas Kay, Raphael Braunschweig, Opaline A. Journeau, Matthias Ruegg, Sean McGregor, Paolo De Los Rios & Laurent Keller
The remarkable ecological success of social insects is often attributed to their advanced division of labour, which is closely associated with temporal polyethism in which workers transition between different tasks as they age. Young nurses are typically found deep within the nest where they tend to the queen and the brood, whereas older foragers are found near the entrance and outside the nest. However, the individual-level maturation dynamics remain poorly understood because following individuals over...

Data from: A novel biomechanical approach for animal behaviour recognition using accelerometers

Pritish Chakravarty, Gabriele Cozzi, Arpat Ozgul & Kamiar Aminian
Data from animal‐borne inertial sensors are widely used to investigate several aspects of an animal's life, such as energy expenditure, daily activity patterns and behaviour. Accelerometer data used in conjunction with machine learning algorithms have been the tool of choice for characterising animal behaviour. Although machine learning models perform reasonably well, they may not rely on meaningful features, nor lend themselves to physical interpretation of the classification rules. This lack of interpretability and control over...

Quantification of Bone Marrow Compartments in Histological Sections

Josefine Tratwal & Olaia Naveiras
We report the development of a semi-automated image analysis plug-in, MarrowQuant, which employs the open-source software QuPath, to systematically quantify multiple bone components in H&E sections in an unbiased manner. MarrowQuant discerns and quantifies the areas occupied by bone, adipocyte ghosts, hematopoietic cells and the interstitial/microvascular compartment. A separate feature, AdipoQuant, fragments adipocyte ghosts in H&E-stained sections of extramedullary adipose tissue sections to render adipocyte area and size distribution. Quantification of BM hematopoietic cellularity with...

Photosynthesis from stolen chloroplasts can support sea slug reproductive fitness

Paulo Cartaxana, Felisa Rey, Charlotte LeKieffre, Diana Lopes, Cedric Hubas, Jorge E. Spangenberg, Stéphane Escrig, Bruno Jesus, Gonçalo Calado, Rosário Domingues, Michael Kühl, Ricardo Calado, Anders Meibom & Sónia Cruz
Some sea slugs are able to steal functional chloroplasts (kleptoplasts) from their algal food sources, but the role and relevance of photosynthesis to the animal host remain controversial. While some researchers claim that kleptoplasts are slowly digestible ‘snacks’, others advocate that they enhance the overall fitness of sea slugs much more profoundly. Our analysis show light-dependent incorporation of 13C and 15N in the albumen gland and gonadal follicles of the sea slug Elysia timida, representing...

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...

Supplementary material from Impact of phylogeny on structural contact inference from protein sequence data

Nicola Dietler, Umberto Lupo & Anne-Florence Bitbol
File containing supplementary figures and results.

Supplementary material from \"Impact of phylogeny on structural contact inference from protein sequence data\"

Nicola Dietler, Umberto Lupo & Anne-Florence Bitbol
Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ancestry, their sequences also feature phylogenetic correlations, which can impair contact inference. We investigate this effect by generating controlled synthetic data from a minimal model where the importance of contacts and of phylogeny can be tuned. We demonstrate that...

Supplementary material from \"Bone conduction facilitates self-other voice discrimination\"

Pavo Orepic, Oliver Alan Kannape, Nathan Faivre & Olaf Blanke
One's own voice is one of the most important and most frequently heard voices. Although it is the sound we associate most with ourselves, it is perceived as strange when played back in a recording. One of the main reasons is the lack of bone conduction that is inevitably present when hearing own voice while speaking. The resulting discrepancy between experimental and natural self-voice stimuli has significantly impeded self-voice research, rendering it one of the...

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  • École Polytechnique Fédérale de Lausanne
  • Swiss Institute of Bioinformatics
  • University of Lausanne
  • University Hospital of Lausanne
  • German Cancer Research Center
  • University College London
  • Swiss Federal Institute for Forest, Snow and Landscape Research
  • University of Oxford
  • University of Neuchâtel
  • University of Bern