Miracle-dz/UniFAR-FTUs huggingface dataset:
Extreme migration and the individual quality spectrum

Costs of migration, in terms of time, energy, and mortality risk, have a strong theoretical and empirical foundation in the study of birds. We expect these costs to be most severe for extreme long-distance migratory landbirds, whose demanding annual routines (e.g. non-stop flights > 8000 km and return journeys > 30 000 km) may approach their maximum physiological capabilities. To explore whether this is true, we review evidence in long-jump migratory shorebirds (Scolopacidae), focusing most on the prototypical example, the Alaska-breeding bar-tailed godwit Limosa lapponica baueri. Contrary to expectations, these and similar birds demonstrate high adult survival, little evidence for elevated mortality during migration, no apparent minimisation of non-stop flight distances, and low inter- and intra-individual variation in migration performance. Two key aspects of extreme migrants may explain these findings: 1) a counter-intuitively conservative annual-cycle strategy, which minimises risks and enables dissipation of carry-over effects before fitness consequences arise; and 2) selection pressure during early life, which quickly removes low-performing individuals from the population. We hypothesise that these two factors, applicable to extreme strategies in a wide range of taxa, act to truncate the range of individual quality in a population, and decrease the prevalence and detectability of carry-over effects. Testing these hypotheses is challenging, as it requires comparative studies of demography and individual quality spectra along a continuum of extremeness. However, it has important potential implications for interpreting individual variation, designing studies of cross-seasonal interactions or costs of migration, and recognising early-warning signs of population decline. For example, the most extreme shorebird migrations rely on abundant but difficult-to-access resources; the high minimum individual performance required for survival predicts that degradation of these resource hot-spots will propel rapid population collapse, rather than incremental declines in condition or performance. Therefore, in extreme migrants, we may paradoxically view populations as operating close to the edge, even while individuals are not.
Structural Behavior of SFRC Beams strengthened with GFRP Laminates: An Experimental and Analytical Investigation

This paper presents the experimental results of a reinforced concrete beams (RC) strengthened with internal steel fibers (SF) and external glass fiber reinforced polymer laminates (GFRP). The research work studied the load carrying capacity, deformation, crack width and ductility of the reinforced concrete beams strengthened with different steel fiber ratios and steel fiber reinforced concrete beams strengthened with three different glass fiber reinforced polymer laminates of two different thickness. The experimental results clearly shows that incorporating steel fibers in to the reinforced concrete beams reduced the crack width and distribute the crack evenly and also increases the bonding between tension face of the beam with glass fiber reinforced polymer laminates. The results also shows that glass fiber reinforced polymer laminates strengthened steel fiber reinforced concrete beams increases the flexural strength and ductility as compared with unstrengthened counterpart. In addition to this experimental work, theoretical calculations were done to find the ultimate load carrying capacity of the beam tested, and also compared with the experimental results.
Migration and parasitism: habitat use, not migration distance, influences helminth species richness in Charadriiform birds

Habitat use and migration strategies of animals are often associated with spatial variation in parasite pressure, but how they relate to one another is not well understood. Here, we use a large dataset on helminth species richness of Charadriiform birds to test whether higher habitat diversity and seasonal migration increase parasite richness in avian hosts.
Effect of landscape variables on the long-term decline of Great Argus in the rainforest of Southern Thailand

Summary In Thailand, as for most of South-East Asia, large vertebrates are declining rapidly due to habitat degradation and increasing hunting pressure. Once relatively common in the evergreen forest of Southern Thailand, the Great Argus Argusianus argus is currently limited to a few populations, whose status is currently unknown. In this study we investigated changes in Great Argus abundance over the past 13 years in Hala-Bala Wildlife Sanctuary. Our aim was to estimate and compare the abundance and density of this species from an earlier two-year survey in 2001–2002 and ours in 2014, and to assess the effect of landscape change on its status of the species. We conducted surveys from March to August 2014 during the breeding season. We placed point counts that overlapped the line transects from the 2001–2002 survey. The results indicated a decline of > 35% in mean abundance from 2001 to 2014. In addition, male abundance has shifted and is now positively related to distance from the forest edge. High levels of human disturbance close to the forest edge may have resulted in the birds moving to the core of the forest, suggesting a need to increase protection and management of forest edge areas. In common with other studies of large vertebrates, our results confirm the importance of long-term studies to highlight the negative effects of human disturbance.
A trait‐based framework for discerning drivers of species co‐occurrence across heterogeneous landscapes

