Search

Abstract Background The functional and metabolic properties of skeletal muscles are partly a function of the spatial arrangement of fibers across the muscle belly. Many muscles feature a non-uniform spatial pattern of fiber types, and alterations to the arrangement can reflect age or disease and correlate with changes in muscle mass and strength. Despite the significance of this event, descriptions of spatial fiber-type distributions across a muscle section are mainly provided qualitatively, by eye. Whilst several quantitative methods have been proposed, difficulties in implementation have meant that robust statistical analysis of fiber type distributions has not yielded new insight into the biological processes that drive the age- or disease-related changes in fiber type distributions. Methods We review currently available approaches for analysis of data reporting fast/slow fiber type distributions on muscle sections before proposing a new method based on a generalized additive model. We compare current approaches with our new method by analysis of sections of three mouse soleus muscles that exhibit visibly different spatial fiber patterns, and we also apply our model to a dataset representing the fiber type proportions and distributions of the mouse tibialis anterior. Results We highlight how current methods can lead to differing interpretations when applied to the same dataset and demonstrate how our new method is the first to permit location-based estimation of fiber-type probabilities, in turn enabling useful graphical representation. Conclusions We present an open-access online application that implements current methods as well as our new method and which aids the interpretation of a variety of statistical tools for the spatial analysis of muscle fiber distributions.

Background: Strawberry is a fruit with a high antioxidant capacity due to its richness in phenolic compounds that suffer a rapid post-harvest deterioration. Spray drying is an alternative to reduce losses; however, these powders present problems of instantanisation, making it necessary to implement agglomeration processes. During storage, powdered food products can undergo a series of changes in their amorphous state from a product initially in a vitreous state to a gummy state, where all properties are substantially modified due to the increased mobility of water in the matrix. Methods: The research objective was to evaluate the storage stability (6 months) of a fluidized bed agglomerated strawberry powder mixture at three temperatures (15, 25 and 25°C), a controlled environment at 65% relative moisture, and PET foil laminated film bags as packaging. Moisture, water activity, bulk and compacted density, Carr and Hausner indices, solubility, hygroscopicity, wettability, angle of repose, antioxidant capacities, total phenols, anthocyanins, vitamin C, color (CIE-Lab) and particle size were monitored. Results: ANOVA showed statistically significant differences (p0.05) on S, ABTS, DPPH, Hu and L. The agglomerate showed moisture and aw values that confer excellent stability against deterioration reactions; it retained good fluidity, low cohesiveness, and retentions above 50% for antioxidant capacity, 76% for total phenols, 39% for anthocyanins, and 40% for vitamin C; particle size was retained during the evaluation. The color was only affected in the 35°C treatment from the fifth month onwards. Conclusions: The study will serve as a tool for the determination of the shelf life of the chipboard once the critical values of the attributes selected as predictors of shelf life are defined.

The present study investigates the impact of water level regulation on the growth of common reed (Phragmites australis), a globally widespread helophytic plant. The investigation has been carried out in the Bolle di Magadino (municipalities of Locarno, Gambarogno, Gordola and Tenero; Ticino, Switzerland), a lacustrine-riparian nature reserve in the context of the Lake Maggiore (that stretches between Italy and Switzerland). This is an oligotrophic, artificially regulated lake. Our initial hypothesis was that variation in water table regulation is the most influential factor for explaining observed local reed dieback. To test this, culm height of P. australis was measured at each significant change in lake water level (water table height increase greater than 20 cm), or monthly in the case of a relatively constant lake level. The study took place between 2020 and 2022, monitoring 14 plots of 400 m2, placed at three different relative elevation classes with respect to the level of the lake (5 plots at low elevation, 193.701 m). The results showed that P. australis growth is significantly influenced by the lake water level and thus the relative elevation of the stands, with lower lake levels leading to better growth, especially during the early phases of the growing season. On the other hand, prolonged flooding of shoots significantly impaired common reed growth. The study identifies two relevant relative elevation thresholds for winter mowing, a management practice that enhances reedbeds health. Mowing below 193.20 m elevation is considered risky, as no healthy reedbeds have been observed below this threshold. Mowing below an elevation of 193.50 m was defined as possibly risky, due to observed dieback in some areas as well as healthy reedbeds in other locations at the same or lower elevations. The research also discussed the potential impact of future changes in water level regulation, including the planned change in the spring regulation threshold (+1.50 m above the hydrometric zero in Sesto Calende). This is expected to result in a further rearrangement in lacustrine vegetation, with the growth optimum for P. australis becoming higher and an increase in clumping habit. In conclusion, this study provides valuable insights into the impact of water level regulation on the growth of P. australis in the Bolle di Magadino nature reserve. The research highlights the need for careful management of water level regulation to preserve the reedbed ecosystem and identifies relevant elevation thresholds for winter mowing to mitigate the risks of reed dieback. The findings can inform future management strategies for the Bolle di Magadino reserve and other similar ecosystems facing the challenges of artificial regulation of water levels.

