Miracle-dz/UniFAR-FTUs huggingface dataset:
Modelling primary branch growth based on a multilevel nonlinear mixed‑effects model: a Pinus koraiensis plantation case study in north‑east China

On the basis of a multilevel nonlinear mixed‑effects model approach, branch diameter and length growth models were developed for a Pinus koraiensis plantation in north‑east China. The models developed were able to better capture the residual variation successfully by partitioning the residual variance into plot‑, tree‑ and branch‑ level variations via random parameter modeling at the three levels. In addition to random effects, various time series correlation structures were evaluated to account for residual autocorrelation, and the AR(1) and ARMA(1,1) structures were selected for the branch diameter and length growth models, respectively. Model validation results using an independent data set confirmed that multilevel mixed models with an appropriate correlation structure produced more accurate and precise branch‑specified diameter and length predictions. Overall, the models were suitable in describing the trends and inherent variability of crown profile and good enough to be included in growth simulation systems for Pinus koraiensis plantations.
Effect of honey and starter culture on growth, acidification, sensory properties and bifidobacteria cell counts in fermented skimmed milk

Bifidobacteria strains (BLR, BLE, Bbv-1 and Bbv-2) were investigated throughout changes in their growth and acidifying activity in the presence of yogurt starters (Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus) on reconstituted skimmed milk (10% w/v) supplemented with 5 or 10% (w/v) polyfloral or unifloral honey as a sweetener. A positive association (P>0.05) between S. thermophilus and each one of the four Bifidobacterium strains was observed and acidity of milk containing (5 or 10%)polyfloral or unifloral honey was acceptable (P>0.05). In associated cultures between oneBifidobacterium strain and Lactobacillus bulgaricus, only 10% of honey stimulated (P>0.05) growth and acid production of both organisms. However, the level of 5% has at the same time both stimulatory (P>0.05) and inhibitory effect (P>0.05) on bifidobacteriaand lactobacilli, respectively. A significant (P<0.05) improvement in bifidobacteria biomass (1.51 to 9.55%) co-cultivated with both lactic acid bacteria was observed in milk containing 5 or 10% honey. However, only 10% honey seems to stimulate (P<0.05) lactic acid bacteria growth in this co-culture. Viability of all bacteria was improved (P<0.05) in the presence of honey, and acidity of fermented milks during storage was regulated, which is probably the cause of the good sensory properties of all honey-added yogurts. Key words: Bifidobacteria, Streptococcus thermophilus, Lactobacillus delbrueckii subsp.bulgaricus, honey, sensory properties, acidification, viability
Reproduction and population structure of the sea cucumber Holothuria tubulosa in the Dardanelles Strait, Turkey

In this study, Holothuria tubulosa Gmelin 1791 was investigated from April 2013 to March 2014 in the Dardanelles Strait, to outline the morphological characteristics, reproductive patterns and the relationship between population characteristics and environmental parameters. Between 15 and 30 individuals of this species were sampled monthly from three stations. There was a negative allometry between length and weight, being gutted weight the most reliable measurement for this species. Reproductive patterns of the species were identified the first time for Turkish coasts. By macroscopic examination of the gonads, smallest sizes (gutted length) were measured as 8.4 and 8.1 cm for female and male, respectively. Sex ratio was calculated as 1: 1.1 with differences between seasons. The reproduction of sea cucumbers occurred between August and September after Gonadosomatic Index (GSI) values reached their maximum in July. The species was found down to 10 m depth with a population density of 0.21 / m 2 , which was rather low compared to previously reported values for Mediterranean populations of this species. There was a high positive correlation between population density and GSI of the species. The highest population density was observed where the largest sea grass meadows are found.
Effects of Salbutamol on growth performance and carcass characteristics of Japanese quail (Coturnix japonica)

