Effects of nonlinear thermal radiation on magnetized Al2 O3 -Blood nanofluid flow through an inclined microporous channel: An investigation of second law analysis.

This study aimed at studying the variational effect of nonlinear thermal radiation on the flow of Casson nanofluid ( Al 2 O 3 - Blood ${\rm Al}_2 {\rm O}_3\text{-}{\rm Blood}$ ) through a porous microchannel with entropy generation. The novelty of this investigation includes the incorporation of porous media, nonlinear radiative heat flux, and convective heat transfer at the channel interface into the energy equation, which results in an enhanced analysis for the cooling design and heat transfer of microdevices that utilize Al 2 O 3 - Blood ${\rm Al}_2 {\rm O}_3\text{-}{\rm Blood}$ nanofluid flow. Particularly, alumina (Al2 O3 ) is considered as the nanoparticles in this blood base fluid due to associated advanced pharmaceutical applications. With dimensionless variables being utilized, the governing equations are minimized to their simplest form. The Chebysev-based collocation technique was employed to numerically solve the resultant ordinary differential equations with the associated boundary conditions and the impact of flow, thermal, and irreversibility distribution fields are determined through graphs. The findings identified that higher levels of Hartmann number produce the Lorentz force, which limits fluid flow and lowers velocity, the response of nonlinear thermal radiation diminishes the heat transfer rate, and a rise in the Casson parameter also reduces the Bejan number. The results of this research can be used to improve heat transfer performance in biomedical devices, design-efficient energy conversion cycles, optimize cooling systems, and cover a wide range of energy technologies from renewable energy to aerospace propulsion.

Representation learning in the artificial and biological neural networks underlying sensorimotor integration.

The integration of deep learning and theories of reinforcement learning (RL) is a promising avenue to explore novel hypotheses on reward-based learning and decision-making in humans and other animals. Here, we trained deep RL agents and mice in the same sensorimotor task with high-dimensional state and action space and studied representation learning in their respective neural networks. Evaluation of thousands of neural network models with extensive hyperparameter search revealed that learning-dependent enrichment of state-value and policy representations of the task-performance-optimized deep RL agent closely resembled neural activity of the posterior parietal cortex (PPC). These representations were critical for the task performance in both systems. PPC neurons also exhibited representations of the internally defined subgoal, a feature of deep RL algorithms postulated to improve sample efficiency. Such striking resemblance between the artificial and biological networks and their functional convergence in sensorimotor integration offers new opportunities to better understand respective intelligent systems.

Behavioral and Cellular Tagging in Young and in Early Cognitive Aging.

The ability to maintain relevant information on a daily basis is negatively impacted by aging. However, the neuronal mechanism manifesting memory persistence in young animals and memory decline in early aging is not fully understood. A novel event, when introduced around encoding of an everyday memory task, can facilitate memory persistence in young age but not in early aging. Here, we investigated in male rats how sub-regions of the hippocampus are involved in memory representation in behavioral tagging and how early aging affects such representation by combining behavioral training in appetitive delayed-matching-to-place tasks with the "cellular compartment analysis of temporal activity by fluorescence in situ hybridization" technique. We show that neuronal assemblies activated by memory encoding were also partially activated by novelty, particularly in the distal CA1 and proximal CA3 subregions in young male rats. In early aging, both encoding- and novelty-triggered neuronal populations were significantly reduced with a more profound effect in encoding neurons. Thus, memory persistence through novelty facilitation engages overlapping hippocampal assemblies as a key cellular signature, and cognitive aging is associated with underlying reduction in neuronal activation.

Soil fertility management among smallholder farmers in Mount Kenya East region.

