On the diffusion of lattice matched InGaAs/InP microstructures

Copyright (2003) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in F. Bollet et al., J. Appl. Phys. 93, 3881 (2003) and may be found at http://link.aip.org/link/?jap/93/388

Photoluminescence and x-ray diffraction studies of the diffusion behavior of lattice matched InGaAs/InP heterostructures

Copyright (2003) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in (F. Bollet and W. P. Gillin, J. Appl. Phys. 94, 988 (2003) and may be found at http://link.aip.org/link/?jap/94/988

Random copying in space

Random copying is a simple model for population dynamics in the absence of selection, and has been applied to both biological and cultural evolution. In this work, we investigate the effect that spatial structure has on the dynamics. We focus in particular on how a measure of the diversity in the population changes over time. We show that even when the vast majority of a population's history may be well-described by a spatially-unstructured model, spatial structure may nevertheless affect the expected level of diversity seen at a local scale. We demonstrate this phenomenon explicitly by examining the random copying process on small-world networks, and use our results to comment on the use of simple random-copying models in an empirical context.Comment: 26 pages, 11 figures. Based on invited talk at AHRC CECD Conference on "Cultural Evolution in Spatially Structured Populations" at UCL, September 2010. To appear in ACS - Advances in Complex System

Ecological indicators for abandoned mines, Phase 1: Review of the literature

Mine waters have been identified as a significant issue in the majority of Environment Agency draft River Basin Management Plans. They are one of the largest drivers for chemical pollution in the draft Impact Assessment for the Water Framework Directive (WFD), with significant failures of environmental quality standards (EQS) for metals (particularly Cd, Pb, Zn, Cu, Fe) in many rivers linked to abandoned mines. Existing EQS may be overprotective of aquatic life which may have adapted over centuries of exposure. This study forms part of a larger project to investigate the ecological impact of metals in rivers, to develop water quality targets (alternative objectives for the WFD) for aquatic ecosystems impacted by long-term mining pollution. The report reviews literature on EQS failures, metal effects on aquatic biota and effects of water chemistry, and uses this information to consider further work. A preliminary assessment of water quality and biology data for 87 sites across Gwynedd and Ceredigion (Wales) shows that existing Environment Agency water quality and biology data could be used to establish statistical relations between chemical variables and metrics of ecological quality. Visual representation and preliminary statistical analyses show that invertebrate diversity declines with increasing zinc concentration. However, the situation is more complex because the effects of other metals are not readily apparent. Furthermore, pH and aluminium also affect streamwater invertebrates, making it difficult to tease out toxicity due to individual mine-derived metals. The most characteristic feature of the plant communities of metal-impacted systems is a reduction in diversity, compared to that found in comparable unimpacted streams. Some species thrive in the presence of heavy metals, presumably because they are able to develop metal tolerance, whilst others consistently disappear. Effects are, however, confounded by water chemistry, particularly pH. Tolerant species are spread across a number of divisions of photosynthetic organisms, though green algae, diatoms and blue-green algae are usually most abundant, often thriving in the absence of competition and/or grazing. Current UK monitoring techniques focus on community composition and, whilst these provide a sampling and analytical framework for studies of metal impacts, the metrics are not sensitive to these impacts. There is scope for developing new metrics, based on community-level analyses and for looking at morphological variations common in some taxa at elevated metal concentrations. On the whole, community-based metrics are recommended, as these are easier to relate to ecological status definitions. With respect to invertebrates and fish, metals affect individuals, population and communities but sensitivity varies among species, life stages, sexes, trophic groups and with body condition. Acclimation or adaptation may cause varying sensitivity even within species. Ecosystem-scale effects, for example on ecological function, are poorly understood. Effects vary between metals such as cadmium, copper, lead, chromium, zinc and nickel in order of decreasing toxicity. Aluminium is important in acidified headwaters. Biological effects depend on speciation, toxicity, availability, mixtures, complexation and exposure conditions, for example discharge (flow). Current water quality monitoring is unlikely to detect short-term episodic increases in metal concentrations or evaluate the bioavailability of elevated metal concentrations in sediments. These factors create uncertainty in detecting ecological impairment in metal-impacted ecosystems. Moreover, most widely used biological indicators for UK freshwaters were developed for other pressures and none distinguishes metal impacts from other causes of impairment. Key ecological needs for better regulation and management of metals in rivers include: i) models relating metal data to ecological data that better represent influences on metal toxicity; ii) biodiagnostic