Miracle-dz/UniFAR-FTUs huggingface dataset:
PERSPECTIVE:SIGN EPISTASIS AND GENETIC CONSTRAINT ON EVOLUTIONARY TRAJECTORIES

Abstract Epistasis for fitness means that the selective effect of a mutation is conditional on the genetic background in which it appears. Although epistasis is widely observed in nature, our understanding of its consequences for evolution by natural selection remains incomplete. In particular, much attention focuses only on its influence on the instantaneous rate of changes in frequency of selected alleles via epistatic contribution to the additive genetic variance for fitness. Thus, in this framework epistasis only has evolutionary importance if the interacting loci are simultaneously segregating in the population. However, the selective accessibility of mutational trajectories to high fitness genotypes may depend on the genetic background in which novel mutations appear, and this effect is independent of population polymorphism at other loci. Here we explore this second influence of epistasis on evolution by natural selection. We show that it is the consequence of a particular form of epistasis, which we designate sign epistasis. Sign epistasis means that the sign of the fitness effect of a mutation is under epistatic control; thus, such a mutation is beneficial on some genetic backgrounds and deleterious on others. Recent experimental innovations in microbial systems now permit assessment of the fitness effects of individual mutations on multiple genetic backgrounds. We review this literature and identify many examples of sign epistasis, and we suggest that the implications of these results may generalize to other organisms. These theoretical and empirical considerations imply that strong genetic constraint on the selective accessibility of trajectories to high fitness genotypes may exist and suggest specific areas of investigation for future research.
Practical uses for ecdysteroids in mammals including humans: and update

Abstract Ecdysteroids are widely used as inducers for gene-switch systems based on insect ecdysteroid receptors and genes of interest placed under the control of ecdysteroid-response elements. We review here these systems, which are currently mainly used in vitro with cultured cells in order to analyse the role of a wide array of genes, but which are expected to represent the basis for future gene therapy strategies. Such developments raise several questions, which are addressed in detail. First, the metabolic fate of ecdysteroids in mammals, including humans, is only poorly known, and the rapid catabolism of ecdysteroids may impede their use as in vivo inducers. A second set of questions arose in fact much earlier with the pioneering “heterophylic” studies of Burdette in the early sixties on the pharmacological effects of ecdysteroids on mammals. These and subsequent studies showed a wide range of effects, most of them being beneficial for the organism (e.g. hypoglycaemic, hypocholesterolaemic, anabolic). These effects are reviewed and critically analysed, and some hypotheses are proposed to explain the putative mechanisms involved. All of these pharmacological effects have led to the development of a wide array of ecdysteroid-containing preparations, which are primarily used for their anabolic and/or “adaptogenic” properties on humans (or horses or dogs). In the same way, increasing numbers of patents have been deposited concerning various beneficial effects of ecdysteroids in many medical or cosmetic domains, which make ecdysteroids very attractive candidates for several practical uses. It may be questioned whether all these pharmacological actions are compatible with the development of ecdysteroid-inducible gene switches for gene therapy, and also if ecdysteroids should be classified among doping substances.
Species composition and invasion in NW Argentinian secondary forests: Effects of land use history, environment and landscape

Abstract Successional patches are a large component of forest ecosystems throughout the world and their vegetation composition is conditioned by multiple factors such as land use history, disturbances, environmental conditions and landscape context. We investigated the relative contribution of historical, environmental, biotic and spatial factors in determining vegetation composition and invasion by exotic species in secondary forest patches of Sierra de San Javier, Tucumán, Argentina. We estimated canopy cover for shrub, vine and tree species distributed over 51 patches with known land use history. We also recorded environmental, historical and spatial variables and used multivariate techniques to explore the relationship between forest composition and explanatory variables. Land use, time since abandonment, altitude, slope and cover of different strata were related to the vegetation pattern in the study site, and they were all significantly structured over space. Exotic species appeared to differ from natives in their response to explanatory variables. Overall, exotic species were dominant on the edges of young patches originated from herbaceous crops, but the total number of exotic species was related to the distance to urban areas and small farms identified as potential sources of exotic propagules. Vegetation composition of secondary forests in NW Argentina was related to historical and environmental factors, but spatial variables strongly influenced vegetation composition as well as the variation in explanatory variables. Nomenclature: Dimitri (1988); Digilio & Legname (1966). Abbreviations: GPS = Global positioning system; MRPP = Multi response permutation procedure; NMDS = Non-metric Multidimensional Scaling; PBSSJ = Parque Biológico Sierra de San Javier; UTM = Universal Transverse Mercator system.
The Swedish Regional Climate Modelling Programme, SWECLIM: A Review