Background: Strawberry is a fruit with a high antioxidant capacity due to its richness in phenolic compounds that suffer a rapid post-harvest deterioration. Spray drying is an alternative to reduce losses; however, these powders present problems of instantanisation, making it necessary to implement agglomeration processes. During storage, powdered food products can undergo a series of changes in their amorphous state from a product initially in a vitreous state to a gummy state, where all properties are substantially modified due to the increased mobility of water in the matrix. Methods: The research objective was to evaluate the storage stability (6 months) of a fluidized bed agglomerated strawberry powder mixture at three temperatures (15, 25 and 25°C), a controlled environment at 65% relative moisture, and PET foil laminated film bags as packaging. Moisture, water activity, bulk and compacted density, Carr and Hausner indices, solubility, hygroscopicity, wettability, angle of repose, antioxidant capacities, total phenols, anthocyanins, vitamin C, color (CIE-Lab) and particle size were monitored. Results: ANOVA showed statistically significant differences (p0.05) on S, ABTS, DPPH, Hu and L. The agglomerate showed moisture and aw values that confer excellent stability against deterioration reactions; it retained good fluidity, low cohesiveness, and retentions above 50% for antioxidant capacity, 76% for total phenols, 39% for anthocyanins, and 40% for vitamin C; particle size was retained during the evaluation. The color was only affected in the 35°C treatment from the fifth month onwards. Conclusions: The study will serve as a tool for the determination of the shelf life of the chipboard once the critical values of the attributes selected as predictors of shelf life are defined.

ABSTRACT Staphylococcus aureus is a Gram-positive commensal and opportunistic pathogen able to cause diseases ranging from mild skin infections to life-threatening endocarditis and toxic shock syndrome. The ability to cause such an array of diseases is due to the complex S. aureus regulatory network controlling an assortment of virulence factors, including adhesins, hemolysins, proteases, and lipases. This regulatory network is controlled by both protein and RNA elements. We previously identified a novel regulatory protein called ScrA, which, when overexpressed, leads to the increased activity and expression of the SaeRS regulon. In this study, we further explore the role of ScrA and examine the consequences to the bacterial cell of scrA gene disruption. These results demonstrate that scrA is required for several virulence-related processes, and in many cases, the phenotypes of the scrA mutant are inverse to those observed in cells overexpressing ScrA. Interestingly, while the majority of ScrA-mediated phenotypes appear to rely on the SaeRS system, our results also indicate that ScrA may also act independently of SaeRS when regulating hemolytic activity. Finally, using a murine model of infection, we demonstrate that scrA is required for virulence, potentially in an organ-specific manner. IMPORTANCE Staphylococcus aureus is the cause of several potentially life-threatening infections. An assortment of toxins and virulence factors allows such a wide range of infections. However, an assortment of toxins or virulence factors requires complex regulation to control expression under all of the different conditions encountered by the bacterium. Understanding the intricate web of regulatory systems allows the development of novel approaches to combat S. aureus infections. Here, we have shown that the small protein ScrA, which was previously identified by our laboratory, influences several virulence-related functions through the SaeRS global regulatory system. These findings add ScrA to the growing list of virulence regulators in S. aureus.

Background: The functional and metabolic properties of skeletal muscles are partly a function of the spatial arrangement of fibers across the muscle belly. Many muscles feature a non-uniform spatial pattern of fiber types, and alterations to the arrangement can reflect age or disease and correlate with changes in muscle mass and strength. Despite the significance of this event, descriptions of spatial fiber-type distributions across a muscle section are mainly provided qualitatively, by eye. Whilst several quantitative methods have been proposed, difficulties in implementation have meant that robust statistical analysis of fiber type distributions has not yielded new insight into the biological processes that drive the age- or disease-related changes in fiber type distributions. Methods: We review currently available approaches for analysis of data reporting fast/slow fiber type distributions on muscle sections before proposing a new method based on a generalized additive model. We compare current approaches with our new method by analysis of sections of three mouse soleus muscles that exhibit visibly different spatial fiber patterns, and we also apply our model to a dataset representing the fiber type proportions and distributions of the mouse tibialis anterior. Results: We highlight how current methods can lead to differing interpretations when applied to the same dataset and demonstrate how our new method is the first to permit location-based estimation of fiber-type probabilities, in turn enabling useful graphical representation. Conclusions: We present an open-access online application that implements current methods as well as our new method and which aids the interpretation of a variety of statistical tools for the spatial analysis of muscle fiber distributions. [ABSTRACT FROM AUTHOR]

Abstract Background Cerebral malaria (CM) is a preeminent cause of severe disease and premature deaths in Sub-Saharan Africa, where an estimated 90% of cases occur. The key features of CM are a deep, unarousable coma that persists for longer than 1 h in patients with peripheral Plasmodium falciparum and no other explanation for encephalopathy. Significant research efforts on CM in the last few decades have focused on unravelling the molecular underpinnings of the disease pathogenesis and the identification of potential targets for therapeutic or pharmacologic intervention. These efforts have been greatly aided by the generation and study of mouse models of CM, which have provided great insights into key events of CM pathogenesis, revealed an interesting interplay of host versus parasite factors that determine the progression of malaria to severe disease and exposed possible targets for therapeutic intervention in severe disease. Main Body This paper reviews our current understanding of the pathogenic and immunologic factors involved in CM. We present the current view of the roles of certain gene products e.g., the var gene, ABCA-1, ICAM-1, TNF-alpha, CD-36, PfEMP-1 and G6PD, in CM pathogenesis. We also present alterations in the blood–brain barrier as a consequence of disease proliferation as well as complicated host and parasite interactions, including the T-cell immune reaction, reduced deformation of erythrocytes and cytoadherence. We further looked at recent advances in cerebral malaria treatment interventions by emphasizing on biomarkers, new diagnostic tools and emerging therapeutic options. Conclusion Finally, we discuss how the current understanding of some of these pathogenic and immunologic factors could inform the development of novel therapeutic interventions to fight CM.

