Miracle-dz/UniFAR-FTUs huggingface dataset:
Marine mammals and seabirds in Mauritanian waters : pilot study April 2004

The upwelling zones in Mauritanian coastal waters provide food-rich conditions for fish. Fish-stocks are exploited by a large international fleet of freeze-trawlers. Trawlers, fish and fish predators therefore congregate in a relatively narrow strip where the upwelling takes place. As an unwanted side-effect large animals, such as cetaceans, sharks and rays are accidentally caught in the nets. To be able to estimate the effect of by-catches on local populations of these groups informationon densities and occurrence in relation to season and environmental variables is needed. In April 2004 the Netherlands Institute for Fisheries Research (RIVO) and Alterra conducted a pilot survey of marine mammals and seabirds in cooperation with the Mauritanian Institute for Oceanographic and Fisheries Research (IMROP). As sea mammals often interact and form multi- species feeding associations with seabirds, the census included both sea mammals and seabirds. The main aim of the project was to investigate the suitability of the combination of a survey of marine mammals and seabirds with an acoustic survey that is carried out twice per year to assess pelagic fish stocks. The ultimate goal is to set up a monitoring program with several surveys per year. If the combination with the acoustic survey is useful and successful, the monitoring program can be carried out at relatively low cost. Between 16 and 28 April 2004 two observers joined the acoustic survey on board the Al Awam, the research vessel of IMROP. A total of 28 transects positioned East-West at distances of 10 nm apart were sampled, at depths varying from 20 m to 500 m. All marine mammals and seabirds encountered were noted, using standard seabirds at sea counting methods. Besides assessing numbers, also behaviour was recorded, following the observation protocol for ship-based seabird surveys in Europe. Observations were carried out when the ship was steaming. During fishing operations (2-5 times per day) observations were interrupted.In this report a short overview of the results is presented. Cetaceans were only rarely encountered during the survey. In total, ten groups or singles were observed during 91.5 hours of counts. The sightings included two large whales (Fin Whale and Humpback Whale), three species of small whales (Killer Whale, Long- or Short-finned Pilot Whale and unidentified Beaked Whale) and two species of dolphin (Common and Bottlenose Dolphin). In total 51.838 seabirds and 314 species were recorded of which Common/Arctic Tern, Black Tern, Wilson’s Storm-petrel and Sabine’s gull were the most abundant species. The general pattern can be characterised by a clear near shore-offshore gradient, with peak densities of most species at the drop-off of the continental shelf. The majority of birds was associated with trawlers.
MATING WITHOUT SEXUAL CANNIBALISM IN TIDARREN SISYPHOIDES (ARANEAE, THERIDIIDAE)

Abstract Copulatory behavior of Tidarren sisyphoides is described for the first time. Courtship proceeds without construction of a mating thread. The male dies during insertion and remains coupled to the female epigynum for 2.4 hours on average (n = 15). In contrast to other species hitherto studied, females of T. sisyphoides do not consume their mates after copulation. Instead, the dead males are removed from the webs by the females.
Antigen-specific cellular hyporesponsiveness in a chronic human helminth infection is mediated by Th3/Tr1-type cytokines IL-10 and transforming growth factor-β but not by a Th1 to Th2 shift