The Swedish Regional Climate Modelling Programme, SWECLIM, was a 6.5-year national research network for regional climate modeling, regional climate change projections and hydrological impact assessment and information to a wide range of stakeholders. Most of the program activities focussed on the regional climate system of Northern Europe. This led to the establishment of an advanced, coupled atmosphere-ocean-hydrology regional climate model system, a suite of regional climate change projections and progress on relevant data and process studies. These were, in turn, used for information and educational purposes, as a starting point for impact analyses on different societal sectors and provided contributions also to international climate research.
INBREEDING IN THE GREATER WHITE-TOOTHED SHREW, CROCIDURA RUSSULA

Abstract We combined mark-and-recapture studies with genetic techniques of parentage assignment to evaluate the interactions between mating, dispersal, and inbreeding, in a free-ranging population of Crocidura russula. We found a pattern of limited and female-biased dispersal, followed by random mating within individual neighborhoods. This results in significant inbreeding at the population level: mating among relatives occurs more often than random, and FIT analyses reveal significant deficits in heterozygotes. However, related mating partners were not less fecund, and inbred offspring had no lower lifetime reproductive output. Power analyses show these negative results to be quite robust. Absence of phenotypic evidence of inbreeding depression might result from a history of purging: local populations are small and undergo disequilibrium gene dynamics. Dispersal is likely caused by local saturation and (re)colonization of empty breeding sites, rather than inbreeding avoidance.
The Vertebrate Body Axis: Evolution and Mechanical Function1

Synopsis. The body axis of vertebrates is an integrated cylinder of bones, connective tissue, and muscle. These structures vary among living and extinct vertebrates in their orientation, composition, and function in ways that render useless simplistic models of the selective pressures that may have driven the evolution of the axis. Instead, recent experimental work indicates that the vertebrate axis serves multiple mechanical functions simultaneously: bending the body, storing elastic energy, transmitting forces from limbs, and ventilating the lungs. On the biochemical level, research on human intervertebral discs has shown that collagens resist tension and torsion while proteoglycans bind water to resist compression. This molecular behavior predicts mechanical behavior of the entire joint, which, in turn helps determine the mechanical behavior of the vertebral column. The axial skeleton, in turn, is reconfigured by axial muscles that work by way of three-dimensional connective tissues that derive mechanical advantage for the muscle force by using the skin to increase leverage. Models may eventually help determine which evolutionary changes in the vertebrate body axis have had important functional and possibly adaptational consequences. Current reconstruction of the hypothetical stem lineage of early chordates and vertebrates suggests that the gradual mineralization of the vertebral elements, appearance of fin rays and new median fins, and transverse and then horizontal segmentation of the axial musculature are all features correlated with increases in swimming speed, maneuverability, and body size.
Influence of Ozone-Related Increases in Ultraviolet Radiation on Antarctic Marine Organisms1

