Miracle-dz/UniFAR-FTUs huggingface dataset:
Recovery of oyster reefs (Crassostrea virginica) in a gulf estuary following disturbance by two hurricanes

During the summer and fall of 1985, two hurricanes struck the Apalachicola Bay system, a center for oyster (Crassostrea virginica) production in the northeast Gulf of Mexico. The first storm, Hurricane Elena, physically destroyed the major oyster-producing reefs in the Apalachicola estuary in early September (9/1/85). This disturbance was followed a month later by considerable accumulations of spat on those reefs most affected by the storm. The second hurricane, Kate, struck the bay in late November (11/21/85) and probably contributed to the natural mortality of young-of-the-year oysters. However, overall oyster biomass did not seem to be affected by Kate. Subsequent oyster growth was substantial with full recovery of the oyster stock noted within a 12-mo period. A detailed evaluation was made of the response of this important estuarine population to these disturbances. The timing and nature of the disturbances relative to the natural history of the oyster were crucial to the overall recovery pattern of the population. Hurricane Elena occurred at the end of the oyster spawning activity in 1985. Effects of the storm probably increased habitat availability and reduced direct competition and predation such that the oyster population benefited from the successful recruitment. The subsequent storm, Kate, coming after the spawning period, was not as destructive to oyster populations as Elena and could have even enhanced growth of the survivors. Hurricanes are common along the Gulf coast during the spawning period of the oysters; it appears that C. virginica is well adapted for such natural disturbances. The observed response of the Apalachicola oyster population to successive disturbances has significant meaning in terms of the long-term ecological stability of estuarine populations and the evolutionary aspects of such biological response to temporally unstable habitats. In this case, such populations can be viewed as highly resilient under even the most extreme conditions of physical instability. However, the exact biological response to temporally irregular disturbances is highly dependent on the timing of such events relative to the natural history of population in question.
Integrating ecosystem functions into restoration ecology—recent advances and future directions

Including ecosystem functions into restoration ecology has been repeatedly suggested, yet there is limited evidence that this is taking place without bias to certain habitats, species, or functions. We reviewed the inclusion of ecosystem functions in restoration and potential relations to habitats and species by extracting 224 publications from the literature (2004–2013). Most studies investigated forests, fewer grasslands or freshwaters, and fewest wetlands or marine habitats. Of all studies, 14% analyzed only ecosystem functions, 44% considered both biotic composition and functions, 42% exclusively studied the biotic component, mostly vascular plants, more rarely invertebrates or vertebrates, and least often microbes. Most studies investigating ecosystem functions focused on nutrient cycling (26%), whereas productivity (18%), water relations (16%), and geomorphological processes (14%) were less covered; carbon sequestration (10%), decomposition (6%), and trophic interactions (6%) were rarely studied. Monitoring of ecosystem functions was common in forests and grasslands, but the functions considered depended on the study organisms. These associations indicate research opportunities for certain habitats, species, and functions. Overall, the call to include ecosystem functions in restoration has been heard; however, a lack of clarity about the ecosystem functions to be included and deficits of feasible field methods are major obstacles for a functional approach. Restoration ecology should learn from recent advances in rapid assessment of ecosystem functions, and by a closer integration with biodiversity–ecosystem functioning research. Not all functions need to be measured in all ecosystems, but more functions than the few commonly addressed would improve the understanding of restored ecosystems.
Stratégies alimentaires de Synodontis bastiani (Siluriformes : Mochokidae) dans le complexe fluvio-lacustre de la Bia, Côte d'Ivoire

Le regime alimentaire de 81 specimens (dont l'estomac de 63 d'entre eux contenait des aliments) de Synodontis bastiani, provenant de la riviere Bia (Cote d'Ivoire) a ete etudie en fonction de la taille des specimens, de la saison hydrologique et des stations d'etude. Un indice alimentaire calcule en combinant les pourcentages d'occurrence, numerique et ponderal a ete utilise. L'espece es omnivore et consomme des invertebres benthiques et des macrophytes avec comme aliments principaux les larves de Chironomidae, l'Insecte Povilla adusta (Polymitarcyidae), des fruits et des debris de vegetaux. Une variation du regime alimentaire a ete observee en fonction de la taille, de la saison et des stations a l'exception du lac ou aucune difference statistiquement significative n'a ete mise en evidence entre les saisons hydrologiques.
Establishment of Native Vaccinium Species on a Mineral Soil