indices to reflect metal effects; iii) better methods to identify metal acclimation or adaptation among sensitive taxa; iv) better investigative procedures to isolate metal effects from other pressures. Laboratory data on the effects of water chemistry on cationic metal toxicity and bioaccumulation show that a number of chemical parameters, particularly pH, dissolved organic carbon (DOC) and major cations (Na, Mg, K, Ca) exert a major influence on the toxicity and/or bioaccumulation of cationic metals. The biotic ligand model (BLM) provides a conceptual framework for understanding these water chemistry effects as a combination of the influence of chemical speciation, and metal uptake by organisms in competition with H+ and other cations. In some cases where the BLM cannot describe effects, empirical bioavailable models have been successfully used. Laboratory data on the effects of metal mixtures across different water chemistries are sparse, with implications for transferring understanding to mining-impacted sites in the field where mixture effects are likely. The available field data, although relatively sparse, indicate that water chemistry influences metal effects on aquatic ecosystems. This occurs through complexation reactions, notably involving dissolved organic matter and metals such as Al, Cu and Pb. Secondly, because bioaccumulation and toxicity are partly governed by complexation reactions, competition effects among metals, and between metals and H+, give rise to dependences upon water chemistry. There is evidence that combinations of metals are active in the field; the main study conducted so far demonstrated the combined effects of Al and Zn, and suggested, less certainly, that Cu and H+ can also contribute. Chemical speciation is essential to interpret and predict observed effects in the field. Speciation results need to be combined with a model that relates free ion concentrations to toxic effect. Understanding the toxic effects of heavy metals derived from abandoned mines requires the simultaneous consideration of the acidity-related components Al and H+. There are a number of reasons why organisms in waters affected by abandoned mines may experience different levels of metal toxicity than in the laboratory. This could lead to discrepancies between actual field behaviour and that predicted by EQS derived from laboratory experiments, as would be applied within the WFD. The main factors to consider are adaptation/acclimation, water chemistry, and the effects of combinations of metals. Secondary effects are metals in food, metals supplied by sediments, and variability in stream flows. Two of the most prominent factors, namely adaptation/ acclimation and bioavailability, could justify changes in EQS or the adoption of an alternative measure of toxic effects in the field. Given that abandoned mines are widespread in England and Wales, and the high cost of their remediation to meet proposed WFD EQS criteria, further research into the question is clearly justified. Although ecological communities of mine-affected streamwaters might be over-protected by proposed WFD EQS, there are some conditions under which metals emanating from abandoned mines definitely exert toxic effects on biota. The main issue is therefore the reliable identification of chemical conditions that are unacceptable and comparison of those conditions with those predicted by WFD EQS. If significant differences can convincingly be demonstrated, the argument could be made for alternative standards for waters affected by abandoned mines. Therefore in our view, the immediate research priority is to improve the quantification of metal effects under field circumstances. Demonstration of dose-response relationships, based on metal mixtures and their chemical speciation, and the use of better biological tools to detect and diagnose community-level impairment, would provide the necessary scientific information

Concave Switching in Single and Multihop Networks

Switched queueing networks model wireless networks, input queued switches and numerous other networked communications systems. For single-hop networks, we consider a {($\alpha,g$)-switch policy} which combines the MaxWeight policies with bandwidth sharing networks -- a further well studied model of Internet congestion. We prove the maximum stability property for this class of randomized policies. Thus these policies have the same first order behavior as the MaxWeight policies. However, for multihop networks some of these generalized polices address a number of critical weakness of the MaxWeight/BackPressure policies. For multihop networks with fixed routing, we consider the Proportional Scheduler (or (1,log)-policy). In this setting, the BackPressure policy is maximum stable, but must maintain a queue for every route-destination, which typically grows rapidly with a network's size. However, this proportionally fair policy only needs to maintain a queue for each outgoing link, which is typically bounded in number. As is common with Internet routing, by maintaining per-link queueing each node only needs to know the next hop for each packet and not its entire route. Further, in contrast to BackPressure, the Proportional Scheduler does not compare downstream queue lengths to determine weights, only local link information is required. This leads to greater potential for decomposed implementations of the policy. Through a reduction argument and an entropy argument, we demonstrate that, whilst maintaining substantially less queueing overhead, the Proportional Scheduler achieves maximum throughput stability.Comment: 28 page

