A minimal model for congestion phenomena on complex networks

We study a minimal model of traffic flows in complex networks, simple enough to get analytical results, but with a very rich phenomenology, presenting continuous, discontinuous as well as hybrid phase transitions between a free-flow phase and a congested phase, critical points and different scaling behaviors in the system size. It consists of random walkers on a queueing network with one-range repulsion, where particles can be destroyed only if they can move. We focus on the dependence on the topology as well as on the level of traffic control. We are able to obtain transition curves and phase diagrams at analytical level for the ensemble of uncorrelated networks and numerically for single instances. We find that traffic control improves global performance, enlarging the free-flow region in parameter space only in heterogeneous networks. Traffic control introduces non-linear effects and, beyond a critical strength, may trigger the appearance of a congested phase in a discontinuous manner. The model also reproduces the cross-over in the scaling of traffic fluctuations empirically observed in the Internet, and moreover, a conserved version can reproduce qualitatively some stylized facts of traffic in transportation networks

Catalytic Hydrogen Production by Ruthenium Complexes from the Conversion of Primary Amines to Nitriles: Potential Application as a Liquid Organic Hydrogen Carrier

The potential application of the primary amine/nitrile pair as a liquid organic hydrogen carrier (LOHC) has been evaluated. Ruthenium complexes of formula [(p-cym)Ru(NHC)Cl2] (NHC=N-heterocyclic carbene) catalyze the acceptorless dehydrogenation of primary amines to nitriles with the formation of molecular hydrogen. Notably, the reaction proceeds without any external additive, under air, and under mild reaction conditions. The catalytic properties of a ruthenium complex supported on the surface of graphene have been explored for reutilization purposes. The ruthenium-supported catalyst is active for at least 10 runs without any apparent loss of activity. The results obtained in terms of catalytic activity, stability, and recyclability are encouraging for the potential application of the amine/nitrile pair as a LOHC. The main challenge in the dehydrogenation of benzylamines is the selectivity control, such as avoiding the formation of imine byproducts due to transamination reactions. Herein, selectivity has been achieved by using long-chain primary amines such as dodecylamine. Mechanistic studies have been performed to rationalize the key factors involved in the activity and selectivity of the catalysts in the dehydrogenation of amines. The experimental results suggest that the catalyst resting state contains a coordinated amine.The authors thank the financial support from MINECO (CTQ2015-69153-C2-2-R), Generalitat Valenciana (AICO/2015/ 039), and the UniversitatJaume I(P1.1B2015-09).The authors are very grateful to the “Serve is Centrals d’Instr umentac ij Cien- t&fica (SCIC)” of the Universitat Jaume I

The recovery of European freshwater biodiversity has come to a halt

Owing to a long history of anthropogenic pressures, freshwater ecosystems are among the most vulnerable to biodiversity loss$^{1}$. Mitigation measures, including wastewater treatment and hydromorphological restoration, have aimed to improve environmental quality and foster the recovery of freshwater biodiversity$^{2}$. Here, using 1,816 time series of freshwater invertebrate communities collected across 22 European countries between 1968 and 2020, we quantified temporal trends in taxonomic and functional diversity and their responses to environmental pressures and gradients. We observed overall increases in taxon richness (0.73% per year), functional richness (2.4% per year) and abundance (1.17% per year). However, these increases primarily occurred before the 2010s, and have since plateaued. Freshwater communities downstream of dams, urban areas and cropland were less likely to experience recovery. Communities at sites with faster rates of warming had fewer gains in taxon richness, functional richness and abundance. Although biodiversity gains in the 1990s and 2000s probably reflect the effectiveness of water-quality improvements and restoration projects, the decelerating trajectory in the 2010s suggests that the current measures offer diminishing returns. Given new and persistent pressures on freshwater ecosystems, including emerging pollutants, climate change and the spread of invasive species, we call for additional mitigation to revive the recovery of freshwater biodiversity

