Miracle-dz/UniFAR-FTUs huggingface dataset:
Benefit-cost analysis of DNA marker-based selection in progenies of Pinus radiata seed orchard parents

The financial viability of DNA marker-based within-family selection (MBS) compared with full-sib family forestry was evaluated for Pinus radiata Donn. ex D. Don. Two traits were investigated: wood density (WD) and diameter at breast height (DBH, 1.4 m). Assuming 20 biallelic loci of equal additive effect controlling trait variation in 15 unrelated top full-sib families of P. radiata, marginal costs of quantitative trait loci (QTL) detection and selection were estimated based on an average of slightly less than five loci per family. We assumed a program where 10 genotypes per family per year were deployed over a 5-year period, and each replicated 100 000 times via fascicle cuttings methods. Estimated marginal costs were NZ$32 and NZ$72 per 1000 plants for WD and DBH, respectively. Genotyping costs were the single largest component for both traits. Genetic gains were estimated by modifying predicted log volumes (DBH) or proportion of structural-grade timber (WD) with and without pruning. Estimated genetic g.
Influenza A virus directly modulates mouse eosinophil responses

Allergic asthma and influenza are common respiratory diseases with a high probability of co‐occurrence. During the 2009 influenza pandemic, hospitalized patients with influenza experienced lower morbidity if asthma was an underlying condition. We have previously demonstrated that acute allergic asthma protects mice from severe influenza and have implicated eosinophils in the airways of mice with allergic asthma as participants in the antiviral response. However, very little is known about how eosinophils respond to direct exposure to influenza A virus (IAV) or the microenvironment in which the viral burden is high. We hypothesized that eosinophils would dynamically respond to the presence of IAV through phenotypic, transcriptomic, and physiologic changes. Using our mouse model of acute fungal asthma and influenza, we showed that eosinophils in lymphoid tissues were responsive to IAV infection in the lungs and altered surface expression of various markers necessary for cell activation in a niche‐specific manner. Siglec‐F expression was altered in a subset of eosinophils after virus exposure, and those expressing high Siglec‐F were more active (IL‐5RαhiCD62Llo). While eosinophils exposed to IAV decreased their overall transcriptional activity and mitochondrial oxygen consumption, transcription of genes encoding viral recognition proteins, Ddx58 (RIG‐I), Tlr3, and Ifih1 (MDA5), were up‐regulated. CD8+ T cells from IAV‐infected mice expanded in response to IAV PB1 peptide‐pulsed eosinophils, and CpG methylation in the Tbx21 promoter was reduced in these T cells. These data offer insight into how eosinophils respond to IAV and help elucidate alternative mechanisms by which they regulate antiviral immune responses during IAV infection.
Species richness of limestone grasslands increases with trait overlap: evidence from within‐ and between‐species functional diversity partitioning

Considering both within‐ and between‐species functional diversities in plant communities has been recently suggested as a way to understand potential assembly mechanisms that control species coexistence. In particular, relating variations in species richness to within‐ and between‐species functional diversities can provide a useful framework for evaluating the importance of alternative community assembly theories. In addition, little is known about whether the relationship between species richness and functional diversity components arises from direct or indirect effects of the abiotic environment. We tested the relationship between functional diversity and species richness by disentangling functional diversity components into within‐species, between‐species and total functional diversities and by considering potential direct and indirect effects of the abiotic conditions. Multi‐ and single‐trait approaches were applied using three key plant functional traits (height, specific leaf area (SLA), LDMC). Traits were measured on species coexisting across sixteen species‐rich limestone grasslands. Direct and indirect effects of the abiotic conditions were evaluated using multiple soil properties including heterogeneity in soil depths. The within‐species functional diversity ranged between 13.5% and 33.6% of the total functional diversity. Within‐species diversity was the main functional component linked to variations in species richness, despite the within‐species functional diversity being lower than between‐species functional diversity. Environmental soil properties had a direct effect on species richness but did not affect functional diversity components. Synthesis: Our results provide evidence that increasing the trait overlap between species, due to an increase in within‐species diversity, may relate to greater species coexistence. Disentangling multiple functional diversity components indicated that there may be equalizing mechanisms that act as potential drivers of species coexistence. In addition, it suggests the possibility that this approach may provide a better understanding of the processes involved in the structure of plant communities.
Habitat use by Nightingales in a scrub–woodland mosaic in central England