Application of an absorbent starch-acrylate polymer (ASAP) to bare-rooted plants of 4 Vaccinium genotypes did not affect plant height, vigor, or chlorosis, but it increased plant mortality significantly. About 25% of all plants treated with ASAP either alone or in combination with peat died during the first year after transplanting. Surviving plants grew at about the same rate as those from other treatments during the 2nd year. A V. ashei (Reade) collection from Mississippi showed least response to soil amendments. Untreated plants of this collection grew well during the 2nd growing season and compared favorably in size with ‘Tifblue’ grown in plots with peat added.
Comparison of heritability estimates of first lactation traits by different methods in Phule Triveni cattle

The first lactation records of 493 Phule Triveni cows sired by 55 sires on production traits viz. FL300DMY, FLL, FDP and reproduction traits like AFC, FCI and FSP were collected/generated from RCDP on cattle, MPKV, Rahuri. The effect of season of calving was found significant on FL300DMY and nonsignificant on FLTMY, FLL, FDP, AFC, FCI and FSP. The effect of period of calving had highly significant effect on all the first lactation traits except FSP. The effect of age groups on FLL was found significant and nonsignificant on rest of the first lactation traits. On AFC the effect of season of birth was found nonsignificant and the period of birth had highly significant effect. The heritability estimates of FLTMY by LSML, ST-SM and ST-AM were 0.35±0.16, 0.15±0.11 and 0.18±0.07; for FL300DMY0.32±0.15, 0.23±0.12 and 0.29±0.07; for FLL 0.07±0.11,0.02±0.04 and 0.06±0.02; for FDP0.22±0.13,0.18±0.14 and 0.30±0.10; for AFC0.48±0.19, 0.07±0.08 and 0.36±0.06 ; for FCI 0.28±0.17,0.05±0.06 and 0.04±0.03; for FSP 0.25±0.17, 0.06±0.03 and 0.17±0.02, respectively. The heritability estimates of first lactation traits from single-trait animal model (ST-AM) were found more accurate and less biased than corresponding single- trait sire model (ST-SM) and LSML.
Continental‐scale analysis of feral cat diet in Australia, prey‐switching and the risk: benefit of rabbit control

Recent analyses of geographical variation in cats’ diet across Australia have been used to highlight rabbit control as a conservation risk, on the basis that prey‐switching by cats following rabbit control is likely to threaten Australian fauna. There is no direct evidence to support that proposition. However, there is direct evidence of repeated prey‐switching due to seasonal fluctuations in uncontrolled rabbit populations, of long‐term suppression of rabbit numbers by effective rabbit control, and that reduced rabbit abundance leads to reduced cat abundance, reduced predation of native fauna and recovery of threatened prey populations. Furthermore, rabbits are a known threat to many Australian native plants and rabbit control has proven benefits for their recovery, thereby offering long‐term benefits for dependent fauna and broader ecosystem function. On the balance of evidence, rabbit control should be encouraged in Australia wherever possible, as a national conservation priority.
Direct somatic embryogenesis in Epipactis veratrifolia, a temperate terrestrial orchid

ABSTRACT Most temperate terrestrial orchids are endangered species. Attempts to produce plantlets from plants of the genus Epipactis by asexual methods have totally failed. This study was conducted using somatic embryogenesis as a rapid vegetative propagation technique for conservation of E. veratrifolia. For these purposes, effects of different types of plant growth regulators (PGRs), different types of explants, light and dark conditions, and the effect of gibberellic acid (GA3) and Paclobutrazol (PBZ) were investigated on somatic embryogenesis induction. Abscisic acid (ABA) pre-treatment effectiveness on inducting somatic embryogenesis and increasing the number of embryos per explant were investigated. Subsequently, 16 media were tested to find the best medium for plant regeneration and shoot and root proliferation. BA (3 mg L−1) resulted in a better response than the other PGRs by supporting the development of 17 embryos per protocorm. PBZ, which resulted in 11 embryos per explant, was better than GA3. FAST medium supplemented with organic substances was recognized as the best medium for plant regeneration and shoot and root proliferation. ABA pre-treatment had positive effect on somatic embryogenesis initiation. This study, for the first time, succeeded in finding a rapid and suitable protocol for propagation and genetic resource conservation of E. veratrifolia.
Description et comportement d'espèces d'Actinidia à fruits glabres dans le Sud-Ouest de la France

