Free-algebra functors from a coalgebraic perspective

Given a set $\Sigma$ of equations, the free-algebra functor $F_{\Sigma}$ associates to each set $X$ of variables the free algebra $F_{\Sigma}(X)$ over $X$. Extending the notion of \emph{derivative} $\Sigma'$ for an arbitrary set $\Sigma$ of equations, originally defined by Dent, Kearnes, and Szendrei, we show that $F_\Sigma$ preserves preimages if and only if $\Sigma \vdash \Sigma'$, i.e. $\Sigma$ derives its derivative $\Sigma'$. If $F_\Sigma$ weakly preserves kernel pairs, then every equation $p(x,x,y)=q(x,y,y)$ gives rise to a term $s(x,y,z,u)$ such that $p(x,y,z)=s(x,y,z,z)$ and $q(x,y,z)=s(x,x,y,z)$. In this case n-permutable varieties must already be permutable, i.e. Mal'cev. Conversely, if $\Sigma$ defines a Mal'cev variety, then $F_\Sigma$ weakly preserves kernel pairs. As a tool, we prove that arbitrary $Set-$endofunctors $F$ weakly preserve kernel pairs if and only if they weakly preserve pullbacks of epis

Bisimulation of Labeled State-to-Function Transition Systems of Stochastic Process Languages

Labeled state-to-function transition systems, FuTS for short, admit multiple transition schemes from states to functions of finite support over general semirings. As such they constitute a convenient modeling instrument to deal with stochastic process languages. In this paper, the notion of bisimulation induced by a FuTS is proposed and a correspondence result is proven stating that FuTS-bisimulation coincides with the behavioral equivalence of the associated functor. As generic examples, the concrete existing equivalences for the core of the process algebras ACP, PEPA and IMC are related to the bisimulation of specific FuTS, providing via the correspondence result coalgebraic justification of the equivalences of these calculi.Comment: In Proceedings ACCAT 2012, arXiv:1208.430

Dissolved noble gases and stable isotopes as tracers of preferential fluid flow along faults in the Lower Rhine Embayment, Germany

Groundwater in shallow unconsolidated sedimentary aquifers close to the Bornheim fault in the Lower Rhine Embayment (LRE), Germany, has relatively low δ2H and δ18O values in comparison to regional modern groundwater recharge, and 4He concentrations up to 1.7 × 10−4 cm3 (STP) g–1 ± 2.2 % which is approximately four orders of magnitude higher than expected due to solubility equilibrium with the atmosphere. Groundwater age dating based on estimated in situ production and terrigenic flux of helium provides a groundwater residence time of ∼107 years. Although fluid exchange between the deep basal aquifer system and the upper aquifer layers is generally impeded by confining clay layers and lignite, this study’s geochemical data suggest, for the first time, that deep circulating fluids penetrate shallow aquifers in the locality of fault zones, implying  that sub-vertical fluid flow occurs along faults in the LRE. However, large hydraulic-head gradients observed across many faults suggest that they act as barriers to lateral groundwater flow. Therefore, the geochemical data reported here also substantiate a conduit-barrier model of fault-zone hydrogeology in unconsolidated sedimentary deposits, as well as corroborating the concept that faults in unconsolidated aquifer systems can act as loci for hydraulic connectivity between deep and shallow aquifers. The implications of fluid flow along faults in sedimentary basins worldwide are far reaching and of particular concern for carbon capture and storage (CCS) programmes, impacts of deep shale gas recovery for shallow groundwater aquifers, and nuclear waste storage sites where fault zones could act as potential leakage pathways for hazardous fluids

Assessing the effectiveness of a three-stage on-farm biobed in treating pesticide contaminated wastewater