Summary The effects of feeding diets containing Salbutamol (0, 1, 3, 5 and 7 mg/kg diet) from 21 to 49 days of age on growth performance and carcass characteristics in 180 male and 180 female Japanese quails (Coturnix japonica) were studied using a factorial arrangement based on completely randomized design. Gender had significant effect on weight gain (P 0.05). Salbutamol increased (P 0.05) by Salbutamol administration. Gender affected leg weight (P<0.05), breast weight, relative weight of leg and liver weight (P<0.01). The breast weight, leg weight and liver weight were significantly higher in females than males but relative weight of leg was significantly lower (P<0.01) in females. The breast weight, relative weight of breast and relative weight of leg were significantly affected by Salbutamol. Gender, Salbutamol and their interactions did not affect the chemical composition of breast muscle. The results of the experiment demonstrated that, Salbutamol had beneficial effects on growth performance and carcass characteristics and it seems that feeding 7 mg Salbutamol/kg diet was more effective in female than male Japanese quails.
The effect of environmental factors on estimated viable and total populations of planktonic bacteria in lakes and experimental enclosures

SUMMARY. The difference between the results of viable and total counting procedures for bacteria are exemplified by vertical profiles from a deep and a shallow lake and from seasonal changes in the epilimnion and hypolimnion of a shallow eutrophic lake. The viable count was, on average, 0.25% of the total count, the greatest difference being noted in the anoxic hypolimnion, probably due to the inadequacy of the viable counting procedure for the isolation of bacteria from such samples. There was a general trend for the more nutrient-rich waters to support larger bacterial populations but such observations did not provide any further information on the factors responsible for the population changes observed. Seasonal fluctuations in the counts are studied and the qualitative and quantitative changes resulting from artificial enclosure of water are discussed. Not all the temporal changes could be explained and short-term changes resulting from nutrient additions to the experimental enclosures were not always reproducible. Horizontal variability was examined, found to be significant and could play an important role where water movement and turbulence is considerable. Results from six sites sampled between 1969 and 1974, representing total and viable bacterial population estimates and a total of eighteen independent or regressor variables were then subjected to principal components analysis. Results taken from the whole water column showed the overwhelming effect of the process of stratification on the bacterial population accounting for 30%-60% of its variability. Secondary components representing algal productivity could account for 10% to 20% of the variability. Many of the chosen regressor variables were acting as measures of the same phenomenon without providing significant information on what affected the bacterial population. To overcome this problem results from the hypolimnion and epilimnion were analysed separately. The analysis demonstrated the importance of seasonal changes in nutrient concentrations in the epilimnion and the development of anoxic conditions in the hypolimnion. Algal biomass, phosphate concentration and the interaction of pH and ammonia appeared to be important. It was concluded that most of the variability in the bacterial population estimates could have been explained by five of the regressor variables and that the factors most likely to provide more information would include some measure of predation and lake retention time.
Reproductive biology of the Brazilian sharpnose shark (Rhizoprionodon lalandii) from southeastern Brazil

Motta, F. S. , Namora, R. C. , Gadig, O. B. F. , and Braga, F. M. S. 2007. Reproductive biology of the Brazilian sharpnose shark (Rhizoprionodon lalandii) from southeastern Brazil. - ICES Journal of Marine Science, 64: 1829-1835.The reproductive biology of the Brazilian sharpnose shark, Rhizoprionodon lalandii, off southeastern Brazil was investigated using data from gillnet landings. The size-at-maturity for males and females was estimated to be 59 and 62 cm total length (L T ), respectively. Ovarian fecundity ranged from 3 to 7 follicles (mean = 4.54), and uterine fecundity from 1 to 5 embryos (mean = 3.3). There was a slight positive relationship between female L T and the number of ovarian follicles, but uterine fecundity was not related to female L T . Embryonic growth is fast following fertilization during summer and autumn. Gestation requires 11-12 months, and peak parturition is between August and September. A comparison of size-at-maturity between animals from northeastern and southeastern Brazil suggests the existence of at least two stocks of R. lalandii along the Brazilian coast.
Composition and Structure of the Lacustrine Bird Communities of Seasonally Flooded Wetlands of Western Brazilian Amazonia at High Water

