Miracle-dz/UniFAR-FTUs huggingface dataset:
Statistical analysis of catch-at-age data with correlated errors

We extend the statistical model used to estimate abundance from commercial catch-at-age data for many of the major commercial fish species in the world. The model we consider combines commercial catch-at-age data and research survey estimates of fish abundance; we extend the model to allow correlated errors among ages within a year for the survey estimates of fish abundance. We also formulate a method for modeling the fishing mortality on the oldest ages of the fish caught. Estimates are obtained using maximum likelihood. We conclude that the level of correlation among ages is sufficiently large to produce large biases in the standard methods for some stocks. The statistical model that includes correlated errors greatly reduces bias and increases efficiency if the correlation in the estimation error is large.
Size-dependent impacts of the endangered white-clawed crayfish (Austropotamobius pallipes) (Lereboullet) on the littoral community

The demise of Britain’s only native crayfish (Austropotamobius pallipes (Lereboullet)) has prompted conservation-led translocations to safe isolated stillwaters (Ark sites). Many translocations represent introductions rather than re-stocking; hence it is important to ensure that there will not be a detrimental impact on communities already present. Current knowledge is insufficient to predict likely effects, although gut contents analyses suggest that A. pallipes is omnivorous and exhibits ontogenic diet shifts. A mesocosm study was conducted with the aim to first, determine community impacts of introducing A. pallipes on the benthic invertebrate community, and second investigate if impacts vary with crayfish life-stage. All crayfish life-stages strongly reduced shredder and grazer abundance, particularly thin-shelled Lymnaea snails. The small snail Physa fontinalis was preferentially consumed by juveniles, perhaps reflecting different prey-handling ability. Adults showed greater reliance on terrestrially derived detritus compared to juveniles. There were limited effects on other trophic levels, although by reducing shredders that process basal resources, crayfish impacts may be felt through the community in the long-term.
Density-dependent population regulation in a Texas grassland

This study examines the extent to which plant population dynamics are affected by density—dependent processes, and at what stage(s) in the life cycle density—dependent effects occur. A natural population of Bouteloua rigidiseta, a perennial grass, was subjected to two changes of density, the addition of seeds and the removal of 30—40% of the adult plants. Censuses were conducted before and after these treatments, one year apart. Survival, growth, and reproduction were all highly size dependent. Seed additions increased proportionately the number of new recruits to the population, indicating that the size of this age class was limited by seed input; seed additions decreased the size of new recruits. Adult removal tended to increase the sizes of both new recruits and adults. Thus competition among adults, among recruits, and by adults against recruits, but not competition by recruits against adults, affected this population in a density—dependent fashion. No density—dependent treatment effects involving rep.
Distribution, Abundance, and Reproductive Success in the Coral Reef Fish Acanthochromis polyacanthus

The relationships between population density, adult size, and various reproductive parameters (including summed reproductive effort and reproductive success) were examined for the planktivorous coral reef fish Acanthochromis polyacanthus. Data were based on multiple censuses conducted over a 2—yr period on One Tree Reef (southern Great Barrier Reef), at 10 sites that cover the range of habitats occupied by the species. Although several reproductive parameters varied significantly over this habitat range, between—site differences in mean reproductive effort per pair were not significant, and mean reproductive success per pair were significantly reduced at only 2 of the 10 sites. Multivariate analysis suggested that heterogeneity among sites in the mean number of broods produced per pair per spawning season is the major determinant of between—site differences in reproductive success, alone accounting for 69% of the among—site variance in reproductive success in 1979—1980, and 67% in 1980—1981. Principal components analysis of nine apparently independent population and fitness parameters over the 10 sites indicates 82.9% of the communal variance can be accounted for by three orthogonal source variables. These appear to relate to food availability, rates of predation, and, most likely, seasonal variation in water temperature. Results are consistent, overall, with the hypothesis that local populations of A. polyacanthus are equilibrial and resource limited. If this hypothesis is correct, adult density is a valid index of habitat quality. Theoretical considerations suggest that this is not likely to be true for most other small, site—attached species of reef fishes.
Marine temperatures experienced by postsmolts and the survival of Atlantic salmon, Salmo salar L., in the North Sea area

