On the estimation of average treatment effects with right-censored time to event outcome and competing risks

We are interested in the estimation of average treatment effects based on right-censored data of an observational study. We focus on causal inference of differences between t-year absolute event risks in a situation with competing risks. We derive doubly robust estimation equations and implement estimators for the nuisance parameters based on working regression models for the outcome, censoring, and treatment distribution conditional on auxiliary baseline covariates. We use the functional delta method to show that these estimators are regular asymptotically linear estimators and estimate their variances based on estimates of their influence functions. In empirical studies, we assess the robustness of the estimators and the coverage of confidence intervals. The methods are further illustrated using data from a Danish registry study.     

Long-range alteration of the physical environment mediates cooperation between Pseudomonas aeruginosa swarming colonies

Pseudomonas aeruginosa makes and secretes massive amounts of rhamnolipid surfactants that enable swarming motility over biogel surfaces. But how these rhamnolipids interact with biogels to assist swarming remains unclear. Here, I use a combination of optical techniques across scales and genetically engineered strains to demonstrate that rhamnolipids can induce agar gel swelling over distances >10,000× the body size of an individual cell. The swelling front is on the micrometric scale and is easily visible using shadowgraphy. Rhamnolipid transport is not restricted to the surface of the gel but occurs through the whole thickness of the plate and, consequently, the spreading dynamics depend on the local thickness. Surprisingly, rhamnolipids can cross the whole gel and induce swelling on the opposite side of a two-face Petri dish. The swelling front delimits an area where the mechanical properties of the surface properties are modified: water wets the surface more easily, which increases the motility of individual bacteria and enables collective motility. A genetically engineered mutant unable to secrete rhamnolipids (ΔrhlA), and therefore unable to swarm, is rescued from afar with rhamnolipids produced by a remote colony. These results exemplify the remarkable capacity of bacteria to change the physical environment around them and its ecological consequences.     

Cauliflower mosaic virus protein P6-TAV plays a major role in alteration of aphid vector feeding behaviour but not performance on infected Arabidopsis

Emerging evidence suggests that viral infection modifies host plant traits that in turn alter behaviour and performance of vectors colonizing the plants in a way conducive for transmission of both nonpersistent and persistent viruses. Similar evidence for semipersistent viruses like cauliflower mosaic virus (CaMV) is scarce. Here we compared the effects of Arabidopsis infection with mild (CM) and severe (JI) CaMV isolates on the feeding behaviour (recorded by the electrical penetration graph technique) and fecundity of the aphid vector Myzus persicae. Compared to mock-inoculated plants, feeding behaviour was altered similarly on CM- and JI-infected plants, but only aphids on JI-infected plants had reduced fecundity. To evaluate the role of the multifunctional CaMV protein P6-TAV, aphid feeding behaviour and fecundity were tested on transgenic Arabidopsis plants expressing wild-type (wt) and mutant versions of P6-TAV. In contrast to viral infection, aphid fecundity was unchanged on all transgenic lines, suggesting that other viral factors compromise fecundity. Aphid feeding behaviour was modified on wt P6-CM-, but not on wt P6-JI-expressing plants. Analysis of plants expressing P6 mutants identified N-terminal P6 domains contributing to modification of feeding behaviour. Taken together, we show that CaMV infection can modify both aphid fecundity and feeding behaviour and that P6 is only involved in the latter.     

The sooner the better: reproductive phenology drives ontogenetic trajectories in a temperate squamate (Podarcis muralis)

Understanding variations in individual trajectories is a crucial evolutionary issue. Terrestrial ectotherms from temperate regions typically face thermal constraints and limited activity periods. Developmental conditions (i.e. embryonic life) and reproductive timing (laying date) should induce phenotypic variations and influence subsequent ontogenetic trajectories (growth and survival). We studied these combined influences in an oviparous squamate, the wall lizard (Podarcis muralis), comprising a multiple clutch species with natural variations in laying date for the first clutch. We experimentally manipulated maternal basking opportunities during gravidity (3, 6 or 9 h per day) and incubation temperature (23 or 29 °C). Early laying date positively influenced winter survival in both incubation treatments. Survival was significantly lower in cool than warm‐incubated individuals (14.8% and 73.6%, respectively) because of delayed hatching date and reduced activity period before winter. Individuals from cool incubation temperature were slightly smaller but had a higher body condition and grew faster during the first month of life. Offspring behaviour was driven by complex interactions between gravidity and incubation treatments. Under cool incubation temperature, defensive behaviour was high, independently of gravidity treatment. Warm incubated individuals showed low defensive response except when maternal basking opportunities were restricted to 3 h. Defensive behaviour at birth had a positive influence on survival in cool‐incubated individuals. The results of the present study highlight the long‐term influence of hatching date that integrates female reproductive timing and incubation conditions. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 00, 000–000.     