SUMMARY Capsule Nightingales Luscinia megarhynchos with song territories in scrub vegetation also used adjacent woodland. Aims To examine spatial use by Nightingales of vegetation mosaics and associated selection of vegetation height classes. Methods We examined habitat selection by male Nightingales through territory mapping and radiotracking within a mosaic of dry scrub and woodland adjacent to water-filled gravel pits in eastern England. Results Fourteen song territories were exclusively in scrub, 2 were exclusively in woodland, and 13 comprised both habitat types. Densities were greatest in scrub vegetation of 3–5 m height. Best-supported models for territory density indicated the importance of considering optimal vegetation height within management prescriptions. Despite song territories being in scrub, kernel home-ranges of all radiotracked Nightingales contained areas of mature trees. Birds also spent more time there than expected based on availability of woodland within kernels. Conclusions Habitat quality has been implicated in the decline of Nightingales in lowland woodland in Britain (and an associated increase in the proportion found in scrub). Our results indicate that woodland habitat characteristics provide resources for Nightingales with song territories located in dry scrub and may be a factor in territory establishment, and are therefore relevant for conservation practitioners at such sites.
Optimisation of probiotic yoghurt production containing Zedo gum

A BoxâBehnken design was applied to optimise the viability of Lactobacillus acidophilus and Bifidobacterium bifidum in probiotic yoghurt containing a novel exudative Zedo gum. The effect of incubation temperature, probiotic inoculation rate, storage time and Zedo gum concentration on quality indices of the yoghurt were explored. With respect to probiotics viability, probiotic inoculation rate was the most important factor followed by the storage time. Zedo gum did not show any significant effect on probiotics viability. The optimum conditions of probiotic yoghurt production were as follows: probiotic inoculation level, 12. 8âg/100âkg of milk; incubation temperature, 41. 6âÂ°C; and Zedo gum concentration, 0.13%.
Investigation of native isolates of entomopathogenic fungi for the biological control of three citrus pests

The pathogenicity of 15 isolates of Beauveria bassiana (Balsamo) Vuillemin, five isolates of Metarhizium anisopliae (Metschnikoff) Sorokin and one isolate of M. flavoviride (Gams and Rozsypal) were tested under laboratory conditions against the subterranean life stages of the citrus pests, Ceratitis rosa Karsch, C. capitata Wiedemann (Diptera: Tephritidae) and Thaumatotibia leucotreta Meyrick. (Lepidoptera: Tortricidae). When these citrus pests were treated with a concentration of 1×107 conidia mL−1, fungal isolates had a significantly greater effect on the adults of C. rosa and C. capitata than they did on the puparia of these two fruit fly species. Further, C. rosa and C. capitata did not differ significantly in their response to entomopathogenic fungi when adult and pupal mycosis were considered. Depending on fungal isolate, the percentage of T. leucotreta adults which emerged from fungal treated sand ranged from 5 to 60% and the percentage of pupae with visible signs of mycosis ranged from 21 to 93%. The relative virulence of the four most promising fungal isolates, as well as the commercially available B. bassiana product, BroadBand® (Biological Control Products, South Africa), were compared against one another as log-probit regressions of mortality against T. leucotreta which exhibited a dose-dependent response. The estimated LC50 values of the three most virulent B. bassiana isolates ranged from 6.8×105 to 2.1×106 conidia mL−1, while those of the least pathogenic ranged from 1.6×107 to 3.7×107 conidia mL−1.
Optimal Rates of Nitrogen Fertilization for First‐Year Corn after Alfalfa