The survival of two Atlantic salmon stocks that inhabit rivers confluent with the North Sea was examined in respect to historical distributions of sea surface water temperatures. The rivers Figgjo and North Esk are relatively small salmon rivers in southern Norway and eastern Scotland, respectively. Wild salmon smolts have been tagged in these rivers since 1965. Tag returns were used to evaluate the survival of salmon in the North Sea. Survival rates of one-sea-winter (1SW) and 2SW fish were correlated within stocks, as well as between stocks. Survival rates were compared with the areal extent of thermal habitat in the north-eastern Atlantic Ocean. A positive correlation was found between the area of 8–10°C water in May and the survival of salmon. A reciprocal negative correlation was also found between survival and 5–7°C water in the same month. An analysis of sea surface temperature distributions for periods of good vs. poor salmon survival showed that when cool surface waters dominate the Norwegian coast and North Sea during May, salmon survival has been poor. Conversely, when the 8°C isotherm has extended northward along the Norwegian coast during May, survival has been good. The effect of water temperature distributions on the growth of postsmolts and other survival factors are discussed.
Spatial and seasonal variation in niche partitioning between blue manakin (Chiroxiphia caudata) and greenish schiffornis (Schiffornis virescens) in southeastern Brazil

The diet of Chiroxiphia caudata and Schiffornis virescens were studied over three years in four forest sites in the southeastern Atlantic Forest of Brazil. Theory suggests that coexistence of similar species is possible by resource-use differences. To test this, patterns of niche overlap and niche breadth in diet were measured in different seasons and forest sites, based on fruit morphological traits and plant life forms. The results suggest seasonal and spatial variation in resource partitioning. During periods of high fruit availability, there was no evidence of fruit trait selection. In contrast, during periods of fruit scarcity in primary forests, there was evidence of niche partitioning, where C. caudata foraged for larger fruits in canopy and S. virescens searched for understory plants. The niche overlap was higher in secondary forest during periods of scarcity, when both species used small understory fruits. Foi estudada a dieta de Chiroxiphia caudata e Schiffornis virescens durante três anos, em quatro tipos de fisionomias florestais no sudeste da Mata Atlântica, Brasil. A teoria sugere que a coexistência de espécies semelhantes é possível pelas diferenças no uso dos recursos. Assim, nós mensuramos a amplitude e sobreposição de nicho considerando a morfologia dos frutos consumidos e a forma de vida das espécies de plantas utilizadas em quatro tipos florestais e em diferentes estações. Os resultados sugerem mudanças sazonais e espaciais na partilha de recursos. Durante períodos de alta disponibilidade de frutos, não há evidências de partilha de recursos. Já em períodos de escassez de frutos nas florestas primárias, C. caudata consumiu frutos grandes presentes no dossel enquanto S. virescens utilizou os frutos pequenos do sub-bosque. Na floresta secundária, o período de escassez foi marcado por sobreposição intensa de nicho onde ambas as espécies consumiram frutos pequenos de sub-bosque.
Climate, snow, ice, crashes, and declines in populations of reindeer and caribou (Rangifer tarandus L.)

Snow is a major determinant of forage availability for reindeer and caribou (Rangifer tarandus; hereafter Rangifer) in winter and is, consequently, a medium through which climate variation may influence population dynamics in this species. Periodic “icing” of winter ranges, where interludes of mild weather result in formation of crusted snow and basal ice that restrict access to forage, is held to be a cause of mass starvation, catastrophic declines in numbers, and even extirpation of local populations. It has been suggested that warming of the Arctic may result in increased frequency of winters with unfavorable snow and ice conditions, with serious consequences for Rangifer. This paper examines data on major declines in populations of Rangifer to determine the mechanism(s) of these events and the role of snow and ice conditions in them. Thirty-one declines, involving numerical decreases between 25% and 99%, were identified in 12 populations. Declines were of two types: the negative phase of irruptive osc.
Fosfato e micorriza na estabilidade de agregados em amostras de latossolos cultivados e não-cultivados

