Miracle-dz/UniFAR-FTUs huggingface dataset:
Current structure of strongly nonlinear interfacial solitary waves

The characteristics of highly nonlinear solitary internal waves (solitons) in two-layer flow are computed within the fully nonlinear Navier-Stokes equations with use of numerical model of the Massachusetts Institute of Technology (MITgcm). The verification and adaptation of the model is based on the data from laboratory experiments [Carr & Davies, 2006]. The present paper also compares the results of our calculations with the computations performed in the framework of the fully nonlinear Bergen Ocean Model [Thiem et al, 2011]. The comparison of the computed soliton parameters with the predictions of the weakly nonlinear theory based on the Gardner equation is given. The occurrence of reverse flow in the bottom layer directly behind the soliton is confirmed in numerical simulations. The trajectories of Lagrangian particles in the internal soliton on the surface, on the interface and near the bottom are computed. The results demonstrated completely different trajectories at different depths of the model area. Thus, in the surface layer is observed the largest displacement of Lagrangian particles, which can be more than two and a half times larger than the characteristic width of the soliton. Located at the initial moment along the middle pycnocline fluid particles move along the elongated vertical loop at a distance of not more than one third of the width of the solitary wave. In the bottom layer of the fluid moves in the opposite direction of propagation of the internal wave, but under the influence of the reverse flow, when the bulk of the velocity field of the soliton ceases to influence the trajectory, it moves in the opposite direction. The magnitude of displacement of fluid particles in the bottom layer is not more than the half-width of the solitary wave.
Technical assistance and seasonality in the diet and production of dairy herds in household agriculture of Western Paraná

The objective of the present study was to characterize the food sources, as well as the composition and quality of milk obtained from household farms of western Parana State (Brazil) with and without technical assistance during the different seasons. For such, 24 properties were selected, 12 of which only received assistance and technical support. Four milk samples were taken (summer, autumn, winter and spring) to assess the physicochemical composition, somatic cell count and total bacterial count and feed supplied to the animals to assess the chemical composition (crude protein, ash, dry matter and neutral detergent fiber). The data were analyzed in a completely randomized design with a 2 × 4 factorial arrangement; the first factor was the presence and absence of technical assistance and the second factor was the four seasons of the year. Due to the dairy tradition of properties in the region, technical assistance had no significant effects on the health and nutritional quality of food, the number of animals, the production, or total bacterial count, which suffered oscillations only depending on the seasons of the year. However, the presence of assistance contributed to reducing somatic cell counts of milk produced and marketed. The technical assistance does not affect the quality of forages and concentrates used or the milk composition; however, it improves the sanitary quality of the milk produced throughout the four seasons of the year in household farms of western Parana.
Infestation of the black cormorants (Phalacrocorax carbo sinensis L. 1758) from the colony on the Selment Wielki, with the nematode Contracaecum rudolphii Hartwich, 1964 (Nematoda, Anisakidae)

Abstract Seasonal changes in the intensity and prevalence of infestation of the black cormorants from the colony on Lake Selment Wielki were investigated. In 2006, the cormorants were procured in April, August, and October, while in 2007, they were collected in August and September. The prevalence of the infestation was very high and reached 100%. The highest intensity (mean values of 102.46 and 82.17 nematodes/bird in 2006 and 2007, respectively) was revealed in the cormorants shot in August. Intensity of infestation of those birds procured in autumn 2006 was more than twice that found in spring and one-fourth of that found in summer of that year. Similarly, in autumn of 2007, the birds' stomachs contained less than half of the number of nematodes recorded in summer of that year.
Comparisons of Social Structure of Columbus Crabs Living on Loggerhead Sea Turtles and Inanimate Flotsam

Columbus crabs, Planes minutus (Crustacea: Brachyura) live in the open ocean attached to floating substrata including Sargassum, flotsam, and sea turtles. Eighty-two percent of 128 loggerhead turtles (Caretta caretta) checked, harboured a total of 172 crabs. Crabs inhabiting flotsam occurred in mixed sex groups of adults and juveniles, with a mean group size of 8.2 ±;11.8 (N=17). In contrast, crabs living on sea turtles around Madeira occur in smaller groups 1.6 ±0.5 (N=105) which are typically adult heterosexual pairs (61 out of 105). Crabs on turtles were bigger than on flotsam and a higher proportion of female crabs were brooding eggs. Columbus crabs exhibit different life history strategies depending on the substratum they inhabit.
Distribution and activity of Drosophila suzukii in cultivated raspberry and surrounding vegetation