Declining soil fertility continues to hinder agricultural production especially among resource-constrained smallholder farmers in sub-Saharan Africa, prompting for evaluation of the strategies used by these farming communities. In this study, we assess soil fertility management among smallholder farmers in Mount Kenya East region. The aim is to examine underlying factors conditioning the uptake of integrated soil fertility management (ISFM) practices in this region; determine the adoption relationship between the practices; and to cluster these techniques. Data for this study was collected between January-March 2019 through a household survey based on a farm household questionnaire and complemented with semi-structured interview with farmers and extension officers. Statistical analyses were generated using SPSS. We use hierarchical clustering analysis to visualize ISFM combination patterns, and correlation matrix in factor analysis to determine the inter-relationship between different ISFM practices. Fisher's exact test and Welch's t-test were used to examine the association between explanatory variables and adoption of ISFM practices. Results show that the decision to invest in fertility practices was correlated with a number of farmers' socio-economic, farm-related factors and institutional characteristics. Fertilizer application correlated significantly with manure use, agroforestry and minimum tillage. ISFM techniques were separated into 3 sets following Ward's hierarchical clustering, namely, manure, fertilizer use and agroforestry (cluster 1 or C1), slash-no-burn, residue burn and fallowing (C2); and residue application and minimum tillage (C3). The study recommends creation of an enabling environment including innovative financing opportunities to facilitate farmers' investment capacities in ISFM and cushion them from potential income loss resulting from implementation of some technologies.

Genetic analysis of Boletus edulis suggests that intra-specific competition may reduce local genetic diversity as a woodland ages.

Ectomycorrhizal fungi are key players in terrestrial ecosystems yet their mating systems and population dynamics remain poorly understood. We investigated the fine-scale relatedness structure and genetic diversity of Boletus edulis, one of the world's most commercially important wild mushrooms. Microsatellite genotyping of fruiting bodies from 14 different sites around Bielefeld in Germany revealed little in the way of population structure over a geographic scale of several kilometres. However, on a more local scale we found evidence for elevated relatedness as well as inbreeding. We also observed a significant negative association between the genetic diversity of fruit and the age of the trees under which they were sampled. Taken together, our results suggest that as genets mature, they compete and potentially create conditions under which further spores struggle to become established. By implication, even though this species is widely picked, propagules remain common enough to create strong competition when new habitats become available.

Application of the Mesolens for subcellular resolution imaging of intact larval and whole adult Drosophila.

In a previous paper, we showed a new giant lens called the Mesolens and presented performance data and images from whole fixed and intact fluorescently-stained 12.5-day old mouse embryos. Here, we show that using the Mesolens we can image an entire Drosophila larva or adult fly in confocal epifluorescence and show subcellular detail in all tissues. By taking several hundreds of optical sections through the entire volume of the specimen, we show cells and nuclear details within the gut, brain, salivary glands and reproductive system that normally require dissection for study. Organs are imaged in situ in correct 3D arrangement. Imaginal discs are imaged in mature larvae and it proved possible to image pachytene chromosomes in cells within ovarian follicles in intact female flies. Methods for fixing, staining and clearing are given.

Rat eradication comes within a whisker! A case study of a failed project from the South Pacific.

To enhance their conservation value, several hundred islands worldwide have been cleared of invasive alien rats, Rattus spp. One of the largest projects yet undertaken was on 43 km(2) Henderson Island in the Pitcairn group, South Pacific, in August 2011. Following massive immediate mortality, a single R. exulans was observed in March 2012 and, subsequently, rat numbers have recovered. The survivors show no sign of resistance to the toxicant used, brodifacoum. Using pre- and post-operation rat tissue samples from Henderson, plus samples from around the Pacific, we exclude re-introduction as the source of continued rat presence. Microsatellite analysis of 18 loci enabled comparison of genetic diversity of Henderson rats before and after the bait drop. The fall in diversity measured by allele frequency change indicated that the bottleneck (N e) through which the breeding population passed was probably around 50 individuals, representing a census population of about 60-80 animals. This is the first failed project that has estimated how close it was to success.

Exploration of the two-photon excitation spectrum of fluorescent dyes at wavelengths below the range of the Ti:Sapphire laser.

We have studied the wavelength dependence of the two-photon excitation efficiency for a number of common UV excitable fluorescent dyes; the nuclear stains DAPI, Hoechst and SYTOX Green, chitin- and cellulose-staining dye Calcofluor White and Alexa Fluor 350, in the visible and near-infrared wavelength range (540-800 nm). For several of the dyes, we observe a substantial increase in the fluorescence emission intensity for shorter excitation wavelengths than the 680 nm which is the shortest wavelength usually available for two-photon microscopy. We also find that although the rate of photo-bleaching increases at shorter wavelengths, it is still possible to acquire many images with higher fluorescence intensity. This is particularly useful for applications where the aim is to image the structure, rather than monitoring changes in emission intensity over extended periods of time. We measure the excitation spectrum when the dyes are used to stain biological specimens to get a more accurate representation of the spectrum of the dye in a cell environment as compared to solution-based measurements.