In the tropics there is little information on the contribution of soil microorganisms on aggregate stability in the soils. Soil management, crop and fertilization can affect the fungi specie in soil, and also affect aggregate stability. This study attempted to evaluate the effect of earlier cropping, phosphate, inoculation with AMF, and brachiaria and soybean on the geometric mean diameter (GMD), particle flocculation index, root dry matter, and total hyphal length, in dystrophic Red Latosol and dystroferric Red Latosol (both Oxisols). Samples of both soils under natural condition and previously cultivated were brought to the green house and received P fertilization and inoculation. Then, they were cultivated twice with brachiaria and soybean. The results showed that the previously cultivated soils had lower total hyphal length and lower aggregate stability (lower GMD), whereas inoculation increased these parameters according to P level. Phosphate fertilization had an indirect benefit on aggregate stability by increasing total hyphal length and root dry matter.
Microfilaments Anchor Chloroplasts along the Outer Periclinal Wall in Vallisneria Epidermal Cells through Cooperation of PFR and Photosynthesis

In the cytoplasmic layer that faces the outer periclinal wall in epidermal cells of leaves of the aquatic angiosperm Vallisneria gigantea Graebner, we examined a possible interrelationship among the configuration of microfilaments, chloroplast motility, and anchoring of chloroplasts. In dark-adapted cells, microfilaments are arranged in a network array. During a 10-min incubation in darkness 10 to 20 min after irradiation with red light (650 nm, 0.41 W m~ 2 ) for 5 min, the number of cells containing a network array decreased substantially while the number of cells containing microfilaments in a honeycomb array increased. Irradiation with red light rapidly produces an increase in chloroplast motility, but chloroplast motility declined almost to initial levels during the 10-min incubation in darkness after the irradiation. Simultaneously, the chloroplasts in these cells became extremely resistant to centrifugal forces. These effects of red light were negated either by far-red light or by the presence of DCMU, and were sensitive to cytochalasin B. It appears, therefore, that microfilaments not only drive the movement of chloroplasts but also play a crucial role in accumulation of the chloroplasts along the outer periclinal wall through dynamic changes in the configuration under cooperative regulation by P FR and photosynthesis.
UJI DAYA HAMBAT ANTIBAKTERI AIR SEDUHAN BUNGA ROSELLA (Hibiscus sabdariffa L) TERHADAP BAKTERI Staphylococcus aureus SECARA DIFUSI AGAR

Telah dilakukan penelitian efek antibakteri dari bunga rosella ( Hibiscus sabdariffa L ) terhadap pertumbuhan bakteri Staphylococcus aureus. Sampel yang digunakan adalah simplisia kering bunga rosella yang dijual. Hasil penelitian dengan tiga merk berbeda air seduhan bunga rosella ( Hibiscus sabdariffa L ) dapat menghambat pertumbuhan bakteri Staphylococcus aureus. Merk A rata-rata diameter zona hambat dengan konsentrasi 0,80% adalah 10,98 mm, 1,43% adalah 11,11 mm, 1,63% adalah 11,59 mm. Merk B dengan konsentrasi 0,84% adalah 11,00 mm, 1,38% adalah 11,08 mm, 1,63% adalah 11,60 mm. Merk C dengan konsentrasi 1,41% didapatkan 11,47 mm. Sebagai pembanding menggunakan antibiotik Tetrasiklin Hidroklorida diameter zona hambat 18,31 mm. Kata kunci : bunga rosella, antibiotik, Staphylococcus aureus
Estrogen protects neuronal cells from amyloid β-induced apoptotic cell death

Accumulating studies have shown that estrogen replacement therapy reduces the risk of Alzheimer's disease. In this study, we clarified that 17β-estradiol (E2) significantly rescues PC12 neuronal cells from amyloid β protein (Aβ)-induced cell death. We found that the amino acid residues of 25 to 35 (Aβ25-35) were more cytotoxic than the full length protein (Aβ1-40) and these residues induced DNA fragmentation typical for apopto- sis. In addition, E2 was confirmed to inhibit calcium influx and cytochrome c release induced by Aβ25-35. Since these sequential events cause apoptosis, the protective effect of E2 may be exerted not by the direct interaction with Aβ, but by the blockade of the mitochondrial apoptotic pathway induced by Aβ.
Fontes e níveis de glicerina para frangos de corte no período de 8 a 21 dias de idade

