Miracle-dz/UniFAR-FTUs huggingface dataset:
Subcellular phenomena in colorectal cancer

The Wnt signalling pathway is involved in stem cell maintenance, differentiation and tissue development, and in so doing plays a key role in controlling the homeostasis of colorectal crypts. In response to an external Wnt stimulus, the intracellular levels of the protein beta-catenin are regulated by the proteins which make up the Wnt signalling pathway. Abnormalities in the Wnt signalling pathway have been implicated in the initiation of colorectal and other cancers. In this thesis we analyse and simplify existing models of the Wnt signalling pathway, formulate models for Wnt's control of the cell cycle in a single cell, and incorporate these into a multiscale model to describe how Wnt may control the patterns of proliferation in a colorectal crypt. A systematic asymptotic analysis of an existing ODE-based model of the Wnt signalling pathway is undertaken, highlighting the operation of different pathway components over three different timescales. Guided by this analysis we derive a simplified model which is shown to retain the essential behaviour of the Wnt pathway, recreating the accumulation and degradation of beta-catenin. We utilise our simple model by coupling it to a model of the cell cycle. Our findings agree well with the observed patterns of proliferation in healthy colon crypts. Furthermore, the model clarifies a mechanism by which common colorectal cancer mutations may cause elevated beta-catenin and Cyclin~D levels, leading to uncontrolled cell proliferation and thereby initiating colorectal cancer. A second model for the influence of the Wnt pathway on the cell cycle is constructed to incorporate the results of a recent set of knockout experiments. This model reproduces the healthy proliferation observed in crypts and additionally recreates the results of knockout experiments by additionally including the influence of Myc and CDK4 on the cell cycle. Analysis of this model leads us to suggest novel drug targets that may reverse the effects of an early mutation in the Wnt pathway. We have helped to build a flexible software environment for cell-based simulations of healthy and cancerous tissues. We discuss the software engineering approach that we have used to develop this environment, and its suitability for scientific computing. We then use this software to perform multiscale simulations with subcellular Wnt signalling models inside individual cells, the cells forming an epithelial crypt tissue. We have used the multiscale model to compare the effect of different subcellular models on crypt dynamics and predicting the distribution of beta-catenin throughout the crypt. We assess the extent to which a common experiment reveals the actual dynamics of a crypt and finally explain some recent mitochondrial-DNA experiments in terms of cell dynamics.
A New Cynepteris from the Upper Triassic of Arizona: Potential Implications for the Early Diversification of Schizaealean Ferns

Cynepteris bolichii is proposed as a new species of the monogeneric fern family Cynepteridaceae on the basis of a single, well‐articulated specimen from the Upper Triassic Chinle Formation in Petrified Forest National Park, Arizona. The specimen consists of an erect rhizome with at least eight attached fronds. As for the other three known Cynepteris species, C. bolichii pinnae exhibit reticulate venation and scattered, solitary, exindusiate sporangia on their abaxial surfaces. Each sporangium is ovoid to pyriform with a short, thick stalk and a complete, apical, caplike annulus consisting of a single row of cells surrounding a multicellular distal plate. These sporangial features are similar to those of several fossil and extant schizaealean ferns. Cynepteris bolichii differs from other Cynepteris species mainly in having once‐pinnate fronds with abundant, elongate hairs on the rachises and veins. Most recent estimates of fern phylogeny consider the Jurassic fossils Stachypteris, Klukiopsis, and Klukia as the oldest fossil representatives of the Schizaeales. It is here proposed that Cynepteris should be considered as a probable Late Triassic record of the order. Features such as reticulate venation, scattered sporangia, and lack of fertile/sterile frond dimorphism are rare and scattered among other fossil and extant ferns currently attributed to the Schizaeales, underscoring the importance of fossils for understanding the early divergence, ancestral morphology, and biogeography of ancient plants groups like the ferns.
Asymmetry, testis and sperm size in Yellow Dung Flies

