Properties of packings and dispersions of superellipse sector particles.

Superellipse sector particles (SeSPs) are segments of superelliptical curves that form a tunable set of hard-particle shapes for granular and colloidal systems. SeSPs allow for continuous parametrization of corner sharpness, aspect ratio, and particle curvature; rods, circles, rectangles, and staples are examples of shapes SeSPs can model. We compare three computational processes: pair-wise Monte Carlo simulations that explore particle-particle geometric constraints, Monte Carlo simulations that reveal how these geometric constraints play out over dispersions of many particles, and Molecular Dynamics simulations that form random loose and close packings. We investigate the dependence of critical random loose and close packing fractions on particle parameters, finding that both values increase with opening aperture and decrease with increasing corner sharpness. The identified packing fractions are compared with the mean-field prediction of the random contact model; we find deviations from the model's prediction due to correlations between particle orientations. The complex interaction of spatial proximity and orientational alignment is also explored with a generalized spatioorientational distribution area (SODA) plot, which shows how higher density packings are achieved through particles assuming a small number of preferred configurations that depend sensitively on particle shape and system preparation.

Development and large-scale production of human milk fat analog by fermentation of microalgae.

Background: Human milk contains a complex mixture of triacylglycerols (TAG), making it challenging to recreate using common ingredients. Objective: The study aimed to develop an innovative fermentation technique to produce essential human milk TAG, effectively tackling a significant hurdle in infant nutrition. Method: An in-depth analysis of the literature has been conducted to identify the specific TAG to be targeted. We used a microalgal oil production platform and a two-step procedure to modify its fatty acid and TAG composition. The palmitic acid (16:0) content has been increased by classical strain improvement techniques, followed by a step involving the expression of a lysophosphatidic acid acyltransferase (LPAAT) sequence capable of esterifying 16:0 specifically at the internal position (sn-2 palmitate) of TAG. Once the strain was stabilized, the fermentation was scaled up in a 50-L reactor to yield several kilograms of biomass. Subsequently, the oil was extracted and refined using standard oil processing conditions. Liquid chromatography-mass spectrometry was employed to monitor the TAG profile and the region specificity of 16:0 at the internal position (sn-2 palmitate) of TAG. Results: The initial strain had a 16:0 level of 25% of total fatty acids, which was increased to 30% by classical strain improvement. Simultaneously, the oleic acid level decreased from 61% to 57% of total fatty acids. Upon expression of an exogenous LPAAT gene, the level of the 16:0 esterified in the internal position of the TAG (sn-2 palmitate) increased by a factor of 10, to reach 73% of total palmitic acid. Consequently, the concentration of oleic acid in the internal position decreased from 81% to 22% of total fatty acids, with TAG analysis confirming that the primary TAG species in the oil was 1,3-dioleoyl-2-palmitoyl-glycerol (OPO). The 50-L-scale fermentation trial confirmed the strain's ability to produce oil with a yield of >150 g of oil per liter of fermentation broth in a timeframe of 5 days, rendering the process scalable for larger-scale industrialization. Conclusion: We have demonstrated the feasibility of producing a suitable TAG composition that can be effectively integrated into the formulations of infant nutrition in combination with other fats and oils to meet the infant feeding requirements.

Improving models for student retention and graduation using Markov chains.

Graduation rates are a key measure of the long-term efficacy of academic interventions. However, challenges to using traditional estimates of graduation rates for underrepresented students include inherently small sample sizes and high data requirements. Here, we show that a Markov model increases confidence and reduces biases in estimated graduation rates for underrepresented minority and first-generation students. We use a Learning Assistant program to demonstrate the Markov model's strength for assessing program efficacy. We find that Learning Assistants in gateway science courses are associated with a 9% increase in the six-year graduation rate. These gains are larger for underrepresented minority (21%) and first-generation students (18%). Our results indicate that Learning Assistants can improve overall graduation rates and address inequalities in graduation rates for underrepresented students.

Reimagine fire science for the anthropocene.

