Miracle-dz/UniFAR-FTUs huggingface dataset:
Comprehensive assessment of carbon productivity, allocation and storage in three Amazonian forests

The allocation and cycling of carbon (C) within forests is an important component of the biospheric C cycle, but is particularly understudied within tropical forests. We synthesise reported and unpublished results from three lowland rainforest sites in Amazonia (in the regions of Manaus, Tapajós and Caxiuanã), all major sites of the Large‐Scale Biosphere–Atmosphere Programme (LBA). We attempt a comprehensive synthesis of the C stocks, nutrient status and, particularly, the allocation and internal C dynamics of all three sites. The calculated net primary productivities (NPP) are 10.1±1.4 Mg C ha−1 yr−1 (Manaus), 14.4±1.3 Mg C ha−1 yr−1 (Tapajós) and 10.0±1.2 Mg C ha−1 yr−1 (Caxiuanã). All errors bars report standard errors. Soil and leaf nutrient analyses indicate that Tapajós has significantly more plant‐available phosphorus and calcium. Autotrophic respiration at all three sites (14.9–21.4 Mg C ha yr−1) is more challenging to measure, with the largest component and greatest source of uncertainty being leaf dark respiration. Comparison of measured soil respiration with that predicted from C cycling measurements provides an independent constraint. It shows general good agreement at all three sites, with perhaps some evidence for measured soil respiration being less than expected. Twenty to thirty percent of fixed C is allocated belowground. Comparison of gross primary productivity (GPP), derived from ecosystem flux measurements with that derived from component studies (NPP plus autotrophic respiration) provides an additional crosscheck. The two approaches are in good agreement, giving increased confidence in both approaches to estimating GPP. The ecosystem carbon‐use efficiency (CUEs), the ratio of NPP to GPP, is similar at Manaus (0.34±0.10) and Caxiuanã (0.32±0.07), but may be higher at Tapajós (0.49±0.16), although the difference is not significant. Old growth or infertile tropical forests may have low CUE compared with recently disturbed and/or fertile forests.
Four years' entomological study of the transmission of seasonal malaria in Senegal and the bionomics of Anopheles gambiae and A. arabiensis

From 1993 to 1996, an entomological survey was conducted in the village of Ndiop, Senegal, as part of a research programme on malaria epidemiology and the mechanisms of protective immunity. Mosquitoes were captured on human bait and by indoor spraying. Species from theAnapheles gainbiae complex were identified using the polymerase chain reaction, and Plasmodiunz falciparum infections were detected by enzyme-linked immunosorbent assay for circumsporozoite protein. The vector species identified were A. ganzbiae (33*9%), A. arabiensis (63.2%), A. melas (0.3%) and A. funestus (2.5%). Similar proportions of A. ganzbiae (74.2%) and A. arabiensis (73.8%) contained human blood; 27.0% ofA. gambiae and 28.3% ofA. arabiensis had fed on cattle. The sporozoite rates were similar forA. ganzbiae (3.2%) and A. arabiensis (3.7%). The annual entomological inoculation rates varied greatly depending on the year. There were 63, 17,37 and 7 infected bites per person per year in 1993, 1994, 1995 and 1996 respectively.Transmission was highly seasonal, from July to 0ctober.A. arabiensis was responsible for 66% of malaria transmission, A. gambiae for 31 %, and A. funestus for 3%.
LARVAL INSTAR DETERMINATION AND TEMPERATURE‐DEVELOPMENT STUDIES OF IMMATURE STAGES OF THE COMMON ARMYWORM, MYTHIMNA CONVECTA (WALKER) (LEPIDOPTERA: NOCTUIDAE)

Larvae of the common armyworm, Mythimna convecta had 6 or 7 instars when reared on artificial diet at 25°C. Instars could be clearly separated on the basis of head capsule widths, but larval growth did not follow “Dyar's Rule”. Seven instar larvae lived longer and yielded heavier pupae than 6 instar larvae. The developmental periods of eggs, larvae and pupae were measured over a range of temperatures between 10°C to 35°C. Both Pradhan's and Stinner's equations provided a better fit to the observed values than thermal summation. In Victoria, M. convecta would have more generations/year but lower winter survival than the southern armyworm, Persectania ewingii (Westwood).
Intergeneric transfer (rye to wheat) of a gene(s) for Russian wheat aphid resistance

