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The generalized circumradius of a set of points A ⊆ R d with respect to a convex body K equals the minimum value of λ ≥ 0 such that a translate of λ K contains A. Each choice of K gives a different function on the set of bounded subsets of R d ; we characterize which functions can arise in this way. Our characterization draws on the theory of diversities, a recently introduced generalization of metrics from functions on pairs to functions on finite subsets. We additionally investigate functions which arise by restricting the generalized circumradius to a finite subset of R d . We obtain elegant characterizations in the case that K is a simplex or parallelotope. [ABSTRACT FROM AUTHOR]

The essay titled "We are the system" explores the role of personal experiences and diversity in academic discourse, specifically in the field of cell biology. The author argues that acknowledging personal perspectives is important because the academic system is made up of fallible and biased individuals. The essay focuses on the challenges faced by the LGBT+ community in STEM fields and emphasizes the need for open dialogue and understanding. The author suggests that academic conferences and initiatives should address diversity and encourages listening to colleagues with different characteristics to gain a better understanding of their experiences. The article emphasizes the importance of having difficult conversations about equity, diversity, and inclusion in academic spaces, and highlights the need for respectful and inclusive dialogue. The author also emphasizes the importance of compassion and understanding for perspectives that may differ from one's own, and encourages the academic community to create space for diverse voices and experiences. [Extracted from the article]

The Journal of Cell Science has published a special issue on cell and tissue polarity. Cell polarization refers to the asymmetric distribution of cellular components, allowing for specialization and different cellular processes within individual cells. This concept is fundamental to various biological functions, such as feeding, propulsion, and the formation of tissues. The issue includes original research articles, reviews, and commentaries that explore the mechanisms and implications of cell and tissue polarity. The issue also highlights the work of early-career researchers and provides insights into the peer review process. [Extracted from the article]

Microbial studies typically involve the sequencing and assembly of draft genomes for individual microbes or whole microbiomes. Given a draft genome, one first task is to determine its phylogenetic context, that is, to place it relative to the set of related reference genomes. We provide a new interactive graphical tool that addresses this task using Mash sketches to compare against all bacterial and archaeal representative genomes in the Genome Taxonomy Database taxonomy, all within the framework of SplitsTree5. The phylogenetic context of the query sequences is then displayed as a phylogenetic outline, a new type of phylogenetic network that is more general than a phylogenetic tree, but significantly less complex than other types of phylogenetic networks. We propose to use such networks, rather than trees, to represent phylogenetic context, because they can express uncertainty in the placement of taxa, whereas a tree must always commit to a specific branching pattern. We illustrate the new method using a number of draft genomes of different assembly quality. [ABSTRACT FROM AUTHOR]

Tree comparison metrics have proven to be an invaluable aide in the reconstruction and analysis of phylogenetic (evolutionary) trees. The path-length distance between trees is a particularly attractive measure as it reflects differences in tree shape as well as differences between branch lengths. The distance equals the sum, over all pairs of taxa, of the squared differences between the lengths of the unique path connecting them in each tree. We describe an O (n log n) time for computing this distance, making extensive use of tree decomposition techniques introduced by Brodal et al. (Algorithmica 38(2):377–395, 2004). [ABSTRACT FROM AUTHOR]

Natural grasslands in southern Australia commonly exist in altered states. One widespread altered state is grassland pasture dominated by cool-season (C3) native grasses maintained by ongoing grazing. This study explores the consequences of removing grazing and introducing fire as a conservation management tool for such a site. We examined the abundance of two native and three exotic species, across a mosaic of fire regimes that occurred over a three-year period: unburnt, summer wild-fire (>2 years previous), autumn management fire (<1 year previously) and burnt in both fires. Given that one aim of conservation management is to increase native species at the expense of exotics, the impacts of the fires were largely positive. Native grasses were at higher cover levels in the fire-managed vegetation than in the unburnt vegetation. Of the three exotic species, one was consistently at lower density in the burnt plots compared to the unburnt plots, while the others were lower only in those plots burnt in summer. The results show that the response of a species varies significantly between different fire events, and that the effects of one fire can persist through subsequent fires. Importantly, some of the effects were large, with changes in the density of plants of over 100-fold. Fire is potentially a cost-effective tool to assist the ecological restoration of retired grassland pastures at large scales. [ABSTRACT FROM AUTHOR]

Consensus methods are widely used for combining phylogenetic trees into a single estimate of the evolutionary tree for a group of species. As more taxa are added, the newsource trees may begin to tell a different evolutionary story when restricted to the original set of taxa. However, if the newtrees, restricted to the original set of taxa,were to agree exactly with the earlier trees, then we might hope that their consensus would either agree with or resolve the original consensus tree. In this article,we ask under what conditions consensus methods exist that are "future proof" in this sense. Whilewe showthat some methods (e.g., Adams consensus) have this property for specific types of input, we also establish a rather surprising "no-go" theorem: there is no "reasonable" consensus method that satisfies the future-proofing property in general.We then investigate a second notion of "future proofing" for consensus methods, in which trees (rather than taxa) are added, and establish some positive and negative results. We end with some questions for future work. [ABSTRACT FROM AUTHOR]

Split networks are a popular tool for the analysis and visualization of complex evolutionary histories. Every collection of splits (bipartitions) of a finite set can be represented by a split network. Here we characterize which collection of splits can be represented using a planar split network. Our main theorem links these collections of splits with oriented matroids and arrangements of lines separating points in the plane. As a consequence of our main theorem, we establish a particularly simple characterization of maximal collections of these splits. [ABSTRACT FROM AUTHOR]

