Miracle-dz/UniFAR-FTUs huggingface dataset:
Vertical distribution of fish eggs and larvae in the Irish Sea and southern North Sea

Fish eggs and larvae were analysed from 63 vertically stratified plankton hauls in the Irish Sea and southern North Sea. The dominant species were sprat (Sprattus sprattus), dragonet (Callionymus spp.), dab (Limanda limanda) and to a lesser extent rockling species, sandeel (Ammodytes spp.), whiting (Merlangius merlangus) and flounder (Platichthys flesus). There was little diVerence between species in the vertical distribution of either eggs or larvae. Most were concentrated in the upper 50 m of the water column, eggs in progressively increasing numbers towards the surface and larvae with a sub-surface peak at a depth of 10‐15 m. The vertical distribution of eggs extended deeper in the water column than larvae, possibly due to some combination of eggs being spawned deeper and their passive susceptibility to turbulent mixing. There were no significant diVerences between day and night distributions and under mixed or isothermal conditions. 1997 International Council for the Exploration of the Sea
The nematode–arthropod clade revisited: phylogenomic analyses from ribosomal protein genes misled by shared evolutionary biases

Phylogenetic analysis of major groups of Metazoa using genomic data tends to recover the sister relationships of arthropods and chordates, contradicting the proposed Ecdysozoa (the molting animals), which group the arthropods together with nematodes and relatives. Ribosomal protein genes have been a major data source in phylogenomic studies because they are readily detected as Expressed Sequence Tags (ESTs) due to their high transcription rates. Here we address the debate about the recovery of Ecdysozoa in genomic data by building a new matrix of carefully curated EST and genome sequences for 25 ribosomal protein genes of the small subunit, with focus on new insect sequences in addition to the Diptera sequences generally used to represent the arthropods. Individually, each ribosomal protein gene showed low phylogenetic signal, but in simultaneous analysis strong support emerged for many expected groups, with support increasing linearly with increased gene number. In agreement with most studies of metazoan relationships from genomic data, our analyses contradicted the Ecdysozoa (the putative sister relationship of arthropods and nematodes), and instead supported the affinity of arthropods with chordates. In addition, relationships among holometabolan insects resulted in an unlikely basal position for Diptera. To test for biases in the data that might produce an erroneous arthropod–chordate affinity we simulated sequence data on tree topologies with the alternative arthropod–nematode sister relationships, applying a model of amino acid sequence evolution estimated from the real data. Tree searches on these simulated data still revealed an arthropod–chordate grouping, i.e., the topologies used to simulate the data were not recovered correctly. This suggests that the arthropod–chordate relationships may be obtained erroneously also from the real data even if the alternative topology (Ecdysozoa) represents the true phylogeny. Whereas denser taxon sampling in the future may recover the Ecdysozoa, our analyses demonstrate that recent phylogenomic studies may be affected by as yet unspecified biases in amino acid sequence composition in the model organisms with available genomic data.
Residual correlations, and not individual properties, determine a nest defense boldness syndrome

Different behavioral traits often covary, forming a behavioral syndrome. It is poorly known whether this covariance occurs on the between-individual level and what its selective consequences are. We used repeated measures (N = 562 observation events) of individual tawny owl Strix aluco females (N = 237) to study the integrated effects of seasonal timing of reproduction and clutch size on boldness displayed during defense of their clutch, in relation to plumage coloration, including local recruit production as a selective force on these traits. Using a Bayesian multivariate mixed model, we quantified the covariances between these traits on phenotypic, residual, and between-individual level and used a structural equation modeling approach to test the significance of presumed causal relationship between these traits in an a priori hypothesized path. On the phenotypic level, boldness was determined through early timing of breeding and larger clutch size, and early breeding increased recruitment probability. However, this relationship was entirely due to residual covariances and was not present on the between-individual level. The low individual-level correlations did not constrain the capacity of the population to respond to evolution as quantified by average autonomy (a metric summarizing evolutionary constraint on multiple traits). In the tawny owl, the association between early breeding and bold behavior, which is favored by selection, is solely due to extrinsic, nonheritable factors. We conclude that phenotypic evidence is insufficient to demonstrate syndrome covariance.
Humoral encapsulation in Diptera (Insecta): comparative studies in vitro