Fire is an integral component of ecosystems globally and a tool that humans have harnessed for millennia. Altered fire regimes are a fundamental cause and consequence of global change, impacting people and the biophysical systems on which they depend. As part of the newly emerging Anthropocene, marked by human-caused climate change and radical changes to ecosystems, fire danger is increasing, and fires are having increasingly devastating impacts on human health, infrastructure, and ecosystem services. Increasing fire danger is a vexing problem that requires deep transdisciplinary, trans-sector, and inclusive partnerships to address. Here, we outline barriers and opportunities in the next generation of fire science and provide guidance for investment in future research. We synthesize insights needed to better address the long-standing challenges of innovation across disciplines to (i) promote coordinated research efforts; (ii) embrace different ways of knowing and knowledge generation; (iii) promote exploration of fundamental science; (iv) capitalize on the "firehose" of data for societal benefit; and (v) integrate human and natural systems into models across multiple scales. Fire science is thus at a critical transitional moment. We need to shift from observation and modeled representations of varying components of climate, people, vegetation, and fire to more integrative and predictive approaches that support pathways toward mitigating and adapting to our increasingly flammable world, including the utilization of fire for human safety and benefit. Only through overcoming institutional silos and accessing knowledge across diverse communities can we effectively undertake research that improves outcomes in our more fiery future.

Excluded area of superellipse sector particles.

Superellipse sector particles (SeSPs) are segments of superelliptical curves that form a tunable set of hard-particle shapes for granular and colloidal systems. SeSPs allow for continuous parametrization of corner sharpness, aspect ratio, and particle curvature; rods, circles, rectangles, and staples are examples of shapes SeSPs can model. We investigate the space of allowable (nonoverlapping) configurations of two SeSPs, which depends on both the center-of-mass separation and relative orientation. Radial correlation plots of the allowed configurations reveal circular regions centered at each of the particle's two end points that indicate configurations of mutually entangled particle interactions. Simultaneous entanglement with both end points is geometrically impossible; the overlap of these two regions therefore represents an excluded area in which no particles can be placed regardless of orientation. The regions' distinct boundaries indicate a translational frustration with implications for the dynamics of particle rearrangements (e.g., under shear). Representing translational and rotational degrees of freedom as a hypervolume, we find a topological change that suggests geometric frustration arises from a phase transition in this space. The excluded area is a straightforward integration over excluded states; for arbitrary relative orientation this decreases sigmoidally with increasing opening aperture, with sharper SeSP corners resulting in a sharper decrease. Together, this work offers a path towards a unified theory for particle shape control of bulk material properties.

Black Soldier Fly Larvae Rearrange under Compression.

Thousands of black soldier larvae hatch simultaneously from eggs laid within rotting vegetation or animal carcasses. Over the next few weeks, they grow while compressed by both their surroundings and each other. When compressed, these larvae rearrange to reduce the forces upon them. How quickly can larvae rearrange, and what final state do they choose? In this experimental study, we use a universal testing machine to conduct creep tests on larvae, squeezing them to set volume fractions and measuring the time course of their reaction force. Live larvae come to equilibrium at a rate 10 times faster than dead larvae, indicating that their small movements can rearrange them faster than just settling. The relaxation of dead larvae is well described by stretched exponentials, which also characterize hierarchical self-avoiding materials such as polymers or balls of crumpled aluminum foil. The equilibrium pressures of live larvae are comparable to those of dead larvae, suggesting that such pressures are dictated by the physics of their bodies rather than their behavior. Live larvae perform fluctuations to actively maintain this equilibrium pressure. This ability to survive large pressures might have applications in the larvae-rearing industry, where both live and dead larvae are packed in containers for shipping.

Elephant trunks form joints to squeeze together small objects.

Wild African elephants are voracious eaters, consuming 180 g of food per minute. One of their methods for eating at this speed is to sweep food into a pile and then pick it up. In this combined experimental and theoretical study, we elucidate the elephant's unique method of picking up a pile of food by compressing it with its trunk. To grab the smallest food items, the elephant forms a joint in its trunk, creating a pillar up to 11 cm tall that it uses to push down on food. Using a force sensor, we show the elephant applies greater force to smaller food pieces, in a manner that is required to solidify the particles into a lump solid, as calculated by Weibullian statistics. Elephants increase the height of the pillar with the force required, achieving up to 28% of the applied force using the self-weight of the pillar alone. This work shows that elephants are capable of modulating the force they apply to granular materials, taking advantage of their transition from fluid to solid. In the future, heavy robotic manipulators may also form joints to compress and lift objects together.