Background: Cerebral malaria (CM) is a preeminent cause of severe disease and premature deaths in Sub-Saharan Africa, where an estimated 90% of cases occur. The key features of CM are a deep, unarousable coma that persists for longer than 1 h in patients with peripheral Plasmodium falciparum and no other explanation for encephalopathy. Significant research efforts on CM in the last few decades have focused on unravelling the molecular underpinnings of the disease pathogenesis and the identification of potential targets for therapeutic or pharmacologic intervention. These efforts have been greatly aided by the generation and study of mouse models of CM, which have provided great insights into key events of CM pathogenesis, revealed an interesting interplay of host versus parasite factors that determine the progression of malaria to severe disease and exposed possible targets for therapeutic intervention in severe disease. Main Body: This paper reviews our current understanding of the pathogenic and immunologic factors involved in CM. We present the current view of the roles of certain gene products e.g., the var gene, ABCA-1, ICAM-1, TNF-alpha, CD-36, PfEMP-1 and G6PD, in CM pathogenesis. We also present alterations in the blood–brain barrier as a consequence of disease proliferation as well as complicated host and parasite interactions, including the T-cell immune reaction, reduced deformation of erythrocytes and cytoadherence. We further looked at recent advances in cerebral malaria treatment interventions by emphasizing on biomarkers, new diagnostic tools and emerging therapeutic options. Conclusion: Finally, we discuss how the current understanding of some of these pathogenic and immunologic factors could inform the development of novel therapeutic interventions to fight CM. [ABSTRACT FROM AUTHOR]

Abstract Multicellular organisms appeared on Earth through several independent major evolutionary transitions. Are such transitions reversible? Addressing this fundamental question entails understanding the benefits and costs of multicellularity versus unicellularity. For example, some wild yeast strains form multicellular clumps, which might be beneficial in stressful conditions, but this has been untested. Here, we show that unicellular yeast evolve from clump‐forming ancestors by propagating samples from suspension after larger clumps have settled. Unicellular yeast strains differed from their clumping ancestors mainly by mutations in the AMN1 (Antagonist of Mitotic exit Network) gene. Ancestral yeast clumps were more resistant to freeze/thaw, hydrogen peroxide, and ethanol stressors than their unicellular counterparts, but they grew slower without stress. These findings suggest disadvantages and benefits to multicellularity and unicellularity that may have impacted the emergence of multicellular life forms.

Multicellular organisms appeared on Earth through several independent major evolutionary transitions. Are such transitions reversible? Addressing this fundamental question entails understanding the benefits and costs of multicellularity versus unicellularity. For example, some wild yeast strains form multicellular clumps, which might be beneficial in stressful conditions, but this has been untested. Here, we show that unicellular yeast evolve from clump‐forming ancestors by propagating samples from suspension after larger clumps have settled. Unicellular yeast strains differed from their clumping ancestors mainly by mutations in the AMN1 (Antagonist of Mitotic exit Network) gene. Ancestral yeast clumps were more resistant to freeze/thaw, hydrogen peroxide, and ethanol stressors than their unicellular counterparts, but they grew slower without stress. These findings suggest disadvantages and benefits to multicellularity and unicellularity that may have impacted the emergence of multicellular life forms. [ABSTRACT FROM AUTHOR]

Characterisation of the wettability of five poor wetting food powders was performed using static immersion and contact angle measurements. The effect of temperature (20, 50 and 70 °C) on wettability showed varying effects on the powders. Higher temperatures majorly improved the wettability of chocolate and high fat powders but worsened the wettability of sodium caseinate and milk protein isolate. Rate-limiting regime testing was performed by pouring a fixed mass of powder on to the surface of water in an agitated beaker and visually assessing what was rate-limiting rehydration after 1 minute. The rate limiting regime tended to be floating at lower agitation speeds and dispersed clumps of varying sizes at higher speeds. However, there were major differences observed between the powders. Some of the powders formed strong films at powder/water interfaces, that could act as a barrier to water penetration and wettability. Consequently, force displacement testing was performed on a layer of powder on the water surface to assess the strength of any powder film formed. Some of the powders formed strong films that may in-part explain their poor wetting behaviour and their propensity to form strong clumps that were difficult to disrupt.

Background: Cirrhinus mrigala, one of the important fish widely consumed in India, was used for karyological observations and to evaluate the toxic effect of butachlor, an extensively used herbicide in rice fields in terms of chromosomal aberration test. Methods: Fishes were collected from “National Fish Seed Farm” Jyotisar with mean body weight of 20-50g. The experimental fishes were kept in two treatments each with replicate of two. There were 15 fish each in the control group (T1) without exposure to butachlor and in T2 where fishes were exposed to butachlor. Results: Karyotype revealed the 2n=50 chromosome from the somatic cell. Chromosomal aberrations were reported after 24 hrs, 48 hrs, 72 hrs, and 96 hrs from kidney cell preparation in fishes exposed to 1.0 ppm, sublethal concentration of butachlor. Frequencies of chromosomal aberration revealed a significant (P

