Thermodynamics of exponential Kolmogorov-Nagumo averages

This paper investigates generalized thermodynamic relationships in physical systems where relevant macroscopic variables are determined by the exponential Kolmogorov-Nagumo average. We show that while the thermodynamic entropy of such systems is naturally described by R\'{e}nyi's entropy with parameter $\gamma$, their statistics under equilibrium thermodynamics are still described by an ordinary Boltzmann distribution, which can be interpreted as a system with inverse temperature $\beta$ quenched to another heat bath with inverse temperature $\beta' = (1-\gamma)\beta$. For the non-equilibrium case, we show how the dynamics of systems described by exponential Kolmogorov-Nagumo averages still observe a second law of thermodynamics and H-theorem. We further discuss the applications of stochastic thermodynamics in those systems - namely, the validity of fluctuation theorems - and the connection with thermodynamic length.Comment: 12 pages, 1 table. arXiv admin note: text overlap with arXiv:2203.1367

An overview of generalized entropic forms

The aim of this focus letter is to present a comprehensive classification of the main entropic forms introduced in the last fifty years in the framework of statistical physics and information theory. Most of them can be grouped into three families, characterized by two-deformation parameters, introduced respectively by Sharma, Taneja, and Mittal (entropies of degree $(\alpha,\,\beta$)), by Sharma and Mittal (entropies of order $(\alpha,\,\beta)$), and by Hanel and Thurner (entropies of class $(c,\,d)$). Many entropic forms examined will be characterized systematically by means of important concepts such as their axiomatic foundations {\em \`{a} la} Shannon-Khinchin and the consequent composability rule for statistically independent systems. Other critical aspects related to the Lesche stability of information measures and their consistency with the Shore-Johnson axioms will be briefly discussed on a general ground.Comment: 14 pages, 6 tables, no figures, to appear on EPL: Focus Issues "Progresses on Statistical Physics and Complexity

ElaD, a Deubiquitinating Protease Expressed by E. Coli

Background: Ubiquitin and ubiquitin-like proteins (Ubl) are designed to modify polypeptides in eukaryotes. Covalent binding of ubiquitin or Ubls to substrate proteins can be reversed by specific hydrolases. One particular set of cysteine proteases, the CE clan, which targets ubiquitin and Ubls, has homologs in eukaryotes, prokaryotes, and viruses. Findings: We have cloned and analyzed the E. coli protein elaD, which is distantly related to eukaryotic CE clan members of the ULP/SENP protease family that are specific for SUMO and Nedd8. Previously misannotated as a putative sulfatase/phosphatase, elaD is an efficient and specific deubiquitinating enzyme in vitro. Interestingly, elaD is present in all intestinal pathogenic E. coli strains, but conspicuously absent from extraintestinal pathogenic strains (ExPECs). Further homologs of this protease can be found in Acanthamoeba Polyphaga Mimivirus, and in Alpha-, Beta-and Gammaproteobacteria. Conclusion: The expression of ULP/SENP-related hydrolases in bacteria therefore extends to plant pathogens and medically relevant strains of Escherichia coli, Legionella pneumophila, Rickettsiae, Chlamydiae, and Salmonellae, in which the elaD ortholog sseL has recently been identified as a virulence factor with deubiquitinating activity. As a counterpoint, our phylogenetic and functional examination reveals that ancient eukaryotic ULP/SENP proteases also have the potential of ubiquitin-specific hydrolysis, suggesting an early common origin of this peptidase clan

Spin-Dependent Mass Enhancement under Magnetic Field in the Periodic Anderson Model

In order to study the mechanism of the mass enhancement in heavy fermion compounds in the presence of magnetic field, we study the periodic Anderson model using the fluctuation exchange approximation. The resulting value of the mass enhancement factor z^{-1} can become up to 10, which is significantly larger than that in the single-band Hubbard model. We show that the difference between the magnitude of the mass enhancement factor of up spin (minority spin) electrons z^{-1}_up and that of down spin (majority spin) electrons z^{-1}_down increases by the applied magnetic field B//z, which is consistent with de Haas-van Alphen measurements for CeCoIn_5, CeRu_2Si_2 and CePd_2Si_2. We predict that z^{-1}_up >z^{-1}_down in many Ce compounds, whereas z^{-1}_up < z^{-1}_down in Yb compounds.Comment: 5 pages, 4 figure

A dynamical approach to the spatiotemporal aspects of the Portevin-Le Chatelier effect: Chaos,turbulence and band propagation

