Miracle-dz/UniFAR-FTUs huggingface dataset:
Can Functional Traits Predict Ecological Interactions? A Case Study Using Rain forest Frugivores and Plants in Australia

In rain forest, the large numbers of species of fleshy‐fruited plants and frugivorous animals result in a large number of potential fruit–frugivore interactions, which are challenging to survey in the field. Yet, knowledge of these relationships is needed to predict consequences of changes in the frugivore assemblage for seed dispersal. In the absence of comprehensive dietary information, it may be possible to delineate between frugivores that disperse different plants using ‘functional traits,’ or morphological and behavioral attributes of frugivores that interact with differences in salient characteristics of plant species. Here we use data on the consumption of 244 Australian rain forest plant species by 38 bird species to test for associations between patterns of frugivory and birds': (1) degree of frugivory, (2) gape width, and (3) seed treatment (seed crushing or seed dispersing). Degree of frugivory and gape width explain 74 percent of the variation in the sizes of fruits consumed by frugivorous birds. Among birds that consume a substantial dietary proportion of fruit, birds with wider gapes consume larger fruits. In contrast, this relationship was not shown by birds for which fruit is only a minor dietary component. Degree of frugivory and gape width, together with seed treatment, also strongly predict the overall taxonomic composition and diversity of plants consumed by bird species. Functional classifications of frugivore species may prove useful in developing a predictive understanding of fruit–frugivore interactions in other rain forest regions where detailed dietary information is not available for most frugivores.
Trophic discrimination of nitrogen stable isotopes in amino acids varies with diet quality in a marine fish

Analysis of individual amino acid (AA) δ15N values is increasingly common in studies of food web architecture, movement ecology, and biogeochemical cycling. However, observations that nitrogen isotope fractionation of AAs may vary across species and trophic positions (TP) complicate the application of compound‐specific stable isotope analysis (CSIA) in studies of aquatic food webs. We reared a common estuarine fish (Fundulus heteroclitus) on four diets to test the hypothesis that diet composition significantly affects AA trophic discrimination factors (TDFs) derived from normalizing fractionation of trophic AAs to the canonical source AA phenylalanine. Phenylalanine showed little trophic fractionation regardless of diet composition, confirming its use as a proxy for δ15N values at the base of food webs. However, TDF values showed significant negative relationships with two important measures of diet quality, protein content and AA imbalance between diet and consumer. As a result, consumers feeding on high protein diets with AA compositions matching their own had significantly lower TDF values than previous literature values, while consumers feeding on contrasting low quality diets had significantly higher TDF values than previously reported. Our results provide an explanation for the apparent relationship between TDF value and TP, and highlight a significant limitation when using a single TDF value among all trophic transfers within a food web. Accurate determination of TPs using CSIA will likely require multiple TDF values across trophic levels or further exploration of other trophic AAs, such as proline, that may show less variation in TDF with diet composition than glutamic acid.
Long-Term Diagnostic Studies for Detection of Brucella spp. in Milk Samples

3 Abstract: Five diagnostic techniques (Milk Ring Test (MRT); Isolation; ELISA; Polymerase Chain Reaction (PCR) and Dot Blot Hybridization Assay (DBH)) in detection of Brucella spp. in milk samples collected from cows, buffaloes, sheep, goats and camels were evaluated. A total number of 1685 serum samples were collected from the different species in the period between 2001to 2009 and examined by Rose Bengal agglutination assays (RBT) and revealed an overall incidence of 52.3%. A total number of 881 milk samples examined by different assays that showed an incidence of 47.8% by MRT, 42.8% by ELISA; 33.8% by isolation, 50.2% by PCR assays and 45.3% by DBH assays. Molecular diagnosis including both PCR and DBH assays found to be more sensitive with maintaining reliable specificity when compared with conventional techniques. In conclusion, molecular diagnosis (PCR and DBH) proved to be more suitable tools for brucella diagnosis than the other conventional techniques (MRT and isolation). A combination between molecular techniques and conventional techniques found to be a good reliable policy for controlling the disease. Nomadic habits concerning drinking of raw milk from camels and goats is incriminated in human cases. Avoid mixing between cattle and buffaloes especially dairy farms with sheep flocks.
An allometric tridimensional model of self-thinning for a gregarious tunicate