Deriving Bisimulation Congruences: 2-categories vs precategories

G-relative pushouts (GRPOs) have recently been proposed by the authors as a new foundation for Leifer and Milner’s approach to deriving labelled bisimulation congruences from reduction systems. This paper develops the theory of GRPOs further, arguing that they provide a simple and powerful basis towards a comprehensive solution. As an example, we construct GRPOs in a category of ‘bunches and wirings.’ We then examine the approach based on Milner’s precategories and Leifer’s functorial reactive systems, and show that it can be recast in a much simpler way into the 2-categorical theory of GRPOs

Reversibility, heat dissipation and the importance of the thermal environment in stochastic models of nonequilibrium steady states

We examine stochastic processes that are used to model nonequilibrium processes (e.g, pulling RNA or dragging colloids) and so deliberately violate detailed balance. We argue that by combining an information-theoretic measure of irreversibility with nonequilibrium work theorems, the thermal physics implied by abstract dynamics can be determined. This measure is bounded above by thermodynamic entropy production and so may quantify how well a stochastic dynamics models reality. We also use our findings to critique various modeling approaches and notions arising in steady-state thermodynamics.Comment: 8 pages, 2 figures, easy-to-read, single-column, large-print RevTeX4 format; version with modified abstract and additional discussion, references to appear in Phys Rev Let

Elevated O-GlcNAc levels activate epigenetically repressed genes and delay mouse ES cell differentiation without affecting naive to primed cell transition

The differentiation of mouse embryonic stem (ES) cells is controlled by the interaction of multiple signaling pathways, typically mediated by post-translational protein modifications. The addition of O-linked N-acetylglucosamine (O-GlcNAc) to serine and threonine residues of nuclear and cytoplasmic proteins is one such modification (O-GlcNAcylation), whose function in ES cells is only now beginning to be elucidated. Here we demonstrate that the specific inhibition of O-GlcNAc hydrolase (Oga) causes increased levels of protein O-GlcNAcylation and impairs differentiation of mouse ES cells both in serum-free monolayer and in embryoid bodies (EBs). Use of reporter cell lines demonstrates that Oga inhibition leads to a reduction in the number of Sox1-expressing neural progenitors generated following induction of neural differentiation, as well as maintained expression of the ES cell marker Oct4 (Pou5f1). In EBs expression of mesodermal and endodermal markers is also delayed. However, the transition of naïve cells to primed pluripotency indicated by Rex1 (Zfp42), Nanog, Esrrb and Dppa3 downregulation and Fgf5 upregulation remains unchanged. Finally, we demonstrate that increased O-GlcNAcylation results in upregulation of genes normally epigenetically silenced in ES cells, supporting the emerging role for this protein modification in the regulation of histone modifications and DNA methylation. Stem Cells 2014

Implications of flexible spacer rotational processes on the liquid crystal behavior of 4,5-dihydroisoxazole benzoate dimers

