Miracle-dz/UniFAR-FTUs huggingface dataset:
Keratin Immunoreactivity in the Late Cretaceous Bird Rahonavis ostromi.

ABSTRACT Immunohistochemical studies, supported by additional lines of evidence, suggest that original proteinaceous components of keratin claw sheath material may be preserved in the pedal ungual phalanx associated with the primitive bird, Rahonavis ostromi, from the Late Cretaceous of Madagascar. This conclusion is based upon immunohistochemical analyses, and supported by brightfield, transmission, and scanning electron microscopy, mass spectrometry, and x-ray photoelectron spectroscopy. Although keratinous structures such as hair, nails, claws, scales and feathers have been identified in the fossil record, these identifications were based on morphological similarity rather than molecular analyses. Chemical or immunological evidence for the survival of keratin has not previously been established in fossils older than ~33,000 BP. This study demonstrates immunological staining and amino acid composition consistent with the presence of fragments of beta keratin, a protein family unique to reptiles and bird.
Teaching forest operations planning and operations research: An integrated approach to learning

The Forest Engineering program at the University of New Brunswick is the only accredited forest engineering program in Canada, and one of the few in North America. One of the primary learning outcomes of the program includes the ability to design and analyze production systems, especially forest operations. This requires that Forest Engineering students be competent in use of operations research tools and techniques. Experience to date has confirmed that a progressive learning approach that requires students to apply operations research techniques to increasingly complex and realistic problems is essential for achieving these learning outcomes. Key words: forest management, operations design, modelling, learning outcomes, forest engineers, curriculum, wood supply chain, progressive learning, education
Assessing uncertainty of a multispecies size-spectrum model resulting from process and observation errors

Ecosystem models, specifically multispecies dynamic models, have been increasingly used to project impacts of fishing activity on the trophodynamics of ecosystems to support ecosystem-basedfisheriesmanagement.Uncertainty is unavoidable inmodellingprocesses andneeds tobe recognized and properly quantified before models are utilized. Uncertainty was assessed in this study for a multispecies size-spectrum model that quantifies community structure and ecological characteristics. The uncertainty was assumed to result fromerrors in fish life-history andmetabolic scale parameters, environmental variability, fishing variability, and sampling errors. Given the same level of imprecision,metabolic scale parameters had the dominant influence on the uncertainty of the size spectrummodelling results, followed by life-history parameters. Both types of errors led to “scenario uncertainty”, suggesting the possible existence of alternative states of community structure. Environmental variability, fishing variability, and observation errors resulted in “statistical uncertainty”, implying that such uncertainty can be described adequately in statistical terms. The results derived from such a simulation study can provide guidance for identifying research priorities to help narrow the gap in scientific knowledge and reduce the uncertainty in fisheries management.
Density‐dependent accumulation of phase characteristics in a natural population of the desert locust Schistocerca gregaria

Abstract. Phase characteristics of locusts from parents that experienced different population densities were investigated under field conditions in Morocco. The density experienced by adults induced a marked phase change in colour, behaviour and morphometry of their offspring. A high‐density subpopulation gave rise to a preponderance of black hatchlings that exhibited a high level of aggregation as later stage nymphs and showed gregarious morphometric features as adults, whereas a low‐density subpopulation produced a majority of green hatchlings with a lesser tendency to group as final‐instar nymphs and more solitarious morphometry as adults. The constrained isolation of insects from the low‐density subpopulation, or crowding of insects from the high‐density subpopulation, resulted in a behavioural and morphometric change towards even more solitarious characteristics in the former and more pronounced gregarious characteristics in the latter, relative to field‐caught insects of the same age. These results from the field are consistent with those in the laboratory and provide more evidence for the dual roles of an individual locust's experience of crowding as well as that of its parents in density‐dependent phase change.
Strip‐management in rape crop: is winter rape endangered by negative impacts of sown weed strips?