Abstract We describe and analyze the bird community composition of the lacustrine water bodies of the seasonally flooded wetlands of the Mamirauá and Amanã Reserves, Amazonas, Brazil. Bird surveys were conducted in 54 water bodies within four water body systems aboard a speedboat, in July 2003, at the peak of the high water season. We recorded 2,823 individuals representing 79 bird species associated with aquatic environments, mostly resident; of these, 34 were aquatic (exclusively associated with aquatic environments), and 19 were primarily piscivorous. The aquatic bird communities of Mamirauá and Amanã comprise a few abundant species and a higher number of rare species. Seven species accounted for 71.7% of all 34 aquatic birds recorded. In general, the more elongated the water bodies, the lower the aquatic and piscivorous bird species richness, and the lower the bird abundance. Piscivorous bird abundance was not significantly related to water body shape. Matrices of bird species by water body were subjected to multivariate analysis using Principal Co-ordinate Analysis (PCoA). For the quantitative data (species abundance) and qualitative data (species presence/absence), the composition of the community of aquatic birds changed significantly among lacustrine water body systems, and was significantly affected by water body shape. The quantitative and qualitative composition of the piscivorous bird community did not change significantly among water body systems, and were not affected by water body shape. The numerical analyses revealed a remarkably different behavior of the communities of aquatic birds and piscivorous birds, the former changing significantly with lacustrine water body morphology and local geography (water body system), and the latter being relatively insensitive to variation in these parameters. Water body shape is one of the determinants of aquatic bird community composition in the seasonally flooded wetlands of this part of Amazonia.
Degradação de pastagens na Região Amazônica: propriedades físicas do solo e crescimento de raízes

The objective of this study was to evaluate: (i) the relation between the degradation of burned Guinea grass pastures and the modifications of some physical and morphological properties of an Amazonian Ultisol; (ii) the root growth of pastures in different degradation stages; and (iii) the potential of rehabilitation of degraded Guinea grass pastures by introducing Gamba grass. On a farm at the eastern Amazon, region of Maraba, PA, Brazil, four pasture types were studied: productive Guinea grass (Panicum maximum Jacq.) pasture; Guinea grass pasture on yield decline; degraded Guinea grass pasture (fallow), and degraded Guinea grass pasture recovered with Gamba grass (Andropogon gayanus Kunth). As reference of the soil original characteristics before clearing, a native forest area was also studied. Burning was an usual practice; moreover, the pastures did not receive fertilizers. Pasture degradation decreased soil covering and exposed the soil surface to the direct impact of rain drops and cattle compaction, what resulted in soil bulk density increase in the superficial layer and decrease in clay flocculation and soil total porosity. Forage yield decline on degraded pasture was accompanied by a decrease on the number of roots on the soil profile, and there was a concentration of the root system close to the surface. Andropogon gayanus showed good potential for the rehabilitation of degraded pastures on the Amazon Region.
Volatile metabolite profiling to discriminate diseases of McIntosh apple inoculated with fungal pathogens

Gas chromatography-mass spectrometry (GC/MS) technology was used to profile volatile metabolites from the headspace gas of McIntosh apple (Malus domestica Borkh.), which were non- inoculated or inoculated with four different fungi, Botrytis cinerea Pers, Penicillium expansum Link, Mucor piriformis Fischer and Monilinia sp. The study yielded a total of 498 different volatile metabolites. Among them only 35 occurred relatively consistently in six replicates over three incubation periods. Of the consistent metabolites, 20 were specific to one or more inoculation agents/diseases, including seven that were unique to apples inoculated with different pathogens. Fluoroethene and 3,4-dimethyl-1-hexene were specific for Penicillium, while butanoic acid butyl ester, 4-methyl-1-hexene and 2-methyltetrazole were specific for Mucor. Similarly, acetic acid methyl ester and fluoroethane were specific to Botrytis and Monilinia, respectively. The method developed in this study can be used by storage managers to detect apple diseases at an early stage of disease progress and use this to manage apple diseases in storage, after further validation under commercial conditions.  2004 Society of Chemical Industry
A combination of functionally different plant traits provides a means to quantitatively predict a broad range of species assemblages in NW Europe