(.) La collection d'Actinidiaceae implantee en 1982 au Lycee agricole de Montauban-Capou a permis d'examiner le comportement de plusieurs especes lors des gels exceptionnels des hivers 1985 (−25 o C) et 1987 (−20 o C). Seules ont survecu, parmi les especes determinees avec precision: arguta, kolomikta, polygama et melanandra. Dans la meme parcelle, les plants d'Actinidia chinensis du meme âge furent detruits et durent etre recepes a la base. Ces quatre especes sont decrites avec leurs caracteristiques botaniques et la comparaison de leur comportement agronomique avec Actinidia chinensis
Daily Movement and Microhabitat Use by the Blacksmith Treefrog Hypsiboas faber (Anura: Hylidae) during the Breeding Season in a Subtemperate Forest of Southern Brazil

Abstract. We studied the patterns of daily movement and habitat use of 20 males and five females of the blacksmith treefrog, Hypsiboas faber, during the breeding season in a subtemperate forest of southern Brazil. Treefrogs were tracked with externally attached thread bobbins. There were no differences between sexes in the mean straight line distance moved (HSD) or in the effective distance moved (HDM), which ranged from 0.06–3.1 m/h and 0.4–9.8 m/h, respectively). Males showed higher site fidelity and less habitat overlap than females. Despite being an arboreal species, most of the tracked individuals used the herbaceous stratum on the ground as microhabitat, which indicates a particular microhabitat use during breeding activities. Estimates of the distance moved obtained from released thread lines revealed that animals moved distances five times greater than the distances calculated by drawing a straight line between consecutive points. Therefore, our findings suggest that the sedentary behavior attributed to some tropical and subtropical anuran species in tropical and subtropical anuran species forests might not be accurate.
Description of two new species of the Neotropical genus Yphthimoides Forster, 1964 (Lepidoptera: Nymphalidae: Satyrinae) from the ‘renata clade’

This paper describes two new species of Neotropical butterflies: Yphthimoides blanquita Barbosa, Marín and Freitas sp. nov., from the dry forest of northwestern Colombia, and Yphthimoides nareta Barbosa & Freitas sp. nov. from northeastern Brazil, based on morphological and molecular data. Adult morphology, including wing shape and pattern as well as male genitalia, is described in detail. Furthermore, analysis of the mitochondrial CoxI ‘barcode’ showed that both new species are quite distinct from all similar Yphthimoides species and additionally, the ‘renata clade’ is defined based on the presence of cornuti in the aedeagus. http://zoobank.org/urn:lsid:zoobank.org:pub:22CA85FF-9682-4016-A300-AB11C71CEDA2
Characters Associations and Path Analysis in Safflower ( Carthamus tinctorious ) Accessions

Safflower as a potential oil crops which can be used as an alternative to the existing widely cultivated oil crops in Ethiopia needs seed yield improvement which inturn relies on its component characters. Examining character association and their interrelationships is helpful in selecting the breeding material for improving the complex trait such as seed yield. A study was carried out during 2012 cropping season to determine the associations of characters and partition of this association into direct and indirect effects on seed yield of safflower. Correlation coefficient analysis showed that seed yield recorded significant positive association with days to flowering (0.190), plant height (0.234), number of capitula (0.172), number of seed per plant (0.834) and hundred seed weight (0.197). The highest positive direct effect was revealed by number of seed per plant (0.89) followed by hundred seed weight (0.106) as depicted by path coefficient analysis. This study showed that number of seed per plant is the most important yield component followed by seed weight. Therefore, this suggests that direct selection based on these characters would be effective for the improvement of safflower.
Closing the loop: A combined computational modeling and experimental approach provides novel insights into immune cell signaling systems and their global effects.