The formation of distinct subdomains of the cell surface is crucial for multicellular organism development. The most striking example of this is apical-basal polarization. What is much less appreciated is that underpinning an asymmetric cell surface is an equally dramatic intracellular endosome rearrangement. Here, we review the interplay between classical cell polarity proteins and membrane trafficking pathways, and discuss how this marriage gives rise to cell polarization. We focus on those mechanisms that regulate apical polarization, as this is providing a number of insights into how membrane traffic and polarity are regulated at the tissue level. [ABSTRACT FROM AUTHOR]

Context: Extracorporeal shockwave lithotripsy (SWL) is the first-line treatment for renal calculi in most cases. Recent technology has allowed lithotriptor machines to localize stones using fluoroscopy or ultrasound (US). Aim: The aim of this study is to compare stone free rates (SFR) using two techniques. Methods: This is a single center retrospective cohort study. We have studied 95 patients with renal calculi undergoing first SWL treatment with localization using US (48 pts) and fluoroscopy (47 pts). SFR was defined as fragments ≤2 m at 4 weeks post procedure on x-ray or US. Patient records were reviewed. Results: Stone size and location, age and body mass index were comparable between groups. Stones ≤7 mm had better SFR with US 86% (18/21) compared to fluoroscopy 59% (10/17) P = 0.08. Overall the US group had similar SFR to the fluoroscopy group for stones of all sizes and locations with 60% (29/48) compared to 45% (21/47) P = 0.18. Radiation exposure was the biggest difference between techniques with a mean radiation dose (mGy/cm2) in the US group of 103 (0-233) and 2113 (241-7821) in the fluoroscopy group. Radiation use in the US group was due to the use of a single shot pre-and post-procedure, this could be reduced to zero. Conclusions: Our data show equivalent outcomes using US compared to the traditional fluoroscopy localization technique. We would encourage departments to develop the use of US localization to reduce radiation exposure to patients. [ABSTRACT FROM AUTHOR]

Monophyletic groups--groups that consist of all of the descendants of a most recent common ancestor--arise naturally as a consequence of descent processes that result in meaningful distinctions between organisms. Aspects of monophyly are therefore central to fields that examine and use genealogical descent. In particular, studies in conservation genetics, phylogeography, population genetics, species delimitation, and systematics can all make use of mathematical predictions under evolutionary models about features of monophyly. One important calculation, the probability that a set of gene lineages is monophyletic under a two-species neutral coalescent model, has been used in many studies. Here, we extend this calculation for a species treemodel that contains arbitrarilymany species. We study the effects of species tree topology and branch lengths on the monophyly probability. These analyses reveal new behavior, including the maintenance of nontrivial monophyly probabilities for gene lineage samples that span multiple species and even for lineages that do not derive from a monophyletic species group. We illustrate the mathematical results using an example application to data from maize and teosinte. [ABSTRACT FROM AUTHOR]

Simulation experiments are used widely throughout evolutionary biology and bioinformatics to compare models, promote methods, and test hypotheses. The biggest practical constraint on simulation experiments is the computational demand, particularly as the number of parameters increases. Given the extraordinary success of Monte Carlo methods for conducting inference in phylogenetics, and indeed throughout the sciences, we investigate ways in which Monte Carlo framework can be used to carry out simulation experiments more efficiently. The key idea is to sample parameter values for the experiments, rather than iterate through them exhaustively. Exhaustive analyses become completely infeasible when the number of parameters gets too large, whereas sampled approaches can fare better in higher dimensions. We illustrate the framework with applications to phylogenetics and genetic archaeology. [ABSTRACT FROM AUTHOR]

In epithelial cells, the polarized orientation of the apical–basal axis determines the position of the apical lumen and, thereby, the collective tubular tissue architecture. From recent studies employing 3D cell cultures, animal models, and patient material, a model is emerging in which the orientation and positioning of the apical surface and lumen is controlled by the relationships between the extracellular matrix (ECM), Rho family GTPase signaling, recycling endosome dynamics, and cell division. Different epithelial cells adjust these relationships to establish their specific cell polarity orientation and lumen positioning, according to physiologic need. We provide an overview of the molecular mechanisms required to construct and orient the apical lumen. [ABSTRACT FROM AUTHOR]

Plant production systems globally must be optimized to produce stable high yields from limited land under changing and variable climates. Demands for food, animal feed, and feedstocks for bioenergy and biorefining applications, are increasing with population growth, urbanization and affluence. Low-input, sustainable, alternatives to petrochemical-derived fertilizers and pesticides are required to reduce input costs and maintain or increase yields, with potential biological solutions having an important role to play. In contrast to crops that have been bred for food, many bioenergy crops are largely undomesticated, and so there is an opportunity to harness beneficial plant-microbe relationships which may have been inadvertently lost through intensive crop breeding. Plant-microbe interactions span a wide range of relationships in which one or both of the organisms may have a beneficial, neutral or negative effect on the other partner. A relatively small number of beneficial plant-microbe interactions are well understood and already exploited; however, others remain understudied and represent an untapped reservoir for optimizing plant production. There may be near-term applications for bacterial strains as microbial biopesticides and biofertilizers to increase biomass yield from energy crops grown on land unsuitable for food production. Longer term aims involve the design of synthetic genetic circuits within and between the host and microbes to optimize plant production. A highly exciting prospect is that endosymbionts comprise a unique resource of reduced complexity microbial genomes with adaptive traits of great interest for a wide variety of applications. [ABSTRACT FROM AUTHOR]