The airborne laser scanner (ALS) provides great potential for mapping the leaf area index (LAI) at the landscape scale using grid cell statistics, while its application is restricted by the lack of clumping information, which has been an unsolved issue highlighted for a long time. ALS generally provides an effective LAI because its footprint is too large to capture small gaps to apply traditional ground-based clumping correction methods. Here, we present a grid cell method based on path length distribution model to calculate the clumping-corrected LAI using ALS data without the requirement of additional field measurements. We separated the within- and between-crown areas to consider between-crown clumping, and used the path length distribution as estimated by local canopy height distribution to consider 3-D foliage profile and within-crown clumping. The path length distribution model takes advantage of the 3-D information rather than the gap size distribution, thus avoiding the limitation of large ALS footprint. With the 0.4-m-footprint ALS data, the results are generally promising and a multilevel clumping analysis is consistent with landscape flown. The ALS LAIs of different resolutions are consistent, with a difference of less than 5% from 5- to 250-m resolutions. Due to its consistency and simple configuration, the method provides an opportunity to map the clumping-corrected LAI operationally and strengthens the ability of airborne lidar to monitor vegetation change and validate the satellite product. This grid cell method based on path length distribution is worth further testing and application using more recent laser technology. [ABSTRACT FROM AUTHOR]

Significant progress has been made in the development of cover data and derived products based on remotely sensed fractional cover information and field data across Australia, and these cover data sets are now used for quantifying and monitoring grazing land condition. The availability of a dense time-series of nearly 30 years of cover data to describe the spatial and temporal patterns in landscape changes over time can help with monitoring the effectiveness of grazing land management practice change. With the advent of higher spatial resolution data, such as that provided by the Copernicus Sentinel 2 series of satellites, we can look beyond reporting purely on cover amount and more closely at the operational monitoring and reporting on spatial arrangement of cover and its links with land condition. We collected high spatial resolution cover transects at 20 cm intervals over the Wambiana grazing trials in the Burdekin catchment in Queensland, Australia. Spatial variance analysis was used to determine the cover autocorrelation at various support intervals. Coincident Sentinel-2 imagery was collected and processed over all the sites providing imagery to link with the field data. We show that the spatial arrangement and temporal dynamics of cover are important indicators of grazing land condition for both productivity and water quality outcomes. The metrics and products derived from this research will assist land managers to prioritize investment and practice change strategies for long term sustainability and improved water quality, particularly in the Great Barrier Reef catchments. [ABSTRACT FROM AUTHOR]

The objective of the present study was to determine the best concentration of urea solution and rinsing time to remove adhesiveness of African catfish eggs. Four different concentrations of rinse solution were used in this experiment comprising of 2 g, 4 g, 6 g and 8 g of urea diluted in 4 g NaCl/L of water producing a concentration of 0.486 mM, 0.973 mM, 1.458 mM, and 1.946 mM of urea concentration respectively, while 4 g NaCl/L of water without urea were used as control. The fish eggs were rinsed with the solutions at different durations namely; 1, 5 and 10 minutes. Each rinsing solution concentration and rinsing time were conducted in three replicates. The fertilization and hatching rates increased and peaked from the control (0 mM of urea) to 0.466 mN urea and decreased when concentration of urea was increased to 0.973 mM urea and 1.458 mM urea, then increased again at 1.946 mM urea, but these values were lower than at 0.486 mM urea. Thus, the best concentration for fertilization and hatching rates were 0.486 urea of urea. However 0.973 mM of urea was optimum in reducing clumping of eggs.

Brucella spp. are Gram-negative, facultative intracellular bacteria that cause brucellosis in mammals. Brucella strains containing the O-polysaccharide in their cell wall structure exhibit a smooth phenotype whereas the strains devoid of the polysaccharide show rough phenotype. B. abortus strain RB51 is a stable rough attenuated mutant which is used as a licensed live vaccine for bovine brucellosis. Previous studies have shown that the wboA gene, which encodes a glycosyltransferase required for the synthesis of O-polysaccharide, is disrupted in B. abortus RB51 by an IS711 element. Although complementation of strain RB51 with a functional wboA gene results in O-polysaccharide synthesis in the cytoplasm, it does not result in smooth phenotype. The aim of this study was to determine if overexpression of Brucella WbkA or WbkE, two additional putative glycosyltransferases essential for O-polysaccharide synthesis, in strain RB51 would result in the O-polysaccharide synthesis and smooth phenotype. Our results demonstrate that overexpression of wbkA or wbkE gene in RB51 does not result in O-polysaccharide expression as shown by Western blotting with specific antibodies. However, wbkA, but not wbkE, overexpression leads to the development of a clumping phenotype and the production of exopolysaccharide(s) containing mannose, galactose, N-acetylglucosamine and N-acetylgalactosamine. Moreover, we found that the clumping recombinant strain displays increased adhesion to polystyrene plates. The recombinant strain was similar to strain RB51 in its attenuation characteristic and in its ability to induce protective immunity against virulent B. abortus challenge in mice.

Humans and animals are colonized by members of the genus Staphylococcus , however only some of these species evolved to cause invasive disease. The genetic basis for conversion of commensal staphylococci into pathogens is not known. We hypothesized that Staphylococcus aureus genes for coagulation and agglutination in vertebrate blood ( coa , vwb and clfA ) may support pathogenic conversion. Expression of coa and vwb in Staphylococcus epidermidis or Staphylococcus simulans supported a coagulase-positive phenotype but not the ability to cause disease in a mouse model of bloodstream infection. However, the simultaneous expression of coa , vwb and clfA in coagulase-negative staphylococci enabled bacterial agglutination in plasma and enhanced survival of S. simulans in human whole blood. Agglutination of S. simulans in the bloodstream of infected mice upon expression of coa , vwb and clfA provided also a mean for dissemination and replication in distal organs. Thus, the acquisition of genes for bacterial agglutination with fibrin appear sufficient for the conversion of commensal staphylococci into invasive pathogens. [ABSTRACT FROM AUTHOR]