Spotted wing drosophila, Drosophila suzukii (Matsumura) (Diptera: Drosophilidae), may utilize wild ‘Himalaya’ blackberry (HB) Rubus armeniacus Focke or other non‐crop plants as refugia and possibly exploit adjacent field margins before colonizing cultivated fruiting crops. Studies were conducted to determine the role of field margins containing HB and their effect on D. suzukii activity, density and distribution in an adjacent commercial red raspberry crop. One‐ha plots adjacent to field margins containing HB or known non‐host (NH) grass crops were established in 2011 and 2012 and replicated three times. Each plot contained two transects with monitoring traps for D. suzukii in the field margin (0 m) and spaced approximately 10 (crop boundary), 40, 70 and 100 m into the adjacent crop (n = 10 traps/plot). Field margin vegetation was treated with a 10% chicken egg white mark solution weekly from pre‐harvest until the end of harvest using a cannon sprayer. Adult D. suzukii were collected from traps weekly and analysed for the presence of the egg white mark using an egg white‐specific enzyme‐linked immunosorbent assay (ELISA). During both years, marked flies and total flies were captured in higher numbers in HB field margins, whereas virtually no flies were captured in field margins containing no known alternative host. Similarly, more flies were captured in the crop near HB than near NH. Spatial Analysis by Distance IndicEs (SADIE) and mean D. suzukii trap captures additionally displayed significantly higher fly densities in the raspberry field near HB than near NH. These results suggest that HB may contribute to elevated D. suzukii populations and pest pressure in comparison with field margins containing no known alternate host vegetation for D. suzukii. Having closely adjacent non‐crop alternate host landscapes may result in increased D. suzukii pest pressure.
Changes in Water Hardness Influence Colonization of Saprolegnia diclina

Abstract Experiments were conducted to determine the effects of different water hardness concentrations on colonization of Saprolegnia diclina in an attempt to explain some of the differences in fungal growth and antifungal chemical effectiveness observed at various fish hatcheries. Fungal growth on nonviable seeds of hemp Cannabis sativa was observed significantly sooner in water where hardness was elevated due to the addition of calcium sulfate dihydrate in each of the experiments. Seeds in test tubes containing water with a hardness of 300 mg/L exhibited fungal colonization in approximately one-half the amount of time observed with seeds in water with hardness less than 150 mg/L. In petri dishes containing inoculated corn meal plugs, the growth of S. diclina was observed at only 24 h on seeds in water with a hardness of 450 mg/L, which was significantly quicker than the 31 h from seeds in water hardness of 150 and 300 mg/L. This, in turn, was significantly quicker than the 35 h required for growth in t.
VITAMIN C STATUS: METHODS AND FINDINGS

: Although vitamin C nutritional status in man may be determined on the basis of dietary intake findings and on clinical signs of a dietary deprivation, biochemical measurements represent the most objective approach. Without the availability of a functional biochemical procedure that relates to vitamin C status, information concerning inadequacies in this nutrient has been derived mainly from measuring ascorbate levels in serum (plasma), leukocytes, blood, and urine. The measurement of serum levels of ascorbic acid is the most commonly used and practical procedure for determining vitamin C nutritional status in individuals or population groups. Although leukocyte ascorbate levels provide information concerning the body stores of the vitamin, the measurement is technically more difficult to perform, and, hence, its use is largely confined to clinical situations as an aid in the diagnosis of scurvy. The clinical diagnosis of scurvy can be aided also by information on the urinary levels of ascorbic acid and the use of vitamin C loading or saturation tests. With recognized limitations, ascorbic acid can be measured in biological samples with the use of automated or manual colorimetric and fluorometric procedures. Nutrition surveys conducted in Canada and the United States have indicated vitamin C deficits among certain population groups.
Annual and interannual CO2 exchanges of the terrestrial biosphere: process-based simulations and uncertainties