Alfalfa (Medicago sativa L.) contributes substantial N to grain crops that follow, but there is uncertainty concerning the amounts. The objective of this study was to determine optimal rates of N fertilization for first-year corn (Zea mays L.) grown after alfalfa. Fertilizer N was applied at seven rates, ranging from 0 to 200 Ib/acre, at 29 trials conducted over 4 yr in northeast Iowa. Concentrations of soil nitrate in late spring and concentration of nitrate in cornstalks at the end of the season were used to help determine optimal N rates. Fertilizer significantly increased yields at six of the 29 trials. The rate of N fertilization most profitable when applied across the 29 fields was mainly determined by cost of fertilization and value of grain. At prices prevailing in the Corn Belt, applications of 0 and 25 Ib N/acre were the most profitable [. ]
Nutritional value of some feedstuffs used in the diet of captive capybaras

Five pen-raised adult female capybaras were used in five digestibility trials in a Latin square design, to determine, for capybaras, the nutritional values of Cameroon grass (Pennisetum purpureum cv. Cameroon); Napier grass (P. purpureum cv. Napier); corn grain; cassava hay, comprising leaves and stems; and palm kernel (Elaeis guineensis) cake. These feedstuffs were provided separately or mixed, in a completely randomized manner, in different experimental periods. The digestibility of each feedstuff not supplied alone was estimated by difference. The animals were individually introduced in metabolism pens. Following a 10-day period of adaptation to each diet, feed intake was recorded and total fecal output was collected over five consecutive days. Energy, crude protein and neutral detergent fiber digestibilities of Cameroon grass were, respectively, 0.88 (±0.07, standard deviation), 0.63 (±0.39) and 0.82 (±0.15). For Napier grass they were 0.84 (±0.05), 0.63 (±0.12) and 0.72 (±0.10); for corn grain, 0.92 (±0.05), 0.97 (±0.20) and 0.83 (±0.14); for cassava hay, 0.86 (±0.12), 0.84 (±0.14) and 0.43 (±0.16); and for palm kernel cake 0.94 (±0.05), 0.85 (±0.14), and 0.97 (±0.05). These digestibilities in capybaras were higher than the digestibilities of the same feedstuffs in other livestock. These results can be explained by the anatomical and physiological characteristics of the capybara, which lead to a high rate of nutrient digestion and absorption.
Race shift in Xanthomonas campestris pv. vesicatoria within a season in field-grown pepper

Race shifts in Xanthomonas campestris pv. vesicatoria, (proposed: X. axonopodis pv. vesicatoria), the pepper bacterial spot pathogen, were studied in the field during 1993 and 1994. In 1993, Early Calwonder (ECW) pepper plants inoculated with rifampicin-resistant race 1 strain Xcv 33 rif , which carries avirulence gene avrBs3, were planted in a plot of ECW-30R plants, which carry the Bs3 gene for resistance to race 1 of the pathogen. Disease was observed on plants adjacent to the inoculum plants 2 weeks after inoculation, and within 10 weeks, all plants were diseased. Rifampicin-resistant single colonies isolated from diseased ECW-30R plants were screened for race reaction on pepper differentials, and all were race 3 because they were compatible on ECW-30R. Total DNA from 25% of the single colonies hybridized to an avrBs3 gene probe, and the plasmid carrying avrBs3 was not detected in the colonies that did not hybridize to avrBs3. Similarly, in 1994 the population derived from a strain of race 2 that carries avrBs1 rapidly shifted to race 3 when inoculated plants were placed in a plot of ECW-10R plants carrying the single resistance gene Bs1. Total DNA from all isolated single colonies with the race 3 phenotype hybridized with avrBs1 and insertion element IS476. Thus, a race 3 pathogen population of X. campestris pv. vesicatoria rapidly developed from race 1 and 2 populations within a growing season in the field when exposed to a resistant pepper cultivar carrying a single resistance gene. The race shift from race 1 to 3 was due to loss of the plasmid carrying the avirulence gene or to inactivation of avrBs3. Shift from race 2 to 3 apparently resulted from insertion element IS476 inactivating avirulence gene avrBs1.
Larval rearing and production of spat of the oysterCrassostrea madrasensis (Preston) in anExperimental hatchery