Characterisation of the wettability of five poor wetting food powders was performed using static immersion and contact angle measurements. The effect of temperature (20, 50 and 70 °C) on wettability showed varying effects on the powders. Higher temperatures majorly improved the wettability of chocolate and high fat powders but worsened the wettability of sodium caseinate and milk protein isolate. Rate-limiting regime testing was performed by pouring a fixed mass of powder on to the surface of water in an agitated beaker and visually assessing what was rate-limiting rehydration after 1 minute. The rate limiting regime tended to be floating at lower agitation speeds and dispersed clumps of varying sizes at higher speeds. However, there were major differences observed between the powders. Some of the powders formed strong films at powder/water interfaces, that could act as a barrier to water penetration and wettability. Consequently, force displacement testing was performed on a layer of powder on the water surface to assess the strength of any powder film formed. Some of the powders formed strong films that may in-part explain their poor wetting behaviour and their propensity to form strong clumps that were difficult to disrupt. [ABSTRACT FROM AUTHOR]

Spatial heterogeneity within canopies and woody components are two factors that limit the accuracy of indirect leaf area index (LAI) measurements, but they have not been fully considered because of the limitations of commercial instruments. This study combined the path length distribution model and multispectral canopy imager for the first time to improve the accuracy of indirect LAI measurements. Indirect and direct in situ measurements were conducted in broadleaf and coniferous forests. Results show that spatial heterogeneity within canopies underestimates the LAI by 16–25%, whereas woody components overestimate LAI by 14–28% in four forest sites. These two factors exhibit opposing effects, which may be misleading and may thus complicate the quantification and validation of the effect of each factor. Ignoring woody components underestimates the degree of spatial heterogeneity or clumping in forests. Considering both nonrandomness within canopies and woody components is necessary in indirect LAI measurements. [ABSTRACT FROM PUBLISHER]

Brucella spp. are Gram-negative, facultative intracellular bacteria that cause brucellosis in mammals. Brucella strains containing the O-polysaccharide in their cell wall structure exhibit a smooth phenotype whereas the strains devoid of the polysaccharide show rough phenotype. B. abortus strain RB51 is a stable rough attenuated mutant which is used as a licensed live vaccine for bovine brucellosis. Previous studies have shown that the wboA gene, which encodes a glycosyltransferase required for the synthesis of O-polysaccharide, is disrupted in B. abortus RB51 by an IS711 element. Although complementation of strain RB51 with a functional wboA gene results in Opolysaccharide synthesis in the cytoplasm, it does not result in smooth phenotype. The aim of this study was to determine if overexpression of Brucella WbkA or WbkE, two additional putative glycosyltransferases essential for O-polysaccharide synthesis, in strain RB51 would result in the O-polysaccharide synthesis and smooth phenotype. Our results demonstrate that overexpression of wbkA or wbkE gene in RB51 does not result in Opolysaccharide expression as shown by Western blotting with specific antibodies. However, wbkA, but not wbkE, overexpression leads to the development of a clumping phenotype and the production of exopolysaccharide(s) containing mannose, galactose, N-acetylglucosamine, and N-acetylgalactosamine. Moreover, we found that the clumping recombinant strain displays increased adhesion to polystyrene plates. The recombinant strain was similar to strain RB51 in its attenuation characteristic and in its ability to induce protective immunity against virulent B. abortus challenge in mice. [ABSTRACT FROM AUTHOR]

Fire is an indissoluble component of ecosystems, however quantifying the effects of fire on vegetation is a challenging task as fire lies outside the typical experimental design attributes. A recent simulation study showed that under increased fire regimes positive tree–tree interactions were recorded (Bacelar et al., 2014). Data from experimental burning plots in an African savanna, the Kruger National Park, were collected across unburnt and annual burn plots. Indices of aggregation and spatial autocorrelation of the distribution of trees between different fire regimes were explored. Results show that the distribution of trees under fire were more clumped and exhibited higher spatial autocorrelation than in unburnt plots. In burnt plots spatial autocorrelation values were positive at finer scales and negative at coarser scales potentially indicating co-existence of facilitation and competition within the same ecosystem depending on the scale. The pattern derived here provides inference for (a) fire acting as an increasing aggregation & spatial autocorrelation force, (b) tree survival under fire regimes is potentially facilitated by forming patches of trees and (c) scale-dependent facilitation and competition coexisting within the same ecosystem with finer scale facilitation and coarser scale competition. [ABSTRACT FROM AUTHOR]

Copyright of African Population Studies is the property of Union for African Population Studies and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Background and Aims Proper characterization of the clumped structure of forests is needed for calculation of the absorbed radiation and photosynthetic production by a canopy. This study examined the dependency of crown-level clumping on tree size and growth conditions in Scots pine (Pinus sylvestris), and determined the ability of statistical canopy radiation models to quantify the degree of self-shading within crowns as a result of the clumping effect. Methods Twelve 3-D Scots pine trees were generated using an application of the LIGNUM model, and the crown-level clumping as quantified by the crown silhouette to total needle area ratio (STARcrown) was calculated. The results were compared with those produced by the stochastic approach of modelling tree crowns as geometric shapes filled with a random medium. Key Results Crown clumping was independent of tree height, needle area and growth conditions. The results supported the capability of the stochastic approach in characterizing clumping in crowns given that the outer shell of the tree crown is well represented. Conclusions Variation in the whole-stand clumping index is induced by differences in the spatial pattern of trees as a function of, for example, stand age rather than by changes in the degree of self-shading within individual crowns as they grow bigger. [ABSTRACT FROM AUTHOR]

