Quantum pumping and dissipation: from closed to open systems

Current can be pumped through a closed system by changing parameters (or fields) in time. The Kubo formula allows to distinguish between dissipative and non-dissipative contributions to the current. We obtain a Green function expression and an $S$ matrix formula for the associated terms in the generalized conductance matrix: the "geometric magnetism" term that corresponds to adiabatic transport; and the "Fermi golden rule" term which is responsible to the irreversible absorption of energy. We explain the subtle limit of an infinite system, and demonstrate the consistency with the formulas by Landauer and Buttiker, Pretre and Thomas. We also discuss the generalization of the fluctuation-dissipation relation, and the implications of the Onsager reciprocity.Comment: 4 page paper, 1 figure (published version) + 2 page appendi

Exact scaling in the expansion-modification system

This work is devoted to the study of the scaling, and the consequent power-law behavior, of the correlation function in a mutation-replication model known as the expansion-modification system. The latter is a biology inspired random substitution model for the genome evolution, which is defined on a binary alphabet and depends on a parameter interpreted as a \emph{mutation probability}. We prove that the time-evolution of this system is such that any initial measure converges towards a unique stationary one exhibiting decay of correlations not slower than a power-law. We then prove, for a significant range of mutation probabilities, that the decay of correlations indeed follows a power-law with scaling exponent smoothly depending on the mutation probability. Finally we put forward an argument which allows us to give a closed expression for the corresponding scaling exponent for all the values of the mutation probability. Such a scaling exponent turns out to be a piecewise smooth function of the parameter.Comment: 22 pages, 2 figure

Classical and quantum pumping in closed systems

Pumping of charge (Q) in a closed ring geometry is not quantized even in the strict adiabatic limit. The deviation form exact quantization can be related to the Thouless conductance. We use Kubo formalism as a starting point for the calculation of both the dissipative and the adiabatic contributions to Q. As an application we bring examples for classical dissipative pumping, classical adiabatic pumping, and in particular we make an explicit calculation for quantum pumping in case of the simplest pumping device, which is a 3 site lattice model.Comment: 5 pages, 3 figures. The long published version is cond-mat/0307619. This is the short unpublished versio

A segmented and clawed male foreleg in a newly described genus and species of eumaeine butterfly (Lepidoptera: Lycaenidae)

Grishinata Robbins and Busby, new genus (Lepidoptera: Lycaenidae: Eumaeini), possesses a five-segmented foretarsus with a clawed pretarsus, a trait that differentiates it from all eumaeine genera except Theclopsis Godman and Salvin. Grishinata penny Busby, Hall, and Robbins, new species, differs from all species of Theclopsis (and most Eumaeini) in lacking male secondary sexual organs on the wings or in the abdomen. It is recorded from the eastern slope of the Andes in Ecuador and Peru. We cannot place Grishinata penny in an existing Eumaeini genus based upon its wing pattern, male foreleg structure, lack of male second­ary sexual organs, and male genitalic morphology. We propose names for the genus and species to document its leg morphology and to provide a name for a genome sequencing project, which will allow us to place the genus in the eumaeine Linnaean hierarchy. There are two morphological types of male forelegs in the lepidopteran butterfly family Lycaenidae, each of which is functionally and structurally different from male forelegs in other diurnal butterfly families. The first male foreleg type is superficially similar to that of Nymphalidae and Riodinidae in that the tarsus is unsegmented, lacks a pretarsus, and is not used to groom the antennae (Robbins 1988, 1990). It differs functionally from these families in that it is used for walking. It differs morphologically in that it possesses tarsal alpha and beta trichoid sensilla (terminology from Chun and Schoonhoven 1973), which are lacking in Nymphalidae and Riodinidae with few exceptions (Robbins 1988). This male foreleg type occurs in more than 98% of lycaenid species (Mattoni and Fiedler 1991). The second lycaenid male foreleg type is superficially similar to that of Hesperiidae, Papilionidae, and Pieridae in that the foretarsus is segmented with a clawed pretarsus. It differs functionally from these families in that it is not used to groom the antennae (Jander 1966; Robbins 1990). It differs morphologically in that it lacks the tibial epiphysis of Hesperiidae and Papilionidae or the vestigial remnant of an epiphysis that occurs in some Pieridae (Robbins 1990). Within Eumaeini, this male foreleg type is restricted to some species of Theclopsis Godman and Salvin, 1887 (Godman and Salvin 1887; Robbins 2004). We discovered a species (Fig. 1) belonging to the Eumaeini with a male foreleg that has a clawed pretarsus and a five-segmented tarsus (Fig. 2), but the male genitalia, secondary sexual characters, and wing pattern (Fig. 1, 3) are dissimilar from those of Theclopsis. The males lack secondary sexual organs on the wings or in the abdomen (Fig. 1, 3), which is highly unusual in Eumaeini (Valencia-Montoya et al. 2021). The male genitalia (Fig. 3) lack structures that would be useful in determining its closest phylogenetic relatives. More generally, we find no clear-cut morphological evidence to place this species in an available eumaeine genus. The purpose of this paper is to propose new generic and specific names for this newly discovered taxon. One reason is that we need a name to document its unusual leg morphology. Another is that we are currently sequencing its genome for a phylogenetic project. Phylogenetic analysis of the sequence data will allow us to place the genus in the eumaeine Linnaean hierarchy. We predict that it will show, in accord with the findings of Mattoni and Fiedler (1991), that its male foreleg with a clawed pretarsus and five-segmented tarsus evolved from a tarsus that was fused without a pretarsus