A tridimensional allometric model of self-thinning was tested in a tunicate population of Pyura praeputialis in the Antofagasta Bay, northern Chile. The theory tested follows the bidimensional allometric theory of Osawa and Allen for the self-thinning rule proposed for plants, except that in addition to mean individual mass we included three new concepts: the number of layers (an equivalent of the leaf area index, [LAI] used in plants), the effective unit area, and the density per unit effective area. We assumed constant tunicate mass per effective unit area and allometry for mean dimensions of the population. The tridimensional model can be reduced to a bidimensional one if density is expressed as the density per unit effective area, which corresponds to the number of individuals relative to the effective area occupied by individuals when they conform a monolayer. The model allows for random sampling and rules out the selection for samples or stands at maximum crowding. The self-thinning of P. praeputialis through a tridimensional model showed an exponent of −1.518 (95% ci,−1.635 to −1.401) for mean tunicate visceral mass, and an exponent of −1.489 (95% ci, −1.588 to −1.390) for the corrected bidimensional model. The two exponents were identical to those predicted from tridimensional allometric theory. The results of this new approach increase the variance explained in comparison to that of classical bidimensional models.
Screening of endophytic fungi from tubers of Dahlia variabilis.

Researches on plant-derived endophytic fungi have grown in recent decades. Dahlia variabilis is one of natural products which potential as a source of antimicrobial agents. The purpose of this research was to isolate and characterize endophytic fungi from the tubers of Dahlia variabilis because derivation of bioactive compounds directly from the plants needs too many biomasses. Direct seeds method was used to isolate endophytic fungi from the samples. Samples were surface-sterilized by immersing in 70% ethanol, soaked in 15% peroxide acid, rinsed in sterile distilled water, and then put on the surface of Sabouraud-4% Dextrose Agar (SDA). Four isolates of endophytic fungi were isolated and characterized morphologically i.e., Monilia sp. , Aureobasidium sp. , Moniliella sp. , and Sporothrix sp.
A new deep-sea genus of the family Polyceridae (Nudibranchia) possesses a gill cavity, with implications for the cryptobranch condition and a ‘Periodic Table’ approach to taxonomy

A new genus and species of a deep-sea dorid nudibranch is described. Elfdaliana profundimontana n. gen, n. sp. is the first taxon of the family Polyceridae with a gill cavity. The new genus possesses diagnostic characters of other polycerids, including globular structures on the branched lateral processes, a radula with broad rachis and differentiated outer lateral teeth. This discovery agrees with recently proposed phylogenetic frameworks and supports a development-based model for the evolution of the dorid nudibranchs, placing the cryptobranch condition as ancestral. A synopsis of the ontogenetic stages representing major dorid cryptobranch and phanerobranch lineages (including novel data on three species) is presented for the first time. Phylotypic periods for the dorid nudibranchs are indicated. It is suggested that the phenomenon of conserved phylotypic periods makes it possible to apply a Periodic Table-like approach to biological taxonomy and phylogenetics.
Inhibition of leptin receptors through plant-derived ligands for liver fibrosis drug development