Exposure to infective larvae of the filarial nematode Onchocerca volvulus (Ov) either results in patent infection (microfilaridermia) or it leads to a status called putative immunity, characterized by resistance to infection. Similar to other chronic helminth infections, there is a T cell proliferative hyporesponsiveness to Ov antigen (OvAg) by peripheral blood mononuclear cells (PBMC) from individuals with patent infection, i.e. generalized onchocerciasis (GEO), compared to PBMC from putatively immune (PI) individuals. In this study, mechanisms mediating this cellular hyporesponsiveness in GEO were investigated: the low proliferative response in PBMC from GEO individuals was associated with a lack of IL-4 production and significantly lower production of IL-5 compared to those from PI individuals, arguing against a general shift towards a Th2 response being the cause of hyporesponsiveness. In contrast, IL-10 and transforming growth factor (TGF)-β, two cytokines associated with a Th3 response, seemed to mediate hyporesponsiveness: PBMC from individuals with GEO produced significantly more IL-10, and T cell proliferative hyporesponsiveness in this group could be reversed by the addition of anti-IL-10 and anti-TGF-β antibodies. Hyporesponsiveness was specific for OvAg and not observed upon stimulation with related nematode antigens, arguing for a T cell-mediated, Ov-specific down-regulation. Ov-specific T cells could be cloned from GEO PBMC which have a unique cytokine profile (no IL-2 but high IL-10 and/or TGF-β production), similar to the T cell subsets known to suppress ongoing inflammation (Th3 and Tr1), indicating that this cell type which has not been found so far in infectious diseases may be involved in maintaining Ov-specific hyporesponsiveness.
Linking forest fires to lake metabolism and carbon dioxide emissions in the boreal region of Northern Québec

Natural fires annually decimate up to 1% of the forested area in the boreal region of Québec, and represent a major structuring force in the region, creating a mosaic of watersheds characterized by large variations in vegetation structure and composition. Here, we investigate the possible connections between this fire‐induced watershed heterogeneity and lake metabolism and CO2 dynamics. Plankton respiration, and water–air CO2 fluxes were measured in the epilimnia of 50 lakes, selected to lie within distinct watershed types in terms of postfire terrestrial succession in the boreal region of Northern Québec. Plankton respiration varied widely among lakes (from 21 to 211 μg C L−1 day−1), was negatively related to lake area, and positively related to dissolved organic carbon (DOC). All lakes were supersaturated in CO2 and the resulting carbon (C) flux to the atmosphere (150 to over 3000 mg C m2 day−1) was negatively related to lake area and positively to DOC concentration. CO2 fluxes were positively related to integrated water column respiration, suggesting a biological component in this flux. Both respiration and CO2 fluxes were strongly negatively related to years after the last fire in the basin, such that lakes in recently burnt basins had significantly higher C emissions, even after the influence of lake size was removed. No significant differences were found in nutrients, chlorophyll, and DOC between lakes in different basin types, suggesting that the fire‐induced watershed features influence other, more subtle aspects, such as the quality of the organic C reaching lakes. The fire‐induced enhancement of lake organic C mineralization and C emissions represents a long‐term impact that increases the overall C loss from the landscape as the result of fire, but which has never been included in current regional C budgets and future projections. The need to account for this additional fire‐induced C loss becomes critical in the face of predictions of increasing incidence of fire in the circumboreal landscape.
A model‐based reconstruction of Holocene treeline dynamics in the Central Swiss Alps

1 We used the forest succession model ForClim to simulate Holocene treeline dynamics along an elevational transect in the Central European Alps, in order to explore the extent and cause of changes in treeline altitude and composition. 2 A temperature reconstruction independent of vegetation proxies was used to drive the model, and the simulation results were compared with Holocene pollen and macrofossil records from a nearby site close to the present‐day treeline. 3 The simulation results yielded treeline fluctuations of about ± 100 m (2375–2600 m a.s.l.), confirming earlier palaeoecological studies and quantitatively corroborating the interpretation of most palaeoecologists that decadal‐ to centennial‐scale Holocene fluctuations of pollen and plant macrofossil frequencies reflect treeline shifts rather than productivity changes alone. 4 The simulated changes in species composition and treeline position show general agreement with palaeobotanical data between 11 000 and 4500 calibrated radiocarbon years BP. In the late Holocene, however, palaeobotanical evidence indicates a distinct lowering of the treeline, while simulation projected continuous forest cover up to an altitude of 2400 m a.s. l. 5 Our results indicate that changes in temperature alone can account for changes in treeline elevation for the first half of the Holocene. The discrepancy between simulation results and palaeobotanical records since 4500 cal. BP supports the hypothesis of a strong human influence on the Alpine treeline during the late Holocene. 6 Combining palaeoecological methods with vegetation modelling can disentangle climatic effects and early human impacts on long‐term vegetation dynamics. Forest succession models may not only help palaeoecologists to achieve a better understanding of the factors driving past vegetation changes, but their validation with long‐term empirical data is also an important step towards applying these models to the assessment of future vegetation dynamics in a changing climate.
Pulmonary Cryptococcosis Secondary to Bronchial Asthma Presenting asType I Respiratory Failure- A Case Report with Review of Literature