1 Assessments of climate change impacts on the global carbon cycle have to rely on accurate models describing the contribution of the terrestrial biosphere. Interannual climate fluctuations provide an ideal test case for their reliability because results can be checked against atmospheric measurements. 2 Intercomparisons have so far shown rather large discrepancies between the results of different terrestrial ecosystem models, especially for net primary productivity (NPP). Therefore, identification of the processes contributing most to modelling uncertainties is another necessary step towards more reliable predictions. 3 The Biosphere Energy-Transfer and Hydrology model (BETHY) is used to simulate global photosynthesis, and plant and soil respiration embedded within the full energy and water balance, based on 13 years of meteorological data. A series of sensitivity experiments is defined to assess the effects of estimated global uncertainties in a range of parameters. 4 It is found that modelling uncertainties are responsible for a large range of computed values of global annual NPP, while interannual climate fluctuations create only relatively minor changes. These fluctuations, however, are responsible for imbalances between carbon uptake by and release from the terrestrial biosphere, creating interannual fluctuations of the net biosphere–atmosphere CO2 exchange. Here, different model versions tend to agree with each other, which indicates that the net flux is generally better constrained than average NPP. A comparison with net fluxes derived from atmospheric CO2 data shows a good agreement for most models. 5 The results support the hypothesis that at the time scale of a decade, the terrestrial biosphere causes most of the interannual fluctuations of atmospheric CO2 concentrations, with the tropics playing a dominant role. They also indicate that modelling uncertainties for the net carbon exchanges tend to be less pronounced than for NPP. The method presented here, applied to other modelling studies, should also help in the identification of major uncertainties in biosphere process description, eventually leading to improved predictive capabilities of such models.
Effects of gut passage on the germination of seeds ingested by didelphid marsupials in a neotropical savanna

We analyzed the effects that passage through the guts of seven didelphid species had on the seed germination of 10 plant species. This study was conducted in an area of riparian woodland in a cerrado (savanna) reserve in southeastern Brazil. We found seeds of 23 angiosperm species in 427 fecal samples obtained from seven didelphid species. The plant families most often represented by the seeds found in the fecal samples were Melastomataceae (5 species) and Rubiaceae (4 species) . Most gut-passed seeds showed no significant difference in germinability when compared with the hand-extracted seeds. Among the ingested seeds, only those of Clidemia urceolata DC. (Melastomataceae) and Myrcia sp. (Myrtaceae) showed an increase in germinability (final proportion of germinated seeds), indicating that didelphid gut passage does not always benefit seed germination. The average germination time of consumed seeds ranged from 12 days (Cipocereus minensis (Werderm.) Ritter) to 171 days (Cordiera sessilis (Vell.) Kuntze). The small number of seeds destroyed after gut passage and the results obtained during the germination experiments underscore the importance of didelphid marsupials to the dynamics of plant reproduction, especially those of small-seeded cerrado species.
The Emergence of Behavioral Testing of Fishes to Measure Toxicological Effects

Historically, research in toxicology has utilized non-human mammalian species, particularly rats and mice, to study in vivo the effects of toxic exposure on physiology and behavior. However, ethical considerations and the overwhelming increase in the number of chemicals to be screened has led to a shift away from in vivo work. The decline in in vivo experimentation has been accompanied by an increase in alternative methods for detecting and predicting detrimental effects: in vitro experimentation and in silico modeling. Yet, these new methodologies can not replace the need for in vivo work on animal physiology and behavior. The development of new, non-mammalian model systems shows great promise in restoring our ability to use behavioral endpoints in toxicological testing. Of these systems, the zebrafish, Danio rerio , is the model organism for which we are accumulating enough knowledge in vivo , in vitro , and in silico to enable us to develop a comprehensive, highthroughput toxicology screening system.
AFLP analysis of Lactuca saligna germplasm collections from four European and three Middle Eastern countries

Lactuca saligna L. (least lettuce, willow-leaf lettuce) is widely distributed around the Mediterranean basin and extends to the Caucasus and temperate Europe; its extra-European distribution covers the Middle East. The aim of this study was to estimate the level of molecular variation and the extent of genetic differentiation of L. saligna in accessions collected in natural and semi-natural habitats in Europe and the Middle East. In sum, 67 accessions of L. saligna, originating in four European countries (Czech Republic, France, Italy, Portugal) and three Middle Eastern countries (Israel, Jordan, Turkey), were compared on the basis of AFLP polymorphism. AFLP analysis of the accessions revealed 415 (84.7%) polymorphic fragments out of 490 fragments amplified by means of seven primer pair combinations. The number of bands produced by individual primer pair combinations ranged from 44 to 101. The UPGMA dendrogram generated from Jaccard's similarity matrix showed a similar genetic background of accessions from the Middle East (Turkey, Israel, Jordan), which were quite distinct from the group of accessions from the European part of the Mediterranean basin (Italy, France, Portugal). Surprisingly, two accessions, one from the Czech Republic (central Europe) and one from Israel, proved genetically wholly separate from all other accessions of L. saligna and are themselves wholly separate. Accessions originating in various eco-geographical conditions were found to differ significantly in their genetic polymorphism.
Land snail diversity and composition in relation to ecological variations in Central European floodplain forests and their history