The humoral encapsulation reaction of larvae of Chironomus has been reproduced and studied in vitro. This reaction is activated by entomogenous fungi and certain foreign bodies as well as by nematodes. The different stages of encapsulation and the duration of the process have been determined. In the larvae of a given species of Chironomidae encapsulation does not vary with age or sex. In contrast, the duration of the process differs according to the species of Chironomidae and is modified by temperature or by parasitism of the host by Mermithidae. The capsules contain melanin. Their formation is prevented by glutathion, an inhibitor of phenoloxidase. The humoral type of encapsulation also occurs in vitro in the haemolymph of larvae of the nematocera families, Culicidae and Chaoboridae. However, the reaction of these insects differs in the amount, distribution and pigmentation of the capsular material. The results demonstrate similarities between humoral and cellular encapsulation.
Mapping Quantitative Trait Loci Controlling Low Temperature Germinability in Rice (Oryza sativa L.)

Quantitative trait loci (QTLs) controlling low temperature germinability (LTG) in rice were identified using 98 backcross inbred lines (BILs) derived from a cross between a japonica variety Nipponbare and an indica variety Kasalath. Seeds of each BIL were stored at 30°C in a drying machine for 7 months to exclude the effects of seed dormancy. Then the germination rate at 15°C for 4 days was scored to represent the LTG. The LTG of Nipponbare and Kasalath was 17 and 61%, respectively, and that of the BILs ranged from 0 to 100%. Five putative QTLs, qLTG-2, qLTG-4-1, qLTG-4-2, qLTG-5 and qLTG-11, were detected on chromosome 2 (G1327: nearest marker locus), 4 (two regions, C946 and C513), 5 (R830) and chromosome 11 (G1465). In the case of qLTG-2, qLTG-4-1 and qLTG-11, Kasalath alleles increased the LTG, while Nipponbare alleles increased it in the case of qLTG-4-2 and qLTG-5. These QTLs explained 40.7% of the total phenotypic variation in the BC1F9 lines. Using chromosome segment substitution lines (SLs), the existence of qLTG-4-1 and qLTG-11 was confirmed and the effect of the Kasalath allele on qLTG-11 was more pronounced than that on qLTG-4-1. The effect of the Kasalath allele on qLTG-4-2, which suppressed the germination, was temporary and disappeared after 7 to 8 month’s storage, suggesting that the disappearance was due to the breaking of seed dormancy and that qLTG-4-2 might control it. Kasalath allele in the case of qLTG-5 decreased the germination rate when the effect of dormancy was completely removed. Therefore, we concluded that qLTG-5 was involved in LTG but not in seed dormancy.
Structural characteristics of tiller age categories of continuously stocked marandu palisade grass swards fertilized with nitrogen

The objective of this experiment was to evaluate the structural characteristics of young, mature and old tillers on continuously stocked marandu palisade grass maintained at 30 cm and fertilized with nitrogen. Treatments corresponded to three nitrogen application rates (150, 300 and 450 kg/ha of N) plus control (no fertilization) and were assigned to experimental units (1,200-m2 paddocks) according to a completely randomized block design, with four replications. Measurements were performed during fall/winter 2007 and summer 2008. During summer, young tillers showed longer leaves and shorter stems relative to old tillers. During fall/winter, young and old tillers showed shorter leaves, while mature and old tillers showed longer stems. Tiller age interfered with the number of leaves per tiller mainly through variations in the number of expanding and senescing leaves during both fall/winter and summer. The structural characteristics of individual tillers are affected by plant age, with nitrogen favouring the production of leaf tissue in young tillers during summer.
Association of plasma protein C levels and coronary artery disease in men