Null model analysis of species co-occurrence patterns has long been used to gain insight into community assembly but is often limited to identifying non-random patterns without providing clarity about underlying ecological mechanisms. This challenge is especially apparent when sampling units are spread across a heterogeneous landscape or along an environmental gradient because multiple mechanisms can produce similar co-occurrence patterns. We developed a trait-based approach for discriminating between environmental filtering and biotic interactions as the probable driver of cooccurrence patterns across environmentally heterogeneous sites. We demonstrate our framework by analyzing the co-occurrence of small mammals over elevation in three independent mountain ranges in the Great Basin of the western United States. Our sampling design accounts for landscape scale environmental variability and within-site habitat heterogeneity. We identified 52 non-random species pairs, of which 36 were aggregated and 16 were segregated. For each pair, we determined which mechanism was the likely ecological explanation using a hypothesis-testing framework based on functional trait similarity. Expectations of biotic interactions were based on similarity of diet and body size whereas habitat affinity and geographic range were used for environmental filtering. Only four pairs were consistent with expectations under biotic interactions, including pairs for which competitive exclusion has previously been documented. In addition to analyzing individual pairs, we used binomial tests of observed versus expected totals of intraand inter-guild pairs to determine assemblage-wide deviations from random community structure. Signatures of environmental filtering were consistent across mountain ranges and scales. Despite differences in species composition and significant pairs among data sets, our approach revealed consistent mechanistic conclusions, emphasizing the value of trait-based methods to co-occurrence and community assembly.
An investigation of DNA damage induced by oxidative stress in neuronal cells

This project aimed to investigate the hypothesis that oxidative DNA damage has a role in neuronal dysfunction. Reactive oxygen species (ROS) are known to damage important cellular macromolecules, including DNA. They have been implicated in many pathological conditions, including common neurodegenerative disorders, but the mechanisms of cellular dysfunction and death involved remain unclear. Oxidative DNA damage was therefore studied in an in vitro model system and pathological tissue. A novel, sensitive assay based on the fortuitous finding that avidin binds directly to the DNA lesion 8-oxodeoxyguanosine (8-oxodG) was used in these investigations. Pre-lethal DNA damage was assessed in terminally differentiated human neuroblastoma IMR32 cultures after exposure to various forms of oxidative stress (hydrogen peroxide, UVA irradiation and paraquat). Avidin binding was significantly increased in these cells, indicating the presence of oxidative DNA damage; repairable and non-repairable damage were both detected. Binding was decreased by pre-incubation with the antioxidant a-tocopherol or iron chelator desferrioxamine, demonstrating the involvement of ROS in the mechanism of DNA damage induced during oxidative stress. Avidin binding was also assessed visually in cells exposed to hydrogen peroxide via fluorescent microscopy, and was shown to be located primarily within the nucleus. Once again, levels of damage were decreased after incubation with a-tocopherol. Finally preliminary studies were carried out to assess levels of oxidatively-damaged DNA in spinal cord sections from patients suffering from MND compared to age-matched control subjects. Binding was once again detected directly in situ using immunofluorescence microscopy. The novel methodology used allows the demonstration of oxidative DNA damage directly in situ, something not previously possible, but is only semi-quantitative, and more work is needed to assess the precise site and mechanism of avidin binding. However, the direct demonstration of damage may help elucidate the mechanisms involved in cellular dysfunction produced by oxidative stress, and so might provide a greater understanding of the causes of the most common neurodegenerative diseases
Communities and occurrences of Squamata reptiles in different vegetation types of the Serra de São José, Minas Gerais, Brazil