The Company of Biologists held the workshop 'Intercellular interactions in context: towards a mechanistic understanding of cells in organs' at historic Wiston House in West Sussex, UK, 5-8 February 2017. The meeting brought together around 30 scientists from disparate backgrounds - yet with a common interest of how tissue morphogenesis occurs and its dysregulation leads to pathologies - to intensively discuss their latest research, the current state of the field, as well as any challenges for the future. This report summarises the concepts and challenges that arose as key questions for the fields of cell, cancer and developmental biology. By design of the organizers - Andrew Ewald (John Hopkins University, MA), John Wallingford (University of Texas at Austin, TX) and Peter Friedl (Radboud University, Nijmegen, The Netherlands) - the attendee makeup was cross-sectional: both in terms of career stage and scientific background. This intermingling was mirrored in the workshop format; all participants - irrespective of career stage - were given equal speaking and question time, and all early-career researchers also chaired a session, which promoted an atmosphere for discussions that were open, egalitarian and supportive. This was particularly evident in the scheduled 'out-ofthe- box' sessions, which provided an avenue for participants to raise ideas and concepts or to discuss specific problems they wanted feedback or clarification on. In the following, rather than act as court reporters and convey chronological accounting of presentations, we present the questions that arose from the workshop and should be posed to the field at large, by discussing the presentations as they relate to these concepts. [ABSTRACT FROM AUTHOR]

Summary The formation of epithelial tissues containing lumens requires not only the apical-basolateral polarization of cells, but also the coordinated orientation of this polarity such that the apical surfaces of neighboring cells all point toward the central lumen. Defects in extracellular matrix (ECM) signaling lead to inverted polarity so that the apical surfaces face the surrounding ECM. We report a molecular switch mechanism controlling polarity orientation. ECM signals through a β1-integrin/FAK/p190RhoGAP complex to downregulate a RhoA/ROCK/Ezrin pathway at the ECM interface. PKCβII phosphorylates the apical identity-promoting Podocalyxin/NHERF1/Ezrin complex, removing Podocalyxin from the ECM-abutting cell surface and initiating its transcytosis to an apical membrane initiation site for lumen formation. Inhibition of this switch mechanism results in the retention of Podocalyxin at the ECM interface and the development instead of collective front-rear polarization and motility. Thus, ECM-derived signals control the morphogenesis of epithelial tissues by controlling the collective orientation of epithelial polarization. [ABSTRACT FROM AUTHOR]

People can make use of a range of heuristic and rational, compensatory strategies to perform a multiple-cue judgment task. It has been proposed that people are sensitive to the amount of cognitive effort required to employ decision strategies. Experiment 1 employed a dual-task methodology to investigate whether participants’ preference for heuristic versus compensatory decision strategies can be altered by increasing the cognitive demands of the task. As indicated by participants’ decision times, a secondary task interfered more with the performance of a heuristic than compensatory decision strategy but did not affect the proportions of participants using either type of strategy. A stimulus set effect suggested that the conjunction of cue salience and cue validity might play a determining role in strategy selection. The results of Experiment 2 indicated that when a perceptually salient cue was also the most valid, the majority of participants preferred a single-cue heuristic strategy. Overall, the results contradict the view that heuristics are more likely to be adopted when a task is made more cognitively demanding. It is argued that people employ 2 learning processes during training, one an associative learning process in which cue-outcome associations are developed by sampling multiple cues, and another that involves the sequential examination of single cues to serve as a basis for a single-cue heuristic. [ABSTRACT FROM AUTHOR]

The embedding of finite metrics in ℓ1 has become a fundamental tool for both combinatorial optimization and large-scale data analysis. One important application is to network flow problems as there is close relation between max-flow min-cut theorems and the minimal distortion embeddings of metrics into ℓ1. Here we show that this theory can be generalized to a larger set of combinatorial optimization problems on both graphs and hypergraphs. This theory is not built on metrics and metric embeddings, but on diversities, a type of multi-way metric introduced recently by the authors. We explore diversity embeddings, ℓ1 diversities, and their application to Steiner Tree Packing and Hypergraph Cut problems. [ABSTRACT FROM AUTHOR]

The embedding of finite metrics in l1 has become a fundamental tool for both combinatorial optimization and largescale data analysis. One important application is to network flow problems as there is close relation between max-flow min-cut theorems and the minimal distortion embeddings of metrics into l1. Here we show that this theory can be generalized to a larger set of combinatorial optimization problems on both graphs and hypergraphs. This theory is not built on metrics and metric embeddings, but on diversities, a type of multi-way metric introduced recently by the authors. We explore diversity embeddings, l1 diversities, and their application to Steiner Tree Packing and Hypergraph Cut problems. [ABSTRACT FROM AUTHOR]

Christian ecotheology tends to emphasize human identity with the rest of nature while also arguing that human society requires transformation through appreciation of intrinsic value in non-human nature. Since this sets up a tension between notions of humans as natural beings and as free to choose among alternative motivations, it would benefit Christian ecotheology to think more consistently about implications of humanity's belonging to nature. Science has provided compelling reasons for thinking that egoism is an incorrigible dimension of human life, thereby suggesting that abusive exploitation of nature has deeper roots than cultural constructs. This realization calls for fundamental rethinking of several traditional Christian doctrines, including the Fall, original sin, and free will. In fact, some theologies already anticipate these revisions, though more remains to be done. Moreover, Christian ecotheology's attention to concepts of connections between humans and nature and of nature's value remains important, but some of its emphases need to change. [ABSTRACT FROM AUTHOR]