Several studies have shown the risk factor causes of coronary heart disease. In this study we tested the hypothesis that plasma protein C level might be used as a biomarker for coronary heart disease and myocardial infarction. The study included 60 men that were classified into 3 groups according to clinical examination; group I set as healthy control group, group II set as patients with ischemic heart disease and group III set as patients suffering from myocardial infarction. Different parameters were measured including, coagulation factor prothrombin time, partial thromboplastin time, fibrinogen and protein C. The activity of the cardiac enzymes (creatine phosphokinase, creatine phosphokinase-MB and lactate dehydrogenase) was also measured. Finally, lipids profile (total lipids, phospholipids, triacylglycerol, total cholesterol, low density lipoprotein cholesterone (LDL-C) and high density lipoprotein (HDL-C) were measured. The results demonstrate significant decrease level of protein C and prothrombin concentration (%) in ischemic heart disease and in myocardial infarction (MI) groups, when compared to the control group. Meanwhile, MI group showed more significant decrease comparing to IHD. Plasma protein C might serve as a marker for coronary artery disease in men. Further studies are warranted to bolster the data and to identify pathogenesis links between innate immune system activation and atherosclerosis. Keywords: Ischemic heart disease, myocardial infarction, protein C, coagulation factor, lipids profile. Afr. J. Biotechnol Vol. 12 No. 50
Trophic relations between cyclopoid copepods and ciliated protists: Complex interactions link the microbial and classic food webs

Two field experiments examined the effects of cyclopoid copepods on ciliates. The presence or absence of Cyclops abyssorum, Cyclops kolensis, and zooplankton >64 μm was manipulated to determine the relative importance of direct cyclopoid predation on protists vs. indirect effects mediated through cyclopoid predation on other metazooplankton. In the second experiment, presence or absence of C. abyssorum was cross-classified with five concentrations of the metazooplankton community. Cyclopoid effects on ciliates were dependent on predator and prey species and on the abundance of alternate prey for cyclopoids. A trophic cascade was also observed, but only for two small ciliates, and only with the larger C. abyssorum. C. abyssorum had a stronger predation effect on oligotrich ciliates when metazooplankton had been removed, and this effect appeared at a lower metazooplankton concentration with a larger ciliate, compared to a smaller species of the same genus. These results suggest that for cyclopoid-ciliate interactions, switching behavior in the predator may be at least as important as a trophic cascade.
Factors influencing success among collaborative sage-grouse management groups in the western United States

SUMMARY Considerable efforts have been put into collaborative conservation efforts across the globe. In the western USA, concern about declines of two sage-grouse species (Centrocercus urophasianus and C. minimus) has led to the creation of over 60 collaborative wildlife management partnership groups to develop and implement local sage-grouse management plans. These sage-grouse local working groups (LWGs) share a common goal, information, and policy environment, but were implemented in diverse ways. As a result, they provide a rare opportunity to study systematically the impact of contextual, organizational, institutional and process factors on local collaborative group success. Data from document reviews and an extensive survey of over 700 group participants from 53 sage-grouse LWGs were used to assess the success of this collaborative conservation effort and identify those group attributes that were related to successful implementation and funding of projects. Specifically, external, internal and emergent group characteristics were considered as likely predictors of LWG implementation success. The LWGs varied broadly in their achievements. The presence of a neutral facilitator, participants' feelings of ownership, groups whose local plans had more authority and early-stage group successes were significantly related to implementation success at the group level.
Song repertoire is not affected by stress in an adult male songbird, the Whitethroat Sylvia communis

Summary It is believed that bird song has evolved as a reliable signal of quality of displaying individuals. Recent research has focused on costs of development of complex song. In the present paper we test if the acquired repertoire size is costly to maintain. We compared changes in song structure in male Whitethroats (Sylvia communis) after 48 h exposure to a stressor (5% body mass weight attached to the tail feathers) vs. changes observed within the same time interval in the control group. The strophe length was marginally significantly shorter in the handicapped males comparing to controls. However, the repertoire size (i.e., a measure of diversity of different song elements) remained intact in both groups. We concluded that the song repertoire in Whitethroats is a static secondary sexual trait. A review of literature has revealed no convincing examples of decreasing repertoire size in adult male songbirds. Further research is needed to improve our understanding of evolutionary and proximate mechanisms maintaining the stability of song repertoires.
Allozyme analysis of Australian isolates of Dilophospora alopecuri