Cryptococcus spp, was first isolated and described in 1894 by Sanfelice F in Italy from peach juice and named it as Saccharomyces neoformans, is an yeast like fungus, first isolated from a clinical specimen by Busse in the same year from Germany. Cryptococci are a saprophytic fungi present in soil contaminated with bird droppings mainly of pigeons, roosting sites and decaying vegetables. Previous reports have also showed the presence of Cryptococcus spp colonized in the nasopharynx and on skin of healthy individuals. Belonging to Basidiomyctes group of fungi Cryptococcus spp primarily infects central nervous system causing meningoencephalitis mostly in immunocompromised individuals. Classical and molecular genetic studies have revealed that Cryptococcus spp are closely related to ascomycetes group (Saccharomyces cerevisiae, Schizosaccharomyces pombe) and basidiomycetes pathogens and mushrooms (Ustilago maydis,Coprinus cinereus, Schizophyllum commune)
Chromosome numbers in wild and semidomesticated Brazilian Capsicum L. (Solanaceae) species: do x = 12 and x = 13 represent two evolutionary lines?

species from theEMBRAPA Hortalicas (Brazil) germplasm collection. 2n = 24 was found in C. baccatum var. praetermissum,C. chinense, C. ﬂexuosum and C. parvifolium, while C. buforum, C. campylopodium, C. cornutum, C. schottianum,C. villosum var. villosum and ﬁve other native south-eastern Brazilian species not yet taxonomically named all had2n = 26 chromosomes. These are the ﬁrst chromosome number determinations for C. cornutum, C. schottianum,C. villosum var. villosum and the ﬁve other Brazilian taxa. Our data conﬁrm published data for C. baccatum var. pra-etermissum, C. campylopodium, C. chinense, C. ﬂexuosum and C. parvifolium, but not for C. buforum. The prevalenceof 2n = 26 chromosomes among Brazilian species, along with the morphological and ecological characteristics pre-sented by the wild and semidomesticated species occurring in Brazil, form a pattern different from that found inAndean wild and semidomesticated species. This supports the hypothesis that there are two different evolutionarylines in the genus and that the native south-eastern Brazilian species belong to the ancestral Capsicum gene pool. © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society, 2006, 151, 259–269.
Evolution of adult size depends on genetic variance in growth trajectories: a comment on analyses of evolutionary dynamics using integral projection models

Integral projection models (IPMs) are an extension of stage‐structured population models to continuous classes or traits, such as body size. Recent studies have used age‐structured IPMs to investigate the relative contributions of evolutionary versus demographic responses of quantitative traits to environmental change. However, I argue here that evolutionary responses are likely to be underestimated by this approach, because it does not fully capture how phenotypic differences between individuals and genotypes accumulate along life, and are transmitted across generations. Trait transitions upon survival and reproduction are treated in IPMs by two classes of functions. First, an ‘inheritance’ function relates the trait of a newborn to that of its adult parent, on the time‐scale of a reproductive event. Secondly, growth functions relate the traits of surviving individuals between successive ages. This differs from the quantitative genetic approach, where parent–offspring resemblance is generally quantified for age‐specific trait values, and on the time‐scale of a generation. More importantly, it is unclear to what extent age‐structured IPMs account for the fact that phenotypic and genetic variances of adult size are largely caused by differential growth among individuals and genotypes in multicellular organisms. I use simple simulations of growth trajectories to ask what the transition functions from IPMs can tell us about the contribution of genetic evolution to phenotypic change. These simulations illustrate that a flat inheritance function is perfectly compatible with substantial response to selection in adults. They further show that the growth functions from IPMs may obscure genetic differences in body size that accumulate along life owing to genetic variation in growth trajectories. IPMs are a powerful tool for investigating age‐dependent components of phenotypic selection, and the demographic consequences of plastic responses that act through environmental effects on growth. But using age‐structured IPMs to project evolutionary dynamics requires combining them with measurements of age‐specific additive genetic variances and cross‐age additive genetic covariances, to accurately describe the accumulation of phenotypic differences across ages, and their transmission across generations.
Segmentation of chromosome images