Abstract Background: Liver fibrosis is a common health problem worldwide. Several drug-targets have been identified from the fibrosis pathway namely leptin, leptin receptors, adiponectin, and PPAR ã agonist. Suitable antifibrotic drugs are needed. Objective: Present plant-derived ligands inhibiting the leptin receptor mediated pathway as antifibrotic drugs. Methods: Bioinformatics was used to generate 3D-structure of leptin receptor to explore binding grooves of therapeutic targets. A molecular library with bioactive compounds from SE Asian medicinal plants was developed by using the bioactive compounds, docking with leptin receptor. Results: The homology model of leptin receptor has showed similarities with crystal structures and folds reported previously for other cytokine family members. The Ramachandran plot shows that 89.1% of the residues are most favored region. Besides, 15 possible active sites were identified with active residues such as Ser180, Gln463, Pro477, IIe482, Leu519, Asn550, Pro564, Val600, Glu643, Lys665, Asp671, Ser675, Leu767, Pro803, and Glu834. Conclusion: This study provides data on surface cavity, binding groove, and active sites of the leptin receptor, which will be useful for researchers to understand leptin receptor/complex. We hope that the strandline serve as a potential drug candidate for liver fibrosis in the near future.
Evaluation and calibration of an automated rising plate meter for estimating dry matter yield of pasture

An automatic rising plate meter called the Ellinbank Pasture Meter (EPM) was constructed and evaluated at the Dairy Research Institute (Ellinbank) for measuring the dry matter present on a pasture dominated by green perennial rye grass. The meter readings of pasture height were found to correlate linearly with pasture yield, and the coefficient of variation of calibrations on any one date averaged about 13%. When the data from a large number of calibrations from separate dates were pooled, the coefficient of variation increased to about 18% (RSD 370 kg ha-1). Although there was a high level of repeatability of readings within operators, a substantial degree of variation existed between operators. The diurnal variation in dry matter percentage of pasture had only small effects on the meter readings. The EPM has an advantage over other pasture measuring methods in that its automatic function enables up to one hundred pasture measurements to be made in five minutes. In direct comparison with a manual rising plate meter and a two probe electronic capacitance meter, it was found that there was no significant difference in accuracy between the three meters but the advantages of the EPM are discussed. On perennial rye grass/white clover pastures in an actively growing vegetative state, the EPM has been found to be accurate enough for research purposes yet simple enough for use by farmers and their advisers as an aid to pasture management.
Comparative life history studies of Frankliniella occidentalis and Thrips tabaci (Thysanoptera: Thripidae) on cucumber

Shortly after its invasion into Europe, the western flower thrips, Frankliniella occidentalis (Pergande), became a more severe pest of greenhouse crops than the onion thrips, Thrips tabaci Lindeman. To test whether this differential pest status was due to a larger capacity of population increase, a comparative life history study was carried out on cucumber ( Cucumis sativus cv. Corona). Experiments at 25°C showed that the egg-to-egg period of F. occidentalis was shorter, but its peak ovipositional rate was lower and its offspring sex ratio more male biased. These differences resulted in a slightly lower intrinsic rate of population increase (r m ) for F. occidentalis than for T. tabaci (0.166 vs. 0.176/day). It was shown experimentally that between 15 and 28°C, developmental rate of F. occidentalis is linearly related to temperature, with a theoretical threshold temperature similar to the value reported for T. tabaci (10.9 vs. 11.5°C). It is argued that the r m -value of F. occidentalis will not be higher than that of T. tabaci for any temperature within this range. Alternative explanations for the difference in pest status between the two thrips species are discussed.
Deep-sea decapod crustaceans in the western and central Mediterranean Sea: preliminary aspects of species distribution, biomass and population structure*