Summary 1 Fluctuating asymmetry (FA), small random deviations from perfect bilateral symmetry, is a widely used measure of developmental stability, and has been linked to fitness measures including male primary reproductive traits such as sperm quality. However, there have been relatively few investigations of potential associations between these male traits and FA, and hence the current balance of evidence is equivocal. 2 There is also evidence that levels of FA vary across populations with, for example, organisms inhabiting marginal populations often displaying increased FA. Moreover, environmental variation may select for different levels of developmental buffering across populations that are only revealed in ‘common garden’ experiments. 3 Investigations of potential associations between male leg FA and testis and sperm size in Yellow Dung Flies are reported here. In addition, levels of FA in a mainland and two island populations were compared when flies were reared under common conditions. 4 No associations were found between any measure of FA and sperm size (or variation) or testis size. Additionally, no evidence was found that FA varied across the three populations when flies were reared under identical controlled conditions.
Exposure of pregnant dairy heifer to magnetic fields at 60 Hz and 30 µT

Thirty‐two pregnant Holstein heifers weighing 499 ± 45 kg, at 3.1 ± . 7 months of gestation and 21 ± 2.0 months of age were confined and exposed to 30 µT magnetic fields (MFs) and a 12 h light/12 h dark light cycle. The heifers were divided into two replicates of 16 animals. Each replicate was divided into two groups of eight animals each, one group the non‐exposed and the second, the exposed group. The animals were subjected to the different treatments for 4 weeks. After 4 weeks, the animals switched treatment, the exposed group becoming the non‐exposed group and vice versa. Then the treatment continued for 4 more weeks. Catheters were inserted into the jugular vein, and blood samples were collected twice a week to estimate the concentration of progesterone (P4), melatonin (MLT), prolactin (PRL), and insulin‐like growth factor 1 (IGF‐1). Feed consumption was measured daily. The results indicated that exposure of pregnant heifers to MF similar to those encountered underneath a 735 kV high tension electrical power line for 20 h/day during a period of 4 weeks produces slight effects. This is evidenced by statistically significant higher body weight (1.2%), higher weekly body weight gain (30%), and decreases in the concentration of PRL (15%) and IGF‐1 (4%) in blood serum. The absence of abnormal clinical signs and the absolute magnitude of the significant changes detected during MF exposure, make it plausible to preclude any major animal health hazard. Bioelectromagnetics 28:471–476, 2007. © 2007 Wiley‐Liss, Inc.
Geographical and environmental correlates of big and small game in Andalusia (southern Spain)

In Andalusia, southern Spain, each game estate applies its own rules and presents its results in annual hunting reports, which have been mandatory for Spanish game estates since 1989. We used the information about hunting yields, included in 32 134 annual hunting reports produced during the period 1993/94 to 2001/02 by 6049 game estates, to determine the current distribution of hunting yields of big and small game species in Andalusia. Using generalised linear models and a geographic information system, we determined the most favourable municipalities to big and small game, respectively, and delimited potential areas to attain good hunting yields for big and small game at a 1-km2 resolution. Municipalities and areas favourable to big game are mainly located in the Sierra Morena and the westernmost fringe of the Betic Range, while those favourable to small game occupy the upper Guadalquivir River valley. There is a clear segregation between big and small game species according to the physiography and land uses of the territory. Big game species are typical of Mediterranean woodland areas, while the most emblematic small game species prefer agricultural areas. Our results provide a territorial ordination of hunting yields in southern Spain and have several potential applications in strategic planning for hunting activities and biodiversity conservation in Andalusia that can be extrapolated to other regions.
Ajuste y predicción de la distribución Weibull a las estructuras diamétricas de plantaciones de pino de Durango, México

In this research the parameters of the Weibull distribution were estimated and predicted with stand attributes. Using hypothesis testing procedures, it was demonstrated that the equations to predict parameters, efficiently mimicked the diameter structures of forest stands used in the fitting as well as forest stands used in validating the prediction equations. Therefore, the equations are recommended to estimate the diameter structures of forest plantations of Durango, Mexico (Pinus durangensis, P. cooperi , P. engelmannii y P. arizonica).
The interspecific and intraspecific variation of functional traits in weeds: diversified ecological strategies within arable fields