Agricultural point source pesticide pollution arising from contaminated machinery washings and accidental spillages pose a significant threat to river water and groundwater quality. In this study, we assess the effectiveness of a three-stage on-farm biobed for treating pesticide contaminated waste water from a large (20 km2) commercial arable estate. The facility consisted of an enclosed machinery wash-down unit (stage 1), a 49 m2 lined compost-straw-topsoil biobed (stage 2), and a 200 m2 drainage field with a trickle irrigation system (stage 3). Pesticide concentrations were analysed in water samples collected fortnightly between November 2013 and November 2015 from the biobed input and output sumps and from 20 porous pots buried at 45 cm and 90 cm depth within the drainage field. The results revealed that the biobed removed 68–98% of individual pesticides within the contaminated washings, with mean total pesticide concentrations reducing by 91.6% between the biobed input and output sumps. Drainage field irrigation removed a further 68–99% of individual pesticides, with total mean pesticide concentrations reducing by 98.4% and 97.2% in the 45 cm and 90 cm depth porous pots, respectively. The average total pesticide concentration at 45 cm depth in the drainage field (57 µg L-1) was 760 times lower than the mean concentration recorded in the input sump (43,334 µg L-1). There was no evidence of seasonality in the efficiency of biobed pesticide removal, nor was there evidence of a decline in removal efficiency over the two-year monitoring period. However, higher mean total pesticide concentrations at 90 cm (102 µg L-1) relative to 45 cm (57 µg L-1) depth indicated an accumulation of pesticide residues deeper within the soil profile. Overall, the results presented here demonstrate that a three-stage biobed can successfully reduce pesticide pollution risk from contaminated machinery washings on a commercial farm

Relating coalgebraic notions of bisimulation

The theory of coalgebras, for an endofunctor on a category, has been proposed as a general theory of transition systems. We investigate and relate four generalizations of bisimulation to this setting, providing conditions under which the four different generalizations coincide. We study transfinite sequences whose limits are the greatest bisimulations

Complete Genome Characterisation of a Novel 26th Bluetongue Virus Serotype from Kuwait

Bluetongue virus is the “type” species of the genus Orbivirus, family Reoviridae. Twenty four distinct bluetongue virus (BTV) serotypes have been recognized for decades, any of which is thought to be capable of causing “bluetongue” (BT), an insect-borne disease of ruminants. However, two further BTV serotypes, BTV-25 (Toggenburg orbivirus, from Switzerland) and BTV-26 (from Kuwait) have recently been identified in goats and sheep, respectively. The BTV genome is composed of ten segments of linear dsRNA, encoding 7 virus-structural proteins (VP1 to VP7) and four distinct non-structural (NS) proteins (NS1 to NS4). We report the entire BTV-26 genome sequence (isolate KUW2010/02) and comparisons to other orbiviruses. Highest identity levels were consistently detected with other BTV strains, identifying KUW2010/02 as BTV. The outer-core protein and major BTV serogroup-specific antigen “VP7” showed 98% aa sequence identity with BTV-25, indicating a common ancestry. However, higher level of variation in the nucleotide sequence of Seg-7 (81.2% identity) suggests strong conservation pressures on the protein of these two strains, and that they diverged a long time ago. Comparisons of Seg-2, encoding major outer-capsid component and cell-attachment protein “VP2” identified KUW2010/02 as 26th BTV, within a 12th Seg-2 nucleotype [nucleotype L]. Comparisons of Seg-6, encoding the smaller outer capsid protein VP5, also showed levels of nt/aa variation consistent with identification of KUW2010/02 as BTV-26 (within a 9th Seg-6 nucleotype - nucleotype I). Sequence data for Seg-2 of KUW2010/02 were used to design four sets of oligonucleotide primers for use in BTV-26, type-specific RT-PCR assays. Analyses of other more conserved genome segments placed KUW2010/02 and BTV-25/SWI2008/01 closer to each other than to other “eastern” or “western” BTV strains, but as representatives of two novel and distinct geographic groups (topotypes). Our analyses indicate that all of the BTV genome segments have evolved under strong purifying selection

Learning and Behavior in Reef Fish: Fuel for Microevolutionary Change?