Experimental time series obtained from single and poly-crystals subjected to a constant strain rate tests report an intriguing dynamical crossover from a low dimensional chaotic state at medium strain rates to an infinite dimensional power law state of stress drops at high strain rates. We present results of an extensive study of all aspects of the PLC effect within the context a model that reproduces this crossover. A study of the distribution of the Lyapunov exponents as a function of strain rate shows that it changes from a small set of positive exponents in the chaotic regime to a dense set of null exponents in the scaling regime. As the latter feature is similar to the GOY shell model for turbulence, we compare our results with the GOY model. Interestingly, the null exponents in our model themselves obey a power law. The configuration of dislocations is visualized through the slow manifold analysis. This shows that while a large proportion of dislocations are in the pinned state in the chaotic regime, most of them are at the threshold of unpinning in the scaling regime. The model qualitatively reproduces the different types of deformation bands seen in experiments. At high strain rates where propagating bands are seen, the model equations are reduced to the Fisher-Kolmogorov equation for propagative fronts. This shows that the velocity of the bands varies linearly with the strain rate and inversely with the dislocation density, consistent with the known experimental results. Thus, this simple dynamical model captures the complex spatio-temporal features of the PLC effect.Comment: 17 pages, 18 figure

Systematic Association of Genes to Phenotypes by Genome and Literature Mining

One of the major challenges of functional genomics is to unravel the connection between genotype and phenotype. So far no global analysis has attempted to explore those connections in the light of the large phenotypic variability seen in nature. Here, we use an unsupervised, systematic approach for associating genes and phenotypic characteristics that combines literature mining with comparative genome analysis. We first mine the MEDLINE literature database for terms that reflect phenotypic similarities of species. Subsequently we predict the likely genomic determinants: genes specifically present in the respective genomes. In a global analysis involving 92 prokaryotic genomes we retrieve 323 clusters containing a total of 2,700 significant gene–phenotype associations. Some clusters contain mostly known relationships, such as genes involved in motility or plant degradation, often with additional hypothetical proteins associated with those phenotypes. Other clusters comprise unexpected associations; for example, a group of terms related to food and spoilage is linked to genes predicted to be involved in bacterial food poisoning. Among the clusters, we observe an enrichment of pathogenicity-related associations, suggesting that the approach reveals many novel genes likely to play a role in infectious diseases

PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood

Phylogenetic patterns show the presence or absence of certain genes in a set of full genomes derived from different species. They can also be used to determine sets of genes that occur only in certain evolutionary branches. Previously, we presented a database named PhyloPat which allows the complete Ensembl gene database to be queried using phylogenetic patterns. Here, we describe an updated version of PhyloPat which can be queried by an improved web server. We used a single linkage clustering algorithm to create 241 697 phylogenetic lineages, using all the orthologies provided by Ensembl v49. PhyloPat offers the possibility of querying with binary phylogenetic patterns or regular expressions, or through a phylogenetic tree of the 39 included species. Users can also input a list of Ensembl, EMBL, EntrezGene or HGNC IDs to check which phylogenetic lineage any gene belongs to. A link to the FatiGO web interface has been incorporated in the HTML output. For each gene, the surrounding genes on the chromosome, color coded according to their phylogenetic lineage can be viewed, as well as FASTA files of the peptide sequences of each lineage. Furthermore, lists of omnipresent, polypresent, oligopresent and anticorrelating genes have been included. PhyloPat is freely available at http://www.cmbi.ru.nl/phylopat