Abstract Arable weeds are a key component of the biodiversity of agroecosystems, but have faced a marked decline due to agricultural intensification. Recently, the crop edge has been considered as a potential refugia for many species. Indeed, weed species richness and abundance are higher in the crop edge than in the field margin and the field core. In this study we question whether weed functional diversity also varies among field elements and whether it is higher in the crop edge. We studied the interspecific and intraspecific variation of three functional traits (specific leaf area, canopy height and above-ground biomass) related to the response of weeds to competition and to agricultural practices, for seven weed species sampled in the crop edge, the field margin and the field core area in four winter-wheat fields. We show that trait values varied significantly with the species, the field element and their interaction. Within the field, all species had high specific leaf area, low canopy height and biomass, suggesting a shade-tolerance syndrome that could be a strategy in response to both competition with the crop and the disturbances induced by agricultural practices. In the crop edge, where the functional variation was the highest, two distinct functional strategies were observed, suggesting a resource partitioning under the predominance of weed–weed competition. In conclusion, the crop edge plays a key role in sustaining weed diversity, mostly because of its intermediate environmental properties that allow the coexistence of weeds with different ecological strategies.
Differentiation and molecular detection of Canadian necrotic strains of Potato virus Y

Isolates of Potato virus Y (PVY) from potatoes grown in Canada were identified as tuber necrotic strains on the basis of biological, serological, and molecular characteristics. Only one isolate, however, caused symptoms of potato tuber necrotic ringspot disease (PTNRD) in progeny tubers of inoculated potato plants Solanum tuberosum 'Nadine' under greenhouse conditions. None of the isolates caused symptoms of PTNRD in potato plants 'Russet Burbank' or 'Saco'. A primer set based on the NIb gene for detection of PVYO by RT-PCR was modified to include detection of the Canadian necrotic isolates of PVY. Restriction analysis of amplicons generated from suspected PVYNTN isolates with primers based on the P1 protein gene differentiated two sets of isolates. Subsequent comparison of the P1 gene sequence of the Canadian isolates with published sequences confirmed that the isolates corresponded to North American and European types of PVYNTN. A new primer pair, based on the NIb gene sequence amplified by RT-PCR, allowed the amplification by RT-PCR of a gene fragment from all PVYN and PVYNTN isolates but not from PVYO strains. These primers proved to be useful for detecting the virus in composite samples of potato leaves, sprouts, and tubers.
Atividade alimentar de espécies de peixe do rio Tibagi, relacionada com o desenvolvimento de gordura e das gônadas

The fish assemblage in a stretch of Tibagi river was studied during the period of one year, throught monthly sampling. It was observed that four fish species (Schizodon intermedius Garavello & Britski, 1990, Acestrorhynchus lacustris Reinhardt, 1874, Pimelodus maculatus Lacepede, 1803 and Steindachnerina insculpta Fernandez-Yepez, 1948) were very frequent and they represent all the main trophic groups. In order to characterize feeding activity, fat storage and reproduction the means degree of repletion, fat and maturation, obtained for each species in each month were compared among the four fish species. Steindachnerina insculpta, a detritivovous species was the one with the highest feeding activity while A. lacustris, a piscivorous fish, showed the lowest feeding activity. For these two species it was clearly observed a sequence of events: higher feeding activity followed by higher fat storage followed by reproduction, that was not observed for P. maculatus and S. intermedius. The variations in feeding activity and fat storage showed by P. maculatus and S. intermedius might be related to their diets.
Genetic variation among populations of Pythium irregulare in southern Australia

Isolates of Pythium irregulare were sampled from seven cereal crops throughout South Australia to determine the extent of genetic diversity within this pathogen and the scale of genetic differentiation among populations. Data derived from 29 individual restriction fragment length polymorphism (RFLP) loci differentiated 54 DNA fingerprints among the 92 isolates analysed. Some isolates had two alleles at several RFLP loci and were scored as heterozygous. One such isolate was selfed in vitro and segregation ratios in the progeny were not significantly different from those expected for allelic variation in a diploid. These data provided evidence that outcrossing occurs within P. irregulare and may contribute to the high level of genetic variation within the species (DT = 0·502). Allelic frequencies were significantly different among all seven populations and GST values showed significant genetic differentiation between populations. The average genetic identity among populations was low and hierarchical cluster analysis provided no clear evidence that populations formed geographically related groups. These analyses indicate low levels of interpopulation gene flow within P. irregulare and imply that population differentiation results from genetic drift.
Non-hormonal synchronization of estrus in West Balkan Mountain sheep