Ant aggregations self-heal to compensate for the Ringelmann effect.

Fire ants, Solenopsis invicta, link their bodies together to form structures such as rafts, bivouacs and bridges. Such structures are in danger of being damaged by natural disturbances such as passing water currents. In this combined experimental and theoretical study, we investigate the self-healing of ant assemblages. We press two ant aggregations together and measure the forces to pull them apart. As the group size increases, the contribution of each ant decreases. This phenomenon, known as the Ringelmann effect, or social loafing, has previously been shown for cattle and humans. In this study, we show that it is a challenge for ants as well. We rationalize this effect with an agent-based simulation which exhibits the Ringelmann effect of ants that periodically make and break links with each other, but grip with higher probability if the ants are stretched. Over time, ants compensate for the Ringelmann effect by building more links. We use a mathematical model to show that the rate of new links is proportional to the number of free ants in the cluster. The principles found here may inspire new directions in self-healing and active materials.

Delayed Flowering in Bamboo: Evidence from Fargesia qinlingensis in the Qinling Mountains of China.

Gregarious flowering of bamboo species impacts ecosystem properties and conservation, but documentation of these periodic events is difficult. Here, we compare the characteristics of flowering sites and un-flowered patches of an arrow bamboo (Fargesia qinlingensis) in the Qinling Mountains, China, over a 5-year period (2003-2007) after a mast flowering event (2003). We examined flowering culm and seedling characteristics in relation to questions regarding the evolution of delayed flowering. Density of live culms decreased over the 5 years in both flowering sites and un-flowered patches. New shoots regenerated only in un-flowered patches. Chemical constituent allocation varied among culm parts (stems, branches, and leaves). Crude protein and extract ether in branches and leaves were less in flowering culms than in un-flowered culms. Seedling density was lower than expected based on floret counts, suggesting predation of seeds. Seedling density was significantly greater in flowering sites than in un-flowered patches and decreased over time. Seedlings performed better in flowering sites than in un-flowered patches based on their height, leaf number per seedling, and average leaf length, while fertilization on flowering sites had no significant effect on seedling growth, suggesting a saturation of resources. This study suggested that the characteristics of bamboos and bamboo stands were dramatically altered during this flowering event, enhancing seedling establishment and growth, and supporting mostly the habitat modification hypothesis of delayed reproduction.

Beta diversity determinants in Badagongshan, a subtropical forest in central China.

Niche and neutral theories emphasize different processes contributing to the maintenance of species diversity. In this study, we calculated the local contribution to beta diversity (LCBD) of every cell, using variation partitioning in combination with spatial distance and environmental variables of the 25-ha Badagongshan plot (BDGS), to determine the contribution of environmentally-related variation versus pure spatial variation. We used topography and soil characteristics as environmental variables, distance-based Moran's eigenvectors maps (dbMEM) to describe spatial relationships among cells and redundancy analysis (RDA) to apportion the variation in beta diversity into three components: pure environmental, spatially-structured environmental, and pure spatial. Results showed LCBD values were negatively related to number of common species and positively related to number of rare species. Environment and space jointly explained ~60% of the variation in species composition; soil variables alone explained 21.6%, slightly more than the topographic variables that explained 15.7%; topography and soil together explained 27%, slightly inferior to spatial variables that explained 34%. The BDGS forest was controlled both by the spatial and environmental variables, and the results were consistent across different life forms and life stages.

Safety evaluation of oleic-rich triglyceride oil produced by a heterotrophic microalgal fermentation process.

