Miracle-dz/UniFAR-FTUs huggingface dataset:
Leaf hydraulic architecture and water relations of three ferns from contrasting light habitats

Leaf hydraulic architecture and water relations of three fern species were measured. The species selected were adapted either to deeply shaded (Woodwardia radicans), moderately shaded (Dryopteris affinis) or moderately sunny (Polystichum setiferum) habitats, as confirmed by microclimatic measurements performed in the field. Leaf water potential (Ψleaf) was lower and leaf conductance to water vapour (gL) was higher in P. setiferum than in the shade-adapted ferns. Leaf osmotic potential and water potential at the turgor loss point were lower in the sun-adapted species than in the other ferns. Leaf hydraulic resistance (Rleaf) was lowest in P. setiferum and Rleaf was correlated with gL across species. Low Rleaf was coordinated with low rachis hydraulic resistance (Rrachis). Low values of Rrachis in P. setiferum were not due to the presence of wide xylem conduits as checked on the basis of anatomical measurements, but to increased radial permeability of vascular bundles. This was a consequence of the absence of endodermis surrounding the vascular bundles in P. setiferum, which was observed in the rachis of shade-adapted species. We conclude that hydraulic adjustment of fern fronds is a key component of adaptation of pteridophytes to contrasting light habitats.
Evaluation of drought tolerance of some corn (Zea mays L.) hybrids in Iran.

The effect of drought stress on yield and its components was studied on 28 new hybrids of maize along with 6 commercial control hybrids at the Khorasan Razavi Agricultural Research and Natural Resources Institute Mashhad, Iran in 2010. The study was conducted in a completely randomized block design with three replications under normal irrigation and drought stress conditions. There were significant differences among hybrids under both conditions for all traits. The mean grain yield of SC500 hybrid in the normal irrigation condition and N11 hybrid in the stress condition was highest. Result of simple correlation between traits under stress condition showed that number of kernel in row was the highest correlation with yield and in normal irrigation ear diameter was higher than other traits correlated. In order to identify the tolerant genotypes, drought resistance indices were calculated. SC500 and SC250 hybrids were the best genotypes under normal condition and H11 and SC250 showed the best behavior under drought stress condition. In summary, it seems Harm, STI and GMP indices have a similar ability to separate drought sensitive and tolerant genotypes. We also used cluster analysis (Ward’s method) to classify tolerance hybrids in similar classes. Key words: Corn, drought resistance indices, hybrid, cluster analysis.
A Novel Species of Gliocladiopsis from Freshwater Habitat in China

Abstract Gliocladiopsis guangdongensis sp. nov. is introduced on the basis of both morphological and on multilocus phylogenetic analysis (&bgr;-tubulin, histone H3, internal transcribed spacer region and translation elongation factor 1-&agr;). The species is compared to other morphologically similar and phylogenetically closely related taxa. Species of Gliocladiopsis are mostly known from soil and terrestrial plants whereas this new species is the first isolation from decaying wood from freshwater habitat.
Assimilation of various organic carbon sources by Haematococcus strains

Differences in the assimilation of individual organic compounds (5 mM sugars and L-asparagine) under mixotrophic growth conditions were described for three naturally occurring Haematococcus strains.The effects of assimilation were measured by the growth intensity and size of algal cells, and the effect of colour changes in the cultures was observed. Some compounds caused the cell colouration to change from green to yellow, being the result of chlorophyll disappearance and the accumulation of yellow secondary carotenoids. In the present experiment none of the cultures turned red, thus excluding the intense accumulation of the commercially interesting carotenoid, astaxanthin.
The fin whale Balaenoptera physalus (L. 1758) in the Mediterranean Sea