Abstract: With crop rotation as a fundamental element of the IPM and organic production, crop plants and their pests change beside permanent sown weed strips. Rape pests which are known to populate the fields from the edges might be augmented by sown weed strips. To evaluate whether weed strips have a negative impact on rape crop, insect pests and their antagonists were studied in a winter rape field near Berne, Switzerland, divided into two parts by a sown weed strip. They were registered at different distances from the weed strip and from the opposite field boundary in 1993. The pollen beetle Meligethes sp. and the cabbage weevils Ceutorhynchus assimilis Payk. , C. napi Gyll. and C. pallidactylus Marsh and the brassica pod midge Dasineura brassicae Winn. were significantly more frequent near the field boundary than in the middle of the field and close to the sown weed strip. This could be because a sown weed strip does not act as a real field edge. For the investigated rape pods, little difference was observed as to the rate of infestation of C. assimilis. It was astonishing that only a few predators were caught by sweep netting in the whole field as well as close to the weed strip. A higher number of parasitoids near the sown weed strip could not be found either, which was probably due to their high mobility. The low rate of parasitization of the rape pests was only once assessed clearly higher near the weed strip than in the rest of the field. Therefore, flower visiting predators and parasitoids might not have been efficiently increased the weed strip. Generally, no negative impact of the weed strip on rape crop was found and therefore sown weed strips could be suitable areas in a farming with crop rotation to diversity an agroecosystem.
Spatial distribution and temporal dynamics of high-elevation forest stands in southern Siberia.

Aim To evaluate the hypothesis that topographic features of high-elevation mountain environments govern spatial distribution and climate-driven dynamics of the forest. Location Upper mountain forest stands (elevation range 1800–2600 m) in the mountains of southern Siberia. Methods Archive maps, satellite and on-ground data from1960 to 2002 were used. Data were normalized to avoid bias caused by uneven distribution of topographic features (elevation, azimuth and slope steepness) within the analysed area. Spatial distribution of forest stands was analysed with respect to topography based on a digital elevation model (DEM). Results Spatial patterns in mountain forests are anisotropic with respect to azimuth, slope steepness and elevation. At a given elevation, the majority of forests occupied slopes with greater than mean slope values. As the elevation increased, forests shifted to steeper slopes. The orientation of forest azimuth distribution changed clockwise with increase in elevation (the total shift was 120°), indicating a combined effect of wind and water stress on the observed forest patterns. Warming caused changes in the forest distribution patterns during the last four decades. The area of closed forests increased 1.5 times, which was attributed to increased stand density and tree migration. The migration rate was 1.5 ± 0.9 m year–1, causing a mean forest line shift of 63 ± 37 m. Along with upward migration, downward tree migration onto hill slopes was observed. Changes in tree morphology were also noted as widespread transformation of the prostrate forms of Siberian pine and larch into erect forms. Main conclusions The spatial pattern of upper mountain forests as well as the response of forests to warming strongly depends on topographic relief features (elevation, azimuth and slope steepness). With elevation increase (and thus a harsher environment) forests shifted to steep wind-protected slopes. A considerable increase in the stand area and increased elevation of the upper forest line was observed coincident with the climate warming that was observed. Warming promotes migration of trees to areas that are less protected from winter desiccation and snow abrasion (i.e. areas with lower values of slope steepness). Climate-induced forest response has significantly modified the spatial patterns of high-elevation forests in southern Siberia during the last four decades, as well as tree morphology.
Clinicopathological correlation in fungal keratitis and a possible evidence of opportunistic infection: a report of two cases

The authors describe two cases of fungal keratitis which, upon histopathological examination, are found to have in common the absence of epithelium, without ulceration and the lack of integrity of the Bowman's layer with the presence of fungal forms in their interior. Through them the authors suggest probable mechanisms of recurrence of fungal keratitis, highlighting the possible existence of an "unusual external route" that would occur by the fungus penetration through the full Bowman layer. Although these findings appear not yet reported or recovered in the ophthalmic literature, the authors suggest that they could be possible opportunistic infection signals which, however, require more evidence to be considered as such.
Plasmid pMOL28-encoded resistance to nickel is due to specific efflux

Two strains of the strictly respiratory bacterium Alcaligenes eutrophus were used to study the kinetics of 63Ni2+ uptake and efflux: the wild type strain N9A and its transconjugant N9A-M243, which harbors plasmid pMOL28.1 encoding constitutive resistance to nickel. When incubated aerobically in 1 μM NiCl2 N9A accumulates high, M243 negligibly small amounts of nickel. When exposed to 1 μM NiCl2 anaerobically, after preincubation at anoxic conditions for 24 h, both strains accumulate almost the same amounts. Aeration results in instantaneous, rapid efflux by M243, but renewed uptake of nickel by N9A. The results suggest that in M243 under normal aerobic conditions two constitutive energy-dependent cation transport systems are functioning concomitantly; a chromosomally determined nickel uptake system and a plasmid-mediated nickel efflux system.
Genetic structure of Japanese Chattonella marina (Raphidophyceae) populations revealed using microsatellite markers