Negative density dependence ( NDD) of recruitment is pervasive in tropical tree species. We tested the hypotheses that seed dispersal is NDD, due to intraspecific competition for dispersers, and that this contributes to NDD of recruitment. We compared dispersal in the palm Attalea butyracea across a wide range of population density on Barro Colorado Island in Panama and assessed its consequences for seed distributions. We found that frugivore visitation, seed removal and dispersal distance all declined with population density of A. butyracea, demonstrating NDD of seed dispersal due to competition for dispersers. Furthermore, as population density increased, the distances of seeds from the nearest adult decreased, conspecific seed crowding increased and seedling recruitment success decreased, all patterns expected under poorer dispersal. Unexpectedly, however, our analyses showed that NDD of dispersal did not contribute substantially to these changes in the quality of the seed distribution; patterns with population density were dominated by effects due solely to increasing adult and seed density. [ABSTRACT FROM AUTHOR]

The objective of the present study was to determine the best concentration of urea solution and rinsing time to remove adhesiveness of African catfish eggs. Four different concentrations of rinse solution were used in this experiment comprising of 2 g, 4 g, 6 g and 8 g of urea diluted in 4 g NaCl/L of water producing a concentration of 0.486 mM, 0.973 mM, 1.458 mM, and 1.946 mM of urea concentration respectively, while 4 g NaCl/L of water without urea were used as control. The fish eggs were rinsed with the solutions at different durations namely; 1, 5 and 10 minutes. Each rinsing solution concentration and rinsing time were conducted in three replicates. The fertilization and hatching rates increased and peaked from the control (0 mM of urea) to 0.466 mN urea and decreased when concentration of urea was increased to 0.973 mM urea and 1.458 mM urea, then increased again at 1.946 mM urea, but these values were lower than at 0.486 mM urea. Thus, the best concentration for fertilization and hatching rates were 0.486 urea of urea. However 0.973 mM of urea was optimum in reducing clumping of eggs. [ABSTRACT FROM AUTHOR]

Aims In the mid- and high-latitude regions, three quarters of the land surface is covered by boreal conifer forests, and snow lasts for 6–8 months of the year. Correctly modeling surface energy balance and snowmelt at mid- and high-latitudes has a significant influence on climate and hydrological processes. However, the heterogeneous and clumped forest structure exerts important control over the radiative energy at the forest floor, which results in large variations of underneath snow cover and snowmelt rate. The goal of this study is to investigate the impact of hierarchically clumped vegetation structure in boreal forest on snowmelt and exchanges of energy and water. Methods We used a simple Clumped Canopy Scheme (CCS) for canopy radiation transfer to characterize the impact of the clumped forest structure on net radiation at the snow surface underneath forests. The CCS was integrated with the Variable Infiltration Capacity macroscale hydrological model (herein referred to as VIC-CCS) to characterize the impact of clumped vegetation structure on surface energy balance and snowmelt during the snow season. A twin simulation, VIC-CCS and the standard VIC model, was performed to isolate the impact of CCS on the energy and water fluxes and snowmelt rates. The simulation results were compared to in situ measurements at four different forest stands: old aspen forest in the Southern Study Area (SOA), black spruce forests in the Southern and Northern Study Areas (SOBS and NOBS) and fen wetland in the Northern Study Area (NFEN) within the Boreal Ecosystem–Atmosphere Study (BOREAS) region in central Canada during 1994 to1996. Important Findings Simulations showed that the implementation of CCS has reduced incoming long-wave radiation at the underlying snow surface and, thereby, lowered the snowmelt rate. Comparison against ground observations of net radiation and surface flux rates showed a reasonable agreement while demonstrating implementation of CCS can markedly improve model surface energy budget and energy inputs computation for snowmelt. The modeled snowmelt matches reasonably well with observations with root mean square error (RMSE) ranging from 16.51 to 19.81 mm using VIC-CCS versus 29.86 to 32.61 mm for VIC only in the four forest sites. The improvement is the most significant for the deciduous forest (old aspen) site, reducing RMSE by16 mm. This study demonstrates that taking into account the effect of the clumped forest structure in land surface parameterization schemes is critical for snowmelt prediction in the boreal regions. [ABSTRACT FROM PUBLISHER]

Cell enumeration and diagnosis using peripheral blood smears are routine tasks in many biological and pathological examinations. Not every area in the smear is appropriate for such tasks due to severe cell clumping or sparsity. Manual working-area selection is slow, subjective, inconsistent, and statistically biased. Automatic working-area classification can reproducibly identify appropriate working smear areas. However, very little research has been reported in the literature. With the aim of providing a preprocessing step for further detailed cell enumeration and diagnosis for high-throughput screening (HTS), we propose an integrated algorithm for area classification and quantify both cell spreading and cell clumping in terms of individual clumps and the occurrence probabilities of the group of clumps over the image. Comprehensive comparisons are presented to compare the effect of these quantifications and their combinations. Our experiments using images of Giemsa-stained blood smears show that the method is efficient, accurate (above 88.9% hit rates for all areas in the validation set of 140 images), and robust (above 78.1% hit rates for a test set of 4878 images). This lays a good foundation for fast working-area selection in HTS. [ABSTRACT FROM AUTHOR]