The ecology and status of fin whales Balaenoptera physalus in the Mediterranean Sea is reviewed. The species' presence, morphology, distribution, movements, population structure, ecology and behaviour in this semi-enclosed marine region are summarized, and the review is complemented with original, previously unpublished data. 2. Although the total size of the fin whale population in the Mediterranean is unknown, an estimate for a portion of the western basin, where most of the whales are known to live, was approximately 3500 individuals. High whale densities, comparable to those found in rich oceanic habitats, were found in well-defined areas of high productivity. Most whales concen- trate in the Ligurian-Corsican-Provencal Basin, where their presence is particularly noticeable during summer; however, neither their movement patterns throughout the region nor their seasonal cycle are clear. 3. Based on genetic studies, fin whales from the Mediterranean Sea are distinct from North Atlantic conspecifics, and may constitute a resident population, separate from those of the North Atlantic, despite the species' historical presence in the Strait of Gibraltar. Fin whales are known to calve in the Mediterranean, with births peaking in November but occurring at lower rates throughout the year. They feed primarily on krill Meganyctiphanes norvegica which they capture by diving to depths in excess of 470 m. It is suggested that the extensive vertical migratory behaviour of its main prey may have influenced the social ecology of this population. 4. Known causes of mortality and threats, including collisions with vessels, entanglement in fishing gear, deliberate killing, disturbance, pollution and disease, are listed and discussed in view of the implementation of appropriate conservation measures to ensure the species' survival in the region.
SALSEA North America: a pelagic ecosystem survey targeting Atlantic salmon in the Northwest Atlantic

Pelagic ecosystem surveys were conducted in the Labrador Sea during 2008 and 2009 as part of SALSEA North America. In total, 107 Atlantic salmon (Salmo salar) were captured using a pelagic surface trawl and multipanel surface gillnets. Surface trawling provided a broad spatial sampling of the fish and macroinvertebrate communities in the upper 10 m of the water column, but caught few salmon (23). Gillnetting was more effective at capturing post-smolt (60) and adult (24) salmon. Multiple smolt cohorts were captured, indicating that post-smolts and returning adults from different rivers in North America have similar autumnal habitat requirements. Postsmolts were caught at night and in water temperatures exceeding 108C, both novel results. Post-smolts and adults consumed similar and diverse prey species, although Themisto compressa was the most important prey item. Intestinal macroparasite loads were substantial and could be a significant source of mortality. Concurrent planktonic assemblage and oceanographic conditions were also quantified. A full exploration of these data, historical datasets, and parallel data collected during SALSEA Greenland and SALSEAMerge will further understanding of the ecology of marine-phase Atlantic salmon and inform investigations into stock-specific differences in marine productivity.
The effect of different dietary vitamin and mineral levels on certain production parameters, including egg shell characteristics of breeding ostriches.

Earlier studies on breeding birds indicated no effect of dietary energy-content on feed intake. This observation is contradictory to results for other animals and/or poultry where feed intake decreases with an increase in dietary energy level. Literature revealed that a lack of certain nutrients may cause animals to consume more feed than necessary to satisfy their nutrient requirements for these limiting nutrients. In this study eight diet groups were evaluated. A standard commercial diet plus one of the following supplements: (i) Standard diet without a vitamin and mineral premix pack (control diet), (ii) with a normal premix pack, (iii) with normal vitamin and 2 x trace elements (M x 2), (iv) with normal trace elements and 2 x vitamins, (v) with a normal premix pack and limestone added as calcium source; (vi) with a normal premix pack and monocalcium phosphate added as phosphorus source, (vii) with a normal premix pack and soybean oilcake added as crude protein source, (viii) with a normal premix pack and linseed added as a fatty acid source. Significant differences were recorded in the quantity of feed ingested by birds between the diet with surplus minerals (M x 2) (Group 3) (2.3 ± 0.3 kg/bird/day), the diet with no vitamins and minerals added (Group 1) (2.7 ± 0.3 kg/bird/day) and the diet with added fatty acids in the form of linseed (Group 5) (2.9 ± 0.5 kg/bird/day). This indicates the possibility that ostriches may adjust feed intake to satisfy their mineral requirements. No statistically significant relationship was found between the thickness and strength of the shell. Significant differences in shell strength (mean value of 154.7, 109.9, 140.4, 142.7, 153.0, 143.4, 138.4 and 151.1 N/cm 2 , respectively) were found between all treatments, but no specific pattern could be identified. Results further revealed no effect of dietary treatment on egg production, dead-in-shell eggs (DIS), infertile eggs or chick production. Further experiments that include certain dietary treatments during the five months rest period are currently being done to quantify the effect of the addition of minerals and vitamins during this period on the production of breeding ostriches. Keywords : Eggshell strength; feed intake, minerals, vitamins
Understanding DNA: The Molecule & How It Works