The emergence of mechanisms for phosphorylating organic and inorganic molecules is a key step en route to the earliest living systems. At the heart of all contemporary biochemical systems reside reactive phosphorus (P) molecules (such as adenosine triphosphate, ATP) as energy currency molecules to drive endergonic metabolic processes and it has been proposed that a predecessor of such molecules could have been pyrophosphate [P2O74-; PPi(V)]. Arguably the most geologically plausible route to PPi(V) is dehydration of orthophosphate, Pi(V), normally a highly endergonic process in the absence of mechanisms for activating Pi(V). One possible solution to this problem recognizes the presence of reactive-P containing mineral phases, such as schreibersite [(Fe,Ni)3P] within meteorites whose abundance on the early Earth would likely have been significant during a putative Hadean-Archean heavy bombardment. Here, we propose that the reduced oxidation state P-oxyacid, H-phosphite [HPO32-; Pi(III)] could have activated Pi(V) towards condensation via the intermediacy of the condensed oxyacid pyrophosphite [H2P2O52-; PPi(III)]. We provide geologically plausible provenance for PPi(III) along with evidence of its ability to activate Pi(V) towards PPi(V) formation under mild conditions (80 °C) in water. [ABSTRACT FROM AUTHOR]

Background: The multispecies coalescent model has become popular in recent years as a framework to infer a species phylogeny from multilocus genetic data collected from multiple individuals. The model assumes that speciation occurs at a specific point in time, after which the two sub-species evolve in total isolation. However in reality speciation may occur over an extended period of time, during which sister lineages remain in partial contact. Inference of multispecies phylogenies under those conditions is difficult. Indeed even designing simulators which correctly sample gene histories under these conditions is non-trivial. Results: In this paper we present a method and software which simulates gene trees under both the multispecies coalescent and migration. Our approach allows for both population sizes and migration rates to change over the species lifetime. Also, migration rates are specified in units of fraction of emigrants per time unit, which makes them easier to interpret. Overall this setup covers a wide range of migration scenarios. The software can be used to investigate properties of gene trees under different migration settings and to generate test cases for programs which infer species trees and/or migration from sequence data. Using simulated data we investigate the effect of migrations between sister lineages on the inference of multispecies phylogenies and on post analysis detection. Conclusions: Our results indicate that while estimation of species tree topology can be quite robust to the presence of gene flow, the inference and detection of migration is problematic, even with methods based on full likelihood models. [ABSTRACT FROM AUTHOR]

Abstract: The Sikhote-Alin (SA) meteorite is an example of a type IIAB octahedrite iron meteorite with ca. 0.5wt% phosphorus (P) content principally in the form of the siderophilic mineral schreibersite (Fe,Ni)3P. Meteoritic in-fall to the early Earth would have added significantly to the inventory of such siderophilic P. Subsequent anaerobic corrosion in the presence of a suitable electrolyte would produce P in a form different to that normally found within endogenous geochemistry which could then be released into the environment. One environment of specific interest includes the low pH conditions found in fumaroles or volcanically heated geothermal waters in which anodic oxidation of Fe metal to ferrous (Fe2+) and ferric (Fe3+) would be coupled with cathodic reduction of a suitable electron acceptor. In the absence of aerobic dioxygen (E o =+1.229V), the proton would provide an effective final electron acceptor, being converted to dihydrogen gas (E o =0V). Here we explore the hydrothermal modification of sectioned samples of the Sikhote-Alin meteorite in which siderophilic P-phases are exposed. We report on both, (i) simulated volcanic conditions using low pH distilled water and (ii) geothermally heated sub-glacial fluids from the northern Kverkfjöll volcanic region of the Icelandic Vatnajoküll glacier. A combination of X-ray photoelectron spectroscopy (XPS) and electrochemical measurements using the scanning Kelvin probe (SKP) method reveals that schreibersite inclusions are significantly less susceptible to anodic oxidation than their surrounding Fe–Ni matrix, being some 550mV nobler than matrix material. This results in preferential corrosion of the matrix at the matrix-inclusion boundary as confirmed using topological mapping via infinite focus microscopy and chemical mapping through Raman spectroscopy. The significance of these observations from a chemical perspective is that electrochemically noble inclusions such as schreibersite are likely to have been released into the geological environment through an undermining corrosion of the surrounding matrix, thus affording localised sources of available water-soluble, chemically reactive P in the form of H-phosphite [, Pi(III) as determined by 31P NMR spectroscopy]. This compound has been shown to have considerable prebiotic chemical potential as a source of condensed P-oxyacids. Here we demonstrate that Pi(III) resulting from the hydrothermal modification of Sikhote-Alin by sub-glacial geothermal fluids can be readily dehydrated into the condensed P-oxyacid pyrophosphite [, PPi(III)] by dry-heating under mild (85°C) conditions. The potential significance of this latter condensed P-compound for prebiotic chemistry is discussed in the light of its modified chemical properties compared to pyrophosphate [, PPi(V)]. [Copyright &y& Elsevier]

Objective: We examined the effectiveness of blue force tracking (BFT) decision support for dismounted infantry soldiers.Background: Technologies to support combat identification (CID) are rapidly evolving and may be deployable to dismounted soldiers in the future. BFT systems are designed to mitigate the risk of fratricide by supplying positional information regarding friendly units to enhance situation awareness.Method: Participants played the role of a dismounted infantry soldier in a first-person perspective gaming environment and made engagement decisions for a series of simulated targets, half of which were enemies and half of which were friends.Results: Participants performed better overall when they were able to use a BFT system than when they performed the task without assistance. When a 10-s latency was added to the updating of position information in the BFT, participants made significantly more false alarms (engaged a friendly target) regardless of whether they knew about the latency.Conclusion: The results indicate the promise of a personal BFT device to reduce the likelihood of fratricide by dismounted infantry soldiers. The results, however, also indicate that the effectiveness of such a device can be dramatically reduced when it does not provide real-time data.Application: Potential applications of this research include development of performance standards for BFT devices and assessment of decision support for dismounted soldiers. [ABSTRACT FROM AUTHOR]