An octoploid triticale was derived from the F 1 of a Russian wheat aphid-resistant rye, «Turkey 77», and «Chinese Spring» wheat. The alloploid was crossed to common wheat, and to «Imperial» rye/«Chinese Spring» disomic addition lines. F 2 progeny from these crosses were tested for Russian wheat aphid resistance and C-banded. A resistance gene(s) was found to be associated with chromosome arm 1RS of the «Turkey 77» rye genome. A monotelosomic 1RS («Turkey 77») addition plant was then crossed with the wheat cultivar «Gamtoos», which has the 1BL.1RS «Veery» translocation. Unlike the 1RS segment in «Gamtoos», the «Turkey 77»-derived 1RS telosome did not express the rust resistance genes Sr31 and Lr26, which could then be used as markers. From the F 1 a monotelosomic 1RS addition plant that was also heterozygous for the 1BL.1RS translocation was selected and testcrossed with an aphid-susceptible common wheat, «Inia 66». Meiotic pairing between the rye arms resulted in the recovery of five euploid Russian-wheat-aphid-resistant plants. One recombinant also retained Sr31 and Lr26 and was selfed to produce translocation homozygotes
Identification of polymorphic allozyme markersfor population structure analysis in Horabagrusbrachysoma (Gunther, 1864).

Fourteen polymorphic allozyme loci were identified in yellow catfish, Horabagrus brachysoma. The genetic variation detected at each allozyme locus was assessed for samples collected from three rivers. The observed heterozygosities per locus ranged from 0.0286 to 0.4000. Significant genotype heterogeneity indicated that the samples are not drawn from same gene pool. The results suggest the potential of the identified loci to analyze stock structure of natural populations of H. brachysoma.
Tainiterma, a new genus of the subfamily Euphorinae (Hymenoptera: Braconidae) from Vietnam and China

A new tribe (Tainitermini) and genus (Tainiterma) of the subfamily Euphorinae (Hymenoptera: Braconidae) are described and illustrated. A key to the two known species (the type species from Vietnam and China: T. pachytarsis spec. nov., and T. maiphuquyi spec. nov. from Vietnam) is added.
Descriptive update on gull taxonomy: 'West Siberian Gull'

Information on the appearance, behaviour and ecology of taxa within the evolutionarily young 'large white-headed gull' complex (taxa currently grouped by three species, Lesser Black-backed Gull Larus fuscus, Herring Gull L. argentatus and Yellow-legged Gull L. cachinnans) is of interest to those ornithologists who study their identification, systematics and speciation. A sharp discrepancy has arisen between the demand for information about some of these taxa and the lack of elementary primary data.The delay in gathering data is due to the inaccessibility of the breeding grounds of some forms and to difficulties with systematic methodologies within the group.There is a critical lack of information about three forms in particular:'West Siberian Gull' L. heuglini antelius,'Taimyr Gull' L. h. heuglini (= 'taimyrensis') and 'Baraba Gull' L. cachinnans barabensis. This paper presents data on the plumage, biometrics, sexual dimorphism and geographical variation of West Siberian Gull.The identification of the Stuttgart type-specimen of heuglini is reviewed. It is suggested that this specimen is, in fact, a Taimyr Gull, and that West Siberian Gull should, therefore, be reassigned the subspecific name 'antelius'. Footnote: In this paper, the vernacular and scientific names used for the key taxa of interest are those preferred by the author, although this does not necessarily reflect editorial policy.
ISOLATION AND PHYSIOLOGICAL ACTIVITIES OF PINITOL IN LESPEDEZA CUNEATA