Fluorite Precipitation in a Calcareous Soil Irrigated with High Fluoride Water

Lysimeters filled with Freedom silt loam soil (fine-silty, mixed, mesic, Xerollic Calciorthids) were irrigated with geothermal well water from south central Idaho. The water contained 7 mg F/L. Alfalfa (Medicago sativa L.) was grown in the lysimeters and the water was applied at a rate to give either a 0.30 or 0.15 leaching fraction. After irrigating the 1.0 m deep soil samples for 600 d, over 98% of the added F remained in the soil. Soil extract and lysimeter leachate analysis showed that fluorite precipitation was occurring in the upper profile, but only after another fluoride adsorption mechanism was saturated and the fluoride and calcium ion activities exceeded the CaF? ion activity product. The F concentration in the upper profile extracts exceeded 20 mg F/L and with the additional high F water irrigation, the soluble F would be expected to leach deeper in the soil. Under field conditions the F would be expected to eventually move into the groundwater with continued irrigation with high F water

An important developmental role for oligosaccharides during early embryogenesis of cyprinid fish

Derivatives of chitin oligosaccharides have been shown to play a role in plant organogenesis at nanomolar concentrations. Here we present data which indicate that chitin oligosaccharides are important for embryogenesis in vertebrates. We characterize chitin oligosaccharides synthesized in vitro by zebrafish and carp embryos in the late gastrulation stage by incorporation of radiolabeled N-acetyl-D-[(UC)-C-14]glucosamine and by HPLC in combination with enzymatic conversion using the Bradyrhizobium NodZ alpha-1,6-fucosyltransferase and chitinases. A rapid and sensitive bioassay for chitin oligasaccharides was also used employing suspension-cultured plant cells of Catharanthus roseus. We show that chitin oligosaccharide synthase activity is apparent only during late gastrulation and can be inhibited by anti-serum raised against the Xenopus DG42 protein. The DG42 protein, a glycosyltransferase, is transiently expressed between midblastula and neurulation in Xenopus and zebrafish embryogenesis. Microinjection of the DG42 antiserum or the Bradyrhizobium NodZ enzyme in fertilized eggs of zebrafish led to severs defects in trunk and tail development.Animal science