umidade da cama de pintos de corte recebendo racoes com diferentes niveis e fontes de glicerina. Foram utilizados 1300 pintos de corte machos Cobb 500, num arranjo fatorial 4x3+1, com delineamento inteiramente casualizados, sendo quatro niveis de inclusao (17,5; 35,0; 52,5 e 70,0g/kg) de tres glicerinas (bruta de soja (GS), bruta mista (GM) e semipurificada (GPUR) nas dietas isonutritivas e um tratamento sem glicerina, sendo que para as fontes e niveis de glicerina foram teste de Student-Newman-Keuls e analise de regressao, respectivamente; e para o tratamento, teste de Dunnett. Utilizou-se quatro repeticoes e 25 aves por parcela. O consumo de racao foi influenciado (P<0,05) pelas fontes de glicerina, sendo a GM a fonte que promoveu menor consumo nas aves, porem, nao houve diferenca dos tratamentos em relacao ao controle. Nao houve diferenca significativa para o ganho de peso. Houve interacao dos niveis e fontes de glicerina para a conversao alimentar. Para a GS, a melhor conversao alimentar com a inclusao de 50,35g; para a GM, houve uma piora linear com o aumento da inclusao de glicerina. Houve interacao para a concentracao de glicerol serico nas aves, obtendo aumento linear nas aves que ingeriram a GS e GPUR, e reducao linear para a GM. O ganho de umidade da cama foi influenciado pelas fontes de glicerina, sendo que a mista apresentou menor umidade. As glicerinas estudadas podem ser incluidas nas racoes para pintos de corte ate 70,0g/kg, sem prejudicar o desempenho dos animais. Palavras-chave: aves, desempenho, glycerol, umidade de cama.
Isolation and characterization of a general amino acid permease from the ectomycorrhizal fungus Amanita muscaria

A cDNA coding for a fungal amino acid transporter (AmAAP1) was identified from Amanita muscaria ectomycorrhizas. The transporter gene was expressed at a basal level under all conditions investigated, but its expression was enhanced 10-fold in the absence of a N source utilized by the fungus. Nitrate was not a suitable N source for A. muscaria and resulted in maximal AmAAP1 expression. The expression of AmAAP1 in a yeast mutant revealed its function as a high-affinity amino acid transporter with a broad substrate spectrum. AmAAP1 takes up all investigated amino acids with Km values between 22 μM for histidine and up to 100 μM for proline. Gene expression and amino acid uptake data together indicate two main functions for AmAAP1: uptake of amino acids from soil for fungal nutrition, and prevention of an amino acid loss by hyphal leakage in the absence of a suitable N source.
Predicting the biodiversity response to climate change: challenges and advances

This Perspective examines progress, challenges and emerging directions in bioclimatic modelling. The field of bioclimatic modelling provides a toolkit which is widely used to examine the biodiversity response to climate, including future scenarios of climate change. Bioclimatic modelling has been the subject of intense research in statistical ecology; here I trace its development from a highly researched statistical foundation towards a framework that increasingly incorporates the ecological detail of a species’ climatic sensitivity. However, as models become more complex (with greater ecological realism) a choice emerges between two approaches: (i) greater model complexity and biological realism – especially where applied to specific conservation problems; and (ii) acceptance of simple bioclimatic tools as a useful albeit limited component, within a mixed evidence-base to assess climate change threat and conservation action. I conclude that whole-organism biologists working at museums and botanic gardens should claim an increasing stake in the bioclimatic framework, especially as the field develops towards an improved biology, towards the integration of new forms of evidence (evolutionary biology, long-term monitoring, expert knowledge, etc.), and in order to force the expansion from model systems (e.g. birds, butterflies, trees), to biodiversity more generally.
The structure of a tropical host-parasitoid community

1. A parasitoid web is a subset of a food web containing data on parasitoids and their hosts; connectance parasitoid webs embody information only about the presence or absence of an interaction, while quantitative parasitoid webs include information about the relative densities of all species. 2. Connectance and quantitative parasitoid webs are described for a community of leaf-mining insects and their parasitoids in regrowth tropical dry forest in Costa Rica. The webs were centred on a study site that contained 88 species of plants, 92 species of leaf miners and 93 species of parasitoids. 3. An average of 1.22 species of miner were found per species of plant, with more species on monocots than on plants with other growth forms. Leaf-miners were highly host-specific
To flee or not to flee: detection, avoidance and attraction of profitable resources by Daphnia magna studied with olfactometer