Objective: We examined the effectiveness of blue force tracking (BFT) decision support for dismounted infantry soldiers. Background: Technologies to support combat identification (CID) are rapidly evolving and may be deployable to dismounted soldiers in the future. BFT systems are designed to mitigate the risk of fratricide by supplying positional information regarding friendly units to enhance situation awareness. Method: Participants played the role of a dismounted infantry soldier in a first-person perspective gaming environment and made engagement decisions for a series of simulated targets, half of which were enemies and half of which were friends. Results: Participants performed better overall when they were able to use a BFT system than when they performed the task without assistance. When a 10-s latency was added to the updating of position information in the BFT, participants made significantly more false alarms (engaged a friendly target) regardless of whether they knew about the latency. Conclusion: The results indicate the promise of a personal BFT device to reduce the likelihood of fratricide by dismounted infantry soldiers. The results, however, also indicate that the effectiveness of such a device can be dramatically reduced when it does not provide real-time data. Application: Potential applications of this research include development of performance standards for BFT devices and assessment of decision support for dismounted soldiers. [ABSTRACT FROM AUTHOR]

Abstract: Dielectric spectroscopy (DS) has been used to monitor the simultaneous saccharification and fermentation of lignocellulosic biomass by measuring its dielectric state. However, it is unknown whether following steam explosion (SE) pre-treatment, lignocellulose would still maintain a dielectric state, and, if maintained, whether the dissipation during enzymatic hydrolysis could be monitored. Distillers Dried Grains with Solubles (DDGS), pre-treated by SE, was found to have a capacitance (C =580kHz) of approximately 24pFcm−1. Following addition of full-strength cellulolytic cocktail A (CC-A; R 2 =0.97) and 1/3 strength cocktail B (CC-B; R 2 =0.96), a natural logarithmic decay in capacitance was determined. Furthermore, the DS biomass probes quantified the initial linear rate of dissipation in capacitance during hydrolysis. The rate of CC-B was 34% that of CC-A. These data extend scope and utility of DS biomass probes for monitoring the enzymatic hydrolysis of SE-pre-treated lignocellulosic substrates in real-time. [Copyright &y& Elsevier]

Abstract: The tight span, or injective envelope, is an elegant and useful construction that takes a metric space and returns the smallest hyperconvex space into which it can be embedded. The concept has stimulated a large body of theory and has applications to metric classification and data visualisation. Here we introduce a generalisation of metrics, called diversities, and demonstrate that the rich theory associated to metric tight spans and hyperconvexity extends to a seemingly richer theory of diversity tight spans and hyperconvexity. [Copyright &y& Elsevier]

The standard models of sequence evolution on a tree determine probabilities for every character or site pattern. A flattening is an arrangement of these probabilities into a matrix, with rows corresponding to all possible site patterns for one set A of taxa and columns corresponding to all site patterns for another set B of taxa. Flattenings have been used to prove difficult results relating to phylogenetic invariants and consistency and also form the basis of several methods of phylogenetic inference. We prove that the rank of the flattening equals r ν T (A | B) , where r is the number of states and ν T (A | B) is the minimum size of a vertex cut separating A from B. When T is binary the rank of the flattening equals r ℓ T (A | B) where ℓ T (A | B) equals the parsimony length of the binary character separating A and B. We provide a direct proof that requires little more than undergraduate algebra, but note that the formula could also be derived from work by Casanellas and Fernández-Sánchez (2011) on phylogenetic invariants. [ABSTRACT FROM AUTHOR]

Abstract: We say that a collection of subsets of is bureaucratic if every maximal hierarchy on contained in is also maximum. We characterize bureaucratic set systems and show how they arise in phylogenetics. This framework has several useful algorithmic consequences: we generalize some earlier results and derive a polynomial-time algorithm for a parsimony problem arising in phylogenetic networks. [Copyright &y& Elsevier]

Increasing the extractable sugar yield from perennial crops is one strategy to generate renewable fuels such as bio-ethanol. Lolium perenne L. (perennial ryegrass) can contain significant (>30% dry matter) water-soluble sugars in the form of polymeric fructan which is readily extracted, broken down and fermented to bio-ethanol. A population of L. perenne generated from four parents which differed in water-soluble carbohydrate (WSC) content was subjected to multiple rounds of selection and recombination on the basis of early spring WSC content to produce a high WSC, and a low WSC population. A control population was generated by selecting the same number of plants at random. The alleles present at six candidate gene loci were analysed before and after selection and correlated to WSC content. Significant differences in the allele frequency of L. perenne soluble-acid invertase1:4 were observed between the three populations with one haplotype significantly associated with the high WSC C2 population (after three rounds of selection and two rounds of recombination). Moreover, WSC content was also associated with biomass accumulation. Thus, in addition to a 2.84-fold increase in WSC yield, the C2 population also had 1.48-fold more biomass per plant, resulting in 3.9-fold higher WSC yield per plant than the control population. [ABSTRACT FROM AUTHOR]

We derive an invertible transform linking two widely used measures of species diversity: phylogenetic diversity and the expected proportions of segregating (non-constant) sites. We assume a bi-allelic (two-state), symmetric, finite site model of substitution. Like the Hadamard transform of Hendy and Penny, the transform can be expressed independently of the underlying phylogeny. Our results bridge work on diversity from two quite distinct scientific communities. [ABSTRACT FROM AUTHOR]

