Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolution moléculaire de la fonction de liaison du sulfure d'hydrogène par les hémoglobines de Riftia pachyptila, annélide tubicole des sources hydrothermales profondes

Les hemoglobines en bicouches hexagonales du vestimentifere Riftia pachyptila des sources hydrothermales profondes de la dorsale du Pacifique Est, ont la propriete de lier et transporter simultanement de l'oxygene et du sulfure d'hydrogene (H2S) des branchies du ver aux bacteries endosymbiotiques sulfo-oxydantes qu'il heberge. Ces dernieres relarguent des composes organiques qu'elles synthetisent par chimiosynthese a partir de H2S, O2 et CO2. Ces composes sont directement assimilables par leur hote. Pour comprendre comment la fonction de fixation de H2S est apparue et a ete maintenue au cours de l'evolution nous avons caracterise (clone et sequence) la famille multigenetique des hemoglobines de Riftia pachyptila. L'etude de l'evolution moleculaire de ces globines montre que les paralogues de cette famille ont des vitesses evolutives differentes: les deux globines impliquees dans la fixation de H2S grâce a la presence de residus cysteine libre presentent des vitesses evolutives plus lentes (forte pression de selection)que les autres globines impliquees dans le seul transport de l'oxygene. l'environnement moleculaire des cysteines est fortement conserve dans les globines orthologues des especes d'annelides fixant ou non le sulfure d'hydrogene. L'analyse des substitutions synonymes et non-synonymes entre globines orthologues montre que le site occupe par la cysteine chez les annelides des milieux reduits et occupe par d'autres acides amines chez les annelides des milieux oxydes, est sous selection positive chez les especes vivant dans des milieux sans H2S. En confrontant ces resultats aux contraintes selectives (presence de H2S) des milieux intertidaux, hydrothermaux et terrestres, nous avons propose un scenario evolutif qui suggere que la fonction de fixation de H2S via une cysteine libre a ete perdue chez les annelides modernes des milieux dans H2S (relaxation des contraintes suivie de selection positive). La perte des cysteines libres suggere que cette adaptation aux milieux reduits (riches en H2S) est un caractere plesiomorphe, et que par consequent l'ancetre des annelides aurait pu vivre dans un environnement reduit.
The effects of sources of supplemental fat on performance, egg quality, and fatty acid composition of egg yolk in laying hens

BACKGROUND: The objective of this study was to determine the effects of sources of supplemental fat on laying performance, egg quality, and fatty acid composition of egg yolk. RESULTS: Two hundreds Isa Brown layers were assigned randomly to be fed ad libitum a standard commercial layer feed (BD), basal diet plus 2% tallow (T), basal diet plus a mixture of 1% tallow and 1% flaxseed oil (MTFO), basal diet plus 2% sunflower oil (SO), or basal diet plus 2% flaxseed oil (FO), which were offered for 8 weeks. Each diet was given to five groups, each containing 10 hens. The feed efficiency and egg production were 2.78 and 53.51% for BD; 2.30 and 63.47% for T; 2.45 and 60.14% for MTFO; 2.29 and 64.30% for SO, and 2.62 and 61.18% for FO groups, respectively. Dietary fat supplementation affected the laying performance but had no significant effects on egg quality parameters. The fatty acid composition of egg yolk lipids were significantly affected by dietary fatty acid composition. The supplemental tallow increased palmitic fatty acid. The proportions of linoleic and arachidonic fatty acids in egg yolks for layers fed the SO diet were higher than in the BD group and those on diets containing other fats. Concentrations of oleic and omega-3 fatty acids were the highest in layers fed the FO diet during the laying period. CONCLUSION: The results indicated that dietary animal and plant fats changed the fatty acid composition of egg yolk. Copyright © 2008 Society of Chemical Industry
Early Pruning Effects on ‘Florida-47’ and ‘Sungard’ Tomato