Numbers of macro- and microalgae have been used as food sources in various cultures for centuries. Several microalgae are currently being developed as modern food ingredients. The dietary safety of oleic-rich microalgal oil produced using a heterotrophic fermentation process was assessed in a 13-week feeding trial in rats with genotoxic potential evaluated using in vitro and in vivo assays. In the genotoxicity assays, the test oil was not mutagenic in Salmonella typhimurium or Escherichia coli tester strains (⩽5000µg/plate) with or without metabolic activation. Further, no clastogenic response occurred in chromosome aberration assays in the bone marrow of mice administered a single intraperitoneal dose (2000mg/kg). In the subchronic study, rats consumed feed containing 0, 25,000, 50,000 or 100,000ppm oleic-rich oil for 90days. No treatment-related mortalities or adverse effects occurred in general condition, body weight, food consumption, ophthalmology, urinalysis, hematology, clinical chemistry, gross pathology, organ weights or histopathology. Although several endpoints exhibited statistically significant effects, none were dose-related or considered adverse. Taking all studies into consideration, the NOAEL for the oleic-rich oil was 100,000ppm, the highest concentration tested and equivalent to dietary NOAELs of 5200mg/kg bw/day and 6419mg/kg bw/day in male and female rats, respectively.

Bioinformatics analyses reveal age-specific neuroimmune modulation as a target for treatment of high ethanol drinking.

BACKGROUND: Use of in silico bioinformatics analyses has led to important leads in the complex nature of alcoholism at the genomic, epigenomic, and proteomic level, but has not previously been successfully translated to the development of effective pharmacotherapies. In this study, a bioinformatics approach led to the discovery of neuroimmune pathways as an age-specific druggable target. Minocycline, a neuroimmune modulator, reduced high ethanol (EtOH) drinking in adult, but not adolescent, mice as predicted a priori. METHODS: Age and sex-divergent effects in alcohol consumption were quantified in FVB/NJ × C57BL/6J F1 mice given access to 20% alcohol using a 4 h/d, 4-day drinking-in-dark (DID) paradigm. In silico bioinformatics pathway overrepresentation analysis for age-specific effects of alcohol in brain was performed using gene expression data collected in control and DID-treated, adolescent and adult, male mice. Minocycline (50 mg/kg i.p., once daily) or saline alone was tested for an effect on EtOH intake in the F1 and C57BL/6J (B6) mice across both age and gender groups. Effects of minocycline on the pharmacokinetic properties of alcohol were evaluated by comparing the rates of EtOH elimination between the saline- and minocycline-treated F1 and B6 mice. RESULTS: Age and gender differences in DID consumption were identified. Only males showed a clear developmental increase difference in drinking over time. In silico analyses revealed neuroimmune-related pathways as significantly overrepresented in adult, but not in adolescent, male mice. As predicted, minocycline treatment reduced drinking in adult, but not adolescent, mice. The age effect was present for both genders, and in both the F1 and B6 mice. Minocycline had no effect on the pharmacokinetic elimination of EtOH. CONCLUSIONS: Our results are a proof of concept that bioinformatics analysis of brain gene expression can lead to the generation of new hypotheses and a positive translational outcome for individualized pharmacotherapeutic treatment of high alcohol consumption.

16S and 23S plastid rDNA phylogenies of Prototheca species and their auxanographic phenotypes.

Because algae have become more accepted as sources of human nutrition, phylogenetic analysis can help resolve the taxonomy of taxa that have not been well studied. This can help establish algal evolutionary relationships. Here, we compare Auxenochlorella protothecoides and 23 strains of Prototheca based on their complete 16S and partial 23S plastid rDNA sequences along with nutrient utilization (auxanographic) profiles. These data demonstrate that some of the species groupings are not in agreement with the molecular phylogenetic analyses and that auxanographic profiles are poor predictors of phylogenetic relationships.

Entangled granular media.

We study the geometrically induced cohesion of ensembles of granular "u particles" that mechanically entangle through particle interpenetration. We vary the length-to-width ratio l/w of the u particles and form them into freestanding vertical columns. In a laboratory experiment, we monitor the response of the columns to sinusoidal vibration (with peak acceleration Γ). Column collapse occurs in a characteristic time τ which follows the relation τ∝exp(Γ/Δ). Δ resembles an activation energy and is maximal at intermediate l/w. A simulation reveals that optimal strength results from competition between packing and entanglement.

