Anharmonic properties from a generalized third order ab~initio approach: theory and applications to graphite and graphene

We have implemented a generic method, based on the 2n+1 theorem within density functional perturbation theory, to calculate the anharmonic scattering coefficients among three phonons with arbitrary wavevectors. The method is used to study the phonon broadening in graphite and graphene mono- and bi-layer. The broadening of the high-energy optical branches is highly nonuniform and presents a series of sudden steps and spikes. At finite temperature, the two linearly dispersive acoustic branches TA and LA of graphene have nonzero broadening for small wavevectors. The broadening in graphite and bi-layer graphene is, overall, very similar to the graphene one, the most remarkable feature being the broadening of the quasi acoustical ZO' branch. Finally, we study the intrinsic anharmonic contribution to the thermal conductivity of the three systems, within the single mode relaxation time approximation. We find the conductance to be in good agreement with experimental data for the out-of-plane direction but to underestimate it by a factor 2 in-plane

Ab initio variational approach for evaluating lattice thermal conductivity

We present a first-principles theoretical approach for evaluating the lattice thermal conductivity based on the exact solution of the Boltzmann transport equation. We use the variational principle and the conjugate gradient scheme, which provide us with an algorithm faster than the one previously used in literature and able to always converge to the exact solution. Three-phonon normal and umklapp collision, isotope scattering and border effects are rigorously treated in the calculation. Good agreement with experimental data for diamond is found. Moreover we show that by growing more enriched diamond samples it is possible to achieve values of thermal conductivity up to three times larger than the commonly observed in isotopically enriched diamond samples with 99.93% C12 and 0.07 C13

Spatio-temporal patterns of the European wildcat in a Mediterranean coastal area

Like most small felids, the European wildcat Felis silvestris is a rather elusive species, poorly detectable in the wild, due to several aspects of its biology. Camera trapping can represent a suitable tool to understand temporal activity patterns and habitat preferences of such elusive species. We used intensive camera trapping over two full years to investigate spatio-temporal patterns of the wildcat in a Mediterranean coastal protected area (Maremma Regional Park, central Italy). At the seasonal scale, the wildcat showed a marked twilight activity in summer and winter (mating period), and nocturnal activity in autumn. Conversely, a peak of activity during the day, i.e., in broad daylight, was reported in spring. Reproductive females may limit their nocturnal movements in spring to increase protection from predators to their kittens at the den, although further data are required to support this conclusion. At seasonal, semestral, and yearly temporal scales, the frequency of wildcat detections increased along with availability of shrubwood. These results emphasise the importance for this small felid of areas with dense vegetation cover (Mediterranean maquis and shrubwood, in our study area). Areas densely covered with shrubby vegetation are expected to provide benefits to this elusive small cat in terms of reduced human disturbance (included tourists), availability of prey (e.g., small mammals), as well as shelter, essential to ensure protection towards potential larger predators

The Mobilome-Enriched Genome of the Competence-Deficient Streptococcus pneumoniae BM6001, the Original Host of Integrative Conjugative Element Tn5253, Is Phylogenetically Distinct from Historical Pneumococcal Genomes

Streptococcus pneumoniae is an important human pathogen causing both mild and severe diseases. In this work, we determined the complete genome sequence of the S. pneumoniae clinical isolate BM6001, which is the original host of the ICE Tn5253. The BM6001 genome is organized in one circular chromosome of 2,293,748 base pairs (bp) in length, with an average GC content of 39.54%; the genome harbors a type 19F capsule locus, two tandem copies of pspC, the comC1-comD1 alleles and the type I restriction modification system SpnIII. The BM6001 mobilome accounts for 15.54% (356,521 bp) of the whole genome and includes (i) the ICE Tn5253 composite; (ii) the novel IME Tn7089; (iii) the novel transposon Tn7090; (iv) 3 prophages and 2 satellite prophages; (v) 5 genomic islands (GIs); (vi) 72 insertion sequences (ISs); (vii) 69 RUPs; (viii) 153 BOX elements; and (ix) 31 SPRITEs. All MGEs, except for the GIs, produce excised circular forms and attB site restoration. Tn7089 is 9089 bp long and contains 11 ORFs, of which 6 were annotated and code for three functions: integration/excision, mobilization and adaptation. Tn7090 is 9053 bp in size, flanked by two copies of ISSpn7, and contains seven ORFs organized as a single transcriptional unit, with genes encoding for proteins likely involved in the uptake and binding of Mg2+ cations in the adhesion to host cells and intracellular survival. BM6001 GIs, except for GI-BM6001.4, are variants of the pneumococcal TIGR4 RD5 region of diversity, pathogenicity island PPI1, R6 Cluster 4 and PTS island. Overall, prophages and satellite prophages contain genes predicted to encode proteins involved in DNA replication and lysogeny, in addition to genes encoding phage structural proteins and lytic enzymes carried only by prophages. & phi;BM6001.3 has a mosaic structure that shares sequences with prophages IPP69 and MM1 and disrupts the competent comGC/cglC gene after chromosomal integration. Treatment with mitomycin C results in a 10-fold increase in the frequency of & phi;BM6001.3 excised forms and comGC/cglC coding sequence restoration but does not restore competence for genetic transformation. In addition, phylogenetic analysis showed that BM6001 clusters in a small lineage with five other historical strains, but it is distantly related to the lineage due to its unique mobilome, suggesting that BM6001 has progressively accumulated many MGEs while losing competence for genetic transformation

Spatiotemporal Overlap between the European Brown Hare and Its Potential Predators and Competitors