The effects of early pruning on the growth and yield of ‘Florida-47’ and ‘Sungard’ tomato (Solanum lycopersicum) were assessed in west-central Florida. Each cultivar was established in separate experiments. The four pruning treatments consisted of leaving one, two, and three main stems in the tomato plants below the first flower cluster, and a nonpruned control. Pruning shoots had significant effects on the plant height of ‘Sungard’ and ‘Florida-47’ at 4 and 3 weeks after transplanting, respectively. Tomato plants with a single stem were 13% and 10% taller than the ones in the nonpruned control, respectively. However, this effect disappeared 1 and 2 weeks later in both cultivars. Regardless of the cultivar, early pruning did not influence foliar disease incidence or early and total tomato marketable yield. This cultural practice did not affect the partitioning to different fruit categories in either cultivars. This data showed that early pruning can temporarily change the plant architecture of ‘Sungard’ and ‘Florida-47’ tomato, explaining the perceived increased plant vigor in comparison with the nonpruned control. However, the effect disappeared during the growing season and did not reflect on marketable yields of either tomato cultivars. If no pruning were performed in these cultivars, growers would be able to save an estimated $40/acre of tomato.
PROTEASE PRODUCTION BY Humicola grisea THROUGH SSF

Microbial proteases are the most important industrial enzymes with considerable applications in food, medicine and pharmacy. Fungi elaborate a wide variety of proteolytic enzymes than bacteria and also offer an advantage as the mycelium can be grown on cheaper substrate, broad range of pH and the mycelium can also be easily removed from the final product. Hence the present study was aimed to study the protease produced by a thermophilic fungus Humicola grisea, isolated from the cow dung. The protease production was evaluated in solid state fermentation (SSF) with different substrates and also under the influence of different activators and inhibitors. The most satisfactory results were obtained when wheat bran was used as substrate in SSF. The enzyme activity was also studied under immobilization for all the parameters.
Shrimp polyculture: a potentially profitable, sustainable, but uncommon aquacultural practice

Shrimp polyculture is not yet a common practice among farmers; however, this activity represents an important alternative to solving and ⁄or minimizing some of the problems that shrimp aquaculture has faced in the past two decades (environmental pollution, diseases and decreasing prices). In this context, many benefits have been achieved with some polyculture practices. Several species from diverse trophic levels have the potential to be co-cultured with shrimps. A good knowledge of the species that are candidates for polyculture and an adequately designed culture system are the most important points to consider when co-culturing shrimp with other species. The present paper is a review of the past, present and future of shrimp polyculture with other organisms.
Bioinformatics analysis of TYR within and among species

The comprehensive bioinformatics of TYR within and among species was analyzed based on variation of nucleotide and amino acid sequence. The stop codon, TAA was used in Sus scrofa , Pan troglodytes , Canis familiaris , Equus caballus , Felis catus , Macaca mulatta , Oryctolagus cuniculus , and Homo sapiens , but thermal gravimetric analysis (TGA) in Bos taurus , Ovis aries , and Mus musculus . The phylogenetic analysis showed that there was the closest relationship between Homo sapiens and P. troglodytes , and the farmost between M. muculus and O. aries . The signal peptide and the transmembrane domain of TYR gene for species were found at 1 to 20 AA and 470 to 500 AA, respectively. The five continuous random coils (5c) in TYR secondary structure of O. aries were found due to the substitution of polar Thr (T) for nonpolar Ile (I) and Leu (L) compared with other species. There was also a secondary structure variation of 2 c in H. sapiens due to the Pro that could break off the alpha helix simultaneous with a kink in polypeptide chain. The TYR is a kind of hydrophilic protein based on the hydropathy profile analysis, and the N-terminal and C-terminal hydrophobic region represents the signal peptide and the transmembrane domain, respectively.
A Compound Multifractal Model for High-Frequency Asset Returns