The recovery of European freshwater biodiversity has come to a halt

Owing to a long history of anthropogenic pressures, freshwater ecosystems are among the most vulnerable to biodiversity loss1. Mitigation measures, including wastewater treatment and hydromorphological restoration, have aimed to improve environmental quality and foster the recovery of freshwater biodiversity2. Here, using 1,816 time series of freshwater invertebrate communities collected across 22 European countries between 1968 and 2020, we quantified temporal trends in taxonomic and functional diversity and their responses to environmental pressures and gradients. We observed overall increases in taxon richness (0.73% per year), functional richness (2.4% per year) and abundance (1.17% per year). However, these increases primarily occurred before the 2010s, and have since plateaued. Freshwater communities downstream of dams, urban areas and cropland were less likely to experience recovery. Communities at sites with faster rates of warming had fewer gains in taxon richness, functional richness and abundance. Although biodiversity gains in the 1990s and 2000s probably reflect the effectiveness of water-quality improvements and restoration projects, the decelerating trajectory in the 2010s suggests that the current measures offer diminishing returns. Given new and persistent pressures on freshwater ecosystems, including emerging pollutants, climate change and the spread of invasive species, we call for additional mitigation to revive the recovery of freshwater biodiversity.publishedVersio

Trends in flow intermittence for European rivers

Intermittent rivers are prevalent in many countries across Europe, but little is known about the temporal evolution of intermittence and its relationship with climate variability. Trend analysis of the annual and seasonal number of zero-flow days, the maximum duration of dry spells and the mean date of the zero-flow events is performed on a database of 452 rivers with varying degrees of intermittence between 1970 and 2010. The relationships between flow intermittence and climate are investigated using the standardized precipitation evapotranspiration index (SPEI) and climate indices describing large-scale atmospheric circulation. The results indicate a strong spatial variability of the seasonal patterns of intermittence and the annual and seasonal number of zero-flow days, highlighting the controls exerted by local catchment properties. Most of the detected trends indicate an increasing number of zero-flow days, which also tend to occur earlier in the year, particularly in southern Europe. The SPEI is found to be strongly related to the annual and seasonal zero-flow day occurrence in more than half of the stations for different accumulation times between 12 and 24 months. Conversely, there is a weaker dependence of river intermittence with large-scale circulation indices. Overall, these results suggest increased water stress in intermittent rivers that may affect their biota and biochemistry and also reduce available water resources

The recovery of European freshwater biodiversity has come to a halt

Owing to a long history of anthropogenic pressures, freshwater ecosystems are among the most vulnerable to biodiversity loss1. Mitigation measures, including wastewater treatment and hydromorphological restoration, have aimed to improve environmental quality and foster the recovery of freshwater biodiversity2. Here, using 1,816 time series of freshwater invertebrate communities collected across 22 European countries between 1968 and 2020, we quantified temporal trends in taxonomic and functional diversity and their responses to environmental pressures and gradients. We observed overall increases in taxon richness (0.73% per year), functional richness (2.4% per year) and abundance (1.17% per year). However, these increases primarily occurred before the 2010s, and have since plateaued. Freshwater communities downstream of dams, urban areas and cropland were less likely to experience recovery. Communities at sites with faster rates of warming had fewer gains in taxon richness, functional richness and abundance. Although biodiversity gains in the 1990s and 2000s probably reflect the effectiveness of water-quality improvements and restoration projects, the decelerating trajectory in the 2010s suggests that the current measures offer diminishing returns. Given new and persistent pressures on freshwater ecosystems, including emerging pollutants, climate change and the spread of invasive species, we call for additional mitigation to revive the recovery of freshwater biodiversity.N. Kaffenberger helped with initial data compilation. Funding for authors and data collection and processing was provided by the EU Horizon 2020 project eLTER PLUS (grant agreement no. 871128); the German Federal Ministry of Education and Research (BMBF; 033W034A); the German Research Foundation (DFG FZT 118, 202548816); Czech Republic project no. P505-20-17305S; the Leibniz Competition (J45/2018, P74/2018); the Spanish Ministerio de Economía, Industria y Competitividad—Agencia Estatal de Investigación and the European Regional Development Fund (MECODISPER project CTM 2017-89295-P); Ramón y Cajal contracts and the project funded by the Spanish Ministry of Science and Innovation (RYC2019-027446-I, RYC2020-029829-I, PID2020-115830GB-100); the Danish Environment Agency; the Norwegian Environment Agency; SOMINCOR—Lundin mining & FCT—Fundação para a Ciência e Tecnologia, Portugal; the Swedish University of Agricultural Sciences; the Swiss National Science Foundation (grant PP00P3_179089); the EU LIFE programme (DIVAQUA project, LIFE18 NAT/ES/000121); the UK Natural Environment Research Council (GLiTRS project NE/V006886/1 and NE/R016429/1 as part of the UK-SCAPE programme); the Autonomous Province of Bolzano (Italy); and the Estonian Research Council (grant no. PRG1266), Estonian National Program ‘Humanitarian and natural science collections’. The Environment Agency of England, the Scottish Environmental Protection Agency and Natural Resources Wales provided publicly available data. We acknowledge the members of the Flanders Environment Agency for providing data. This article is a contribution of the Alliance for Freshwater Life (www.allianceforfreshwaterlife.org).Peer reviewe