The Indian backwater oyster, Crassostrea madrasensis, was spawned in the laboratory at Tuticorin. The larvae were reared and the spat settled in 15-20 days. Two species of jihytoflagellates, Isochrysis galbana and Pavlova sp. were isolated from the natural environment, cultured in mass scale and given as food throughout the larval period. Early stages of the development of fertilized egg, successive stages of developing larvae, and metamorphosis to the spat have been described. The methodology of the production of cultchless spat and rearing the post-set oysters are discussed.
Regional patterns of genetic structure among Australian populations of the mud crab, Scylla serrata (Crustacea : Decapoda): evidence from mitochondrial DNA

The population genetic structure of the estuarine crab, Scylla serrata (Forskal, 1775), was examined among shelf-connected locations and across a historical bio-geographic barrier. Over 300 individuals were sampled from multiple locations within coastal regions (western, northern and eastern) of Australia and analysed for mutational differences at a mitochondrial coding gene (COI). Analysis of molecular variance indicated mitochondrial haplotypes to be structured regionally (P < 0.001), which contrasted with evidence of genetic panmixia within regions. Regional genetic structure broadly correlated with hydrological circulation, supporting the contention that release of propagules away from the estuary may allow genetic connectivity among widespread shelf-connected S. serrata populations. That similar patterns of maternal gene flow are absent among trans-oceanic populations may indicate that the spatial scale of effective dispersal for this species is generally limited to areas of coastal shelf. Two distinct clades of haplotypes were geographically separated either side of the Torres Strait, a narrow sea channel connecting the northern and eastern regions of coastal Australia. This pattern of historical genetic separation is concordant with a number of other marine species across northern Australia and may indicate a shared history of vicariance induced by eustasy. Alternatively, we suggest that sundering of S. serrata populations resulting in cladogenesis may have its origins outside of the northern Australian region.
Genetic diversity assessment in sorghum accessions using qualitative morphological and amplified fragment length polymorphism markers

Qualitative morphological and amplified fragment length polymorphism (AFLP) markers were compared for assessment of genetic diversity. Nine qualitative morphological traits were recorded to compare genetic relationships among 17 sorghum accessions with information derived from six AFLP primer combinations analysis. The mean morphological genetic similarity was lower in comparison to similarity computed using AFLP markers. Genetic similarity measured by AFLP markers was similar within the Ethiopian and South African material, as well as between South African and Ethiopian material. Morphological similarity was much higher in the Ethiopian material than in the South African material, indicating that the genotypes were related. The two techniques described genetic variability in different ways. Dendrogram generated from the morphological data matrix separated accession 216737 as being genetically distinct from the rest of the accessions. Accessions M101 and 97MW6127 were the most dissimilar accessions based on AFLP data.
Biological activities and metabolites from Trevoa trinervis Miers

Chilean folklore medicine uses Trevoa trinervis Miers. (Rhamnaceae), ‘trevo’, for the treatment of inflammation caused by wounds and burns. The antiinflammatory and antipyretic activities of crude methanol, aqueous and successive hexane, dichloromethane, methanol extracts of the aerial part were studied. The fractionation of the most potent extract (dichloromethane), led to the isolation of the pentacyclic triterpenoids betulinic (the major metabolite), oleanolic and ursolic acids, along with β‐sitosterol. Evaluation of the acute oral toxicity of the crude methanol extract showed it to be nontoxic. The crude methanol and the aqueous extracts were assayed for their antineoplastic activity against P‐388 murine leukaemia, A‐549 human lung carcinoma and HT‐29 colon carcinoma showing no activity. Betulinic acid was also assayed showing some activity against the neoplastic cell lines, but only residual activity against Mel‐28 melanona cells. © 1997 John Wiley & Sons, Ltd.
DNA polymorphism of chloroplast SSR regions in various vegetables and its application to analyses of interspecific polymorphisms in Allium species

DNA Polymorphism of Chloroplast SSR Regions in Various Vegetables and its Application to Analyses of Interspecific Polymorphisms in Allium species Naoyuki Araki, Naoki Yamauchi and Masayoshi Shigyo* United Graduate School of Agricultural Sciences, Tottori University, Koyama, Tottori 680-8553 Forensic Science Laboratory, Yamaguchi Prefectural Police Headquarters, Takimachi, Yamaguchi 753-8504 Faculty of Agriculture, Yamaguchi University, Yoshida, Yamaguchi 753-8515
A numerical study of ice-drift divergence by cyclonic wind with a Lagrangian ice model