Small-scale population differentiation among coral reef fishes may be more common than previously thought. New molecular technologies have informed patterns of differentiation, while experimental approaches focusing on larval abilities to limit distribution have explored processes leading to diversification. Building upon a recently published paper by Wismer et al. that examined population level differences in learning and cooperative behaviors in cleaner wrasse (Labroides dimidiatus), we use a phylogenetic framework to explore how social behaviors are distributed among wrasses in the Labrichthyines clade. Establishing links between social behavior and speciation across the phylogeny allows us explore how social behaviors such as learning and cooperation may also act as possible mechanisms driving diversification at the microevolutionary scale

Male Association Preference for Conspecifics in the Redband Darter, Etheostoma luteovinctum (Teleostei: Percidae) Based on Visual Cues

Divergent visual signals and associated mate preferences are frequently hypothesized to result in behavioral isolation between species lineages. Females are traditionally predicted to be the choosier sex, using visual cues such as male color to facilitate mate recognition and assessment. However, a number of authors have hypothesized that males also are selective in choosing mates and that male preferences can be important in maintaining behavioral isolation. Darters of the genus Etheostoma(Percidae) are a diverse group of sexually dimorphic fishes in which males of most species exhibit elaborate nuptial coloration during spawning seasons. Male coloration is hypothesized to play a role in maintaining behavioral isolation between darter species, and females show association preferences for conspecific male coloration. However, the degree to which males exhibit preferences for conspecific female visual cues is less clear. We examined conspecific association preferences based only on visual signals in male Redband Darter, Etheostoma luteovinctum. We presented individuals with a choice of a conspecific female or a female E. hopkinsi, a heterospecific that is almost completely behaviorally isolated from E. luteovinctumand differs in coloration and body shape. Males exhibited a statistically significant association preference for conspecifics in dichotomous choice trials where only visual cues were available. This is the first study to document a significant conspecific association preference in males of a darter species, providing evidence that males may contribute to behavioral isolation from E. hopkinsi. Differences in female coloration, body shape, or behavior appear to serve as important signals that would help maintain behavioral isolation between E. luteovinctum and E. hopkinsi upon secondary contact

No Evidence for Color or Size Preference in Either Sex of a Dichromatic Stream Fish, Percina Roanoka

Sexual dimorphism is hypothesized to be the result of differential selection pressures between the sexes. Dimorphic traits can serve as indicators of mate quality, altering mate preferences in the opposite sex in favor of a conspicuous trait. Common indicators of mate quality include color and size, with traditional assumptions and evidence predicting a preference for more colorful and/or larger sized mates in many species. Both male and female preferences for more colorful and larger mates within a species are rarely examined simultaneously, however. We examined a sexually dichromatic freshwater fish, Percina roanokaand found that male coloration is positively correlated with size, suggesting color may function as an indicator of viability. We tested preferences for coloration and size in both sexes in a dichotomous mate choice setup in which only visual signals were exchanged. Neither females nor males exhibited a color or size preference in individuals of the opposite sex. Visual cues alone therefore appear to be insufficient to elicit a significant preference in both sexes of this species. Male coloration in P. roanoka does not appear to be driven solely by female preference

Data from: Preference for conspecifics evolves earlier in males than females in a sexually dimorphic radiation of fishes

Speciation by sexual selection is generally modeled as the co-evolution of female preferences and elaborate male ornaments leading to behavioral (sexual) reproductive isolation. One prediction of these models is that female preference for conspecific males should evolve earlier than male preference for conspecific females in sexually dimorphic species with male ornaments. We tested that prediction in darters, a diverse group of freshwater fishes with sexually dimorphic ornamentation. Focusing on the earliest stages of divergence, we tested preference for conspecific mates in males and females of seven closely related species pairs. Contrary to expectation, male preference for conspecific females was significantly greater than female preference for conspecific males. Males in four of the fourteen species significantly preferred conspecific females; whereas, females in no species significantly preferred conspecific males. Relationships between the strength of preference for conspecifics and genetic distance revealed no difference in slope between males and females but a significant difference in intercept, also suggesting that male preference evolves earlier than females’. Our results are consistent with other recent studies in darters and suggest that the co-evolution of female preferences and male ornaments may not best explain the earliest stages of behavioral isolation in this lineage