Global population structure and demographic history of the grey seal.

Although the grey seal Halichoerus grypus is one of the most familiar and intensively studied of all pinniped species, its global population structure remains to be elucidated. Little is also known about how the species as a whole may have historically responded to climate-driven changes in habitat availability and anthropogenic exploitation. We therefore analysed samples from over 1500 individuals collected from 22 colonies spanning the Western and Eastern Atlantic and the Baltic Sea regions, represented by 350 bp of the mitochondrial hypervariable region and up to nine microsatellites. Strong population structure was observed at both types of marker, and highly asymmetrical patterns of gene flow were also inferred, with the Orkney Islands being identified as a source of emigrants to other areas in the Eastern Atlantic. The Baltic and Eastern Atlantic regions were estimated to have diverged a little over 10 000 years ago, consistent with the last proposed isolation of the Baltic Sea. Approximate Bayesian computation also identified genetic signals consistent with postglacial population expansion across much of the species range, suggesting that grey seals are highly responsive to changes in habitat availability.

No correlation between multi-locus heterozygosity and fitness in the common buzzard despite heterozygote advantage for plumage colour.

Correlations between heterozygosity and fitness are frequently found but rarely well understood. Fitness can be affected by single loci of large effect which correlate with neutral markers via linkage disequilibrium, or as a result of variation in genome-wide heterozygosity following inbreeding. We explored these alternatives in the common buzzard, a raptor species in which three colour morphs differ in their lifetime reproductive success. Using 18 polymorphic microsatellite loci, we evaluated potential genetic differences among the morphs which may lead to subpopulation structuring and tested for correlations between three fitness-related traits and heterozygosity, both genome wide and at each locus separately. Despite their assortative mating pattern, the buzzard morphs were found to be genetically undifferentiated. Multilocus heterozygosity was only found to be correlated with a single fitness-related trait, infection with the blood parasite, Leucocytozoon buteonis, and this was via interactions with vole abundance and age. One locus also showed a significant relationship with blood parasite infection and ectoparasite infestation. The vicinity of this locus contains two genes, one of which is potentially implicated in the immune system of birds. We conclude that genome-wide heterozygosity is unlikely to be a major determinant of parasite burden and body condition in the polymorphic common buzzard.

Increased signals from short-wavelength-excited fluorescent molecules using sub-Ti:Sapphire wavelengths.

We report the use of an all-solid-state ultrashort pulsed source specifically for two-photon microscopy at wavelengths shorter than those of the conventional Ti:Sapphire laser. Our approach involves sum-frequency mixing of the output from an optical parametric oscillator (λ= 1400-1640 nm) synchronously pumped by a Yb-doped fibre laser (λ= 1064 nm), with the residual pump radiation. This generated an fs-pulsed output tunable in the red spectral region (λ= 620-636 nm, ~150 mW, 405 fs, 80 MHz, M(2) ~ 1.3). We demonstrate the performance of our ultrashort pulsed system using fluorescently labelled and autofluorescent tissue, and compare with conventional Ti:Sapphire excitation. We observe a more than 3-fold increase in fluorescence signal intensity using our visible laser source in comparison with the Ti:Sapphire laser for two-photon excitation at equal illumination peak powers of 1.16 kW or less.

A compact instrument for adjusting laser beams to be accurately coincident and coaxial and its use in biomedical imaging using wave-mixed laser sources.

Biomedical imaging applications that involve nonlinear optical processes such as sum-frequency generation (SFG) and four-wave mixing require that the pulses are synchronized in time and the beams are coaxial to better than 400 µrad. For this reason, folding mirrors are normally used to extend the beam path over a few meters so that detectors can be put into the beams to check their overlap at the start of a long path and also at the end of it. We have made a portable instrument with a footprint of only 22 cm × 11 cm × 16 cm that uses a short focal length lens and a telephoto combination for viewing the near-field and far-field simultaneously. Our instrument is simple to build and use, and we show its application in coherent anti-Stokes Raman scattering microscopy and SFG-based two-photon fluorescence microscopy.

