Publications related to Development and implementation of eco-genomic tools for aquatic ecosystem biomonitoring: the SYNAQUA French-Swiss program

The microbial genomics of glacier-fed streams: adaptations to an extreme ecosystem

Glacier-fed streams are the cold, ultra-oligotrophic, and unstable streams that are fed by glacial meltwater. Despite these extreme conditions, they harbour a diverse and abundant microbial diversity that develops into biofilms, covering the boulders and s ...

EPFL2024

The cost of adaptability: resource availability constrains functional stability under pulsed disturbances

Hannes Markus Peter

Global change exposes ecosystems to changes in the frequency, magnitude, and concomitancy of disturbances, which impact the composition and functioning of these systems. Here, we experimentally evaluate the effects of salinity disturbances and eutrophicati ...

Amer Soc Microbiology2024

At what spatial scale does natural selection operate? Using multiscale frameworks to calibrate the effects of environmental factors across landscape continuums

Annie Sandrine Guillaume

Patterns in nature arise from processes interacting across a continuum of spatial scales, where new relationships emerge at each level of investigation. These patterns are nested features encompassing fine-scale local patterns, such as topography and geolo ...

EPFL2024

Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods

Jaspreet Singh Saini

Understanding the ecological impacts of viruses on natural and engineered ecosystems relies on the accurate identification of viral sequences from community sequencing data. To maximize viral recovery from metagenomes, researchers frequently combine viral ...

Amer Soc Microbiology2024

Microbial genome collection of aerobic granular sludge cultivated in sequencing batch reactors using different carbon source mixtures

Aline Sondra Adler, Christof Holliger, Pilar Natalia Rodilla Ramírez, Laetitia Janine Andrée Cardona, Jaspreet Singh Saini, Ruizhe Pei

Aerobic granular sludge (AGS) consists of a microbial consortium that has an important role in wastewater treatment. This study investigates AGS microorganisms cultivated in a laboratory-scale sequencing batch reactor. Metagenomic sequencing was conducted ...

Amer Soc Microbiology2024

Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics

Tamar Kohn, Xavier Fernandez Cassi

Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preampli ...

2024

Development and clinical validation of computational imaging biomarkers for neurodegenerative diseases

Veronica Lily Ravano

Neurodegenerative and neuroinflammatory disorders often involve complex pathophysiological mechanisms that are â to this date â only partially understood. A more comprehensive understanding of those microstructural processes and their characterization ...

EPFL2024

Collimation simulations for the FCC-ee

Tatiana Pieloni, Félix Simon Carlier, Guillaume Clément Broggi, Milica Rakic, Giovanni Iadarola, Bruce Roderik

The collimation system of the Future Circular Collider, operating with leptons (FCC-ee), must protect not only the experiments against backgrounds, but also the machine itself from beam losses. With a 17.8 MJ stored energy of the electron and positron beam ...

Iop Publishing Ltd2024

Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities

Evangelia Vagena

Microorganisms are a key component in the chain of life. They are essential for agriculture, produce a large proportion of oxygen, and play a central role in the cycle of elements. Microorganisms are widely used in the production of food and alcoholic beve ...

EPFL2024

Atlas Narratives of Anthropogenic Transformations across the Vietnamese Mekong Delta's Urban-Rural Territories: Water Ecosystems as Subject for the Social Ecological Transition

Sylvie Tram Nguyen

Well beyond the impact of climate change, anthropogenic modifications of the Vietnam Mekong Delta's ecosystems have resulted in environmental degradation and subsequent loss in ecosystems. The environmental impacts include but are not limited to accelerate ...

EPFL2023

Structural Insights into Electrophiles and Electrophilic Metabolites Sensing and Signaling: The Missing Information

Chloé Rogg, Yimon Aye

Native reactive electrophilic species (RES) are long-recognized regulators of pathophysiology; yet, knowledge surrounding how RES regulate context-specific biology remains limited. The latest technological advances in profiling and precision decoding of RE ...

WILEY-V C H VERLAG GMBH2023

Host-Pathogen Interactions Through the Genomic Lens

Zhi Ming Xu

Hosts and pathogens are involved in a long-standing evolutionary arms race characterized by successive rounds of evolution. Specifically, while hosts evolve resistance against infections, pathogens adapt to re-establish virulence. Since the signatures of t ...

EPFL2023

Inborn errors of type I interferon immunity in patients with symptomatic acute hepatitis E

Jacques Fellay

Background and Aims:The clinical spectrum of human infection by HEV ranges from asymptomatic to severe acute hepatitis. Furthermore, HEV can cause diverse neurological manifestations, especially Parsonage-Turner syndrome. Here, we used a large-scale human ...

Lippincott Williams & Wilkins2023

Genomic insights into the coupling of a Chlorella-like microeukaryote and sulfur bacteria in the chemocline of permanently stratified Lake Cadagno

Christel Sybille Hassler

Meromictic Lake Cadagno is a permanently stratified system with a persistent microbial bloom within the oxic-anoxic boundary called the chemocline. The association between oxygenic and anoxygenic photosynthesis within the chemocline has been known for at l ...

SPRINGERNATURE2023

Media Coverage of 3D Visual Tools Used in Urban Participatory Planning

Jens Ingensand, Thibaud Nicolas Chassin

The opportunities provided by adopting digitally-generated visual tools in urban participatory planning are compelling. These visual tools can promote interactions between authorities and citizens and among citizens. However, the urban participatory practi ...

IGI GLOBAL2023

Numerical tools for burning plasmas

Laurent Villard, Alberto Bottino, Jonathan Graves, Ben McMillan, Emmanuel Lanti, Emanuele Poli, Xiao Wang, Baruch Rofman

The software stack under development within a European coordinated effort on tools for burning plasma modelling is presented. The project is organised as a Task (TSVV Task 10) under the new E-TASC initiative (Litaudon et al 2022 Plasma Phys. Control. Fusio ...

IOP Publishing Ltd2023

Understanding Revision Behavior in Adaptive Writing Support Systems for Education

Tanja Christina Käser Jacober, Paola Mejia Domenzain, Luca Mouchel, Thiemo Wambsganss

Revision behavior in adaptive writing support systems is an important and relatively new area of research that can improve the design and effectiveness of these tools, and promote students' self-regulated learning (SRL). Understanding how these tools are u ...

Zenodo2023

Digital Intervention for Collaborative and Human-Centered Activities in Design-Based Learning Scenarios

Denis Gillet, Isabelle Barbara Marie-Hélène Cardia

Training science and engineering students to become responsible citizens and professionals requires novel and creative pedagogical approaches, such as design thinking. This concept relies on processes and tools to develop creativity and problem-solving ski ...

IEEE2023

ROSMOSE: A Web-based Optimization Tool to Aid Decision-making for the Design and Operation of Industrial and Urban Energy Systems

François Maréchal, Cédric Terrier, Daniel Alexander Florez Orrego, Michel Lopez, Meire Ellen Gorete Ribeiro Domingos

Energy efficiency is crucial for the sustainable operation of all industrial and urban sectors. However, practicing engineers have seldom access to open-source tools that can readily evaluate and compare scenarios in terms of energy consumption, cost, and ...

2023

Assessing the readiness of municipalities for digital process innovation

Mert Duygan

Pre-adoption phases of innovation are understudied in the innovation literature. This article addresses preadoption phases of innovation by running a prospective analysis. We assess the readiness of municipalities for the adoption of a digital tool that br ...

ELSEVIER SCI LTD2023