We explored patterns of land snail assemblages using 93 alluvial forest sites in six river floodplains of the Elbe drainage basin (northwestern Bohemia, Czech Republic). Differences in species richness and composition across the four floodplain forest types (i.e., alder carrs, ash-alder forests, willow-poplar softwood forests, and hardwood forests) were analysed using generalized linear models, multidimensional scaling and redundancy analysis with the Monte Carlo permutation test. The studied floodplain forest types did not differ in species richness, except for the alder carrs which were significantly poorer. The number of species expressed a significant unimodal response along with elevation and Ellenberg nutrients, and further significantly decreased towards the most humid sites. Contrary to species richness, the main forest types clearly differed based on land snail species composition, with the exception of the ash-alder and willow-poplar forest sites which became completely overlapped in the ordination space. The main changes in species composition were mostly associated with elevation and Ellenberg moisture on the first MDS axis: Ellenberg nutrients and light were fitted on the second and the third axes, respectively. These variables, along with calcium content estimated using Ellenberg indicator values for soil reaction, had significant effects on the variation and snail species composition in the final RDA model. No response of either species richness or compositional changes was found for the measured content of topsoil calcium, most likely due to the higher importance of other variables. On the basis of some recently published data we can conclude that historical development and long-term human activities on the succession of floodplain assemblages have resulted in a sharp impoverishment of strictly land snail species of several hardwood forest sites in the majority of lower river stretches. Whilst in most areas there are no exact palaeoecological data available, these historical influences were closely correlated with the site elevation in our dataset as the main difference in species composition was hard to explain solely using environmental predictors.
A long-term hydrological soil study on the effects of soil and land use on deep seepage dynamics in northeast Germany

Starting in 1993, interactions between land use and precipitation have been investigated in three research areas of northeast Germany. The research based on continuous measurements of soil water tension and water content down to a depth of 5 m at 36 plots situated at diverse soils under different land use (arable land, forest, grass fallow). At arable sites, the main period of deep seepage occurred between February and April during the study period. With 175 mm a−1, the mean annual deep seepage rate under arable land was highest at sandy soils. At loamy soils, the mean seepage rate amounting to 122 mm a−1 appeared significantly less. Smallest seepage rates, however, were determined for forested plots (pine 15 mm a−1, beech 18 mm a−1). Differences were significant as compared to arable land at sandy and loamy soils and grass fallow. It is concluded that deep seepage and groundwater recharge under forest will tend to wane at annual precipitation rates of <550 mm a−1. This should be taken into account in decision making on land use planning and conversion of arable areas to forestry in regions characterised by negative values of the climatic water balance.
Phylogeny of Lycopodiaceae (Lycopsida) and the Relationships of Phylloglossum drummondii Kunze Based on rbcL Sequences

A cladistic analysis based on rbcL sequences from a representative sample of 12 species yields a single most parsimonious tree that supports monophyly of Lycopodiaceae, Lycopodium, and Lycopodiella. Huperzia is resolved as paraphyletic to the morphologically divergent, monotypic Australasian Phylloglossum. The Huperzia-Phylloglossum clade is strongly supported and is sister group to a Lycopodium-Lycopodiella clade. These results provide the first clear evidence for the relationships of the problematic Phylloglossum drummondii. Profound differences in life cycle and morphology between Phylloglossum and other Lycopodiaceae are interpreted in terms of pedomorphosis (specifically, progenesis) and are viewed as adaptive responses to drought and brush fire. Our results show that rbcL sequence divergence among neotropical species of the supposedly ancient genus Huperzia is extremely low and that additional data will be necessary to resolve relationships among epiphytes and ground-living species. These surprisingly low levels of sequence divergence indicate that most living species diversity within Lycopodiaceae is of relatively recent origin Our results are consistent with a late Cretaceous or early Tertiary origin and diversification of epiphytic species within Huperzia, and these events may be linked to the diversification of angiosperms.
Is the Bill of the Male Oystercatcher a Better Tool for Attacking Mussels Than the Bill of the Female

Male Oystercatchers, Haematopus ostralegus, take relatively more large and thick-shelled molluscs, like cockles and mussels, while female Oystercatchers take relatively more deeply buried clams and polychaetes. Opening sturdy prey requires considerable muscular effort and the bill must be strong to resist the stresses. Sexual dimorphism in bill morphology is subtle and consists of the following: the bill of the male is shorter in total length and the distal half (gonys-region) is deeper and wider, suggesting it is stronger in resisting forces operating on the bill when opening mussels. Skull dimensions and the weight of the depressor muscle of the beak Musculus depressor mandibulae do not differ between the sexes. It is argued that with equal effort of the head, neck and jaw muscles, greater forces are exerted at the contact point between the bill and the prey in the male bill than in the female to overcome the resistance required to open mussels.