Systems biology is an approach that marries complimentary disciplines, encouraging the use of quantitative methods to help define, explain, and predict biological processes. By building computational models of biological systems, we can pose new biologically motivated questions and make falsifiable, quantitative predictions. In this thesis I will discuss the cycle of model building and experimental validation, and how it has provided insight into poorly and understood systems and allowed us to predict the effects of perturbations on these systems, which could have real and significant effects in human health and medicine. First, we model the activation of neutrophils in sepsis. By fitting a single model to two sets of data, coming from animals that survive and succumb to the same bacterial challenge, we create a realistic representation of biological variation, showing how a single network architecture can lead to different outcomes. Additionally, this method allows us to identify markers for sepsis susceptibility and identify and optimize a potential treatment option to lead to improved outcomes. Next, we model signaling downstream of the T cell receptor, and how this leads to differentiation decision making in CD4 T cells. By modeling the dynamics of this signaling network under varying antigen doses, we are able to identify network elements critical to dose discrimination, leading to the production of Treg cells following low dose stimulation and Th cells following high dose stimulation. We can then perturb these elements of the network, to potentially fine tune mature T cell populations to alter the trajectories of autoimmune disorders or cancer. Finally, we model the dynamics of IL-17 signaling. This allows us to understand how ubiquitin scaffolds form following cytokine stimulation, leading to the activation of NF-B, and how the ubiquitin editing enzyme A20 acts as a negative feedback regulator by breaking these chains. This allows us to better understand ubiquitin oligomerization as a fulcrum in the system, and how changes in A20 and ubiquitin binding proteins lead to different profiles of NF-B activation and could play a role in inflammatory disorders.
Host reaction of arabica coffee genotypes derived from “Sarchimor” to Meloidogyne paranaensis

Plant parasitic nematodes are responsible to significant decline in coffee crops. In Paraná State, Brazil, the more damaging species are Meloidogyne incognita and M. paranaensis. Resistance sources are available, but only a low number of arabica coffee cultivars carry this characteristic. Therefore, the objective of the present work was to evaluate the host reaction to M. paranaensis of coffee genotypes derived from ‘Sarchimor’ IAPAR 88480-8. Eleven ‘Sarchimor’ genotypes and the cultivars Tupi IAC 1669-33 and Catuaí Vermelho IAC 99 (susceptible standard) were evaluated in two 90 days long experiments. Plants were inoculated with 1,400 or 1,000 eggs, in experiments 1 and 2, respectively. The reproduction factor (RF) and the number of nematodes per gram of roots (Nema/g) were calculated. Great phenotypic variability was observed between the coffee genotypes tested. At least three ‘Sarchimor’ genotypes had lower susceptibility to M. paranaensis. The cultivar Tupi IAC 1669-33 and the other ‘Sarchimor’ genotypes tested were as susceptible as ‘Catuaí Vermelho IAC 99’ to M. paranaensis and must be avoided in infested areas.
Bayesian Analysis for the Comparison of Nonlinear Regression Model Parameters: an Application to the Growth of Japanese Quail

This paper discusses the Bayesian approach as an alternative to the classical analysis of nonlinear models for growth curve data in Japanese quail. A Bayesian nonlinear modeling method is introduced and compared with the classical nonlinear least squares (NLS) method using three non-linear models that are widely used in modeling the growth data of poultry. The Gompertz, Richards and Logistic models were fitted to 499 Japanese quail weekly averaged body weight data. Normal prior was assumed for all growth curve parameters of the models with assuming Jeffreys' non-informative prior for residual variances. Models were compared based on the Bayesian measure of fit, deviance information criterion (DIC), and our results indicated the better fit of Gompertz and Richards models than the Logistic model to our data. Moreover, the parameter estimates of the models fitted by both approaches showed only small differences.
The Creation of A Negative Slope Conductance Region by the activation of The Persistent Sodium Current Prolongs Near-Threshold Synaptic Potentials