Abstract Every spring for the past two decades, depletion of stratospheric ozone has caused increases in ultraviolet B radiation (UVB, 280–320 nm) reaching Antarctic terrestrial and aquatic habitats. Research efforts to evaluate the impact of this phenomenon have focused on phytoplankton under the assumption that ecosystem effects will most likely originate through reductions in primary productivity; however, phytoplankton do not represent the only significant component in ecosystem response to elevated UVB. Antarctic bacterioplankton are adversely affected by UVB exposure; and invertebrates and fish, particularly early developmental stages that reside in the plankton, are sensitive to UVB. There is little information available on UV responses of larger Antarctic marine animals (e.g., birds, seals and whales). Understanding the balance between direct biological damage and species-specific potentials for UV tolerance (protection and recovery) relative to trophic dynamics and biogeochemical cycling is a crucial factor in evaluating the overall impact of ozone depletion. After more than a decade of research, much information has been gathered about UV-photobiology in Antarctica; however, a definitive quantitative assessment of the effect of ozone depletion on the Antarctic ecosystem still eludes us. It is only obvious that ozone depletion has not had a catastrophic effect in the Antarctic region. The long-term consequences of possible subtle shifts in species composition and trophic interactions are still uncertain.
Helophyte germination in a Mediterranean salt marsh: Gut-passage by ducks changes seed response to salinity

Question: In seeds which are regularly consumed by waterbirds in the field, how does gut–passage modify their response to salinity gradients? Location: Donana National Park salt marsh, south-west of Spain. Methods: Seeds of Scirpus litoralis and Scirpus maritimus were collected and force fed to mallards (Anas platyrhynchos). Both the ingested seeds (passage) and non-ingested seeds (controls) were exposed, in germination chambers, to a salinity range similar to that observed in the field (0-32 dS/m). After 30 days, the total percentage germination, the duration of the dormancy period and the germination speed were computed. The response of the different germination parameters to ingestion and salinity was analyzed using generalized lineal models. Recovery tests on seeds that did not germinate in the various treatments and tests of the effect of ingestion on the intrinsic variability in seed response were also performed. Results: An increase in salinity reduced germinability and increased the length of dormancy, while gut passage increased the intrinsic variability of the temporal seed response in both species. In S. litoralis there was a significant interaction between the effects of salinity and passage on germination rate. Passage increased germination rate at low salinities (≤2 dS/m) but decreased it at high salinities (≥4 dS/m). Conclusion: Gut-passage by ducks significantly changes seed response to salinity. The outcome of plant-animal interactions can be influenced by environmental gradients. Studies of germination in response to gut passage that do not take such gradients into account may produce misleading results.
The Behavioral Ecology of Intermittent Locomotion1

Abstract Most physiological and ecological approaches to animal locomotion are based on steady state assumptions, yet movements of many animals are interspersed with pauses lasting from milliseconds to minutes. Thus, pauses, along with changes in the duration and speed of moves, form part of a dynamic system of intermittent locomotion by which animals adjust their locomotor behavior to changing circumstances. Intermittent locomotion occurs in a wide array of organisms from protozoans to mammals. It is found in aerial, aquatic and terrestrial locomotion and in many behavioral contexts including search and pursuit of prey, mate search, escape from predators, habitat assessment and general travel. In our survey, animals exhibiting intermittent locomotion paused on average nearly 50% of their locomotion time (range 6–94%). Although intermittent locomotion is usually expected to increase energetic costs as a result of additional expenditure for acceleration and deceleration, a variety of energetic benefits can arise when forward movement continues during pauses. Endurance also can be improved by partial recovery from fatigue during pauses. Perceptual benefits can arise because pauses increase the capacity of the sensory systems to detect relevant stimuli. Several processes, including velocity blur, relative motion detection, foveation, attention and interference between sensory systems are probably involved. In animals that do not pause, alternative mechanisms for stabilizing the perceptual field are often present. Because movement is an important cue for stimulus detection, pauses can also reduce unwanted detection by an organism's predators or prey. Several models have attempted to integrate energetic and perceptual processes, but many challenges remain. Future advances will require improved quantification of the effects of speed on perception.
PHYLOGENETIC ANALYSIS OF CORRELATION STRUCTURE IN STALK-EYED FLIES (DIASEMOPSIS, DIOPSIDAE)