MHC genotype and near-deterministic mortality in grey seals.

The Major Histocompatability Complex (MHC) is one of the best known and best characterised components of the immune system, yet its functions remain somewhat enigmatic, including both anti-pathogen activity and kin recognition. To explore the importance of the MHC relative to literally hundreds of other components of the immune system, we compared MHC genotype frequencies between pups and adults in the grey seal (Halichoerus grypus), one of many marine mammals that exhibit low allelic diversity. We find that one allele is strongly associated with pup survival, pups being more likely to be found dead if they lack it, while total allele number is a remarkably strong predictor of survivorship to adulthood. We estimate that approximately 70% of mortality can be attributed to the MHC. Our study therefore shows that low MHC allele diversity belies its critical role in determining whether a weaned pup negotiates disease to become a breeding adult.

Use of a white light supercontinuum laser for confocal interference-reflection microscopy.

Shortly after its development, the white light supercontinuum laser was applied to confocal scanning microscopy as a more versatile substitute for the multiple monochromatic lasers normally used for the excitation of fluorescence. This light source is now available coupled to commercial confocal fluorescence microscopes. We have evaluated a supercontinuum laser as a source for a different purpose: confocal interferometric imaging of living cells and artificial models by interference reflection. We used light in the range 460-700 nm where this source provides a reasonably flat spectrum, and obtained images free from fringe artefacts caused by the longer coherence length of conventional lasers. We have also obtained images of cytoskeletal detail that is difficult to see with a monochromatic laser.

Geographic variation of the major histocompatibility complex in Eastern Atlantic grey seals (Halichoerus grypus).

Pathogen-driven balancing selection maintains high genetic diversity in many vertebrates, particularly in the major histocompatibility complex (MHC) immune system gene family, which is often associated with disease susceptibility. In large natural populations where subpopulations face different pathogen pressures, the MHC should show greater genetic differentiation within a species than neutral markers. We examined genetic diversity at the MHC-DQB locus and nine putatively neutral microsatellite markers in grey seals (Halichoerus grypus) from eight United Kingdom (UK) colonies, the Faeroe Islands and Sable Island, Canada. Five DQB alleles were identified in grey seals, which varied in prevalence across the grey seal range. Among the seal colonies, significant differences in DQB allele and haplotype frequencies and in average DQB heterozygosity were observed. Additionally, the DQB gene exhibited greater differentiation among colonies compared with neutral markers, yet a weaker pattern of isolation by distance (IBD). After correcting for the underlying IBD pattern, subpopulations breeding in similar habitats were more similar to one another in DQB allele frequencies than populations breeding in different habitats, but the same did not hold true for microsatellites, suggesting that habitat-specific pathogen pressure influences MHC evolution. Overall, the data are consistent with selection at MHC-DQB loci in grey seals with both varying selective pressures and geographic population structure appearing to influence the DQB genetic composition of breeding colonies.

Candidate genes versus genome-wide associations: which are better for detecting genetic susceptibility to infectious disease?

Technological developments allow increasing numbers of markers to be deployed in case-control studies searching for genetic factors that influence disease susceptibility. However, with vast numbers of markers, true 'hits' may become lost in a sea of false positives. This problem may be particularly acute for infectious diseases, where the control group may contain unexposed individuals with susceptible genotypes. To explore this effect, we used a series of stochastic simulations to model a scenario based loosely on bovine tuberculosis. We find that a candidate gene approach tends to have greater statistical power than studies that use large numbers of single nucleotide polymorphisms (SNPs) in genome-wide association tests, almost regardless of the number of SNPs deployed. Both approaches struggle to detect genetic effects when these are either weak or if an appreciable proportion of individuals are unexposed to the disease when modest sample sizes (250 each of cases and controls) are used, but these issues are largely mitigated if sample sizes can be increased to 2000 or more of each class. We conclude that the power of any genotype-phenotype association test will be improved if the sampling strategy takes account of exposure heterogeneity, though this is not necessarily easy to do.

Evidence that two main bottleneck events shaped modern human genetic diversity.