In polar regions low-pressure systems drive sea ice divergence, which can accelerate summer sea ice melt through energy absorption at resulting open water areas. This paper examines the mechanisms that cause the ice divergence and its seasonal change with a Lagrangian ice model. We focus on the effects of initial ice concentration, ice strength and ocean stratification. A series of idealized simulations (initially at 5 km resolution) are carried out with a Rankine combined vortex as external wind forcing. We have found a characteristic length scale r*1 in free drift, based on the influence of the Coriolis term. The results show that ice concentration decreases most greatly within the range of r*1. In addition, ice divergence becomes small in the inner region for high concentrations (i.e. over 0.95), due to inward internal force blocking divergent deformations. The effects of ocean stratification on ice-drift divergence are also examined. Numerical results show that as the density stratification increases divergent Ekman flows beneath ice further promote the ice-drift divergence and lead to more reduction in the ice concentration through thinning of surface Ekman layer.
Preparing for successful transitions beyond institutional care in Zimbabwe: adolescent girls’ perspectives and programme needs

ABSTRACT This qualitative study explored adolescent girls’ perspectives and programme needs as they transition from two institutions in Highfield, Harare, Zimbabwe. The study was guided by the sustainable livelihood and feminist theoretical frameworks. Semi-structured interviews were conducted with 32 adolescent girls (16 inside and 16 outside) from Institutions A and B. Focus group discussions were held with two groups of eight adolescent girls inside both institutions. Institutions A and B are run by the government and a non-governmental organisation respectively. Findings suggest that adolescent girls associate successful transitions with social, economic and emotional well-being. Thus, they need programmes that provide advocacy skills, relationship-building, educational support, accommodation, financial support, employment opportunities, family tracing and after-care support to address poverty and other social vulnerabilities after leaving care. The study concludes that adolescent girls are active agents of development capable of articulating their views and developmental needs. Thus, the researcher recommends their increased participation in transition planning and programming as well as the development of a support model that incorporates gender-specific concerns and needs addressing poverty in the institutional context.
What is the Chinese caterpillar fungus Ophiocordyceps sinensis (Ophiocordycipitaceae)?

Ophiocordyceps sinensis is a well-known insect fungus, naturally distributed in the Tibetan Plateau of Asia. It has been long known by its synonym Cordyceps sinensis both in scientific and non-scientific communities but was recently transferred to Ophiocordyceps. Over the last 300 years, the morphological characters of this taxon have been studied by different professionals and experts, such as religious persons, travelers, entomologists, pharmacologists and mycologists. Morphological descriptions of mature O. sinensis stroma based on recent studies are compared in this study with those of the type specimens of Berkeley (Lond J Bot. 2:205–211;1843). A literature review indicates that the specimens of Berkeley (1843) are immature. New names have been proposed for O. sinensis-like species from alpine regions, such as O. gansuënsis, O. crassispora, O. kangdingensis, O. multiaxialis and O. nepalensis, and it is not obvious how these differ from O. sinensis. Epitypification and revision of O. sinensis is, therefore, essential to resolve the taxonomic ambiguity of O. sinensis and related species.
Bifidogenic properties of different types of fructo-oligosaccharides

Abstract Batch culture growth of eight species of bifidobacteria utilizing fructo-oligosaccharides was compared to that with glucose. In comparison to other saccharolytic colonic bacteria such as members of the Clostridium and Bacteroides genera, the bifidobacteria preferred fructans as a source of carbon and energy. Variable growth of each of the different species occurred and was largely dependent on the type of oligosaccharide used. Oligofructose, which is a linear chain molecule comprising glucose and fructose (degree of polymerization = 4), had a higher bifidogenic effect than larger molecular weight carbohydrates and branched chain varieties. Specific growth rates, culture pH values and enzyme production data showed that Bifidobacterium infantis growth and activities were especially increased with oligofructose. It is possible that an increase in the concentration of fructose based oligosaccharides in diet will have bifidogenic properties. Bearing in mind the purported beneficial aspects of these bacteria, this may have a positive influence for health of the host.