Twenty-one isolates of the nematode-vectored plant pathogen, Dilophospora alopecuri , were examined by allozyme electrophoresis. The study focused on isolates from Australia, including those associated with populations of the seed-gall nematode, Anguina funesta , in Western Australia (W.A.), where the fungus apparently provides natural control of the A. funesta-Clavibacter toxicus association responsible for annual ryegrass toxicity, and a range of Anguina populations in south-eastern Australia. Reference strains from international culture collections were included. Variation was found in 26 of 27 presumptive loci and 10 electrophoretic types were identified. All Australian isolates fell into six electrophoretic types that formed two groups of three that differed by less than 13% within each group, but differed by over 70% between the groups. Of the isolates from W.A. , six fell into one electrophoretic type and one into a second electrophoretic type that differed at one locus only. Three exotic isolates varied from Australian ones by 27–74%. Dilophospora alopecuri exhibited greater within-species allelic variation than previously reported for asexually-reproducing halophase fungi. The lack of variation within W.A. suggests that (i) a teleomorph does not occur under local conditions, (ii) the W.A. population has arisen from a single introduction and (iii) selection of strains suitable for biocontrol of Anguina funesta and Clavibacter toxicus should include material from eastern Australia.
Patrones de distribución de clorofila a y producción primaria en aguas del Golfo de México y del Mar Caribe

An aceanographic cruise was carried out in the Summer 1994 in the Gulf of Mexico and Caribbean Sea in order to study the spatial variability (horizontal and vertical) of the total chlorophyll a and primary production in relation to thermal structure, irradiance, and the nutricline position in the water column. The highest production rates were measured on the Yucatan shelf (0.84 and 2.11 gC.m-2.d-1) while in the Gulf of Mexico and Caribbeab Sea the rates were much lower (0.07-0.14 gC.m-2.d-1). Vertical profiles with deep chlorophyll maxima (0.16 to 4.24 mg.m-3) were always situated below the mixed layer, between 20 and 120m deep in neritic and oceanic waters, respectively, at low light intensities (between 0.2 and 5% of I) and sometimes in relation to the nutricline. In the Gulf of Mexico and in the Caribbean Sea a vertical profile types which is characteristics for tropical oligotrophic waters, with low chlorophyll concentrations, a deep maximum near the nutricline and low primary production was found. In the Yucatan shelf the profile approximates to the productive extreme of typical tropical structure, with higher chlorophyll concentration, primary production and a shallow thermocline. In oligotrophic waters the phytoplankton fraction < 10um contributes with 50 to 100% of the total chlorophyllic biomass while, in eutrophic waters its contribution ranges between 20 and 67%.
Text Mining applied to Molecular Biology

textabstractThis thesis describes the development of text-mining algorithms for molecular biology, in particular for DNA microarray data analysis. Concept profiles were introduced, which characterize the context in which a gene is mentioned in literature, to retrieve functional associations between genes. The method was shown to efficiently annotate DNA microarray data and complement existing methods. Concept profiles were also used for other types of concepts and were successfully applied for functional annotation of genes through automatic assignment of Gene Ontology terms to genes. A generic framework has been developed based on concept profiles, dubbed Anni (www.biosemantics.org/anni), to provide researchers with an ontology-based interface to the literature and we demonstrated its utility for literature-based knowledge discovery. Use and development of text-mining tools to identify relations between genes and to automatically annotate sets of genes resulting from ! microarray experiments. Comparing DNA microarray studies can reveal interesting parallels. However, such analyses are hampered by the large influences of design, technical and statistical factors on the found differentially expressed genes. Comparisons based on perturbed biological processes could be more robust. Concept profiles were used to reveal overlapping biological processes between microarray studies in a comparative meta- analysis of 102 muscle-related microarray studies. We demonstrated that many more biologically meaningful links could be retrieved between studies, even between studies without differentially expressed genes in common.
The effects of litter layer and soil properties on the soil-atmosphere fluxes of greenhouse gases in karst forest, southwest china