The objective of the present study was to learn which species of Squamata reptiles occur in Protected Area Sao Jose, in Tiradentes, Minas Gerais, Brazil. Between November 2009 and December 2010 reptiles were captured. In total 157 specimens were recorded of 29 species, 16 snakes, 12 lizards and one amphisbaena. Among the snakes, Dipsadidae showed the greatest richness, with a total of nine species. The group of snakes had the highest number of species present in the community, but 79% of sampled specimens were lizards, Enyalius bilineatus being the most abundant species, with 21% of occurrence. The area with the highest richness was the Cerradao. The lower abundance was found in the Gallery Forest area (n=14), but it was the vegetation type with the highest equitability. Areas of Cerradao and Cerrado sensu strictu showed the most similarity. In these areas five species were recorded in common, Bothrops neuwiedi (n=3) being the only species of snake, and the two species of lizards most abundant in both environments were Enyalius bilineatus (n=32) and Ameivula ocellifera (n=19). Ophiodes striatus and Xenodon merremii were common to Cerradao and Dirty Field areas. There was no species recorded that were common to the environments of Cerrado and Dirty Field but two species not sympatric were found of the same genus, Tropidurus torquatus, which was found only in the Cerrado sensu strictu and Tropidurus itambere exclusively in Dirty Field. Since none of the rarefaction curves reached full asymptote, this highlights the need for further study due to the high probability of new species being recorded for the studied area.
Anatomical characters and SEM structure of radula and shell in the species-level taxonomy of freshwater prosobranchs (Mollusca: Gastropoda: Prosobranchia) comparative usefulness study

The paper, based on 15 prosobranch species inhabiting freshwater habitats in Poland, is devoted to a comparative analysis of the usefulness of several taxonomical characters. Such commonly used characters as: shell “macrocharacters”, operculum, soft part external morphology and pigmentation, ctenidium and osphradium, male and female reproductive organs and penis have already been described in detail in earlier papers of the author: in this paper they are essentially characterized and illustrated for comparative purposes. The paper presents descriptions of SEM structures of the radula, protoconch habitus and outer surface, teleoconch outer and inner surfaces and teleoconch inner structure visible on sections parallel and perpendicular to the growth lines of the shell, for all the 15 species. The descriptions are illustrated with 336 SEM micrographs. Then, all the characters are discussed considering their taxonomical usefulness. It is pointed out that all the characters show a more or less restricted usefulness. On the other hand, the SEM shell structural characters prove not less useful in taxonomy than “good” conventionally used ones. In Appendix II the author has described concisely the general organization of the shell of the studied prosobranchs. Key WordS: shell, operculum, soft part, morphology, pigmentation, ctenidium, osphradium, reproductive organs, radula, protoconch sculpture, teleoconch sculpture/inner structure Folia Malacologica 4/1990 was originally published as No. 1276 of Scientific Bulletins of University of Mining and Metallurgy, Cracow. This digitalised version was prepared by the Association of Polish Malacologists and first published on-line on December 30th, 2016. http://dx.doi. org/10.12657/folmal.004. 005 Folia Malacol. 4: 53–142
Morphology, Pathogenicity and Molecular Identification of Fusarium spp. Associated with Anise Seeds in Serbia