Chattonella marina var. antiqua and C. marina var. marina (Raphidophyceae) are red tide‐forming, harmful phytoplankton species. We investigated the genetic diversity and genetic relationship among the populations using microsatellite markers to identify putative sources of C. marina var. antiqua and C. marina var. marina in Japanese coastal populations. A positive correlation between genetic divergence and geographical distance (isolation by distance) was recognized for C. marina var. antiqua. The C. marina var. antiqua populations were established throughout a geological time scale, and genetic divergence had progressed in each population with gene flow depending on geographic distances. In contrast, isolation by distance was not observed for C. marina var. marina populations, and the genetic divergence among populations was extremely high. The Tokyo Bay population of C. marina var. marina, which was first recognized in 2008, had many private alleles but was related to the Kagoshima Bay population. The Tokyo Bay population may have been established by several invasions from the Kagoshima Bay population and other regions.
COLOR DEVELOPMENT DURING NATURAL FERMENTATION AND CHEMICAL ACIDIFICATION OF SALAMI-TYPE PRODUCTS

The impact of using natural fermentation with lactic acid bacteria (LAB), chemical acidification with liquid lactic acid, and encapsulated citric, gluconic or lactic acid were evaluated in raw and cooked salami-type products. Liquid lactic acid resulted in an immediate pH drop and significant increase in L*(lightness) and a*(redness) values, as well as clumping of the ground meat particles that exhibited moisture release due to excessive protein denaturation. Overnight LAB fermentation also resulted in increased L*and a*values, but unlike direct acid addition, did not cause moisture loss or clumping. Spectra data, collected after both treatments reached pH 4.6, revealed pretty similar curve shape, with higher values for the fermented product at 420–550 nm and 610–670 nm. The encapsulated acids, designed to release acid at about 62C, did not affect the color of the raw meat batters. Cooking of all treatments resulted in higher L*and a*values, both by about 50%. L*and a*values were pretty similar for all the acidified and non-acidified control. The only exception was a no-nitrite control, which showed a significantly (P < 0.05) lower a*value. PRACTICAL APPLICATIONS The use of different acidification methods to lower the pH of meat products (bacteria fermentation, direct acid addition, encapsulated acid) does affect the color of the product. When going through the process, care should be given to the rate of acidification. A slow acid production (fermentation) or acid release when the meat proteins have started to go through heat coagulation (by using acid encapsulated in hydrogenated vegetable oil) are recommended. Direct acid addition results in immediate lightening of the product as well as crumbling of the ground meat particles, which later negatively affect color and texture of the product.
From Systems Biology to Gene Function: Discovering New Determinants of Plant Tolerance to Abiotic Stresses

Guaranteeing food security in an era of rising world population, global climate change, and pressure to use land situated in harsh environments for agriculture, is an increasing challenge. In the drive for improved crop performance, efforts have focused on identifying genes controlling many traits including greater tolerance to biotic and abiotic stresses. However, several problems in identifying new candidate genes can be distinguished. Classic forward and reverse genetic screens of plant mutants require the screening of up to hundreds of thousands of plants, yet the return is very low – typically <1%–3% of the mutant population display a desired phenotype [1-8]. Although computational methods have shown potential in identifying sets of candidate genes, very few studies have actually tested their predictions on mutant populations. Moreover, most of those studies that have screened mutants defective in candidate genes, have only screened a few mutants, making it difficult to robustly assess gene discovery rate [9-13].
Home range and activity patterns of red foxes in nadgee nature reserve

Three adult red foxes (Vulpes vulpes) in a 20-km2 wilderness area of coastal south-eastern Australia were studied during pre-denning and denning. Home ranges were defined by geographic featues, but not by roads. The foxes occupied exclusive home ranges, and observations suggest that they were territorial and existed alone or, at most, in mated pairs. Home-range sizes were small (1.2-5.2 km2) compared with those in North America and Europe, but similar to those in England and Wales. During denning the female's activity became almost entirely diurnal. When not active, the vixen was with the cubs. Male activity during denning was nocturnal, but, as found for the female, inactive periods were spent near the suspected den-site in his home range. Habitats that were frequented most by all foxes were those with the highest abundance of either small or medium-sized mammals. Dry sclerophyll forest was used consistently by all foxes but heathland and the beaches were rarely frequented. Small and medium-sized mammals, which were abundant in all habitats except the beach and heathland, made up 52.6% of items in the scats.
On the evolutionary co-adaptation of morphology and distributed neural controllers in adaptive agents