Abstract: Dielectric spectroscopy (DS) is routinely used in yeast and mammalian fermentations to quantitatively monitor viable biomass through the inherent capacitance of live cells; however, the use of DS to monitor the enzymatic break down of lignocellulosic biomass has not been reported. The aim of the current study was to examine the application of DS in monitoring the enzymatic saccharification of high sugar perennial ryegrass (HS-PRG) fibre and to relate the data to changes in chemical composition. DS was capable of both monitoring the on-line decrease in PRG fibre capacitance (C =580kHz) during enzymatic hydrolysis, together with the subsequent increase in conductivity (G =580kHz) resulting from the production of organic acids during microbial growth. Analysis of the fibre fractions revealed >50% of HS-PRG lignocellulose had undergone enzymatic hydrolysis. These data demonstrated the utility of DS biomass probes for on-line monitoring of simultaneous saccharification and fermentation (SSF). [Copyright &y& Elsevier]

Summary [ABSTRACT FROM AUTHOR]

The Rab GTPases are the largest family of proteins regulating membrane traffic. Rab proteins form a nidus for the assembly of multiprotein complexes on distinct vesicle membranes to regulate particular membrane trafficking pathways. Recent investigations have demonstrated that Myosin Vb (Myo5B) is an effector for Rab8a, Rab10, and Rab11a, all of which are implicated in regulating different pathways for recycling of proteins to the plasma membrane. It remains unclear how specific interactions of Myo5B with individual Rab proteins can lead to specificity in the regulation of alternate trafficking pathways. We examined the relative contributions of Rab/Myo5B interactions with specific pathways using Myo5B mutants lacking binding to either Rab11a or Rab8a. Myo5B Q1300L and Y1307C mutations abolished Rab8a association, whereas Myo5B Y1714E and Q1748R mutations uncoupled association with Rab11a. Expression of Myo5B tails containing these mutants demonstrated that Rab11a, but not Rab8a, was required for recycling of transferrin in nonpolarized cells. In contrast, in polarized epithelial cyst cultures, Myo5B was required for apical membrane trafficking and de novo lumen formation, dependent on association with both Rab8a and Rab11a. These data demonstrate that different combinations of Rab GTPase association with Myo5B control distinct membrane trafficking pathways. [ABSTRACT FROM AUTHOR]

This paper considers a study of the thermo-elastic behaviour of a disc brake during heavy braking. The work is concerned with working towards developing design advice that provides uniform heating of the disc, and equally important, even dissipation of heat from the disc blade. The material presented emanates from a combination of modeling, on-vehicle testing but mainly laboratory observations and subsequent investigations. The experimental work makes use of a purpose built high speed brake dynamometer which incorporates the full vehicle suspension for controlled simulation of the brake and vehicle operating conditions. Advanced instrumentation allows dynamic measurement of brake pressure fluctuations, disc surface temperature and discrete vibration measurements. Disc run-out measurements using non-contacting displacement transducers show the disc taking up varying orders of deformation ranging from first to third order during high speed testing. This surface interrogation during braking identifies disc deformation including disc warping, "ripple" and the effects of "hot spotting". The mechanical measurements are complemented by thermal imaging of the brake, these images showing the vane and vent patterns on the surface of the disc. The results also include static surface scanning, or geometry analysis, of the disc which is carried out at appropriate stages during testing. The work includes stress relieving of finished discs and subsequent dynamometer testing. This identifies that in-service stress relieving, due to high heat input during braking, is a strong possibility for the cause of disc "warping". It is also seen that an elastic wave is established during a braking event, the wave disappearing on release of the brake. [ABSTRACT FROM AUTHOR]

The paper overviews the modes of vibration of the principal component parts of a brake and their contribution to system instability during noise generation. It is shown that both in-plane and out-of-plane vibration is present and that both can be related to the vibration of the pad. It is further shown that the pad and its region often provide a solution or "fix" towards noise prevention and it is this area that forms the focus of this investigation. The collective evidence, proposals and associated theory are applied to real brake case studies when it is demonstrated that disc/pad interface "spragging" may be the source of brake noise. Measurements of the position of the dynamic centre of pressure (CoP) support the theoretical predictions that a leading CoP induces brake noise. Design proposals are suggested that may be applied early in the design phase as a means to reduce the propensity of a brake to generate noise. [ABSTRACT FROM AUTHOR]

Polymeric immunoglobulin A (pIgA) transcytosis, mediated by the polymeric immunoglobulin receptor (pIgR), is a central component of mucosal immunity and a model for regulation of polarized epithelial membrane traffic. Binding of pIgA to pIgR stimulates transcytosis in a process requiring Yes, a Src family tyrosine kinase (SFK). We show that Yes directly phosphorylates EGF receptor (EGFR) on liver endosomes. Injection of pIgA into rats induced EGFR phosphorylation. Similarly, in MDCK cells, pIgA treatment significantly increased phosphorylation of EGFR on various sites, subsequently activating extracellular signal-regulated protein kinase (ERK). Furthermore, we find that the Rab11 effector Rab11-FIP5 is a substrate of ERK. Knocking down Yes or Rab11-FIP5, or inhibition of the Yes-EGFR-ERK cascade, decreased pIgA-pIgR transcytosis. Finally, we demonstrate that Rab11-FIP5 phosphorylation by ERK controls Rab11a endosome distribution and pIgA-pIgR transcytosis. Our results reveal a novel Yes-EGFR-ERK-FIP5 signalling network for regulation of pIgA-pIgR transcytosis. [ABSTRACT FROM AUTHOR]