A change of the input resistance (Rin) of the neuron involves a change in the membrane conductances by opening and closing of ion channels. In passive membranes, i.e., membranes with only linear leak conductances, the increase or decrease of these conductances leads to a decrease or increase of the Rin and the membrane time constant (τm). However, the presence of subthreshold voltage dependent currents can produce non-linear effects generating deviations from this relationship, especially the contradictory effect of negative conductances, as produced by the sodium-persistent current (INaP), on the Rin. In this work we aimed to analyze experimentally and theoretically the impact of the negative conductance produced by INaP on Rin. Experiments of whole-cell patch-clamp conducted in CA1 hippocampus pyramidal cells from brain slices showed a paradoxical voltage-dependent decrease of the Rin and the τm in subthreshold membrane potentials close to the firing threshold after the perfusion with TTX, which inhibits INaP. This effect is postulated to be a result of the negative slope conductance in the subthreshold region produced by this conductance. The analysis of the experimental data, together with simulations found that the slope conductance of INaP is negative for subthreshold membrane potentials and its magnitude is voltage dependent in the same range observed for the voltage-dependence of Rin and τm. The injection of an artificial INaP using dynamic-clamp in the presence of TTX restored the Rin and τm to its original values. Additionally the injection of an artificial leak current with a negative conductance in the presence of TTX restored the Rin and τm as the artificial Inap did. On the other hand, the injection of an artificial leak current with a positive conductance in the presence of TTX had no effect on the Rin and τm. We conclude that INaP increases the Rin and τm by the negative slope conductance observed in its non-monotonic I-V relationship. These results demonstrate that the effect of Inap on Rin and τm is stronger in potentials near the firing threshold, which could potentiate the temporal summation of the EPSPs increasing their temporal integration and facilitating action potential firing. Because of its negative slope conductance, INaP is more effective in increasing excitability near threshold than a depolarizing leak current.
Alimentation de la Cardine, Lepidorhombus whiffiagonis en Mer Celtique

La cardine est l'espece de poisson plat la plus abondante sur le plateau celtique et dans le Golfe de Gascogne. L'analyse des contenus stomacaux a permis de preciser la composition de son regime alimentaire en Mer Celtique et ses variations en fonction de la taille. Les poissons occupent une place preponderante dans la nourriture de toutes les cardines d'une longueur superieure a 23 cm. Les principales proies appartiennent toutes aux especes de type nageur: trisopteres, merlan bleu, chinchard. Il n'apparait pas y avoir de correlation entre la taille des proies et celle du predateur. La consommation individuelle a ete evaluee entre 3,14 et 3,33% du poids du corps par jour
Biological evaluation of Jatropha curcas seed as a new source of protein

The effects of autoclaving, roasting, germination and chemical detoxification (treating with ethanol 90% for 2 hours followed by autoclaving in 0.07% sodium bicarbonate at 121°C for 20 min) of Jatropha curcas seeds on the protein quality, liver function, kidney function, organ weight and histology in rats were evaluated. Roasting, autoclaving and germination treatments did not affect the toxicity of Jatropha seed flour. However, detoxification treatment improved the protein quality of Jatropha seed flour. The protein efficiency ratio, true digestibility and biological value of detoxifying Jatropha seed flour were 87.33, 92.33 and 86.11% of the casein. Rats fed detoxified Jatropha seed flour had higher heart and kidney weights and lower lung weight than those fed casein. These differences were not enough to cause any side effects on the tissues of these organs. However, detoxified Jatropha seed flour did not affect in liver and spleen weights. Liver and kidney functions in rats fed detoxified Jatropha seed flour were within the normal and safe range. Gross examination and histopathological of vital organs of rats fed detoxified Jatropha seed flour did not show any atrophy compared to rats fed casein.
COMPARISON OF FOUR METHODS FOR ENUMERATING SOMATIC CELLS IN MILK WITH AN ELECTRONIC COUNTER

Four chemical fat dispersion methods for conducting the Electronic Somatic Cell Count of milk were studied. The four methods were Rapid/Fixation/Dispersion, Somafix/Somaton, and two methods reported by the International Dairy Federation. Results were critically affected by variations in several procedural factors: type of test tube used for cell fixation and fat dispersion; ratio of milk to diluent; duration of cellular fixation; temperature and duration of fat dispersion; aging of milk samples before analysis; aging of fixed and dispersed samples; and method to agitate samples after fixation and dispersion. After standardization of procedures, the four methods were used, under regulatory testing conditions, to determine the cellular content of three groups of 50 samples of bulk herd milk. A Wisconsin Mastitis Test was done on each and a Direct Microscopic Somatic Cell Count was done on the latter two groups of samples. Attempts to fix cells and disperse fat simultaneously with a Rapid/Fixation/Dispersion.