Bélsejt-specifikus jelátviteli útvonalak elemzése az autofágia szabályozásában

I present a workflow of integrating expression data from single-cell RNA sequencing and interaction data from a priori regulatory networks to study cell type specific differences in the complex regulation of autophagy in the gut. I investigated differences in autophagy regulation between colonic and the ileal tissues, in the process of inflammation and in the pathogenesis of the two types of IBD - Crohn’s disease and ulcerative colitis

Oscillation of Autophagy Induction under Cellular Stress and What Lies behind It, a Systems Biology Study

One of the main inducers of autophagy-dependent self-cannibalism, called ULK1, is tightly regulated by the two sensor molecules of nutrient conditions and energy status, known as mTOR and AMPK kinases, respectively. Recently, we developed a freely available mathematical model to explore the oscillatory characteristic of the AMPK-mTOR-ULK1 regulatory triangle. Here, we introduce a systems biology analysis to explain in detail the dynamical features of the essential negative and double-negative feedback loops and also the periodic repeat of autophagy induction upon cellular stress. We propose an additional regulatory molecule in the autophagy control network that delays some of AMPK’s effect on the system, making the model output more consistent with experimental results. Furthermore, a network analysis on AutophagyNet was carried out to identify which proteins could be the proposed regulatory components in the system. These regulatory proteins should satisfy the following rules: (1) they are induced by AMPK; (2) they promote ULK1; (3) they down-regulate mTOR upon cellular stress. We have found 16 such regulatory components that have been experimentally proven to satisfy at least two of the given rules. Identifying such critical regulators of autophagy induction could support anti-cancer- and ageing-related therapeutic efforts

ULK1 and ULK2 are less redundant than previously thought:computational analysis uncovers distinct regulation and functions of these autophagy induction proteins

Macroautophagy, the degradation of cytoplasmic content by lysosomal fusion, is an evolutionary conserved process promoting homeostasis and intracellular defence. Macroautophagy is initiated primarily by a complex containing ULK1 or ULK2 (two paralogs of the yeast Atg1 protein). To understand the differences between ULK1 and ULK2, we compared the human ULK1 and ULK2 proteins and their regulation. Despite the similarity in their enzymatic domain, we found that ULK1 and ULK2 have major differences in their autophagy-related interactors and their post-translational and transcriptional regulators. We identified 18 ULK1-specific and 7 ULK2-specific protein motifs serving as different interaction interfaces. We found that interactors of ULK1 and ULK2 all have different tissue-specific expressions partially contributing to diverse and ULK-specific interaction networks in various tissues. We identified three ULK1-specific and one ULK2-specific transcription factor binding sites, and eight sites shared by the regulatory region of both genes. Importantly, we found that both their post-translational and transcriptional regulators are involved in distinct biological processes—suggesting separate functions for ULK1 and ULK2. Unravelling differences between ULK1 and ULK2 could lead to a better understanding of how ULK-type specific dysregulation affects autophagy and other cellular processes that have been implicated in diseases such as inflammatory bowel disease and cancer