In this study, the segmentation of chromosome images is examined. These banded chromosome arms belong to mosquitoes of the anopheles gambiae complex and are stained and mounted on slides. Spurious breaks in the chromosome arms due to the banded characteristic of the arms, detection of objects which are actually made up of noisy segments of fusion of two or more arms during segmentation due to close proximity of the arms to each other are some of the problems that are encountered during segmentation. <<ETX>>
Growth analysis and canopy architecture of velvetleaf grown under light conditions representative of irrigated Mediterranean-type agroecosystems

Abstract Velvetleaf growth and canopy architecture were compared under a range of light conditions representative of competitive and noncompetitive environments typical of irrigated Mediterranean-type agroecosystems. Velvetleaf biomass and seed production exceeded those reported in the literature. Plants grown in full light produced 1,370 g dry weight and 44,200 seeds per plant and showed low relative variability. Velvetleaf grown with corn was reduced to 21 g dry weight and 349 seeds per plant, and had high relative variability for biomass and seed numbers. Velvetleaf grown with kidney bean, intraspecific neighbors, or under shadecloth had dry weights and seed numbers that were intermediate to plants grown in full light or with corn. Relative growth rate (RGR), net assimilation rate (NAR), and leaf area ratio (LAR) were assessed utilizing Richards functions, which were fitted to the primary biomass and leaf area data by weighted regression. RGR was highest for all plants early in the season, but declined later. Dynamics of NAR and LAR appeared to be correlated with increased self-shading, shading by neighbors, leaf age, and shedding of lower canopy leaves. Dynamics of specific leaf area corresponded with light availability such that the leaves exposed to full light were thicker than those exposed to shade. The branches of plants in all treatments had random azimuths and the foliage area density was concentrated along the perimeter of the plant's canopy. Velvetleaf increased the canopy radius through extensive branching when exposed to full sunlight. Leaf area distribution and branching patterns resulted in leaf area indices of less than 1.0. Leaves maintained a perpendicular angle to the sun throughout the day, but this depended on whether leaves received a consistent directional signal from the sun and not necessarily on whether they received a high-intensity signal. When shaded, the allocation of dry matter went primarily to the stem tissue, which increased the height rather than the girth of the plants. There was a 10- to 20-d delay for allocations to seed in the case of shaded plants relative to those grown in full sunlight. In brief, velvetleaf had a wide range of growth and canopy responses to a variety of light availabilities and it should have little difficulty in becoming fully established in the irrigated agroecosystems of Mediterranean-type regions. Nomenclature: Corn, Zea mays L. ‘NC 4616’; kidney bean, Phaseolus vulgaris L. ‘Sutter Pink’; velvetleaf, Abutilon theophrasti Medikus ABUTH.
Mapping of QTLs Controlling Egg Quality on Chromosomes 6-8, Z and Three Linkage Groups in Chickens