Simple SummaryPredator-prey relationships and competition shape interspecific coexistence in wildlife communities. So far, most published studies have focused on large carnivores and their prey, whereas little is known about medium and small-sized mammal communities. The European brown hare Lepus europaeus is a widespread species in Europe and is part of the diet of many birds of prey and mammalian carnivores of all sizes. Furthermore, competition with other herbivorous mammals at feeding sites has also been suggested. In an area in Central Italy, we have assessed spatiotemporal overlap among brown hare and its potential predators (red fox Vulpes vulpes, pine marten Martes martes, domestic cat Felis catus, and domestic dog Canis familiaris) and a competitor (roe deer Capreolus capreolus). We showed that, outside a fenced area excluding predators and competitors, brown hares become more nocturnal and more active on dark nights to limit encounters with predators, and that they adopt spatial partitioning to avoid competitors, as expected by ecological theory.Analysis of spatiotemporal partitioning is pivotal to shed light on interspecific coexistence. Most research effort has involved large-sized carnivores and their prey, whereas little attention has been devoted to lagomorphs. We assessed spatiotemporal overlap among the European brown hare Lepus europaeus and its potential competitors and predators through camera-trapping in an area in Central Italy. We estimated the interspecific patterns of the spatiotemporal activity rhythms of brown hares, its potential predators (the red fox Vulpes vulpes, the pine marten Martes martes, the domestic cat Felis catus, and the domestic dog Canis familiaris), and a competitor, the roe deer Capreolus capreolus. Brown hare activity was studied in natural conditions as well as in a fenced area that excluded terrestrial predators and competitors. Free-ranging hares developed a more nocturnal behavior to avoid diurnal predators (i.e., domestic carnivores and martens). Although high temporal overlap was observed between free-ranging brown hares and both red foxes (82%) and roe deer (81%), hares avoided fox by being more active on darkest nights, as well as avoided roe deer through spatial partitioning. We suggest that hares may adapt their spatiotemporal behavior to avoid potential predators and competitors

CXCR3 and α_Eβ₇ integrin identify a subset of CD8+ mature thymocytes that share phenotypic and functional properties with CD8+ gut intraepithelial lymphocytes

Background: We previously demonstrated the existence of two distinct subsets of T cell receptor (TCR)αβ+CD8αβ+ single positive (SP) cells in human postnatal thymus which express the chemokine receptor CCR7 or CXCR3 and migrate in vitro in response to their specific ligands. Aim: To investigate whether these two CD8+ thymocyte subsets had distinct peripheral colonisation. Methods: TCRαβ+CD8+ SP cells were obtained from normal postnatal thymus, mesenteric lymph node (LNs), small bowel, and peripheral blood (PB) specimens. Cells were then evaluated for expression of surface molecules, cytolytic potential, telomere length, and profile of cytokine production. Results: CD8+CCR7+CXCR3− thymocytes exhibited CD62L, in common with those which localise to LNs. In contrast, CD8+CCR7−CXCR3+ thymocytes lacked CD62L but exhibited CD103, similar to intraepithelial lymphocytes (IELs) present in the gut mucosa where the CXCR3 ligand, CXCL10, and the CD103 ligand, E-cadherin, are highly and consistently expressed. In addition, thymocytes and gut CD8+CXCR3+CD103+ cells showed comparable telomere length, which was higher than that of PB CXCR3+CD8+ T cells. However, both of these populations contained perforin and granzyme A, and displayed the ability to produce interferon γ and interleukin 2. Of note, CXCR3 deficient, in comparison with wild-type C57Black/6, mice showed decreased proportions of CD3+CD8αβ+ and increased proportions of CD3+CD8αα+ lymphocytes at gut level. Moreover, adoptive transfer of CD3+CD8αβ+ thymocytes from wild-type into CXCR3 deficient mice resulted in a significant increase in CD3+CD8αβ+ T cells in the gut mucosa but not in other tissues. Conclusions: The results of this study demonstrate the existence of a previously unrecognised subset of TCRαβ+CD8αβ+ SP CXCR3+CD103+ thymocytes which share phenotypic and functional features with CD8+ IELs, thus suggesting the possibility of their direct colonisation of the gut mucosa

The rhythm of the night: patterns of~activity of the European wildcat in the Italian peninsula

The European wildcat is a threatened carnivore, whose ecology is still scarcely studied, especially in Mediterranean areas. In this study, we estimated activity rhythm patterns of this felid, by means of camera-trapping at three spatial scales: (i) whole country (Italy); (ii) biogeographical areas; (iii) latitudinal zones. The activity rhythms patterns were also calculated according to temporal scales: (1) warm semester; (2) cold semester and (3) seasonal scales. Lastly, we also tested whether the effect of moon phases affected the wildcat activity. We conducted the analysis on a total of 975 independent events collected in 2009-2021, from 285 locations, in 65,800 camera days. We showed that the wildcat in Italy exhibits a > 70% nocturnal behaviour, with 20% of diurnal activity, at all spatial scales, and throughout the whole year, with peaks at 10.00 p.m. and 04.00 a.m. We observed a high overlap of wildcat activity rhythms between different biogeographical and latitudinal zones. The wildcat was mainly active on the darkest nights, reducing its activity in bright moonlight nights. Diurnal activity was greater in the warm months and decreased with the distance from shrubs and woodlands, most likely according to activity rhythms of its main prey, water presence in summer, the care of offspring and the availability of shelter sites. Conversely, the distance to paved roads seems to have no significant effects on diurnal activity, suggesting that, in presence of natural shelters, the wildcat probably may tolerate these infrastructures. We suggested limited plasticity in activity rhythm patterns of the wildcat, emphasizing the importance of dark hours for this species