There is growing interest in the use of D-pinitol (D-3-methyl-chiro-inositol) as a food supplement because of its reported efficacy in lowering blood glucose levels, decreasing cardiovascular risks, liver protection, weight control and anti-inflammation. The objectives of this study were to quantitate, isolate and examine physiological activities of pinitol in Lespedeza cuneata which has been used as an oriental medicine for years. Pinitol was determined in the whole L. cuneata by gas chromatography, about 2.7% of dried mass. The effective method for the isolation of pinitol from the water extract of L. cuneata was surveyed. The water-soluble proteins were removed from water extract by using 80% ethanol solution prior to being applied into a C18 column. The fraction eluted with water was further loaded into an activated charcoal column. Pinitol-rich fraction was obtained with 10% ethanol eluent and it was dried to yield a final product. Although the final product was at a purity of about 81% by weight, no toxic effects of impurities were observed on the proliferation of liver and macrophage cells in vitro in a concentration range of 50-500 μg/ml. The effects of water extract and pinitol fraction of L. cuneata on lowering blood glucose levels were examined in rats. The antioxidant activities of water extract of L. cuneata were also determined in vitro and in vivo.
The effect of natural and simulated insect herbivory, and leaf age, on the process of infection of Rumex crispus L. and R. obtusifolius L. by Uromyces rumicis (Schum.) Wint.

The development of uredinia of Uromyces rumicis (Schum.) Wint. was studied on Rumex crispus L. and R. obtusifolius L. plants inoculated in the laboratory. Fewer uredinia developed on leaves injured by simulated insect herbivory, those fed upon by Gastrophysa viridula Degeer (Coleoptera: Chrysomelidae), and young, incompletely expanded leaves, than on uninjured, fully expanded control leaves. The effect of simulated herbivory and leaf age on the process of U. rumicis infection was investigated using Calcofluor staining and epifluorescence microscopy. Simulated insect herbivory reduced significantly the proportion of sporelings producing appressoria and the proportion of sporelings with appressoria that entered the substomatal cavity. In R. obtusifolius, leaf injury also reduced the proportion of penetration hyphae that formed substomatal vesicles. The proportion of sporelings that produced intercellular hyphae in injured leaves was reduced by 58 % in R. crispus and 89 % in R. obtusifolius. G. viridula feeding induced similar resistance in R. obtusifolius leaves. Simulated insect herbivory reduced both uredinial density and the area occupied by intercellular hyphae by between 65% and 89%. Injury had a greater effect than leaf age on sporelings in the pre-haustorial stages of development. However, the total area occupied by intercellular hyphae in young leaves was reduced by between 42% and 78% compared to mature leaves, owing to a lower uredinial density and, in R. obtusifolius, also to a significant reduction in the size of individual uredinia.
Applying computer simulation models as learning tools in fishery management

Abstract Computer models can be powerful tools for addressing many problems in fishery management, but uncertainty about how to apply models and how they should perform can lead to a cautious approach to modeling. Within this approach, we expect models to make quantitative predictions but only after all model inputs have been estimated from empirical data and after the model has been tested for agreement with an independent data set. I review the limitations to this approach and show how models can be more useful as tools for organizing data and concepts, learning about the system to be managed, and exploring management options. Fishery management requires deciding what actions to pursue to meet management objectives. Models do not make decisions for us but can provide valuable input to the decision-making process. When empirical data are lacking. preliminary modeling with parameters derived from other sources can help determine priorities for data collection. When evaluating models for management applica.
Molecular diversity of arbuscular mycorrhizal fungi colonising Hyacinthoides non‐scripta (bluebell) in a seminatural woodland

Arbuscular mycorrhizal (AM) fungi form symbiotic associations with plant roots. Around 150 species have been described and it is becoming clear that many of these species have different functional properties. The species diversity of AM fungi actively growing in roots is therefore an important component of ecosystem diversity. However, it is difficult to identify AM fungi below the genus level from morphology in planta, as they possess few informative characters. We present here a molecular method for identifying infrageneric sequence types that estimate the taxonomic diversity of AM fungi present in actively growing roots. Bluebell roots were sampled from beneath two different canopy types, oak and sycamore, and DNA sequences were amplified from roots by the polymerase chain reaction with fungal‐specific primers for part of the small subunit ribosomal RNA gene. Restriction fragment length polymorphism among 141 clones was assessed and 62 clones were sequenced. When aligned, discrete sequence groups emerged that cluster into the three families of AM fungi: Acaulosporaceae, Gigasporaceae and Glomaceae. The sequence variation is consistent with rRNA secondary structure. The same sequence types were found at both sampling times. Frequencies of Scutellospora increased in December, and Acaulospora increased in abundance in July. Sites with a sycamore canopy show a reduced abundance of Acaulospora, and those with oak showed a reduced abundance of Glomus. These distribution patterns are consistent with previous morphological studies carried out in this woodland. The molecular method provides an alternative method of estimating the distribution and abundance of AM fungi, and has the potential to provide greater resolution at the infrageneric level.
Study of behavior of sesame (Sesamum indicum L.) to relative turgidity, diffusion pressure deficit and transpiration intensity under arid conditions of Western Rajasthan.