Abstract: Urban sprawl (dispersed urban development) has increased at alarming rates in Europe and North America over the last 50 years. Quantitative data are urgently needed in monitoring systems for sustainable development. However, there is a lack of reliable measures of urban sprawl that take into account the spatial configuration of the urban areas (not just total amount). This paper introduces four new measures of urban sprawl: degree of urban dispersion (DIS), total sprawl (TS), degree of urban permeation of the landscape (UP), and sprawl per capita (SPC). They characterize urban sprawl from a geometric point of view. The measures are related through TS = DIS ×urban area, UP = TS/size of the landscape studied, and SPC = TS/number of inhabitants. The paper investigates the properties of the new measures systematically using 13 suitability criteria which were derived from a clear definition of urban sprawl as discussed in a previous paper. The scale of analysis is specified by the so-called horizon of perception. Second, the new measures are applied to three examples from Switzerland. Subsequently, the measures are briefly compared to other measures of urban sprawl from the literature. We demonstrate that UP is an intensive and area-proportionately additive measure and is suitable for comparing urban sprawl among regions of differing size, while SPC is most appropriate when comparing sprawl in relation to human population density. The paper also provides practical advice for calculating the new measures. We conclude that the new method is more suitable than previous methods to quantify the indicator “urban sprawl” in monitoring systems as this method distinguishes the phenomenon of urban sprawl from its various causes and consequences. This article is part II of a set of two papers. [Copyright &y& Elsevier]

1 The cultivation and dissemination of alien ornamental plants increases their potential to invade. More specifically, species with bird-dispersed seeds can potentially infiltrate natural nucleation processes in savannas. 2 To test (i) whether invasion depends on facilitation by host trees, (ii) whether propagule pressure determines invasion probability, and (iii) whether alien host plants are better facilitators of alien fleshy-fruited species than indigenous species, we mapped the distribution of alien fleshy-fruited species planted inside a military base, and compared this with the distribution of alien and native fleshy-fruited species established in the surrounding natural vegetation. 3 Abundance and diversity of fleshy-fruited plant species was much greater beneath tree canopies than in open grassland and, although some native fleshy-fruited plants were found both beneath host trees and in the open, alien fleshy-fruited plants were found only beneath trees. 4 Abundance of fleshy-fruited alien species in the natural savanna was positively correlated with the number of individuals of those species planted in the grounds of the military base, while the species richness of alien fleshy-fruited taxa decreased with distance from the military base, supporting the notion that propagule pressure is a fundamental driver of invasions. 5 There were more fleshy-fruited species beneath native Acacia tortilis than beneath alien Prosopis sp. trees of the equivalent size. Although there were significant differences in native plant assemblages beneath these hosts, the proportion of alien to native fleshy-fruited species did not differ with host. 6 Synthesis. Birds facilitate invasion of a semi-arid African savanna by alien fleshy-fruited plants, and this process does not require disturbance. Instead, propagule pressure and a few simple biological observations define the probability that a plant will invade, with alien species planted in gardens being a major source of propagules. Some invading species have the potential to transform this savanna by overtopping native trees, leading to ecosystem-level impacts. Likewise, the invasion of the open savanna by alien host trees (such as Prosopis sp.) may change the diversity, abundance and species composition of the fleshy-fruited understorey. These results illustrate the complex interplay between propagule pressure, facilitation, and a range of other factors in biological invasions. [ABSTRACT FROM AUTHOR]

• Simple models of light interception are useful to identify the key structural parameters involved in light capture. We developed such models for isolated trees and tested them with virtual experiments. Light interception was decomposed into the projection of the crown envelope and the crown porosity. The latter was related to tree structure parameters. • Virtual experiments were conducted with three-dimensional (3-D) digitized apple trees grown in Lebanon and Switzerland, with different cultivars and training. The digitized trees allowed actual values of canopy structure (total leaf area, crown volume, foliage inclination angle, variance of leaf area density) and light interception properties (projected leaf area, silhouette to total area ratio, porosity, dispersion parameters) to be computed, and relationships between structure and interception variables to be derived. • The projected envelope area was related to crown volume with a power function of exponent 2/3. Crown porosity was a negative exponential function of mean optical density, that is, the ratio between total leaf area and the projected envelope area. The leaf dispersion parameter was a negative linear function of the relative variance of leaf area density in the crown volume. • The resulting models were expressed as two single equations. After calibration, model outputs were very close to values computed from the 3-D digitized databases. [ABSTRACT FROM AUTHOR]

The fixation of a new allele can be driven by Darwinian positive selection or can be due to random genetic drift. Identifying instances of positive selection is a difficult task, because its impact is routinely obscured by the action of negative selection. The nature of the genetic code dictates that positive selection in favor of an amino acid replacement should often cause a burst of two or three nucleotide substitutions at a single codon site, because a large fraction of amino acid replacements cannot be achieved after just one nucleotide substitution. Here, we study pairs of successive nonsynonymous substitutions at one codon in the course of evolution of HIV-1 genes within HIV-1 populations inhabiting infected individuals. Such pairs are more numerous and more clumped than expected if different substitutions were independent and than what is observed for pairs of successive synonymous substitutions. Bursts of nonsynonymous substitutions in HIV-1 evolution cannot be explained by mutational biases and must, therefore, be due to positive selection. Both reversals, exact or imprecise, of fixed deleterious mutations and acquisitions of amino acids with new properties are responsible for the bursts. Temporal clumping is strongest at codon sites with a low overall rate of nonsynonymous evolution, implying that a substantial fraction of replacements of conservative amino acids are driven by positive selection. We identified many conservative sites of HIV-1 proteins that occasionally experience positive selection. [ABSTRACT FROM AUTHOR]