An Introduction to Molecular Biology for Non-Scientists Why a Helix? Different Kinds of Double Helix Twisting and Curving Curving in Three Dimensions DNA Supercoiling The Assembly of DNA intor Chromosomes Specific DNA-Protein Interactions Methods Used to Study the Structure of DNA DNA in Disease, Diagnostics and Medicine Cytosine Methylation and DNA Epigenetics Appendix 1: Notes on the Derivation of Some Technical Terms Appendix 2: The Chemical Theory of Base-stacking Interactions in DNA Appendix 3: How to modify Gene Expression by means of Anti-sense Oligonucleotides, Ribozymes or si-RNA
Algoritmo de recocido simulado aplicado al problema de secuenciamiento regular

In this paper a detailed description of the simulated annealing algorithm is presented. This strategy was employed to solve a well know flow-shop problem, which behavior is featured by the combinatorial explosion and non linear modeling. Therefore, the strategy could be focused to analyze the efficiency of the production in facilities with limited resources. Simulations results performed in a problem in the literature are presented. By this mean, the wide versatility, efficiency, and the easy implementation of the proposed algorithm is verified.
Soil carbon balance following conversion of grassland to oil palm

Oil palm (Elaeis guineensis Jacq.) crops are expanding rapidly in the tropics, with implications for the global carbon cycle. Little is currently known about soil organic carbon (SOC) dynamics following conversion to oil palm and virtually nothing for conversion of grassland. We measured changes in SOC stocks following conversion of tropical grassland to oil palm plantations in Papua New Guinea using a chronosequence of plantations planted over a 25‐year period. We further used carbon isotopes to quantify the loss of grassland‐derived and gain in oil palm‐derived SOC over this period. The grassland and oil palm soils had average SOC stocks of 10.7 and 12.0 kg m−2, respectively, across all the study sites, to a depth of 1.5 m. In the 0–0.05 m depth interval, 0.79 kg m−2 of SOC was gained from oil palm inputs over 25 years and approximately the same amount of the original grass‐derived SOC was lost. For the whole soil profile (0–1.5 m), 3.4 kg m−2 of SOC was gained from oil palm inputs with no significant losses of grass‐derived SOC. The grass‐derived SOC stocks were more resistant to decrease than SOC reported in other studies. Black carbon produced in grassfires could partially but not fully account for the persistence of the original SOC stocks. Oil palm‐derived SOC accumulated more slowly where soil nitrogen contents where high. Forest soils in the same region had smaller carbon stocks than the grasslands. In the majority of cases, conversion of grassland to oil palm plantations in this region resulted in net sequestration of soil organic carbon.
Aquatic and Terrestrial Locomotor Performance in a Semiaquatic Plethodontid Salamander (Pseudotriton ruber): Influence of Acute Temperature, Thermal Acclimation, and Body Size