Long-term population demography of Trillium recurvatum on loess bluffs in western Tennessee, USA.

BACKGROUND AND AIMS: Understanding the demography of long-lived clonal herbs, with their extreme modularity, requires knowledge of both their short- and long-term survival and ramet growth patterns. The primary objective of this study was to understand the dynamics of a clonal forest herb, Trillium recurvatum, by examining temporal and small-scale demographic patterns. We hypothesized: (i) there would be more variability in the juvenile age class compared with non-flowering adult and flowering adult classes due to year-to-year fluctuations in recruitment; (ii) rates of population growth (λ) and increase (r) would be highest in non-flowering ramets due to a combination of transitions from the juvenile stage and reversions from flowering adults; and (iii) inter-ramet distances would be most variable between flowering and juvenile ramets due to a combination of clonal growth, seed dispersal by ants and ramet death over time. METHODOLOGY: Census data were collected on the total number of stems in the population from 1990 to 2007, and placed within one of three life stages (juvenile, three-leaf non-flowering and three-leaf flowering). Modified population viability equations were used to assess temporal population viability, and spatial structure was assessed using block krigging. Correlations were performed using current and prior season weather to current population demography. PRINCIPAL RESULTS: The first hypothesis was rejected. The second hypothesis was supported: population increase (r) and growth rate (λ) were highest in non-flowering ramets. Finally, the third hypothesis was rejected: there was no apparent density dependence within this population of Trillium and no apparent spatial structure among life stages. CONCLUSIONS: Overall population density fluctuated over time, possibly due to storms that move soil, and prior year's temperature and precipitation. However, density remained at some dynamic stable level. The juvenile age class had greater variability for the duration of this study and population growth rate was greatest for non-flowering ramets.

Analysis of us-preexposure effects in appetitive conditioning.

In two experiments, rats received preexposure to one type of food followed by autoshaping in which presentation of one lever was associated with the preexposed food, and presentation of another lever with a novel type of food pellet. In both it was found that acquisition of the leverpress response occurred more readily on the lever associated with the novel food. This example of the US (unconditioned stimulus) preexposure effect is not to be explained in terms of the development of competing responses during preexposure. Explanations in terms of blocking by contextual cues and of habituation to the US are considered.

Power-law flow statistics in anisometric (wedge) hoppers.

We find the probability for N particles to exit an anisometric (having unequal dimensions) hopper before jamming to have a broad power-law decay with exponent α = -2, in marked contrast to the exponential decay seen in hoppers with symmetric apertures. The transition from exponential to power law is explained by amodel that assumes particle motion is correlated over a distinct length scale. Hoppers with lengths larger than this length are modeled as a series of adjacent, statistically independent "cells." Experiments with apertures 27-37 particle diameters D long are well fit by a three-cell model, implying that the correlation length is ≈ 9-12D.

Molecular factors affecting the accumulation of recombinant proteins in the Chlamydomonas reinhardtii chloroplast.

In an effort to develop microalgae as a robust system for the production of valuable proteins, we analyzed some of the factors affecting recombinant protein expression in the chloroplast of the green alga Chlamydomonas reinhardtii. We monitored mRNA accumulation, protein synthesis, and protein turnover for three codon-optimized transgenes including GFP, bacterial luciferase, and a large single chain antibody. GFP and luciferase proteins were quite stable, while the antibody was less so. Measurements of protein synthesis, in contrast, clearly showed that translation of the three chimeric mRNAs was greatly reduced when compared to endogenous mRNAs under control of the same atpA promoter/UTR. Only in a few conditions this could be explained by limited mRNA availability since, in most cases, recombinant mRNAs accumulated quite well when compared to the atpA mRNA. In vitro toeprint and in vivo polysome analyses suggest that reduced ribosome association might contribute to limited translational efficiency. However, when recombinant polysome levels and protein synthesis are analyzed as a whole, it becomes clear that other steps, such as inefficient protein elongation, are likely to have a considerable impact. Taken together, our results point to translation as the main step limiting the expression of heterologous proteins in the C. reinhardtii chloroplast.