A field experiment was conducted during kharif season of 2008 and 2009 (from august to october) to investigate the behavior of crop plant Sesame (Sesamum indicum L.) to RT (Relative turgidity), DPD (Diffusion pressure deficit) and TI (Transpiration intensity). The plant species (Sesamum indicum L.) investigated has been found to behave differentially with respect to relative turgidity, Diffusion pressure deficit and Transpiration intensity during different hours of day and at different stages Viz. Vegetative, flowering and capsule stage.
In vitro propagation of endemic plant Centaurea arifolia Boiss. Taxa

Centaurea L. (Asteraceae) is one of the largest genera in the flora of Turkey. Centaurea arifolia belonging to the genus Centaurea is considered as DD (Data Deficient) according to IUCN category. There are no studies identified aiming to propagate this species in vitro. In this study, the seeds were germinated aseptically in Petri dishes containing growth regulator free Murashige and Skoog half-strength (MS ½) medium. Leaf explants of six-week-old grown seedlings were cultured on MS medium supplemented with 1 mg lâˆ’1 BAP plus 0.1 mg lâˆ’1 NAA and 2 mg lâˆ’1 BAP plus 0.2 mg lâˆ’1 NAA for indirect regeneration and after three weeks, actively growing calli appeared and proliferated. Induction of adventitious shoot regeneration from calli was achieved approximately 150% (MS1) and 120% (MS2), within three weeks. Regenerated adventitious shoots were best rooted on MS medium containing 1 mg lâˆ’1 IBA. This protocol provides a successful propagation technique through indirect in vitro organogenesis from leaf segments of C. arifolia. Keywords: C. arifolia, endemic species, micropropagation
Effects of exposure to air and subsequent drying on the phosphate sorption characteristics of sediments from a eutrophic reservoir.

The effects of exposure to air and subsequent drying on the phosphate adsorptive characteristics of sediments taken from Chaffey Dam-a small eutrophic water storage reservoir in New South Wales, Australia-were studied. Sediments were sampled along a transect that covered heavily desiccated, wet-littoral, and submerged sediments, both from above and below the oxycline. Phosphate adsorption isotherms showed that there was a definite transition in P affinity along the transect, with sediments taken from the driest sites displaying the least adsorptive capacity for phosphate and samples taken from beneath the oxycline the highest. A similar transition was observed for the kinetics of phosphate uptake. The order of reaction with respect to phosphate loading decreased from approximately first order for anoxic sediments to fractional order for desiccated sediments. These effects are mostly the result of sediment oxidation and aging rather than desiccation, variation in elemental composition, or differences in the amount of native P adsorbed to the scdimcnt. Release of water is a routine procedure in the operation of most water storages. One consequence of extended water release is the exposure of (mostly anoxic) sediments to the atmosphere and possible desiccation. Because such sediments are potentially both the largest sink for and the largest source of many nutrients (particularly phosphorus), sediment changes induced by exposure may have a marked effect on the nutrient budget of the water storage on rewetting of exposed sediments. Studies (Schoenburg and Oliver 1988; Qui and McComb 1994) have shown a net release of nutrients from sediments that had been exposed to air and were subsequently rcwetted. Qui and McComb (1994) showed by means of isotherm measurements that phosphate affinity decreased in wetland sediment that was dried out in the laboratory. They suggested that this change in affinity could partially explain their observations. Their study is consistent with a report by Twinch (1987) that concerned sediments taken from a large water-storage reservoir in South Africa. Twinch showed that there was a measurable decrease in the phosphate-buffering capacity and an increase in the phosphate equilibrium concentration when sediments were air-dried in the laboratory. In contrast to these studies, Jacoby et al. (1982) reported a net reduction in dissolved P levels in the water column above sediments that had been exposed to the air and were subsequently resubmerged. Several studies on soils (Barrow and Shaw 1980; Haynes and Swift 1985, 1986) and aluminum-organic matter associations (Haynes
Potential toxicity of chrysophytes affiliated with Poterioochromonas and related 'Spumella-like' flagellates