Abstract Current theory predicts that (1) locomotor performance of amphibians should exhibit greater thermal sensitivity in aquatic than in terrestrial habitats, and (2) amphibians lose the ability to acclimate locomotor performance to different temperatures after metamorphosis. To test these predictions for a semiaquatic plethodontid salamander (Pseudotriton ruber), I measured aquatic and terrestrial burst speeds of metamorphosed individuals at 8 C and 18 C after acclimation to 8 C and 18 C. Both aquatic and terrestrial speeds exhibited thermal sensitivity, which paralleled that for cycle frequency (tail or leg), but terrestrial speed had a significantly greater thermal sensitivity. Aquatic speed was significantly greater at 8 C acclimation, whereas terrestrial speed was not affected by thermal acclimation. Scaling of locomotor performance was significantly different in water than on land and was significantly affected by temperature. My results indicate that (1) aquatic burst speed has less thermal sensitivity (perhaps related to a greater importance of burst speed in aquatic habitats), and (2) a partial positive compensation in aquatic burst speed occurs at low acclimation temperature (perhaps related to seasonal activity in cool aquatic habitats). However, because the compensatory increase in swimming speed at low acclimation temperature was much less at low test temperature (a 6% increase) than at high test temperature (an 18% increase), this may not be a beneficial acclimation response.
Effect of nonessential amino acids on phagostimulation and maintenance of the pea aphid, Acyrthosiphon pisum

Eleven nonessential amino acids and amides, at concentrations ranging from 0.001 to 1.0% in 35% sucrose solutions, were individually tested for their role in phagostimulation, growth, and survival in Acyrthosiphon pisum (Harris). Alanine and -γ-amino butyric acid were generally phagostimulatory, whereas asparagine, aspartic acid, cysteine, cystine, glutamic acid, glycine, proline, serine, and tyrosine were generally inhibitory. Asparagine, glutamic acid, glycine, and proline supported growth and prolonged survival; aspartic acid and tyrosine increased weight but did not prolong survival, and alanine, -γ-amino butyric acid, cystine, cysteine, and serine neither promoted growth nor prolonged survival.
High genetic diversity of the endangered Iberian three‐spined stickleback (Gasterosteus aculeatus) at the Mediterranean edge of its range

Summary 1. The three-spined stickleback (Gasterosteus aculeatus) on the Iberian Peninsula is only distributed in freshwater habitats and has completely disappeared from most of its range, mainly as a consequence of habitat degradation and invasive fish introductions. Genetic investigations have shown that Mediterranean-Adriatic sticklebacks constitute an evolutionarily significant unit. Here, we present the first genetic data for Iberian populations living on the southern edge of the stickleback’s range. We used microsatellite markers to study gene diversity, population structure and genetic demography of stickleback populations. 2. High genetic differentiation among collections yielded a model of four genetically homogeneous units related to geography. The observed pattern of isolation by distance resulted mainly from the hydrographical pattern and limited gene flow among rivers. Moreover, low levels of gene diversity, high isolation and recent bottleneck events, which have led to small or even critical effective population sizes in several locations, could be explained by additional recent anthropogenic fragmentation. 3. We defined at least four evolutionarily significant units threatened by habitat fragmentation in north-eastern Iberian sticklebacks. Because they retain long evolutionary histories, these populations should be considered of high conservation priority, and urgent management measures should be implemented.
A simple numerical tool to infer whether a species is extinct

Including uncertain sightings when inferring extinction of a species is relatively new and has proven to be significant. However, including uncertain sightings leads to non‐trivial mathematical problems which are inaccessible to many ecologists. I use the Pohnpei Mountain Starling Aplonis pelzelni to describe an Excel spreadsheet which infers extinction from a sighting record. The spreadsheet implements a Bayesian model which includes uncertainty around the prior, uncertain sightings and survey effort. Survey effort has not been included in extinction models before, but clearly plays a significant role in extinction estimates, which the Pohnpei Mountain Starling example demonstrates. The spreadsheet (included as supplementary material) is user‐friendly, fast and accessible on Windows.
Efeitos de extratos vegetais e antimicrobianos sobre a digestibilidade aparente, o desempenho, a morfometria dos órgãos e a histologia intestinal de leitões recém-desmamados