To form epithelial organs cells must polarize and generate de novo an apical domain and lumen. Epithelial polarization is regulated by polarity complexes that are hypothesized to direct downstream events, such as polarized membrane traffic, although this interconnection is not well understood. We have found that Rab11a regulates apical traffic and lumen formation through the Rab guanine nucleotide exchange factor (GEF), Rabin8, and its target, Rab8a. Rab8a and Rab11a function through the exocyst to target Par3 to the apical surface, and control apical Cdc42 activation through the Cdc42 GEF, Tuba. These components assemble at a transient apical membrane initiation site to form the lumen. This Rab11a-directed network directs Cdc42-dependent apical exocytosis during lumen formation, revealing an interaction between the machineries of vesicular transport and polarization. [ABSTRACT FROM AUTHOR]

Safeners enhance the selectivity of graminicidal herbicides such as fenoxaprop ethyl in cereals, by increasing their rates of detoxification in the crop. While studying the selectivity of fenoxaprop ethyl in wheat, we determined that the safeners mefenpyr diethyl and fenchlorazole ethyl also enhanced herbicide tolerance in the competing weed black-grass ( Alopecurus myosuroides). Fenoxaprop ethyl was detoxified by conjugation with glutathione in both wheat and black-grass, with the resulting metabolites processed to the respective cysteine derivatives, which were then N-glycosylated. In black-grass, these detoxification pathways were only slightly enhanced by safeners, suggesting that metabolism alone was unlikely to account for increased herbicide tolerance. Instead, it was determined that safening was associated with an accumulation of glutathione and hydroxymethylglutathione and enzymes with antioxidant functions including phi and lambda glutathione transferases, active as glutathione peroxidases and thiol transferases respectively. These safener-induced changes closely mirrored those determined in two independent black-grass populations that had acquired multiple herbicide resistance (MHR) in the field. In addition to enhanced glutathione metabolism, both safener treatment and MHR resulted in elevated levels of flavonoids in the foliage of black-grass plants, notably flavone- C-glycosides and anthocyanins. Our results demonstrate that safening in a grass weed is associated with an inducible activation in antioxidant and secondary metabolism which mirrors the biochemical phenotype exhibited in plants that are resistant to multiple classes of herbicides. [ABSTRACT FROM AUTHOR]

The Hadamard transform (Hendy and Penny, Syst. Zool. 38(4):297-309, 1989; Hendy, Syst. Zool. 38(4):310-321, 1989) provides a way to work with stochastic models for sequence evolution without having to deal with the complications of tree space and the graphical structure of trees. Here we demonstrate that the transform can be expressed in terms of the familiar P[τ] = ℯQ[τ] formula for Markov chains. The key idea is to study the evolution of vectors of states, one vector entry for each taxa; we call this the n-taxon process. We derive transition probabilities for the process. Significantly, the findings show that tree-based models are indeed in the family of (multi-variate) exponential distributions. [ABSTRACT FROM AUTHOR]

The mineral schreibersite, (Fe,Ni)3P, a ubiquitous component of iron meteorites, is known to undergo anoxic hydrolytic modification to afford a range of phosphorus oxyacids. H-phosphonic acid (H3PO3) is the principal hydrolytic product under hydrothermal conditions, as confirmed here by 31P-NMR spectroscopic studies on shavings of the Seymchan pallasite (Magadan, Russia, 1967), but in the presence of photochemical irradiation a more reduced derivative, H-phosphinic (H3PO2) acid, dominates. The significance of such lower oxidation state oxyacids of phosphorus to prebiotic chemistry upon the early Earth lies with the facts that such forms of phosphorus are considerably more soluble and chemically reactive than orthophosphate, the commonly found form of phosphorus on Earth, thus allowing nature a mechanism to circumvent the so-called Phosphate Problem. This paper describes the Galvanic corrosion of Fe3P, a hydrolytic modification pathway for schreibersite, leading again to H-phosphinic acid as the key P-containing product. We envisage this pathway to be highly significant within a meteoritic context as iron meteorites are polymetallic composites in which dissimilar metals, with different electrochemical potentials, are connected by an electrically conducting matrix. In the presence of a suitable electrolyte medium, i.e., salt water, galvanic corrosion can take place. In addition to model electrochemical studies, we also report the first application of the Kelvin technique to map surface potentials of a meteorite sample that allows the electrochemical differentiation of schreibersite inclusions within an Fe:Ni matrix. Such experiments, coupled with thermodynamic calculations, may allow us to better understand the chemical redox behaviour of meteoritic components with early Earth environments. [ABSTRACT FROM AUTHOR]

How do animal cells assemble into tissues and organs? A diverse array of tissue structures and shapes can be formed by organizing groups of cells into different polarized arrangements and by coordinating their polarity in space and time. Conserved design principles underlying this diversity are emerging from studies of model organisms and tissues. We discuss how conserved polarity complexes, signalling networks, transcription factors, membrane-trafficking pathways, mechanisms for forming lumens in tubes and other hollow structures, and transitions between different types of polarity, such as between epithelial and mesenchymal cells, are used in similar and iterative manners to build all tissues. [ABSTRACT FROM AUTHOR]

We give formulas for calculating in polynomial time the number of ancestral reconstructions for a tree with binary leaf- and root labels for each number of 0 $$\rightarrow$$ 1 and 1 $$\rightarrow$$ 0 arcs. For trees of fixed degree, the corresponding numbers of 0 $$\rightarrow$$ 0 and 1 $$\rightarrow$$ 1 arcs can be deduced. We calculate intervals for the relative cost of 0 $$\rightarrow$$ 1 and 1 $$\rightarrow$$ 0 transitions over which the same labelings remain the cheapest. [ABSTRACT FROM AUTHOR]