The synthesis of some novel non-symmetric liquid crystal dimers, {3-[4-(octyloxyphenyl)]-4,5-dihydroisoxazol-5-yl}alkyl 4-(decyloxy)benzoates (5a–d) and 4-{3-[4-(octyloxyphenyl)]-4,5-dihydroisoxazol-5-yl}alkyl 4-{[6-(octyloxy)naphthalen-2-yl]ethynyl}benzoate (9a–d), are reported. The liquid-crystalline properties, theoretical calculations based on the conformational aspects of the flexible alkyl spacer and X-ray experiments are discussed. The syntheses of the key intermediates, 2-{3-[4-(octyloxy)phenyl]-4,5-dihydroisoxazol-5-yl}alkanol (3a–d), presenting the flexible alkyl spacer were achieved through [3+2] cycloaddition reactions between nitrile oxides, which were generated in situ by oxidation of the respective aromatic oximes, and dipolarophile alkenols (CH2[double bond, length as m-dash]CH(CH2)nOH, n = 1, 2, 3, and 4). The benzoates 5a–d were synthesized through esterification of 3a–d and p-n-decyloxybenzoic acid (4). The esters 9a–d were synthesized through derivatization of isoxazolines 3a–d into 4-{3-[4-(octyloxyphenyl)]-4,5-dihydroisoxazol-5-yl}alkyl 4-bromobenzoate (7a–d) followed by a Sonogashira reaction with 2-ethynyl-6-octyloxynaphthalene (8). 5a and 5b showed a monotropic smectic C phase. 9a/c displayed a enantiotropic nematic (N) mesophase, whereas 9b/d showed a monotropic nematic mesophase. No mesophase was observed for 7a–d. An odd–even effect was observed for 5a–d and 9a–d associated with the crystal to isotropic phase transition and crystal to nematic phase, respectively, as the length of the spacer was increased from 1 to 4 carbon atoms. The transitional properties were higher for odd-numbered members (n = 1 and 3) for all of the series studied. The X-ray data of compounds 5a and 5b are in agreement with polarizing optical microscopy observations with the assignment of an SmC mesophase. Density functional theory calculations using the B3LYP hybrid functional with the level 6-311G(d,p) basis set were performed for molecules 5a–d to correlate the conformation of the flexible spacer and the transitional properties. The conformational analysis showed that the most stable conformation for 5a–d is one where all of the carbon atoms of the flexible spacer are orientated at 180° (antiperiplanar orientation) except for 5a because the spacer is too short. The odd-numbered members have a more bent shape and are less elongated molecules than the even-numbered members. Thus, mesomorphic behavior is dictated by the conformational constraint imposed by the flexible spacer on the mesogenic groups

Reversal of Pathogen-Induced Barrier Defects in Intestinal Epithelial Cells by Contra-pathogenicity Agents.

“This is a post-peer-review, pre-copyedit version of a protocol published in Digestive Diseases and Sciences The final publication is available at https://doi.org/10.1007/s10620-020-06121-9"BACKGROUND: Environmental enteropathy (EE) is associated with stunting, impairment of responses to oral vaccines, and other adverse health consequences in young children throughout the developing world. EE is characterized by chronic low-grade intestinal inflammation and disrupted epithelial barrier integrity, partly resulting from dysregulation of tight junction proteins, observed in other enteropathies such as celiac disease. During EE, this dysregulation of tight junction expression amplifies translocation of pathogenic bacteria across the intestinal mucosa. AIMS: The aim was to determine whether enteropathogen-mediated epithelial barrier failure can be ameliorated using contra-pathogenicity therapies. METHODS: Intestinal epithelial barrier damage was assessed in Caco-2 cells incubated with three important enteropathogens identified in EE patients: Enteropathogenic Escherichia coli (EPEC), Citrobacter rodentium (C. rodentium), and Cryptosporidium parvum (C. parvum). Potential therapeutic molecules were tested to detect effects on transepithelial resistance (TER), bacterial translocation (BT), claudin-4 expression, and regulation of the inflammatory cytokine response. RESULTS: All three enteropathogens compared to uninfected cells, reduced TER (EPEC; p < 0.0001, C. rodentium; p < 0.0001, C. parvum; p < 0.0007), reduced claudin-4 expression, and permitted BT (EPEC; p < 0.0001, C. rodentium; p < 0.0001, C. parvum; p < 0.0003) through the monolayer. Zinc, colostrum, epidermal growth factor, trefoil factor 3, resistin-like molecule-β, hydrocortisone, and the myosin light chain kinase inhibitor ML7 (Hexahydro-1-[(5-iodo-1-naphthalenyl)sulfonyl]-1H-1,4-diazepine hydrochloride); ML7) improved TER (up to 70%) and decreased BT (as much as 96%). Only zinc demonstrated modest antimicrobial activity. CONCLUSION: The enteropathogens impaired intestinal-epithelial barrier integrity with dysregulation of claudin-4 and increased bacterial translocation. Enteropathogen-mediated damage was reduced using contra-pathogenicity agents which mitigated the effects of pathogens without direct antimicrobial activity