There is a strong consensus that modern humans originated in Africa and moved out to colonize the world approximately 50 000 years ago. During the process of expansion, variability was lost, creating a linear gradient of decreasing diversity with increasing distance from Africa. However, the exact way in which this loss occurred remains somewhat unclear: did it involve one, a few or a continuous series of population bottlenecks? We addressed this by analysing a large published dataset of 783 microsatellite loci genotyped in 53 worldwide populations, using the program 'Bottleneck'. Immediately following a sharp population decline, rare alleles are lost faster than heterozygosity, creating a transient excess of heterozygosity relative to allele number, a feature that is used by Bottleneck to infer historical events. We find evidence of two primary events, one 'out of Africa' and one placed around the Bering Strait, where an ancient land bridge allowed passage into the Americas. These findings agree well with the regions of the world where the largest founder events might have been expected, but contrast with the apparently smooth gradient of variability that is revealed when current heterozygosity is plotted against distance from Africa.

Contrasting patterns of genetic diversity at three different genetic markers in a marine mammal metapopulation.

Many studies use genetic markers to explore population structure and variability within species. However, only a minority use more than one type of marker and, despite increasing evidence of a link between heterozygosity and individual fitness, few ask whether diversity correlates with population trajectory. To address these issues, we analysed data from the Steller's sea lion, Eumetiopias jubatus, where three stocks are distributed over a vast geographical range and where both genetic samples and detailed demographic data have been collected from many diverse breeding colonies. To previously published mitochondrial DNA (mtDNA) and microsatellite data sets, we have added new data for amplified fragment length polymorphism (AFLP) markers, comprising 238 loci scored in 285 sea lions sampled from 23 natal rookeries. Genotypic diversity was low relative to most vertebrates, with only 37 loci (15.5%) being polymorphic. Moreover, contrasting geographical patterns of genetic diversity were found at the three markers, with Nei's gene diversity tending to be higher for AFLPs and microsatellites in rookeries of the western and Asian stocks, while the highest mtDNA values were found in the eastern stock. Overall, and despite strongly contrasting demographic histories, after applying phylogenetic correction we found little correlation between genetic diversity and either colony size or demography. In contrast, we were able to show a highly significant positive relationship between AFLP diversity and current population size across a range of pinniped species, even though equivalent analyses did not reveal significant trends for either microsatellites or mtDNA.

Pinniped phylogenetic relationships inferred using AFLP markers.

Amplified fragment length polymorphisms (AFLPs) are widely used for phylogenetic reconstruction in plants but their use in animal taxa has been limited, and in mammals rare. In addition, their use has been largely limited to shallow relationships amongst species or subspecies. Here, we genotype 23 pinniped species for 310 AFLP markers and find a strong phylogenetic signal, with individuals coclustering within species, and overall a good agreement between our phylogeny and those constructed using mitochondrial DNA and nuclear sequences even at nodes approximately 15 million years old. Although supporting the existing ideas about pinniped relationships, our data shed light on relationships within the hitherto relatively unresolved Phocine species group, and provide further supporting evidence for raising two subspecies of Zalophus californianus, Z. c. californianus and Z. c. wollebaeki, to species level. Plotting AFLP divergence time estimates against those based on both mtDNA and nuclear sequences we find strong linear relationships, suggesting that the different markers are evolving in a clocklike fashion. These data further emphasize the utility of AFLP markers as general tools for phylogenetic reconstruction.

Heterozygosity and lungworm burden in harbour seals (Phoca vitulina).

In several studies, heterozygosity measured at around 10 microsatellite markers correlates with parasite load. Usually the effect size is small, but while this may reflect reality, it may also be possible that too few markers are used or the measure of fitness contains too much error to reveal what is actually a much stronger underlying effect. Here, we analysed over 200 stranded harbour seals (Phoca vitulina) for an association between lungworm burden and heterozygosity, conducting thorough necropsies on the seals and genotyping the samples obtained for 27 microsatellites. We found that homozygosity predicts higher worm burdens, but only in young animals, where the worms have the greatest impact on fitness. Testing each locus separately, we found that a significant majority reveal a weak but similar trend for heterozygosity to be protective against high lungworm burden, suggesting a genome-wide effect, that is, inbreeding. This conclusion is supported by the fact that heterozygosity is correlated among markers in young animals but not in otherwise equivalent older ones. Taken as a whole, our results support the notion that homozygosity increases susceptibility to parasitic infection and suggest that parasites can be effective in removing inbred individuals from the population.