Determining an optimal phylogenetic tree using maximum parsimony, also referred to as the Steiner tree problem in phylogenetics, is NP hard. Here we provide a new formulation for this problem which leads to an analytical and linear time solution when the dimensionality (sequence length, or number of characters) is at most two. This new formulation of the problem provides a direct link between the maximum parsimony problem and the maximum compatibility problem via the intersection graph. The solution for the “two character case” has numerous practical applications in phylogenetics, some of which are discussed. [ABSTRACT FROM AUTHOR]

The parsimony score of a character on a tree equals the number of state changes required to fit that character onto the tree. We show that for unordered, reversible characters this score equals the number of tree rearrangements required to fit the tree onto the character. We discuss implications of this connection for the debate over the use of consensus trees or total evidence and show how it provides a link between incongruence of characters and recombination. [ABSTRACT FROM AUTHOR]

Abstract: An important procedure in the mathematics of phylogenetic analysis is to associate, to any collection of weighted splits, the metric given by the corresponding linear combination of split metrics. In this note, we study necessary and sufficient conditions for a collection of splits of a given finite set to give rise to a linearly independent collection of split metrics. In addition, we study collections of splits called affine split systems induced by a configurations of lines and points in the plane. These systems not only satisfy the linear-independence condition, but also provide a -basis of the -lattice consisting of all integer-valued symmetric maps defined on that vanish on the diagonal and for which, in addition, holds for all . This -lattice is generated by all split metrics considered as vectors in the real vectorspace consisting of all real-valued symmetric maps defined on that vanish on the diagonal — and, hence, is also an -basis of that vectorspace. [Copyright &y& Elsevier]

Genome phylogenies can be inferred from data on the presence and absence of genes across taxa. Logdet distances may be a good method, because they allow expected genome size to vary across the tree. Recently, Lake and Rivera proposed conditioned genome reconstruction (calculation of logdet distances using only those genes present in a conditioning genome) to deal with unobservable genes that are absent from every taxon of interest. We prove that their method can consistently estimate the topology for almost any choice of conditioning genome. Nevertheless, the choice of conditioning genome is important for small samples. For real bacterial genome data, different choices of conditioning genome can result in strong bootstrap support for different tree topologies. To overcome this problem, we developed supertree methods that combine information from all choices of conditioning genome. One of these methods, based on the BIONJ algorithm, performs well on simulated data and may have applications to other supertree problems. However, an analysis of 40 bacterial genomes using this method supports an incorrect clade of parasites. This is a common feature of model-based gene content methods and is due to parallel gene loss. [ABSTRACT FROM AUTHOR]

Abstract: A glutathione transferase (GST) related to the theta (T) class of enzymes found in plants and animals has been cloned from the potato pathogen Phytophthora infestans. The cDNA encoded a 25kDa polypeptide termed PiGSTT1 which was expressed in E. coli as the native protein. The purified recombinant enzyme behaved as a dimer (PiGSTT1-1) and while being unable to catalyse the glutathione conjugation of 1-chloro-2,4-dintrobenzene, was highly active as a glutathione peroxidase with organic hydroperoxide substrates. In addition to reducing the synthetic substrate cumene hydroperoxide, PiGSTT1-1 was shown to be highly active toward 9(S)-hydroperoxy-(10E,12Z,15Z)-octadecatrienoic acid=9(S)-HPOT, which is formed in potato plants during infection by P. infestans as a precursor of the antifungal oxylipin colnelenic acid. An antiserum was raised to PiGSTT1-1 and used to demonstrate that the respective enzyme was abundantly expressed in P. infestans both cultured on pea agar and during the infection of potato plants. [Copyright &y& Elsevier]

Woody debris (WD) is an important component of forest C budgets, both as a C reservoir and source of CO2 to the atmosphere. We used an infrared gas analyzer and closed dynamic chamber to measure CO2 efflux from downed coarse WD (CWD; diameter≥7.5 cm) and fine WD (FWD; 7.5 cm>diameter≥2 cm) to assess respiration in a selectively logged forest and a maturing forest (control site) in the northeastern USA. We developed two linear regression models to predict WD respiration: one based on WD temperature, moisture, and size ( R 2=0.57), and the other on decay class and air temperature ( R 2=0.32). WD respiration (0.28±0.09 Mg C ha−1 year−1) contributed only ≈2% of total ecosystem respiration (12.3±0.7 Mg C ha−1 year−1, 1999–2003), but net C flux from CWD accounted for up to 30% of net ecosystem exchange in the maturing forest. C flux from CWD on the logged site increased modestly, from 0.61±0.29 Mg C ha−1 year−1 prior to logging to 0.77±0.23 Mg C ha−1 year−1 after logging, reflecting increased CWD stocks. FWD biomass and associated respiration flux were ≈7 times and ≈5 times greater, respectively, in the logged site than the control site. The net C flux associated with CWD, including inputs and respiratory outputs, was 0.35±0.19 Mg C ha−1 year−1 (net C sink) in the control site and −0.30±0.30 Mg C ha−1 year−1 (net C source) in the logged site. We infer that accumulation of WD may represent a small net C sink in maturing northern hardwood forests. Disturbance, such as selective logging, can enlarge the WD pool, increasing the net C flux from the WD pool to the atmosphere and potentially causing it to become a net C source. [ABSTRACT FROM AUTHOR]