Mariagiovanna Mazzapioda On the Evolutionary Co-Adaptation of Morphology and Distributed Neural Controllers in Adaptive Agents The attempt to evolve complete embodied and situated artificial creatures in which both morphological and control characteristics are adapted during the evolutionary process has been and still represents a long term goal key for the artificial life and the evolutionary robotics community. Loosely inspired by ancient biological organisms which are not provided with a central nervous system and by simple organisms such as stick insects, this thesis proposes a new genotype encoding which allows development and evolution of morphology and neural controller in artificial agents provided with a distributed neural network. In order to understand if this kind of network is appropriate for the evolution of non trivial behaviours in artificial agents, two experiments (description and results will be shown in chapter 3) in which evolution was applied only to the controller’s parameters were performed. The results obtained in the first experiment demonstrated how distributed neural networks can achieve a good level of organization by synchronizing the output of oscillatory elements exploiting acceleration/deceleration mechanisms based on local interactions. 9 In the second experiment few variants on the topology of neural architecture were introduced. Results showed how this new control system was able to coordinate the legs of a simulated hexapod robot on two different gaits on the basis of the external circumstances. After this preliminary and successful investigation, a new genotype encoding able to develop and evolve artificial agents with no fixed morphology and with a distributed neural controller was proposed. A second set of experiments was thus performed and the results obtained confirmed both the effectiveness of genotype encoding and the ability of distributed neural network to perform the given task. The results have also shown the strength of genotype both in generating a wide range of different morphological structures and in favouring a direct co-adaptation between neural controller and morphology during the evolutionary process. Furthermore the simplicity of the proposed model has showed the effective role of specific elements in evolutionary experiments. In particular it has demonstrated the importance of the environment and its complexity in evolving non-trivial behaviours and also how adding an independent component to the fitness function could help the evolutionary process exploring a larger space solutions avoiding a premature convergence towards suboptimal solutions.
Hemoglobinopathies in Children within a Malaria Holoendemic Region of Western Kenya

Plasmodium falciparum malaria is one of the predominant causes of morbidity and mortality in children under five years of age in sub-Saharan Africa. In malaria endemic regions, the intensity of transmission and the age at which malaria is first acquired are important in conditioning disease outcomes. In addition, inter-individual variability in disease severity among age-matched children (aged <3 yrs) with similar levels of parasite exposure is largely determined by genetic variability. Historical exposure to malaria in endemic populations has exerted tremendous selective pressure on the human genome, particularly in the host-immune response genes that mediate susceptibility and clinical outcomes. Hemoglobinopathies, such as the alpha thalassemia 3.7 kb deletion and sickle-cell trait (HbAS) also confer protection against severe malaria through a mechanism(s) that are yet to be fully elucidated. As such, this study examined the role of alpha thalassemia 3.7 kb deletion and HbAS in protection against severe malaria anemia (SMA) in children (n=468; aged 3-36 months) residing in a holoendemic P. falciparum transmission region of western Kenya. These investigations demonstrated that successful genotyping of the deletion required high-quality genomic DNA from large volumes of whole blood that was unavailable for most of the small, underweight-for-age, severely anemic children in which DNA was isolated from dried blood spots. Results presented here further demonstrated that the HbAS genotype was significantly associated with a reduced burden of both low (<10%; P=0.03) and high (greater than or equal to 10%; P<0.001) pigment-containing monocytes (PCM). In addition, hemoglobin (Hb; P=0.05) and red blood cell (RBC; P=0.04) counts were significantly higher in the HbAS group relative to children with the HbAA genotype. The HbAS genotype was also significantly associated with protection against SMA using both the World Health Organization (i.e., <5.0 g/dL; P=0.04) and modified definitions of SMA (i.e., <6.0 g/dL; P=0.02). Taken together, results presented here suggest that the HbAS genotype confers protection against SMA by reducing the natural acquisition of malarial pigment (hemozoin) in monocytes. This study has significant public health importance by demonstrating that one of the mechanisms by which HbAS provides protection against SMA is through reducing the overall burden of hemozoin in monocytes.