Tissue culture of ornamental cacti

Cacti species are plants that are well adapted to growing in arid and semiarid regions where the main problem is water availability. Cacti have developed a series of adaptations to cope with water scarcity, such as reduced leaf surface via morphological modifications including spines, cereous cuticles, extended root systems and stem tissue modifications to increase water storage, and crassulacean acid metabolism to reduce transpiration and water loss. Furthermore, seeds of these plants very often exhibit dormancy, a phenomenon that helps to prevent germination when the availability of water is reduced. In general, cactus species exhibit a low growth rate that makes their rapid propagation difficult. Cacti are much appreciated as ornamental plants due to their great variety and diversity of forms and their beautiful short-life flowers; however, due to difficulties in propagating them rapidly to meet market demand, they are very often over-collected in their natural habitats, which leads to numerous species being threatened, endangered or becoming extinct. Therefore, plant tissue culture techniques may facilitate their propagation over a shorter time period than conventional techniques used for commercial purposes; or may help to recover populations of endangered or threatened species for their re-introduction in the wild; or may also be of value to the preservation and conservation of the genetic resources of this important family. Herein we present the state-of-the-art of tissue culture techniques used for ornamental cacti and selected suggestions for solving a number of the problems faced by members of the Cactaceae family

Universal DNA methylation age across mammalian tissues

DATA AVAILABILITY STATEMENT : The individual-level data from the Mammalian Methylation Consortium can be accessed from several online locations. All data from the Mammalian Methylation Consortium are posted on Gene Expression Omnibus (complete dataset, GSE223748). Subsets of the datasets can also be downloaded from accession numbers GSE174758, GSE184211, GSE184213, GSE184215, GSE184216, GSE184218, GSE184220, GSE184221, GSE184224, GSE190660, GSE190661, GSE190662, GSE190663, GSE190664, GSE174544, GSE190665, GSE174767, GSE184222, GSE184223, GSE174777, GSE174778, GSE173330, GSE164127, GSE147002, GSE147003, GSE147004, GSE223943 and GSE223944. Additional details can be found in Supplementary Note 2. The mammalian data can also be downloaded from the Clock Foundation webpage: https://clockfoundation.org/MammalianMethylationConsortium. The mammalian methylation array is available through the non-profit Epigenetic Clock Development Foundation (https://clockfoundation.org/). The manifest file of the mammalian array and genome annotations of CpG sites can be found on Zenodo (10.5281/zenodo.7574747). All other data supporting the findings of this study are available from the corresponding author upon reasonable request. The chip manifest files, genome annotations of CpG sites and the software code for universal pan-mammalian clocks can be found on GitHub95 at https://github.com/shorvath/MammalianMethylationConsortium/tree/v2.0.0. The individual R code for the universal pan-mammalian clocks, EWAS analysis and functional enrichment studies can be also found in the Supplementary Code.SUPPLEMENTARY MATERIAL 1 : Supplementary Tables 1–3 and Notes 1–6.SUPPLEMENTARY MATERIAL 2 : Reporting SummarySUPPLEMENTARY MATERIAL 3 : Supplementary Data 1–14.SUPPLEMENTARY MATERIAL 4 : Supplementary Code.Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,754 methylation arrays from our Mammalian Methylation Consortium, which encompass 59 tissue types across 185 mammalian species. These predictive models estimate mammalian tissue age with high accuracy (r > 0.96). Age deviations correlate with human mortality risk, mouse somatotropic axis mutations and caloric restriction. We identified specific cytosines with methylation levels that change with age across numerous species. These sites, highly enriched in polycomb repressive complex 2-binding locations, are near genes implicated in mammalian development, cancer, obesity and longevity. Our findings offer new evidence suggesting that aging is evolutionarily conserved and intertwined with developmental processes across all mammals.https://www.nature.com/nataginghj2024Zoology and EntomologySDG-15:Life on lan

Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial

Dimethyl fumarate (DMF) inhibits inflammasome-mediated inflammation and has been proposed as a treatment for patients hospitalised with COVID-19. This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple treatments in patients hospitalised for COVID-19 (NCT04381936, ISRCTN50189673). In this assessment of DMF performed at 27 UK hospitals, adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. Between 2 March 2021 and 18 November 2021, 713 patients were enroled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients received corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.86-1.47; p = 0.40). There was no significant effect of DMF on any secondary outcome