The cladoceran herbivore Daphnia magna is a major consumer of phytoplankton in lakes. Therefore, this organism may control the phytoplankton community and the proliferation of some algae or cyanobacteria. Cladoceran behaviour and migration in relation to temperature, light or presence of planktivorous fishes have been well studied. In particular, it is known that the detection of kairomones produced by predators may induce avoidance. Avoidance could also occur with other semiochemicals such as cyanotoxins. In order to explore this hypothesis, we used an olfactometer to observe and measure the exploratory behaviour of D. magna individuals based on the motivation for food. Daphnids were allowed to choose between different compounds: water, a pure cyanotoxin, i.e. the microcystin-RR [(MC)-RR], extracts of one MC-producing strain (PMC 75.02) and one MC-free strain (PMC 87.02) of Planktothrix agardhii, or a green algae Scenedesmus obliquus. With this experimental design, we observed that i) cladocerans are able to detect resources with different qualities, ii) they can explore before exhibiting preferences, and iii) daphnids are able to avoid compounds that are potentially toxic (e.g., microcystins). First, daphnids explored the environment, subsequently (after about 1.5 h), they showed a significant tendency to stay where there is a profitable resource such as S. obliquus. These results also suggest that specimens of D. magna cannot detect MC compounds from P. agardhii, but they respond to it as a food resource. The study of zooplankton ability to explore the environment when exposed to semiochemicals needs further investigation.
Genetic adaptation for vernalization requirement in Nepalese wheat and barley

SUMMARY A large number of accessions of covered and naked barley from eastern Nepal were grown without vernalization, and it was found that naked barley accessions were predominantly spring varieties while covered barley accessions were predominantly winter varieties. Seven accessions were subjected to a range of vernalization periods. Four naked varieties were spring varieties, although one showed some response to vernalization, but the three covered barleys were winter varieties. Although the majority of naked barleys are spring forms, they are winter sown at high altitudes and this does not conform to the distribution of naked barley described by Takahashi (1955). Wheat accessions which came from villages situated at high altitudes tended to have higher vernalization requirements than those which came from lower altitudes. This was taken to indicate local adaptation and a low movement of seeds (gene-flow) between villages. The relationship between vernalization requirement and altitude was not found in barley. Marked but contrasting regional patterns for vernalization requirement occurred in the wheat and covered barley. It was concluded that gene-flow was greater within regions than between them. This regional isolation together with environmental heterogeneity are major diversity promoting mechanisms.
LOCAL REDUCTION OF MYCORRHIZAL ARBUSCULE FREQUENCY IN ENRICHED SOIL MICROSITES

Increased nutrient availability reduces vesicular–arbuscular mycorrhizal (VAM) associations with plants, but whether increased nutrients in small volumes of soil affect local VAM colonization is not known. In a field experiment we investigated VAM colonization at different times following fertilization of small soil patches. Soil volumes of ~ 1000 cm3 were treated with a nutrient solution (enriched patch) or distilled water (control patch) on opposite sides of individual plants of the tussock grass Agropyron desertorum and the shrub Artemisia tridentata. Agropyron had significantly lower (p = 0.03) arbuscular infection in the locally enriched patches compared to control patches (32 and 40%, respectively). This reduced arbuscule frequency was apparent at the first sampling (3 days following treatment application) and remained lower in each subsequent sampling (as much as 30% lower than the control patches). Artemisia revealed a similar pattern in arbuscule frequency but was not statistically significant. O.
Gas liquid chromatography-flame ionization detector (GLC-FID) residue analysis of carbamate pesticide in freshwater fish Labeo rohita

In this present study, the identification and quantification of carbosulfan pesticide residues in freshwater fish Labeo rohita is developed. A gas liquid chromatographic (GLC) method was successfully developed for the determination of carbosulfan residues. The fish were exposed to 1/10th sublethal concentration of carbosulfan i.e. 0.12 mg L−1 for 15 days. The fish samples were extracted with n-hexane, cleaned up and purified. The order of tissues where the carbosulfan pesticide bioaccumulation takes place were in the order: gill < kidney < liver < muscle. These results suggest that prolonged exposure to sublethal concentrations of carbosulfan in Labeo rohita leads to increased accumulation of pesticide residues in tissues.