Three deep-sea areas in the Mediterranean Sea were sampled using a bottom otter trawl during the DESEAS oceanographic survey carried out from early June to early July 2001, covering an area in the western Mediterranean from 600 to 2800 m in depth and two areas in the central Mediterranean, the western and eastern Ionian Sea from 600 to 4000 m in depth. Decapod crustaceans were one of the dominant megafaunal groups, together with fishes, in terms of both biomass and abundance. A total of 2799 decapod specimens belonging to 32 species were collected. Abundance and biomass of the decapod crustaceans decreased with depth. For depths below 1000 m, a decrease in total decapod biomass was recorded from west to east. From the data reported in this study and data from the available literature, decapod crustaceans display differential depth distributions in the different areas. For the most abundant species, size and sex distributions versus depth gradient were examined to compare intraspecific population structures between the sampling areas. Despite differences, among areas, in the species biomass compositions by depth strata and differences in their overall bathymetric ranges of distribution, intraspecific population structures of the most abundant species seem to follow similar trends for size and sex distribution versus depth gradient between the western and central areas. This might be an indication that the individual species structure their populations according to a similar basic pattern regardless of differences in local environmental features. The results have been discussed in the general context of the environmental features encountered by the species in each of the sampling areas.
Grateloupia jejuensis (Halymeniales, Rhodophyta): a new species previously confused with G. elata and G. cornea in Korea

Despite specimens` large size and ease of collection in northeast Asian waters, the species diversity of the genus Grateloupia still needs more research in Korea. We investigated plastid rbcL sequences and carried out detailed morphological observation on flattened halymeniacean red alga collected in twelve locations around Korea and Japan. We describe Grateloupia jejuensis sp. nov. based on the distinct clade with high support in our rbcL tree. Grateloupia jejuensis is characterized by solitary or caespitose habit and flattened thalli with discoid holdfast, cartilaginous texture, and blunt or bifid axis. Grateloupia jejuensis was distantly related to G. elata and G. cornea, which have been morphologically confused with the former, and it formed a sister relationship with Prionitis filiformis from California, USA in the rbcL tree.
In vitro cleaning of sugarcane (Saccharum officinarum) explants against the viral infections by application of the viral inhibitors (DHHT and virazol): a preliminary study

The objective of this work was to cleanse explants of Saccharum officinarumcultivated in vitro using the viral inhibitors DHHT and virazol. The basic vegetal material constituted seeds of 4 varieties of sugarcane, Ð¥99-055, Ð¥97-029, X99-071 and X97-035, obtained from the CIRAD of Guadeloupe. The explants of foliar, stem and root origin size 0.7 - 1.5 mm were cultivated on modified medium of Mourassigue and Skougou. The viral inhibitors introduced in the culture medium to proportions of 1%. The diagnosis of the viruses were made by symtomatologic tests confirmed by enzyme linked immunosorbent assay (ELISA). 5 viruses (SCMV, CMV, RLMV and YDBV) were screened. The use of the virazol and DHHT makes possible to obtain 40, 55, 35 and 60 % explants respectively free from SCMV, CMV, RLMV and YDBV on the X97-029 variety for explants size 1.2 - 1.5 mm. The results show that it is possible to obtain a seed-bearer material of sugarcane free from some viruses by the method of cleaning using the viral inhibitors on explants of larger cuts (1.2 - 1.5 mm). Key words: Saccharum officinarum, explants, viral inhibitors
Repeated sampling affects Tree Swallow semen characteristics

Abstract Male Tree Swallows (Tachycineta bicolor) face intense sperm competition because mated pairs copulate frequently, extra-pair copulations are common, and females store sperm. We examined the effects of repeated sampling on the characteristics of Tree Swallow semen by manually expressing semen from 15 males immediately after capture (T0) and then hourly for 4 h (T1–T4). The semen characteristics of individual males varied in response to repeated sampling. The total number of sperm cells we obtained from each male over the 4-h sampling period varied from 104–107. Semen samples lacking sperm increased from 6.7% of T0 samples to 26.7– 33.3% of subsequent samples. Forty percent of males provided at least one semen sample that lacked sperm. There were no significant differences among hourly samples in semen volume, sperm concentration, or in the total number of sperm cells obtained from each male. However, there were significant differences among males in each of these variables. Semen volumes represented small proportions of cloacal protuberance volumes. We did not detect significant correlations between total semen volumes or total number of sperm cells obtained from males from T0–T4 and cloacal protuberance volumes. Total semen volume and number of sperm cells obtained from T0–T4 significantly increased with date. However, sperm concentration was not significantly correlated with date. We did not detect significant correlations between semen characteristics and male morphology. Individual variation in responses to repeated sampling has implications for the copulatory strategies of male and female Tree Swallows.
BREEDING BIRD RESPONSE TO RIPARIAN BUFFER WIDTH IN MANAGED PACIFIC NORTHWEST DOUGLAS‐FIR FORESTS