The practical aim of gene mapping in different organisms is to discover genetic markers and their linkage with quantitative traits loci (QTLs) that can increase the selection response in breeding programs and help to minimize the limitation in using QTL information for marker-assisted selection (MAS), especially for traits that are difficult to improve when using traditional selection (Korstanje and Paigen, 2002; Fadiel et al. 2005). QTL analysis always involves linkage of genetic markers with genome regions influencing the investigated trait (or traits) (Soller, 1991). Prior work using genetic markers has identified the Boroola gene affecting ovulation rate in sheep (fecB), the halothane sensitivity gene in pigs (RYRT), the double muscling gene of cattle (Montgomery at al. 1993; Geldermann et al. 1999; Grobet at al. 1997). Microsatellite markers or simple sequence repeats can satisfy the investigations of quantitative trait loci in animal breeding (Malek et al. 2001; Diez-Tascon et al. 2001). These markers must be characterized by high heterozygosity and polymorphism and should be evenly distributed throughout the genome and broadly dispersed. The effect of QTL mapping depends on: the number of genes underlying a polygenic trait, even markers distribution throughout the genome, interactions between genes, traits hereditary and the size of animal population (Soller, 1991; Hillel, 1997; Malek et al. 2001). The reference population can be obtained by crossing genetically distant breeds, families or inbred lines to obtain the mapping populations with the high level of heterozygosity. Two breeds of chickens were used to develop reference family and detect QTLs affecting egg quality traits: cocks of a native Polish breed Green-Legged Partidgenous (GlP) and hens of Rhode Island Red (RIR). During the first 100 days of the laying period, the GlP hens lay about 40 eggs weighting on average 50 g, whilst the RIR flock laid 83 eggs with a mean weight of 60 g. QTL analysis of egg quality traits was performed on 552 birds of the F2 generation with the aid of 19 microsatellite loci on chromosomes 6, 7, 8, Z and linkage groups 9 (E 36), 19 (E 52) and 26 (E 46). Linkage analysis was performed for 19 microsatellite markers within the mapped population and ten QTLs were found to affect seven egg quality traits: at week 53-shell thickness, shell strength, albumen weight, egg specific gravity and percent of yolk in egg; and at week 33percent of yolk in egg and Hugh’s units.
Yield improvement and adaptation of wheat to water-limited environments in Australia—a case study

Abstract. The improvement in grain yield of wheat throughout Australia through both breeding and management has been impressive. Averaged across all farms, there has been an approximate doubling of yield per unit area since ∼1940. This has occurred across a broad range of environments with different rainfall patterns. Interestingly, the gain in the driest years (9 kg ha–1 year–1 or 0.81% year–1) has been proportionally greater than in the most favourable years (13.2 kg ha–1 year–1 or 0.61% per year) when expressed as yield relative to 2012. These data from all farms suggest that further yield progress is likely, and evidence is presented that improved management practices alone could double this rate of progress. The yield increases achieved have been without any known compromise in grain quality or disease resistance. As expected, improvements have come from both changed management and from better genetics, as well as from the synergy between them. Yield improvements due to changed management have been dramatic and are easiest to quantify, whereas those from breeding have been important but more subtle. The management practices responsible have largely been driven by advances in mechanisation that enable direct seeding, more timely and flexible sowing and nutrient management, and improved weed and pest control, many of which have been facilitated by improved crop sequences with grain legumes and oilseeds that improve water- and nutrient-use efficiency. Most of the yield improvements from breeding in Australia have come from conventional breeding approaches where selection is almost solely for grain yield (together with grain quality and disease resistance). Improvements have primarily been through increased harvest index (HI), although aboveground biomass has also been important. We discuss future opportunities to further increase Australian rainfed wheat yields. An important one is earlier planting, which increases resource capture. This will require knowledge of the genes regulating phenological development so that flowering still occurs at the optimum time; appropriate modifications to sowing arrangements and nutrient management will also be required. To improve yield potential, we propose a focus on physiological traits that increase biomass and HI and suggest that there may be more scope to improve biomass than HI. In addition, there are likely to be important opportunities to combine novel management practices with new breeding traits to capture the synergy possible from variety × management interactions. Finally, we comment on research aimed at adapting agriculture to climate change.