WThis paper builds a model of high-frequency equity returns in clock time by separately modeling the dynamics of trade-time returns and trade arrivals. Our main contributions are threefold. First, we characterize the distributional behavior of high-frequency asset returns both in clock time and trade time and show that when controlling for pre-scheduled market news events, trade-time returns are well characterized by a Gaussian distribution at very fine time scales. Second, we develop a structured and parsimonious model of clock-time returns by subordinating a trade-time Gaussian distribution with a trade arrival process that is associated with a modified Markov-Switching Multifractal Duration (MSMD) model of Chen et al. (2013). Our modification of the MSMD model provides a much better characterization of high-frequency inter-trade durations than the original model of Chen et al. (2013). Over-dispersion in this distribution of inter-trade durations leads to leptokurtosis and volatility clustering in clock-time returns, even when trade-time returns are Gaussian. Finally, we use our model to extrapolate the empirical relationship between trade rate and volatility in an effort to understand conditions of market failure. Our model finds that physical separation of financial markets maintains a natural ceiling on systemic volatility and promotes market stability.
Elephant are not beetles: implications of the ivory trade for the survival of the African elephant

The scientific community now agrees that, more than anything else, it is the killing of African elephants for the ivory trade that has caused the very dramatic declines in elephant populations witnessed over the past decade. Based on samples of ivory trade data, recent population modelling and field data, the authors discuss the implications of the ivory trade for the future survival of viable populations of African elephants.
Seasonality of larvae of Brachyura and Anomura (Crustacea Decapoda) in the Beagle Channel, Argentina*

), H. planatus (143 larvae · 10 m-3) and Pagurus spp. (79 larvae · 10 m-3), which represented 97% of the total larvae collected. Larvae of Pinnotheridae, Eurypodius latreillii, Libidoclaea granaria, and Paralomis granulosa were about an order of magnitude less abundant. Relative abundances of larvae correspond to relative abundances of the respective benthic stages. The absence of certain larval stages or of certain species (Acanthocyclus albatrossis and Lithodes santolla) probably indicates their differential distribution within the Beagle Channel. Particularly, lithodid larvae may have benthic or epibenthic habits.
SPECIFIC LEAF AREA AND PHOTOSYNTHETIC PARAMETERS OF TREE SPECIES IN THE FOREST UNDERSTOREY AS A FUNCTION OF THE MICROSITE LIGHT ENVIRONMENT IN CENTRAL AMAZONIA

MARENCO, R. A. & VIEIRA, G. 2005. Specific leaf area and photosynthetic parameters of tree species in the forest understorey as a function of the microsite light environment in central Amazonia. The effect of the microsite light environment (MLE) on specific leaf area (SLA), light-saturated photosynthesis (Amax), maximum transpiration (Emax) and stomatal conductance (gs-max) was examined in three tree forest species (late successional Minquartia guianensis and Scleronema micranthum, and Goupia glabra, a pioneer species) growing in the forest understorey. Logging of large trees 15 years ago had no significant effect on either SLA or photosynthetic parameters. On a per area basis, species did not differ in gas exchange parameters. However, when photosynthesis was expressed on a per mass basis (ug C g~' DM s-'), higher photosynthetic rates were observed in Goupia (1.07) than in Scleronema (0.71) or Minquartia (0.57). SLA (m2 kg-1) was greater in Goupia (24.4) than in Scleronema (18) or Minquartia (15.9). Amax, Emax and gs-max increased as the MLE in the understorey became brighter, particularly in Goupia. Leaf respiration in the light (0.2 umol m-2 s-1) and the apparent quantum yield (33 mmol COa mol-1 photon) were similar in all examined species. Regardless of logging disturbance, examined species acclimated to the MLE according to their successional status. Goupia, but not Minquartia or Scleronema, responded to its light environment mainly by changing SLA, indicating that physiological processes are involved in the acclimation of late successional species to the forest understorey.
Artículo original Comportamiento biológico de Blastocystis hominis en pacientes tratados con Secnidazol (Unidazol

Blastocystis hominis, classified as Stramenopile, is the most frequent intestinal parasite in humans. In feces and cultures, forms with a central body (FCB), granulose forms (GraF), as well as globulous and ameboid forms in binary division or in cysts are seen. Its elevated prevalence, association with symptoms in humans, and lack of effective treatment, justified the evaluation of secnidazol (Unida- zol ® ZOUZ-PHARMA) in 14 individuals (7 males and 7 females) infected with B. hominis, with ages between 5-79 years, who were clinically and parasitologically evaluated before and after treatment; with one dose of the drug: 2 g for adults and 30 mg/Kg body weight for children. In feces serial examinations we evaluated morphology, number of parasites per microscopic field (400X), reproductive forms, and growth in culture. The study showed that in 14.3% (2/14) of patients the parasite was eliminated, and there was a significant decrease of the number per field (p< 0.05), of the FCB (p= 0.001) and of GraF (p< 0.05) frequency in the rest, as well as a decrease of positive direct examinations (p< 0.001). These preliminary results show that the drug in a single dose occasionally eradicated B. hominis, decreased the excretion of vegetative forms and induced the occurrence of cysts.These studies should be continued.
On the Classification of the Ascaridae. II. The Polydelphis Group; with some account of other Ascarids parasitic in Snakes