We examined the relative importance of riparian vs. upland habitats to breeding birds by comparing species abundance, richness, and similarity of bird communities in managed Douglas-fir forests in western Washington State, USA. We also examined whether forested buffer strips along second- and third-order streams effectively maintain the pre-logging riparian breeding bird community by comparing species abundance, richness, and turnover among three treatments: (1) unharvested controls; (2) sites that were clear-cut, leaving a narrow (∼14 m) forested buffer on both sides of the stream; and (3) sites that were clear-cut, leaving a wide (∼31 m) forested buffer along both sides of the stream. Deciduous trees, berry-producing shrubs, and other deciduous shrubs less common in adjacent upland forest characterized streamside zones. Despite different vegetation features, riparian and upland habitats did not differ in any measures of bird species richness and composition. No species or species group was more abundant.
Towards an acoustic‐based coupled observation and modelling system for monitoring and predicting ecosystem dynamics of the open ocean

Assessment of open-ocean ecosystems relies on understanding ecosystem dynamics, and development of end-to-end ecosystem models represents an approach that addresses these challenges. These models incorporate the population structure and dynamics of marine organisms at all trophic levels. Satellite remote sensing of ocean colour and direct at-sea measurements provide information on the lower trophic levels of the models, and fisheries studies provide information on top predator species. However, these models suffer from a lack of observations for the so-called mid-trophic levels, which are poorly sampled by conventional methods. This restricts further development, and we argue that acoustic observations from a range of platforms (e.g. buoys, moorings) can be linked to the ecosystem models to provide much-needed information on these trophic levels. To achieve this, the models need to be tailored to incorporate the available acoustic data, and the link from acoustic backscatter to biologically relevant variables (biomass, carbon, etc.) needs attention. Methods to progress this issue are proposed, including the development of observation models and focal areas for ground truthing. To ensure full use of the potential of acoustic techniques, we argue that a systematic and long-term strategy incorporating the following elements is required: development of metadata standards and automated data analysis, inclusion of acoustic sensors in large-scale observatory programmes, improvement of observation-model links, and efficient sampling strategies. Finally, these elements should be tied together in an observation-modelling framework, coordinated by international organizations, to improve our understanding and quantification of open-ocean ecosystem dynamics.
Responses in pigmentation and anti-oxidant expression in Arctic Daphnia along gradients of DOC and UV exposure

Responses in carapace melanization and expression of the major anti-oxidant catalase (CAT) and glutathione transferase (GST) in Arctic Daphnia were assessed in enclosures along a gradient of dissolved organic carbon (DOC). This gradient was created by adding freeze-dried humic matter to 2 m 3 UV-transparent enclosures, yielding final nominal concentrations of 1, 2.5, 5 and 10 mg C l -1 . The UV attenuation was strongly affected by additions of DOC, and attenuation coefficients at 320 nm increased from 3.0 in the control to approximately 3.5 and 11.0 m -1 in the 1 and 10 mg DOC treatments respectively. Most Daphnia showed pronounced carapace melanization, and the absorbance of short-wave radiation through the carapace was strongly related to the degree of melanization. Nevertheless, the different UV climate in the enclosures did not cause any short-term adaptation in Daphnia pigmentation over a 3 week period. The levels of CAT and GST were assessed over time in the control and at 10 mg DOC. These enzymes displayed opposite patterns, with somewhat lower activities of CAT at low DOC (control) relative to 10 mg DOC, while the opposite was found for GST. There was also a significant negative correlation between CAT and solar irradiation for GST in both bags, while no sects were found for GST.