The purpose of this trial was to evaluate the effects of antimicrobial and herbal extracts on digestibility, performance, morphology and histology of weanling pigs. One hundred and twenty weaned pigs were used to compare five treatments: control - basal diet; antimicrobial - basal diet plus Zn bacitracina, olaquindox, and colistin (50 ppm of each); herbal extract A, B and C - basal diet plus 700 ppm, 1,400 ppm and 2,100 ppm of herbal extract, respectively, with 12 replications (pens of two pigs each) per treatment in a 35-d randomized complete block design experiment. The herbal extract consisted of mixture of equal amounts of essential oils of thyme, clove, oregano, eugenol and carvacrol. In digestibility assay, 40 pigs (four replications per treatment) were fed a diet with chromium oxide (marker method). On 35th day of experimental period, one animal of each experimental unit was slaughtered and samples were collected for analysis. The herbal extracts increased dietary DM apparent digestibility compared to control and antimicrobial treatments. The antimicrobial agents improved performance of weanling pigs during all phases of the experimental period compared to the other treatments. Pigs fed high dietary level of herbal extract showed better results for pig performance and other variables. The antimicrobial treatment improved the relative weights of intestinal tract and empty small intestine and improved ileum villus height and ileum villus height:crypt depth ratio of animals. However, more studies are necessary to evaluate which type of essential oil should be used and the best combination and inclusion level of herbal extract in the diet.
Diving to extremes: are New Zealand sea lions (Phocarctos hookeri) pushing their limits in a marginal habitat?

When studying diving behaviour, it is important to know whether a species is operating at or close to its maximum physiological capacity, because if it is, it will be less capable of compensating for normal environmental or human-induced fluctuations in its environment. New Zealand (NZ) sea lions Phocarctos hookeri are among the world’s rarest pinnipeds with a restricted distribution and abundance to the most southerly limit of their known range, NZ’s sub-Antarctic. Female NZ sea lions are the deepest and longest diving of the otariids, foraging further from their breeding rookeries than any other sea lion. In this study, the diving behaviours of 18 female NZ sea lions from Enderby Island, Auckland Islands, were recorded during early lactation over two austral summers, 2003 and 2004. While at sea, sea lions dived almost continuously, spending on average 52.7% of their time submerged (46 m). The mean dive depth ( � SE) for all dives was 129.5 � 5.3 m (range 94.6 � 1.1 to 178.9 � 1.6 m). The mean duration of dives was 4.0 � 0.1 min with an average of 40 � 2.9% of all dive times spent in the deepest 85% of the dive. Although there was high variation in diving behaviour among individuals, overall, animals were found to be diving beyond their estimated aerobic dive limits on 68% of all dives. Given that female NZ sea lions have a high percentage of dives that are beyond their theoretical aerobic limits, we ask whether this represents a miscalculation in aerobic limits, is it a species highly adapted to carry an anaerobic load or a species that is physically stretched to their limits? A species that is presumably under physiological stress just to maintain its current low static population numbers is also likely to be more susceptible to external impacts and this needs consideration for their management.
Support vector machine prediction of N-and O-glycosylation sites using whole sequence information and subcellular localization

Background: Glycans, or sugar chains, are one of the three types of chain (DNA, protein and glycan) that constitute living organisms; they are often called “the third chain of the living organism”. About half of all proteins are estimated to be glycosylated based on the SWISS-PROT database. Glycosylation is one of the most important post-translational modifications, affecting many critical functions of proteins, including cellular communication, and their tertiary structure. In order to computationally predict N-glycosylation and O-glycosylation sites, we developed three kinds of support vector machine (SVM) model, which utilize local information, general protein information and/or subcellular localization in consideration of the binding specificity of glycosyltransferases and the characteristic subcellular localization of glycoproteins. Results: In our computational experiment, the model integrating three kinds of information achieved about 90% accuracy in predictions of both N-glycosylation and O-glycosylation sites. Moreover, our model was applied to a protein whose glycosylation sites had not been previously identified and we succeeded in showing that the glycosylation sites predicted by our model were structurally reasonable. Conclusions: In the present study, we developed a comprehensive and effective computational method that detects glycosylation sites. We conclude that our method is a comprehensive and effective computational prediction method that is applicable at a genome-wide level.