The chrysophyte genera Poterioochromonas and Ochromonas and their heterotrophic analogons, i.e. the ‘Spumella-like’ flagellates, account for a significant and often dominating fraction of the pelagic nanoplankton. Even though several osmotrophically and autotrophically grown strains of Ochromonas and Poterioochromonas are assumed to produce toxins, the potential toxicity has been investigated neither for its association with bacterivorous nutrition nor within the related exclusively heterotrophic ‘Spumellalike’ flagellates. We investigated the toxic potential of several flagellate strains using cultures of flagellates, cell extracts and filtrate of flagellate cultures. The effect on potential predators was exemplarily tested for the cladoceran Daphnia magna and the rotifer Platyias sp. All tested heterotrophic and mixotrophic flagellate strains were toxic to zooplankton at abundances exceeding 10 4 flagellates mL � 1 . For the rotifers, survival on any of the flagellate strains was significantly lower than that in the control treatment (P < 0.001) already after 24 h. We conclude that (i) ‘Spumella-like’ flagellates can be toxic to zooplankton, (ii) all tested flagellates, i.e. heterotrophic and mixotrophic flagellates, feeding phagotrophically can be toxic to zooplankton and (iii) sublethal effects may be observed at typical field abundances, even though acute toxicity seems to be restricted to flagellate abundances observed only at peak events.
Nectar feeding increases exploratory behaviour in the aphid parasitoid Diaeretiella rapae (McIntosh)

Feeding on floral nectar has multiple positive effects on parasitic wasps, including increased longevity and fecundity, and in addition, nectar feeding can also alter parasitoid behaviour. To advance understanding of the effects of nectar feeding on Diaeretiella rapae (McIntosh) [Hymenoptera: Braconidae], the activities of 1‐day‐old female D. rapae with or without a prior buckwheat (Fagopyrum esculentum) nectar meal were quantified. Nectar increased searching time of D. rapae by a factor of 40 compared with individuals provided with water only and reduced the time spent stationary. The number of attacks to aphids by nectar‐fed parasitoids was not significantly (P = 0.06) higher than that of unfed D. rapae, suggesting that the conditions of the experiment facilitated host finding by ‘quiet’ parasitoids. Nevertheless, nectar feeding modified the behaviour of D. rapae in a way that parasitoids were more explorative and less inactive. This represents one additional mechanism through which nectar feeding impacts parasitoid biology and suggests that a synergy between increased host searching, increased longevity and increased fecundity should lead to an enhancement of biocontrol when D. rapae females have access to nectar in the field.
Sashimi plots: Quantitative visualization of alternative isoform expression from RNA-seq data

Analysis of RNA sequencing (RNA-Seq) data revealed that the vast majority of human genes express multiple mRNA isoforms, produced by alternative pre-mRNA splicing and other mechanisms, and that most alternative isoforms vary in expression between human tissues. As RNA-Seq datasets grow in size, it remains challenging to visualize isoform expression across multiple samples. We present Sashimi plots, a quantitative multi-sample visualization of RNA-Seq reads aligned to gene annotations, which enables quantitative comparison of isoform usage across samples or experimental conditions. Given an input annotation and spliced alignments of reads from a sample, a region of interest is visualized in a Sashimi plot as follows: (i) alignments in exons are represented as read densities (optionally normalized by length of genomic region and coverage), and (ii) splice junction reads are drawn as arcs connecting a pair of exons, where arc width is drawn proportional to the number of reads aligning to the junction.
DNA Synthesis Studied in Later Growth Cycles and in Zoosporangium Development of Allomyces macrogynus

Synchrony of duplication cycles in Allomyces macrogynus was maintained through five cycles to the end of vegetative growth. In a culture in which hyphal emergence was inhibited the fourth cycle was abnormal. No DNA synthesis occurred before septation when zoosporangia developed in culture medium. When organisms were induced to make sporangia by transfer to water there was a small apparent increase in DNA prior to but not after septation. The unavoidable extraction of wall glycopeptide poses some problems in nucleic acid assays. Partial inhibition by 10µM benomyl allowed continued growth with large rhizoids at every apex. Partial inhibition by mitomycin allowed continued growth without any further morphological differentiation.