Assembly theory predicts that filtering processes will select species by their attributes to build a community. Some filters increase functional similarity among species, while others lead to dissimilarity. Assuming converging processes to be dominant within habitats, we tested in this study whether species assemblages across a wide range of habitats can be distinguished quantitatively by their mean trait compositions. In addition, we investigated how many and which traits are needed to describe the differences between species assemblages best. The approach has been applied on a dataset that included 12 plant traits and 7644 vegetation releves covering a wide range of habitats in the Netherlands. We demonstrate that due to the dominant role of converging processes 1) the functional composition can explain up to 80% of the floristic differences between species assemblages using seven plant traits, showing that plant trait combinations provide a powerful tool for predicting the occurrence of species assemblages across different habitats; 2) to achieve a high performance, traits should be taken from different strategy components, i.e. traits that are functionally orthogonal, which does not necessarily coincide with low trait-trait correlations; 3) the different strategy components identified in this study correspond to the strategy components of some conventional plant ecological strategy schemes (PESS) – schemes to describe the variation between individual species. However, some PESS merge traits into one strategy component that are shown to be functionally different when predicting species assemblages. If such PESS is used to predict assemblages, this leads to a loss in predictive capacity. Potentially, our new approach is globally applicable to quantify community assembly patterns. However this needs to be tested.
Phylogeny of Tragopogon L. (Asteraceae) Based on Internal and External Transcribed Spacer Sequence Data

Tragopogon L. (Lactuceae, Cichorioideae, Scorzonerinae) is an Old World genus of ca. 150 species. To elucidate relationships in this poorly understood genus, we analyzed internal and external transcribed spacer sequences (ITS and ETS, respectively) from 59 species from 14 of the 17 sections recognized by Borisova. Podospermum and Lactuca were used as outgroups. ITS and ETS sequence data provide strong support for the monophyly of Tragopogon under parsimony optimality criteria. Sequence data also support the monophyly of several of the recognized sections within Tragopogon, including the sections Tragopogon, Majores, Hebecarpus, Chromopappus, and Collini. However, the circumscriptions of these groups are often altered from the taxonomic treatment of Borisova. Most members of the recognized sections Brevirostres and Profundisulcati appear within the Brevirostres and Profundisulcati clades, respectively. Species of section Nikitinia are also included in the Brevirostres clade. Sequence data also provide evidence for an Angustissimi clade of T. pusillus, T. filifolius, diploid T. latifolius ( \documentclass{aastex} \usepackage{amsbsy} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{bm} \usepackage{mathrsfs} \usepackage{pifont} \usepackage{stmaryrd} \usepackage{textcomp} \usepackage{portland,xspace} \usepackage{amsmath,amsxtra} \usepackage[OT2,OT1]{fontenc} \newcommand\cyr{ \renewcommand\rmdefault{wncyr} \renewcommand\sfdefault{wncyss} \renewcommand\encodingdefault{OT2} \normalfont \selectfont} \DeclareTextFontCommand{\textcyr}{\cyr} \pagestyle{empty} \DeclareMathSizes{10}{9}{7}{6} \begin{document} \landscape $$2\mathrm{n}\,=12$$ \end{document} ), T. segetum, T. acanthocarpus, T. serotinus, and T. charadzae, species not previously considered closely related. Our analyses also indicate possible relationships for 17 species that had not been previously placed in any section. The diploids T. porrifolius, T. pratensis, and T. dubius, which were introduced into North America and ultimately formed the recent alloploids T. mirus and T. miscellus, are not closely related within Tragopogon; T. dubius and T. porrifolius appear in sister clades, and T. pratensis is more distantly related. Characters often used to establish sectional groupings, such as the length of the achene beak, evolved multiple times in Tragopogon.
A 13-YEAR SURVEY OF THE APHIDOPHAGOUS COCCINELLIDAE IN MAIZE FIELDS IN EASTERN SOUTH DAKOTA