The Ascarids parasitic in snakes present considerable difficulties from the systematic point of view, owing to the incomplete character of many of the descriptions, and to the state of confusion which has long existed in the nomenclature. The writer has made an attempt, by examining such material as was available, and by comparing a number of the existing descriptions, to clear up some of this confusion. It was hoped also that such a comparative treatment would throw some light on the systematic value of the modifications of the female genital apparatus, which occur in some of these forms.
Expression of Glycine Receptor α Subunits and Gephyrin in Cultured Spinal Neurons

The inhibitory glycine receptor is a pentameric membrane protein composed of α and β subunits. In the postsynaptic membrane, the glycine receptor and the copurifying peripheral membrane protein gephyrin are clustered underneath glycine‐releasing nerve terminals. Here, we describe the expression of gephyrin and the neonatal and adult glycine receptor α subunit isoforms α1 and α2 during in vitro differentiation of rat spinal neurons. Analysis by immunoassays and the reverse transcriptase—polymerase chain reaction showed that gephyrin and α subunit mRNA and protein levels exhibited a marked increase from 1 to 5 days in vitro, i.e. prior to the formation of functional synaptic contacts. Using confocal and standard immunofluorescence, we determined the number of immunoreactive cells and the cellular localization of the α subunits and gephyrin. At 3 days in vitro, glycine receptor immunoreactivity revealed by the monoclonal antibody mAb4a was found in >10% of cells and was mainly localized intracellularly; in contrast, gephyrin was detected in <50% of cells. At 7 days in vitro, gephyrin was essentially localized at the neuronal surface. At this stage, the number of glycine receptor‐positive cells approached that of gephyrin‐containing neurons (50%), and glycine receptor antigen was found both intracellularly and at the periphery of the cells. The antibody mAb2b, which binds exclusively to the α1 subunit, revealed aggregates at the surface of a few neurons. At 10 days in vitro, glycine receptor and gephyrin staining was localized in clusters at the periphery of the soma and the neurites. This quantitative analysis corroborates temporal differences in the cellular distribution of gephyrin and glycine receptor α subunits, the former being accumulated first at the neuronal surface.
Arthropod Abundance and Diversity in a Lowland Tropical Forest Floor in Panama: The Role of Habitat Space vs. Nutrient Concentrations

Tropical forest floor characteristics such as depth and nutrient concentrations are highly heterogeneous even over small spatial scales and it is unclear how these differences contribute to patchiness in forest floor arthropod abundance and diversity. In a lowland tropical forest in Panama we experimentally increased litter standing crop by removing litter from five plots (L−) and adding it to five other plots (L+); we had five control plots. After 32 mo of treatments we investigated how arthropod abundance and diversity were related to differences in forest floor physical (mass, depth, water content) and chemical properties (pH, nutrient concentrations). Forest floor mass and total arthropod abundance were greater in L+ plots compared with controls. There were no treatment differences in nutrient concentrations, pH or water content of the organic horizons. Over all plots, the mass of the fermentation horizon (Oe) was greater than the litter horizon (Oi); arthropod diversity and biomass were also greater in the Oe horizon but nutrient concentrations tended to be higher in the Oi horizon. Arthropod abundance was best explained by forest floor mass, while arthropod diversity was best explained by phosphorus, calcium and sodium concentrations in the Oi horizon and by phosphorus concentrations in the Oe horizon. Differences in arthropod community composition between treatments and horizons correlated with phosphorus concentration and dry mass of the forest floor. We conclude that at a local scale, arthropod abundance is related to forest floor mass (habitat space), while arthropod diversity is related to forest floor nutrient concentrations (habitat quality).
Neural modeling of human motor coordination inspired by biological signals aiming for parkinsonian gaits. (Modélisation neuronale de la coordination motrice humaine inspirée de signaux biologiques et visant des allures de marche parkinsoniennes)