Aim The aims of this work were (1) to study how well land-cover and climatic data are capable of explaining distribution patterns of ten bird species breeding and/or feeding primarily on marshes and other wetlands and (2) to compare the differences between red-listed and common marshland species in explanatory variables, and to study the predictability of their distribution patterns. Location Finland, northern Europe. Methods The data of the bird atlas survey carried out in 1986–89 using a 10 × 10 km uniform grid system in Finland were used in the analyses. Land-cover data based on CORINE (Coordination of Information on the Environment) classification and climatic variables were compiled using the same 10 × 10 km grid. Generalized additive models (GAM) with a stepwise selection procedure were used to select relevant explanatory variables and to examine the complexity of the response shapes of the different species to each variable. The original data set was randomly divided into model training (70%) and model evaluation (30%) sets. The final models of common and red-listed bird species richness were validated by fitting them to the model evaluation set, and the correlation between observed and predicted species richness was calculated. We assessed the discrimination ability of the binary models (single species) with the area under the curve (AUC) of a receiver operating characteristic (ROC) plot and the Kappa coefficient. Results Cover of marshland, shoreline length and mean temperature in April–June were significantly ( P < 0.01) related to the common marshland species richness. Cover and clumping of marshland and mean temperature and precipitation in April–June were selected in the model of red-listed marshland species richness. The level of discrimination in our single species models varied in ROC from fair to excellent (AUC values 0.70–0.95). Cover of marshland was included in all GAM models built for the target species, but clumping of marshland, shoreline length and cover of mires also appeared as important predictors in single species models. Seven species had statistically significant relationships with climatic variables in the multivariate GAMs. Cover of marshland was highest in squares in which the red-listed bittern Botaurus stellaris, marsh harrier Circus aeruginosus and great reed warbler Acrocephalus arundinaceus and the water rail Rallus aquaticus were observed. Main conclusions Cover of marshland was the only variable which was included in all the models, reinforcing the close connection between the studied species and marshlands. Broad-scale clumping of marshlands was important for the red-listed species, probably due to the much lower population sizes of red-listed species than those of common species. Land-cover data produced in CORINE seems to be well suited for modelling the distribution patterns of marshland birds. Although climatic variables also strongly affect the studied marshland birds, habitat availability plays a crucial role in their occurrence. The distribution patterns of marshland birds at the scale of 10 × 10 km reflect the interplay between habitat availability and direct climatic variables. [ABSTRACT FROM AUTHOR]

Leaf area index (LAI) is the total one‐sided area of leaf tissue per unit ground surface area. It is a key parameter in ecophysiology, especially for scaling up the gas exchange from leaf to canopy level. It characterizes the canopy–atmosphere interface, where most of the energy fluxes exchange. It is also one of the most difficult to quantify properly, owing to large spatial and temporal variability. Many methods have been developed to quantify LAI from the ground and some of them are also suitable for describing other structural parameters of the canopy. This paper reviews the direct and indirect methods, the required instruments, their advantages, disadvantages and accuracy of the results. Analysis of the literature shows that most cross‐validations between direct and indirect methods have pointed to a significant underestimation of LAI with the latter techniques, especially in forest stands. The two main causes for the discrepancy, clumping and contribution of stem and branches, are discussed and some recent theoretical or technical solutions are presented as potential improvements to reduce bias or discrepancies. The accuracy, sampling strategy and spatial validity of the LAI measurements have to be assessed for quality assurance of both the measurement and the modelling purposes of all the LAI‐dependent ecophysiological and biophysical processes of canopies. [ABSTRACT FROM PUBLISHER]

Airborne lidar point clouds of vegetation capture the 3-D distribution of its scattering elements, including leaves, branches, and ground features. Assessing the contribution from vegetation to the lidar point clouds requires an understanding of the physical interactions between the emitted laser pulses and their targets. Most of the current methods to estimate the gap probability ( P gap ) or leaf area index (LAI) from small-footprint airborne laser scan (ALS) point clouds rely on either point-number-based (PNB) or intensity-based (IB) approaches, with additional empirical correlations with field measurements. However, site-specific parameterizations can limit the application of certain methods to other landscapes. The universality evaluation of these methods requires a physically based radiative transfer model that accounts for various lidar instrument specifications and environmental conditions. We conducted an extensive study to compare these approaches for various 3-D forest scenes using a point-cloud simulator developed for the latest version of the discrete anisotropic radiative transfer (DART) model. We investigated a range of variables for possible lidar point intensity, including radiometric quantities derived from Gaussian Decomposition (GD), such as the peak amplitude, standard deviation, integral of Gaussian profiles, and reflectance. The results disclosed that the PNB methods fail to capture the exact P gap as footprint size increases. By contrast, we verified that physical methods using lidar point intensity defined by either the distance-weighted integral of Gaussian profiles or reflectance can estimate P gap and LAI with higher accuracy and reliability. Additionally, the removal of certain additional empirical correlation coefficients is feasible. Routine use of small-footprint point-cloud radiometric measures to estimate P gap and the LAI potentially confirms a departure from previous empirical studies, but this depends on additional parameters from lidar instrument vendors. [ABSTRACT FROM AUTHOR]