Invertebrate traits, diversity and the vulnerability of groundwater ecosystems

Funding Information: This manuscript evolved from a workshop titled Trait‐based analyses in groundwater ecology and bioassessment held as part of the 24th International Conference on Subterranean Biology, 20–24th August 2018, University of Aveiro, Portugal. The workshop was supported by the conference organisers and the Macquarie University Species Spectrum Research Centre. Financial support was also provided to M.A.D. by the Portuguese government (Fundação para a Ciência e Tecnologia; FCT) through the research unit UIDB/04085/2020 (CENSE). A.S.P.S.R. was supported by the VILLUM FONDEN (research grant 15471) and by Portuguese National Funds through Fundação para a Ciência e a Tecnologia within the cE3c Unit funding UIDB/00329/2020. S.I.S. acknowledges funding through EU Operational Programme Research, Development and Education No. CZ.02.2.69/0.0/0.0/16_027/0008357, and by the Ministry of Education, Youth and Sports of the Czech Republic [grant number CZ.02.1.01/0.0/0.0/16 025/0007417]. K.L.K. was supported in part by Australian Research Council grant LP190100927. The comments of the Editor, Associate Editor and an anonymous reviewer greatly improved the MS. Open access publishing facilitated by Macquarie University, as part of the Wiley ‐ Macquarie University agreement via the Council of Australian University Librarians. Publisher Copyright: © 2022 The Authors. Functional Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.Groundwater comprises the largest freshwater ecosystem on the planet. It has a distinct regime of extreme, yet stable environmental conditions that have favoured the development of similar morphological and functional traits in the resident invertebrate fauna (stygofauna). The analysis of community traits is increasingly used as an alternative to taxonomy-based assessments of biodiversity, especially for monitoring ecosystem status and linking the functions of organisms to ecological processes, yet it has been rarely applied to stygofauna and groundwater ecosystems. In this paper, we review the variation in functional traits among the invertebrate fauna of this important ecosystem. We focus on the stygofauna and processes of alluvium and fractured rock aquifers that are typified by small voids and fissures that constrain the habitats and environmental conditions. As a first step, we compare trait variability between groundwater and surface water invertebrate communities and then examine the significance of the ranges of these traits to the vulnerability of the ecosystem to change. Fifteen potentially useful functional traits are recognised. Eight of these have narrower ranges (i.e. exhibit fewer states, or attributes, of a particular trait) in groundwater than they do in surface water. Two traits have wider ranges. Our synthesis suggests that the relative stability of groundwater environments has led to low trait variability. The low biomass and low reproductive rate of stygofauna suggest that recovery potential following disturbance is likely to be low. For the purposes of both improved understanding and effective management, further work is needed to document additional functional traits and their states in groundwater fauna, enabling a better understanding of the relationship between response and effect traits in these ecosystems. Read the free Plain Language Summary for this article on the Journal blog.publishersversionpublishe

Risk of infection in type 1 and type 2 diabetes compared with the general population: a matched cohort study

OBJECTIVE We describe in detail the burden of infections in adults with diabetes within a large national population cohort. We also compare infection rates between patients with type 1 and type 2 diabetes mellitus (T1DM and T2DM). RESEARCH DESIGN AND METHODS A retrospective cohort study compared 102,493 English primary care patients aged 40–89 years with a diabetes diagnosis by 2008 (n = 5,863 T1DM and n = 96,630 T2DM) with 203,518 age-sex-practice–matched control subjects without diabetes. Infection rates during 2008–2015, compiled from primary care and linked hospital and mortality records, were compared across 19 individual infection categories. These were further summarized as any requiring a prescription or hospitalization or as cause of death. Poisson regression was used to estimate incidence rate ratios (IRRs) between 1) people with diabetes and control subjects and 2) T1DM and T2DM adjusted for age, sex, smoking, BMI, and deprivation. RESULTS Compared with control subjects without diabetes, patients with diabetes had higher rates for all infections, with the highest IRRs seen for bone and joint infections, sepsis, and cellulitis. IRRs for infection-related hospitalizations were 3.71 (95% CI 3.27–4.21) for T1DM and 1.88 (95% CI 1.83–1.92) for T2DM. A direct comparison of types confirmed higher adjusted risks for T1DM versus T2DM (death from infection IRR 2.19 [95% CI 1.75–2.74]). We estimate that 6% of infection-related hospitalizations and 12% of infection-related deaths were attributable to diabetes. CONCLUSIONS People with diabetes, particularly T1DM, are at increased risk of serious infection, representing an important population burden. Strategies that reduce the risk of developing severe infections and poor treatment outcomes are under-researched and should be explored

Repression of the Sumo-Specific Protease SENP1 Induces P53-Dependent Premature Senescence in Normal Human Fibroblasts

The proliferative lifespan of normal somatic human cells in culture terminates in a permanent growth-arrested state known as replicative senescence. In this study, we show that RNA interference-mediated repression of the genes encoding the small ubiquitin-related modifier (SUMO)-specific proteases, Senp1, Senp2, and Senp7, induced low passage primary human fibroblasts to senesce rapidly. Following Senp1 repression, we observed a global increase in sumoylated proteins and in the number and size of nuclear SUMO-containing promyelocytic leukemia (PML) bodies. SUMO/PML bodies also increased during replicative senescence. p53 transcriptional activity was enhanced towards known p53 target genes following repression of Senp1, and inhibition of p53 function prevented senescence after Senp1 repression. These data indicate that Senp1 repression induces p53-mediated premature senescence and that SUMO proteases may thus be required for proliferation of normal human cells