Morphological divergence among species may be constrained by the pattern of genetic variances and covariances among traits within species. Assessing the existence of such a relationship in nature requires information on the stability of intraspecific correlation and covariance structure and the correspondence of this structure to the pattern of evolutionary divergence within a lineage. Here, we investigate these issues for nine morphological traits and 15 species of stalk-eyed flies in the genus Diasemopsis. Within-species matrices for these traits were generated from phenotypic data for all the Diasemopsis species and from genetic data for a single Diasemopsis species, D. dubia. The among-species pattern of divergence was assessed by calculating the evolutionary correlations for all pairwise combinations of the morphological traits along the phylogeny of these species. Comparisons of intraspecific matrices reveal significant similarity among all species in the phenotypic correlations matrices but not the covariance matrices. In addition, the differences in correlation structure that do exist among species are not related to their phylogenetic placement or change in the means of the traits. Comparisons of the phenotypic and phylogenetic matrices suggest a strong relationship between the pattern of evolutionary change among species and both the intraspecific correlation structure and the stability of this structure among species. The phenotypic and the phylogenetic matrices are significantly similar, and pairs of traits whose intraspecific correlations are more stable across taxa exhibit stronger coevolution on the phylogeny. These results suggest either the existence of strong constraints on the pattern of evolutionary change or a consistent pattern of correlated selection shaping both the phenotypic and phylogenetic matrices. The genetic correlation structure for D. dubia, however, does not correspond with patterns found in the phenotypic and phylogenetic data. Possible reasons for this disagreement are discussed.
On the Style and Translation of Benjamins A Lyric Poet in the Era of High Capitalism

W.Benjamin's Charles Baudelaire:A lyric Poet in the Era of High Capitalism has drawn wild attention to Chinese academic circles,and has been,therefore,translated into three Chinese versions.This paper discusses the understanding toward the style of WB's text and its impact on translation.The author argues that,the “poetic thinking” of WB is not literary imagination,but rather,is embodied as “image montage”. All of the images have clear implications from historical or literary references.As this “image montage” is the unique style of WB's text,when being translated,the images involved should be exactly and clearly interpreted according to their signified(signifie)in history or literature.The author specifically discusses several approaches applied to correctly interpret WB's text in the translation:to use or invent a Chinese specific term for the specific image;to interpret image with its signifie;to retain the image of idiom.
Chlorophyll a Self-assembly in Polar Solvent–Water Mixtures†

Abstract The conversion of chlorophyll a (Chl a) monomers into large aggregates in six polar solvents upon addition of water has been studied by means of absorption, fluorescence spectroscopy and fluorescence lifetime measurements for the purpose of elucidating the various environmental factors promoting Chl a self-assembly and determining the type of its organization. Two empirical solvent parameter scales were used for quantitative characterization of the different solvation properties of the solvents and their mixtures with water. The mole fractions of water f1/2 giving rise to the midpoint values of the relative fluorescence quantum yield were determined for each solvent, and then various solvent–water mixture parameters for the f1/2 values were compared. On the basis of their comparison, it is concluded that the hydrogen-bonding ability and the dipole–dipole interactions (function of the dielectric constant) of the solvent–water mixtures are those that promote Chl a self-assembly. The influence of the different nature of the nonaqueous solvents on the Chl aggregation is manifested by both the different water contents required to induce Chl monomer → aggregate transition and the formation of two types of aggregates at the completion of the transition: species absorbing at 740–760 nm (in methanol, ethanol, acetonitrile, acetone) and at 667–670 nm (in pyridine and tetrahydrofuran). It is concluded that the type of Chl organization depends on the coordination ability and the polarizability (function of the index of refraction) of the organic solvent. The ordering of the solvents with respect to the f1/2 values—methanol < ethanol < acetonitrile < acetone < pyridine < tetrahydrofuran—yielded a typical lyotropic (Hofmeister) series. On the basis of this solvent ordering and the disparate effects of the two groups of solvents on the Chl a aggregate organization, it is pointed out that the mechanism of Chl a self-assembly in aqueous media can be considered a manifestation of the Hofmeister effect, as displayed in the lipid-phase behavior (Koynova et al., Eur. J. Biophys. 25, 261–274, 1997). It relates to the solvent ability to modify the bulk structure and to distribute unevenly between the Chl–water interface and bulk liquid.
Using Phylogenies to Study Convergence: The Case of the Ant-Eating Mammals1