Cette these presente une plate-forme de simulation neuro-musculo-squelettique du systeme locomoteur humain pour reproduire des allures de marche saines ou alterees par la maladie de Parkinson, ou par d’autres troubles locomoteurs. Le premier chapitre s’interesse aux grands principes du systeme locomoteur en se focalisant sur les structures neuronales du cerveau qui sont le siege des troubles parkinsoniens. La transmission a la moelle epiniere des signaux de controle de l'activite musculaire au travers de plusieurs boucles fermees est decrite. Differents modeles neuronaux des troubles parkinsoniens issus de la litterature sont presentes. Le second chapitre presente le controleur neuronal implemente dans la plate-forme. Il utilise un modele original de «central pattern generators» (CPG) inspire du reseau locomoteur spinal. Ce CPG peut generer des signaux rythmiques variables selon ses parametres neuronaux controles par des signaux descendants du cerveau. Les signaux des motoneurones du CPG sont appliques en tant qu'excitation au modele de muscles flexeur/extenseur. Le chapitre trois presente les simulateurs musculo-squelettiques GAIT2DE et OpenSim utilises ainsi que les modifications apportees pour simuler, en boucle fermee, le systeme locomoteur marchant sur le sol et les retours proprioceptifs et exteroceptifs exploites par les CPGs. Le chapitre quatre concerne l'analyse du cycle de la marche et l'optimisation des parametres du controleur. Le cycle de marche permet de comparer des donnees de simulation avec des parametres de marche reelle, et d’optimiser le controleur a partir d'une analyse comparative utilisant la correlation croisee. Le chapitre cinq presente les resultats obtenus avec les deux simulateurs en integrant une circuiterie complete a base des CPGs et d’un reflexe du controle d’equilibre. Les resultats montrent qu’on peut generer differentes demarches plus ou moins coordonnees selon les parametres neuronaux reproduisant ainsi les allures observees pour la maladie de Parkinson ou d’autres troubles connus en medecine. Le dernier chapitre conclu et propose certaines ameliorations de la plate-forme dans son ensemble pour simuler des demarches dues a d’autres maladies neurodegeneratives ou a l’impact de protheses ou suite a des interventions chirurgicales.
Effectiveness of commercial harvesting in controlling feral-pig populations

Abstract Context. The feral pig (Sus scrofa) is a widespread pest species in Australia and its populations are commonly controlled to reduce damage to agriculture and the environment. Feral pigs are also a resource and harvested for commercial export as game meat. Although many other control techniques are used, commercial harvesting of feral pigs is often encouraged by land managers, because it carries little or no cost and is widely perceived to control populations. Aims. To use feral-pig harvesting records, density data and simple harvest models to examine the effectiveness of commercial harvesting to reduce feral-pig populations. Methods. The present study examined commercial harvest off-take on six sites (246–657 km2) in southern Queensland, and 20 large blocks (∼2–6000 km2) throughout Queensland. The harvest off-take for each site was divided by monthly or average annual population size, determined by aerial survey, to calculate monthly and annual harvest rates. A simple harvest model assuming logistic population growth was used to determine the likely effectiveness of harvesting. Key results. Commercial harvest rates were generally low (<∼20%) and are likely to provide only modest reductions in population size. Additionally, harvest rates capable of substantial reductions (>50%) in long-term population size were isolated occurrences and not maintained across sites and years. High harvest rates were observed only at low densities. Although these harvest rates may be sufficiently high to hold populations at low densities, the population is likely to escape this entrapment following a flush in food supply or a reduction in harvest effort. Implications. Our results demonstrated that, at current harvest rates, commercial harvesting is ineffective for the landscape-scale control of feral-pig populations. Unless harvest rates can be significantly increased, commercial harvesting should be used as a supplement to, rather than as a substitute for, other damage-control techniques.