The purpose of present study was to determine the possibility and degree of synchronization of estrus by the "ram effect" in West Balkan Mountain sheep breed. An experiment has been carried out for three years and covers a total of 902 ewes aged 18 months to 6 years old. In each flock of 150-180 ewes there were placed in three ram teasers, which were isolated from ewes for 8 months The introduction of rams in the flock was during the transition to estral period and for the first two years it was on first of August and in the third year of experiment - on 18th August (early estral season). The ewes which came in estrus were artificially inseminated with fresh semen, shallow-cervical. The date of insemination and lambing for each ewe were recorded. In the first 15 days after introduction of ram 22% of all ewes came in estrus, which were apparently naturally cycling. From 16 to 28 days of introduction of rams 58% of ewes came in estrus, hence reacted to the effect of ram. The second characteristic peak of the ram effect was significantly higher than the first. Ewes that were naturally cycling also responded to the effect of the ram. By applying the ram effect 40% of ewes lambed within two weeks. Barren ewes were relatively high at an average of 9%, with ranges from 5 to 14% of all ewes during different years. From the barren ewes 67% were not getting pregnant next year too. This justifies their culling.
High CO2 Requiring Mutant of Anacystis nidulans R2

Some physiological characteristics of a mutant (E1) of Anacystis nidulans R2, incapable of growing at air level of CO2, are described. E1 is capable of accumulating inorganic carbon (Ci) internally as efficiently as the wild type (R2). The apparent photosynthetic affinity for Ci in E1, however, is some 1000 times lower than that of R2. The kinetic parameters of ribulose 1,5-bisphosphate carboxylase/oxygenase from E1 are similar to those observed in R2. The mutant appears to be defective in its ability to utilize the intracellular Ci pool for photosynthesis and depends on extracellular supply of Ci in the form of CO2. The very high apparent photosynthetic Km (CO2) of the mutant indicate a large diffusion resistance for CO2. Data obtained here are used to calculate the permeability coefficient for CO2 between the bulk medium and the carboxylation site of cyanobacteria.
Influence of Process Conditions on the Kinetics of the Osmotic Dehydration of Yacon (Polymnia sonchifolia) in Fructose Solution

Yacon is a tuberous root with functional properties that contains near 90% water, promoting its quick degradation. The purpose of this work was to optimize the osmotic dehydration of yacon using response surface methodology (RSM). Water loss, solute gain and water activity were determined as functions of the independent variables such as temperature (30–50C), fructose concentration (40–68% w/w) and use of an edible sodium alginate coating coverage. Correlation equations were constructed describing the effects of the independent variables. By applying RSM, the optimum conditions for dehydration were found to be with sodium alginate coating in a solution at 68°Brix and 30C for 60 min. Practical Applications The process of osmotic dehydration can be used for the preparation of shelf-stable products for the purpose of obtaining a more physicochemically and microbiologically stable final product. The treatment of coating before osmotic dehydration helps in reducing the problem of large solute gain without affecting much on the water loss. The fruits obtained by combining coating and osmotic dehydration exhibit better appearance and extended shelf life. The product can be used in the areas of nonavailability of fruit, and it is also used as an ingredient in the formulation of products such as jellies and yacon syrup.
The Influence of Soil Microorganisms and Bio- or -Organic Fertilizers on Dissipation of Some Pesticides in Soil and Potato Tubers