Coccinellids are a conspicuous group of aphidophagous predators in maize, Zea mays L. , in the Northern Great Plains of the United States. Numerous studies have been conducted on the ecology of coccinellids in maize in North America (Ewert and Chiang 1966a, 1966b; Smith 1971; Foott 1973; Wright and Laing 1980; Corderre and Tourneur 1986; Corderre et al. 1987). However, there have been few long-term surveys of coccinellids in maize. Foott (1973) reported on the abundance of coccinellid species inhabiting maize in eastern Canada over a 4-year period; no surveys of this type have been reported for the Northern Great Plains. We sampled coccinellids in maize fields at three sites in eastern South Dakota for 13 consecutive years to determine the species inhabiting the crop and levels of variation in their abundances among sites and years.
Induced genetic variability for quantitative traits in M2 generation in soybean by mutagens

The various genetic variability parameters were estimated using physical (gamma rays) and chemical (EMS) mutagens using two cultivars i.e. PKV-1 and JS-335. Results indicated that genotypic coefficient of variation and phenotypic coefficient of variation, heritability were significantly high for different characters studied i.e. Plant height, number of Â branches per plant, number of Â clusters per plant, number of Â pods per plant, yield per plant, 100 grain weight. All the mutagenic treatments were effective in inducing genetic variability in both the varieties.
Phenotypic Diversity and Stability of the Intestinal Coliform Flora in Piglets During the First 3 Months of Age

The intestinal coliform bacterial populations in six piglets and their sows from two litters in the same stable were studied by the aid of an automated system for biochemical fingerprinting (The PhenePlate, or PhP system). Faecal samples from sows were collected once a week until weaning, and from piglets once a week during their first 3 mth of life. Altogether 1248 coliform isolates from 52 faecal samples were studied. The phenotypical diversity of the coliform bacteria in each faecal sample was measured as Simpson’s diversity index (D i ), and the similarities between the bacteria in different samples were measured as population similarity coefficients (S p ). The D i of the sows was initially high, but decreased in one sow during an outbreak of diarrhoea which occurred during week 3 of the study. The D i of the piglets varied between samples, and showed no tendency to increase with age. Two piglets included in the study died during the diarrhoeal outbreak, and they generally carried intestinal floras showing lower D i during their first 3 wk of life than those which survived (mean value 0.454 versus 0.744). The coliform population within each piglet was usually quite stable before the diarrhoeal outbreak, but in all piglets the population was drastically changed during and after the outbreak. Piglets within each litter shared similar coliform populations during the first week of life, but piglets from different litters had no coliforms in common. On day 75, the piglets were removed from their sows and mixed with others in different litters, and after that coliform populations of piglets from different sows showed a tendency to become more similar to each other. Samples collected during the diarrhoeal outbreak from different piglets did not contain similar coliform populations which is a strong indication that the aetiological agent of the outbreak was not any coliform bacterium. The present study shows a useful way to investigate intestinal bacteria in both man and animals. The methods are very simple to use, and fully computerised data treatment makes it possible to study large numbers of bacterial isolates. Keywords - Intestinal bacteria; Coliforms; Piglets; Diversity; Stability.
Cockroaches

nutrition, ecology, and evolution of all cockroaches; indeed, it can be difﬁcult to determine the organismal boundaries between them. Here we address microbes as gut and fat body mutualists, as part of the external rumen, the food value of microbes, various mechanisms by which cockroaches may ingest them, and some non-nutritional microbial inﬂuences. Finally, we discuss some strategies used by cockroaches to evade and manage disease in their microbe-saturated habitats.