Anise (Pimpinella anisum L.) is an important medicinal spice plant that belongs to the family Apiaceae. Anise seeds are rich in essential oils and this is a reason why anise production in Serbia has increased over the last decade. During a routine health inspection on anise seeds collected from three localities in the province of Vojvodina (MoAiorin, Veliki Radinci and OstojiA‡evo) during 2012 and 2013, it was found out that Fusarium spp. were a commonly observed fungi. The presence of Fusarium fungion the seed samples ranged from 3.75-13.75%. The aim of this study was to isolate and identify the strains of Fusarium species present on anise seed samples as it is necessary that commercially used anise seeds are completely free of Fusarium. Based on morphological, microscopic characteristics and a molecular identification by sequencing of TEF gene, the presence of the following species was confirmed on the anise seeds: F. tricinctum, F. proliferatum, F. equiseti, F. oxysporum, F. sporotrichoides, F. incarnatum and F. verticillioides. According to our knowledge and research, this is the first report of F. tricinctum and F. sporotrichoides as pathogens on anise seeds in the world. All seven isolates of Fusarium species are pathogenic to the anise seedlings, while the most virulent species were F. oxysporum, F. tricinctum and F. incarnatum.
The role of phosphatidylinositol-specific phospholipase-C in plant defense signaling

Plant innate immunity requires immune receptors that sense the presence of microbes and activate defense reactions. Phosphatidylinositol-phospholipase C (PI-PLC) activity was previously shown to be important for several types of plant defenses although its signaling mechanism is not fully understood. It is also not clear why plants possess several PI-PLC isoforms and how triggering immune receptors activates them. PI-PLC activation induces a transient release of free cytosolic Ca2+ and the turnover of specific low abundant signaling phospholipids in the plasma membrane. Both events are important signals in animals and plants. Here, the first genetic evidence linking PI-PLC signaling to plant defense against pathogens is provided. The structure of the tomato PI-PLC family was determined, the corresponding genes were cloned and the function of individual isoforms during defense was studied. We found that PLC4 and PLC6 encode active enzymes and that they have distinct roles in defense. Optimum activity requirements and substrate preferences were determined for three PI-PLC enzymes and their enzyme activity was found to be important for immune receptor-activated responses. The available information was used to draw a model explaining the role of PI-PLC signaling in immune receptor-mediated defense and resistance in plants.
The effect of strain of Holstein-Friesian cow and feeding system on reproductive performance in seasonal-calving milk production systems

Three strains of Holstein-Friesian (HF) cows: high production North American (HP), high durability North American (HD) and New Zealand (NZ) were assigned, within strain, to one of three pasture-based feeding systems: Moorepark (MP), high concentrate (HC), and high stocking rate (HS). The effects of strain of HF, feeding system and parity on milk production, body condition score (BCS), live weight, energy balance and reproductive performance were studied using a repeated measures model with a factorial arrangement of strain ofHF and feeding systems. Associations between these variables and conception to first service (CONCEPT1), conception to first and second service (CONCEPTl_2), pregnancy rate at 6 weeks (PREG6) and overall pregnancy rate (PREG) were assessed using logistic regressions. When treatment means were compared, the NZ strain had a shorter gestation length and a higher CONCEPT1J2 than both the HP and HD strains. Similarly, the NZ strain had a higher PREG6 and PREG than the HP strain. Feeding system had no significant effect on reproductive performance. The HP strain had the highest milk yield at first AI and peak milk yield, the NZ strain had the lowest milk yield while the HD strain was intermediate. The energy balance of the NZ strain was higher than that of the HP and HD strains. The NZ strain had the lowest live weight and highest BCS; the HD strain had the highest live weight and the HP strain had the lowest BCS. The results show that dairy cows with superior genetic merit for fertility traits have better reproductive performance.
Étude de l’interaction entre L. pneumophila et l’autophagie de la cellule hôte