Temporal variation is a major source of the uncertainty in estimating the flux- es of the greenhouse gases (GHGs) in terrestrial ecosystems, and the GHG fluxes and its affecting factors in the karst region of southwest China re- mains weakly understood. Using the static cham- ber technique and gas chromatography method, the CO 2 , CH 4 and N 2 O fluxes were carried out be- tween 9 and 11 a.m. at 15 day intervals from June 2008 to May 2009 in a Pinus massoniana forest. Two treatments were chosen for this study: undis- turbed (soil with litter layer) and disturbed (sur- face litter removal). Both treatments were found to be the net source of atmospheric CO 2 and N 2 O, but a sink of atmospheric CH 4 . The seasonality of soil CO 2 emission coincided with the seasonal climate pattern, with high CO 2 emission rates in the hot-wet season and low rates in the cool-dry season. In contrast, seasonal patterns of CH 4 and N 2 O fluxes were not clear, although higher CH 4 uptake rates were often observed in autumn and higher N 2 O emission rates were often observed in spring (dry-wet season transition). The litter was active in GHG fluxes, and removal of the lit- ter layer reduced soil CO 2 emission (17%) and increased CH 4 uptake (24%) whereas N 2 O fluxes were not affected distinctly in the pine forest, indi- cating that litter layer had an important effect on C exchanges. In the pine forest, soil CO 2 emissions and CH 4 uptakes correlated significantly with soil temperature (r 2 = 0.87, P <0.01; r 2 = 0.34, P <0.05, respectively), but had no significant relationship with soil moisture. And there was a significant cor- relation between CH 4 flux and NH 4 + -N (r 2 = 0.39, P < 0.05) and soil inorganic N (r 2 = 0.48, P <0.05), but no significant correlation was found between CH 4 flux and NO 3 - -N. Moreover, we found a significant negative logarithmic correlation be- tween N 2 O flux and soil NO 3 - -N concentration (r 2 = 0.41, P <0.05), and the relationship between CO 2 emission and soil inorganic N content (r 2 = 0.35, P < 0.05). These results suggested that soil temperature and mineral N dynamics largely af- fected the temporal GHG exchanges between for- est soil and atmosphere.
Extension of the postharvest life of `Pollock' avocado using modified atmosphere packaging

Introduction. The postharvest life of 'Pollock' avocado, a popular cultivar grown in Sri Lanka, is 7-10 d at room temperature. A short postharvest life limits its export volume by sea freight. Materials and methods. Pollock avocado fruit were packaged in 0.05 mm thick low-density polyethylene (LDPE) bags to create a modified atmosphere (MA), and they were stored at 12 o C and 94% relative humidity. The effect of the potassium permanganate, an ethylene absorber, and of the granular charcoal, a carbon dioxide absorber, on modifying the in-package atmosphere was tested. During storage, carbon dioxide, oxygen and ethylene contents were measured. The packages were opened after MA storage, and the fruit ripened naturally under ambient conditions. The weight loss, changes in firmness, total soluble solids (TSS), pulp color, visual quality rating (VQR), chilling injury index (CI) and disease index (DI) during or after storage were determined. Results. Compared with the samples packaged with- out absorbers, those packaged with absorbers had significantly lower carbon dioxide and eth- ylene contents. MA packaging was effective in extending the postharvest life of Pollock avo- cado up to 17 d. Inclusion of absorbers further extended the postharvest life up to 29 d. Firmness, TSS, pulp color, VQR, CI and DI of the ripened fruits were not significantly affected by the MA conditions. Discussion. The MA conditions did not alter the ripening process and were successful in preventing the chilling injury and diseases. Packaging of Pollock avocado in 0.05 mm LDPE bags at 1:1 surface to weight ratio (cm 2.g -1 ) with ethylene and carbon diox- ide absorbers and storing at 12 °C and 94% relative humidity can be recommended to extend their storage life up to 29 d.