Abstract Identifying when homoplasy is due to convergence requires confidence in trees and precise analysis of potentially convergent characters. Some features of mammals that eat mostly ants and termites are used as examples of convergence; the most speciose assemblages of these mammals are in the orders Xenarthra and Pholidota. My studies on cranial muscles in xenarthrans and pholidotans aim to 1) precisely describe the anatomy in ant-eating and non-ant-eating lineages, 2) assess variation among ant-eating lineages, and 3) compare the most derived conditions (in xenarthran anteaters and pholidotan pangolins). These data clarify the nature of morphological adaptation in ant-eating mammals, and when combined with accumulating phylogenetic studies, allow us to distinguish features that have evolved convergently from those that are variable but not correlated with diet. Interpreting the extreme similarity in anteaters and pangolins remains problematic due to lingering disagreement among phylogenetic hypotheses. Prevailing opinion favors interpretation of these similarities as convergent.
The Binding Characteristics and Intracellular Localization of Temoporfin (mTHPC) in Myeloid Leukemia Cells: Phototoxicity and Mitochondrial Damage¶

Abstract The state of aggregation of the photosensitizer meso-tetrahydroxyphenylchlorin (mTHPC) in both cell free and intracellular environment was elucidated by comparing its absorption and excitation spectra. In methanol, mTHPC existed as monomers and strongly fluoresced. In aqueous solutions such as phosphate-buffered saline (PBS), mTHPC formed nonfluorescent aggregates. Some portion of mTHPC monomerized in the presence of 10% fetal calf serum PBS. In murine myeloid leukemia M1 and WEHI-3B (JCS) cells, cytoplasmic mTHPC were monomeric. By using organelle-specific fluorescent probes, it was found that mTHPC localized preferentially at the mitochondria and the perinuclear region. Photodynamic treatment of mTHPC-sensitized leukemia cells caused rapid appearance of the apoptogenic protein cytochrome c in the cytosol. Results from flow cytometric analysis showed that the release of cytochrome c was especially pronounced in JCS cells, and well correlated with the extent of apoptotic cell death as reported earlier. Electron microscopy revealed the loss of integrity of the mitochondrial membrane and the appearance of chromatin condensation as early as 1 h after light irradiation. We conclude that rapid release of cytochrome c from photodamaged mitochondria is responsible for the mTHPC-induced apoptosis in the myeloid leukemia JCS and M1 cells.
The Rossby Centre Regional Atmospheric Climate Model Part I: Model Climatology and Performance for the Present Climate over Europe

The Rossby Centre Atmospheric Regional Climate Model (RCA2) is described and simulation results, for the present climate over Europe, are evaluated against available observations. Systematic biases in the models mean climate and climate variability are documented and key parameterization weaknesses identified. The quality of near-surface parameters is investigated in some detail, particularly temperature, precipitation, the surface energy budget and cloud cover. The model simulates the recent, observed climate and variability with a high degree of realism. Compensating errors in the components of the surface radiation budget are highlighted and the fundamental causes of these biases are traced to the relevant aspects of the cloud, precipitation and radiation parameterizations. The model has a tendency to precipitate too frequently at small rates, this has a direct impact on the simulation of cloud-radiation interaction and surface temperatures. Great care must be taken in the use of observations to evaluate high resolution RCMs, when they are forced by analyzed boundary conditions. This is particularly true with respect to precipitation and cloudiness, where observational uncertainty is often larger than the RCM bias.