The influence of soil microorganisms, biofertilizer and compost fertilization on the persistence of the two organphosphorus insecticides, chlorpyrifos, ethoprophos and carbamate insecticide, carbofuran were studied under semifield experimental conditions. Residue analysis of the initial samples of the three applied pesticides, chlorpyrifos, ethoprophos and carbofuran was relatively high (68.3, 76.0 and 80.9 ppm, respectively) in uncultivated, unfertilized and unsterilized soil. These amounts were decreased to 10.12, 14.6 and 12.0 ppm showing 85.18, 80.79 and 85.17% loss, respectively at 6 weeks after treatments. The initial deposits of these pesticides in po- tato cultivated soils (control) were 70.77, 74.17 and 81.17 ppm, respectively, graduate dissipation of tested pesticides was noticed through the successive intervals. At the end of the experimental period, residues detected revealed 93.0, 91.5 and 94.37% loss, respectively. Addition of certain bioactive (microbal and compost ) amendments was able to induce the pesticide degradation in the contaminated soil (the highest degradation levels was noticed in biofertilized soil, > 99.99, 99.33 and 96.11%). On the other hands, obtained data clearly showed that microorganisms living in soil play role in pesticide biodegradation. In other words, the percentages of loss of chlorpyrifos, ethoprophos and carbofuran residues were 86.35, 83.91 and 82.32% in sterilized soils, respectively, at 6 weeks after treat- ments. Obtained data indicated also, the residual values of tested insecticides on or in potato tubers were more than the maximum residue limits (MRL) in all treatments, this means that the tested insecticides have a translocation and accumulating properties in potato tubers.
Growth and nutrition of legumes on a high country yellow-brown earth subsoil

Abstract The phosphate response patterns of tropical and temperate legumes were compared in a glasshouse trial on a high country yellow-brown earth subsoil. Differences in growth and P response patterns could be explained by the known differences in tolerance of Al toxicity. The temperate legumes Lotus pedunculatus and Lupinus polyphyllus appeared to be able to tolerate Al toxicity as well as the torpicallegume Lotononis bainsu and more so than Trifolium semipilosum. However Trifolium repens was less tolerant than T. semipilosum. Of the species studied, Lupinus polyphyllus was the only one capable of reasonable growth where no P was added to the soil. The greater seed reserves of Lupinus appeared to contribute substantially to its greater growth and P uptake under conditions of low P input.
Incidência de infecção por Toxoplasma gondii em cães do município de São Paulo

The incidence of toxoplasmic infection in dogs of Sao Paulo city, evaluated by the indirect immunofluorescent technique was 63,8% [LC (58,6 — 69,0) = 95%]. There were not observed differences estatistically significant between the proportion of reagents when considered the sex, the seasons and the differents section of Sao Paulo city. The more frequent value of anti-toxoplasma antibody title was 64.
The timing of nutritional restriction during reproduction influences staple strength

The staple strength of wool from Merino ewes (liveweight 41 kg; condition score 1.5) was assessed in response to a short-term nutritional restriction at different stages of pregnancy and lactation. Single- and twin-bearing ewes were fed to maintain maternal liveweight (control) or restricted to lose 2 kg in maternal liveweight between Days 85 and 98, 113 and 126, or 141 and 154 of pregnancy, or Days 169 and 182 in early lactation. Unmated control ewes were fed to maintenance, and a group of unmated ewes was restricted between the equivalent of Days 141 and 154 of pregnancy. All groups were maintained in group-feeding pens from Day 8 of pregnancy to 4 weeks after weaning of lambs. The ewes were fed lucerne hay. Control ewes fed to maintain liveweight produced sound wool (unmated 52.7, or single-rearing 46.0, and twin-rearing 43.0 N/ktex). Nutritional restriction only reduced the staple strength of wool produced by unmated ewes by 2.2 N/ktex (P > 0.05), but reduced that of reproducing ewes by 0–26.8 N/ktex. The decline in staple strength of reproducing ewes increased as the time of restriction during pregnancy advanced. Restriction during lactation did not significantly (P > 0.05) influence staple strength. The effect of restriction appeared to be mediated via changes in diameter along fibres. The results indicate that there is variation in the sensitivity of staple strength to short-term nutritional restriction, with both pregnancy status and the stage of pregnancy at which the restriction is imposed influencing the impact on staple strength.