L. pneumophila est l'agent responsable de la legionellose, une pneumonie severe associee a 10% de mortalite. Cette bacterie intracellulaire a acquis la capacite de survivre et de se repliquer dans des cellules humaines. Notamment, L. pneumophila secrete un grand nombre d'effecteurs par son systeme de secretion de type IV, qui interagissent avec differentes voies cellulaires, dont l'autophagie. L'autophagie est une voie de degradation conservee qui permet aux cellules eucaryotes de reguler l'homeostasie cellulaire et d'eliminer les agents pathogenes intracellulaires. Neanmoins, nombre d'entre eux ont evolue pour manipuler cette voie a leur propre avantage. Meme si l'interaction entre L. pneumophila et l'autophagie a ete rapportee, aucun modele clair n'est determine. Dans cette etude, nous montrons qu'une infection a L. pneumophila induit une stimulation globale de l'autophagie, mais que ce phenotype depend des souches utilisees, et notamment de la presence de certains effecteurs. De plus, l'inhibition de l'autophagie est liee a un defaut de replication intracellulaire suggerant que cette voie est benefique a la bacterie. Afin de rechercher les determinants genetiques impliques dans cette interaction, nous avons identifie des effecteurs communs secretes par le systeme de secretion de type IV entre L. pneumophila et Coxiella burnetii, une bacterie de l'ordre des Legionellales connue pour stimuler et detourner l'autophagie. La capacite des mutants de ces effecteurs a stimuler l'autophagie chez L. pneumophila a ete analysee. Si aucun d'entre eux ne semble implique dans la modulation de l'autophagie, cette etude suggere d'autres fonctions pour ces effecteurs conserves
Towards a model of grape tannin extraction under wine‐like conditions: the role of suspended mesocarp material and anthocyanin concentration

Background and Aims The study aimed to determine how fresh grape mesocarp modifies the extraction and composition of tannin under wine-like conditions. A further aim was to observe whether addition of anthocyanin during extraction exerted an effect on the concentration of recovered tannin. Methods and Results Fresh red grape berries were dissected into skin, mesocarp and seed. Different combinations of the berry components were extracted in model wine or fermented. Initial results indicated that mesocarp material bound seed tannin more selectively than skin tannin. Further experiments pointed towards a more complex system, whereby adsorption of tannin by mesocarp facilitated ongoing extraction of tannin from the skins. The effect exerted by mesocarp was potentially to increase the concentration gradient between skins and the liquid medium by the continuous removal of tannin. Under these conditions, both skin and seed tannin could be removed from extracts or wines by suspended mesocarp material. White grape skins or mesocarp were also extracted with the addition of a variable concentration of purified anthocyanin and found to facilitate the extraction of otherwise non-extractable tannin. This effect was observed to be greater for grape mesocarp than for white grape skins. Conclusions The concentration and composition of tannin were shown to be modified by the presence of mesocarp material. A role for anthocyanin in enhancing the extraction of tannin was confirmed. Significance of the Study The results show that multiple factors interact to influence tannin extraction and retention from grapes.
Species pools and differential performance generate variation in leaf nutrients between native and exotic species in succession

A central aim of invasion biology has been to identify key functional differences between native and exotic species to determine which traits may be responsible for invasion success and impacts. There are two primary ways that differences may exist between native and exotic species—the traits of the local species pools may differ, or the way that the traits interact with their environment may differ. We explored leaf nutrient concentrations as functional traits that directly link to plant metabolic processes by sampling healthy, mature leaves from 119 native and exotic taxa across a wide range of successional statuses in New Jersey, USA. Leaf nutrient concentration data (carbon, calcium, magnesium, nitrogen, phosphorus, potassium) were paired with long‐term community dynamics from the Buell–Small Succession Study to evaluate abundance‐weighted trait values over succession for native and exotic species. After accounting for differences across growth forms, there were minimal differences in foliar nutrients based on plant origin, with only lower leaf carbon and higher leaf potassium in exotic species. However, these differences were not sufficient to generate overall differences between native and exotic species in a multivariate analysis. In contrast, the successional trajectories of the abundance‐weighted trait values for most leaf nutrients differed strongly between native and exotic plants. While this pattern may be partially attributable to variation in the species pool for carbon and potassium, successional processes generated differential sorting, suggesting underlying differences in how the same traits function in native and exotic assemblages. Synthesis. These results suggest that both variation in the species pool and variation in the successional selection of plant traits can generate functional differences between native and exotic plants. Assessments of trait differences between native and exotic species will require information on traits and plant performance to unambiguously link traits to function in dynamic plant communities.