Vector competence of the African argasid tick Ornithodoros moubata for the Q fever agent Coxiella burnetii

Q fever is a widespread zoonotic disease caused by the intracellular bacterium Coxiella burnetii. While transmission is primarily but not exclusively airborne, ticks are usually thought to act as vectors on the basis of early microscopy studies. However, recent observations revealed that endosymbionts of ticks have been commonly misidentified as C. burnetii, calling the importance of tick-borne transmission into question. In this study, we re-evaluated the vector competence of the African soft tick Ornithodoros moubata for an avirulent strain of C. burnetii. To this end, we used an artificial feeding system to initiate infection of ticks, specific molecular tools to monitor further infections, and culture assays in axenic and cell media to check for the viability of C. burnetii excreted by ticks. We observed typical traits associated with vector competence: The exposure to an infected blood meal resulted in viable and persistent infections in ticks, trans-stadial transmissions of infection from nymphs to adults and the ability of adult ticks to transmit infectious C. burnetii. However, in contrast to early studies, we found that infection differed substantially between tick organs. In addition, while adult female ticks were infected, we did not observe C. burnetii in eggs, suggesting that transovarial transmission is not effective. Finally, we detected only a sporadic presence of C. burnetii DNA in tick faeces, but no living bacterium was further isolated in culture assays, suggesting that excretion in faeces is not a common mode of transmission in O. moubata.     

Benzo[1,2‐b:4,5‐b′]Dithiophene–6,7‐Difluoroquinoxaline Small Molecule Donors with >8% BHJ Solar Cell Efficiency

Solution‐processable small molecule (SM) donors are promising alternatives to their polymer counterparts in bulk‐heterojunction (BHJ) solar cells. While SM donors with favorable spectral absorption, self‐assembly patterns, optimum thin‐film morphologies, and high carrier mobilities in optimized donor–acceptor blends are required to further BHJ device efficiencies, material structure governs each one of those attributes. As a result, the rational design of SM donors with gradually improved BHJ solar cell efficiencies must concurrently address: (i) bandgap tuning and optimization of spectral absorption (inherent to the SM main chain) and (ii) pendant‐group substitution promoting structural order and mediating morphological effects. In this paper, the rational pendant‐group substitution in benzo[1,2‐b:4,5‐b′]dithiophene–6,7‐difluoroquinoxaline SMs is shown to be an effective approach to narrowing the optical gap (E_opt) of the SM donors ( SM1 and SM2 ), without altering their propensity to order and form favorable thin‐film BHJ morphologies with PC₇₁BM. Systematic device examinations show that power conversion efficiencies >8% and open‐circuit voltages (V_OC) nearing 1 V can be achieved with the narrow‐gap SM donor analog ( SM2 , E_opt = 1.6 eV) and that charge transport in optimized BHJ solar cells proceeds with minimal, nearly trap‐free recombination. Detailed device simulations, light intensity dependence, and transient photocurrent analyses emphasize how carrier recombination impacts BHJ device performance upon optimization of active layer thickness and morphology.     

Escherichia coli expression and refolding of E/K-coil-tagged EGF generates fully bioactive EGF for diverse applications

Heterodimerizing peptides, such as the de novo designed E5/K5 peptide pair, have several applications including as tags for protein purification or immobilization. Recently, we demonstrated that E5-tagged epidermal growth factor (EGF), when bound to a K4 expressing adenovirus, promotes retargeting of the adenovirus to EGFR expressing target cells. In this study, we present the Escherichia coli expression, refolding and purification of human EGF fused with the E5-coil (E5-coil-EGF) or with the K5-coil (K5-coil-EGF). EGF receptor phosphorylation and cell proliferation assays demonstrated that the biological activity of the coil-tagged EGF versions was comparable to that of non-tagged EGF. Additionally, analysis of the binding of E5/K5-coil-EGF to cell surface EGFR or to soluble EGFR ectodomain, as measured by cell-based binding competition assays and by SPR-based biosensor experiments, indicated that the coil-tagged EGF versions bound to EGFR with affinities similar to that of non-tagged EGF. Finally, we show that E-coil-tagged EGF, but not non-tagged EGF, can retarget a K-coil containing adenovirus to EGF receptor expressing glioblastoma tumor cells. Overall these results indicate that E. coli expression offers a practical platform for the reproducible production of fully biologically active E5/K5-coil-tagged EGF, and support applications of heterodimerizing coil-tagged ligands, e.g. the targeting of viruses or other entities such as nanoparticles to tumor cells, or growth factor immobilization on cell culture scaffolds for tissue engineering.