Search for Rayleigh scattering in the atmosphere of GJ1214b

We investigate the atmosphere of GJ1214b, a transiting super-Earth planet with a low mean density, by measuring its transit depth as a function of wavelength in the blue optical portion of the spectrum. It is thought that this planet is either a mini-Neptune, consisting of a rocky core with a thick, hydrogen-rich atmosphere, or a planet with a composition dominated by water. Most observations favor a water-dominated atmosphere with a small scale-height, however, some observations indicate that GJ1214b could have an extended atmosphere with a cloud layer muting the molecular features. In an atmosphere with a large scale-height, Rayleigh scattering at blue wavelengths is likely to cause a measurable increase in the apparent size of the planet towards the blue. We observed the transit of GJ1214b in the B-band with the FOcal Reducing Spectrograph (FORS) at the Very Large Telescope (VLT) and in the g-band with both ACAM on the William Hershel Telescope (WHT) and the Wide Field Camera (WFC) at the Isaac Newton Telescope (INT). We find a planet-to-star radius ratio in the B-band of 0.1162+/-0.0017, and in the g-band 0.1180+/-0.0009 and 0.1174+/-0.0017 for the WHT & INT observations respectively. These optical data do not show significant deviations from previous measurements at longer wavelengths. In fact, a flat transmission spectrum across all wavelengths best describes the combined observations. When atmospheric models are considered a small scale-height water-dominated model fits the data best.Comment: Accepted for publication in Ap

MiniBacillus PG10 as a Convenient and Effective Production Host for Lantibiotics

Efficient bacterial cell factories are important for the screening and characterization of potent antimicrobial peptides such as lantibiotics. Although lantibiotic production systems have been established in Lactococcus lactis and Escherichia coli, the industrial workhorse Bacillus subtilis has been left relatively unexplored as a lantibiotic production host. Therefore, we tested different B. subtilis strains for their ability to produce lantibiotic peptides by using the subtilin modification and transport enzymes derived from the natural subtilin producer B. subtilis ATCC 6633. Our study shows that although B. subtilis ATCC 6633 and 168 are able to produce various processed lantibiotic peptides, an evident advantage of using either the 8-fold protease-deficient strain WB800 or the genome-minimized B. subtilis 168 strain PG10 is the lack of extracellular serine protease activity. Consequently, leader processing of lantibiotic precursor peptides is circumvented and thus potential toxicity toward the production host is prevented. Furthermore, PG10 provides a clean secondary metabolic background and therefore appears to be the most promising B. subtilis lantibiotic production host. We demonstrate the production of various lantibiotic precursor peptides by PG10 and show different options for their in vitro activation. Our study thus provides a convenient B. subtilis-based lantibiotic production system, which facilitates the search for novel antimicrobial peptides

Polar Smectic Films

We report on a new experimental procedure for forming and studying polar smectic liquid crystal films. A free standing smectic film is put in contact with a liquid drop, so that the film has one liquid crystal/liquid interface and one liquid crystal/air interface. This polar environment results in changes in the textures observed in the film, including a boojum texture and a previously unobserved spiral texture in which the winding direction of the spiral reverses at a finite radius from its center. Some aspects of these textures are explained by the presence of a Ksb term in the bulk elastic free energy density that favors a combination of splay and bend deformations.Comment: 4 pages, REVTeX, 3 figures, submitted to PR

Joint modelling of mental health markers through pregnancy: a Bayesian semi-parametric approach

Maternal depression and anxiety through pregnancy have lasting societal impacts. It is thus crucial to understand the trajectories of its progression from preconception to postnatal period, and the risk factors associated with it. Within the Bayesian framework, we propose to jointly model seven outcomes, of which two are physiological and five non-physiological indicators of maternal depression and anxiety over time. We model the former two by a Gaussian process and the latter by an autoregressive model, while imposing a multidimensional Dirichlet process prior on the subject-specific random effects to account for subject heterogeneity and induce clustering. The model allows for the inclusion of covariates through a regression term. Our findings reveal four distinct clusters of trajectories of the seven health outcomes, characterising women's mental health progression from before to after pregnancy. Importantly, our results caution against the loose use of hair corticosteroids as a biomarker, or even a causal factor, for pregnancy mental health progression. Additionally, the regression analysis reveals a range of preconception determinants and risk factors for depressive and anxiety symptoms during pregnancy

Black carbon over Mexico: the effect of atmospheric transport on mixing state, mass absorption cross-section, and BC/CO ratios

A single particle soot photometer (SP2) was operated on the NCAR C-130 during the MIRAGE campaign (part of MILAGRO), sampling black carbon (BC) over Mexico. The highest BC concentrations were measured over Mexico City (sometimes as much as 2 μg/m<sup>3</sup>) and over hill-fires to the south of the city. The age of plumes outside of Mexico City was determined using a combination of HYSPLIT trajectories, WRF-FLEXPART modeling and CMET balloon tracks. As expected, older, diluted air masses had lower BC concentrations. A comparison of carbon monoxide (CO) and BC suggests a CO background of around 65 ppbv, and a background-corrected BC/CO<sub>net</sub> ratio of 2.89±0.89 (ng/m<sup>3</sup>-STP)/ppbv (average ± standard deviation). This ratio is similar for fresh emissions over Mexico City, as well as for aged airmasses. Comparison of light absorption measured with a particle soot absorption photometer (PSAP) and the SP2 BC suggests a BC mass-normalized absorption cross-section (MAC) of 10.9±2.1 m<sup>2</sup>/g at 660 nm (or 13.1 m<sup>2</sup>/g @ 550 nm, assuming MAC is inversely dependent on wavelength). This appears independent of aging and similar to the expected absorption cross-section for aged BC, but values, particularly in fresh emissions, could be biased high due to instrument artifacts. SP2-derived BC coating indicators show a prominent thinly-coated BC mode over the Mexico City Metropolitan Area (MCMA), while older air masses show both thinly-coated and thickly-coated BC. Some 2-day-old plumes do not show a prominent thickly-coated BC mode, possibly due to preferential wet scavenging of the likely-hydrophilic thickly-coated BC

Changes to cholesterol trafficking in macrophages by Leishmania parasites infection

Leishmania spp. are protozoan parasites that are transmitted by sandfly vectors during blood sucking to vertebrate hosts and cause a spectrum of diseases called leishmaniases. It has been demonstrated that host cholesterol plays an important role during Leishmania infection. Nevertheless, little is known about the intracellular distribution of this lipid early after internalization of the parasite. Here, pulse‐chase experiments with radiolabeled cholesteryl esterified to fatty acids bound to low‐density lipoproteins indicated that retention of this source of cholesterol is increased in parasite‐containing subcellular fractions, while uptake is unaffected. This is correlated with a reduction or absence of detectable NPC1 (Niemann–Pick disease, type C1), a protein responsible for cholesterol efflux from endocytic compartments, in the Leishmania mexicana habitat and infected cells. Filipin staining revealed a halo around parasites within parasitophorous vacuoles (PV) likely representing free cholesterol accumulation. Labeling of host cell membranous cholesterol by fluorescent cholesterol species before infection revealed that this pool is also trafficked to the PV but becomes incorporated into the parasites’ membranes and seems not to contribute to the halo detected by filipin. This cholesterol sequestration happened early after infection and was functionally significant as it correlated with the upregulation of mRNA‐encoding proteins required for cholesterol biosynthesis. Thus, sequestration of cholesterol by Leishmania amastigotes early after infection provides a basis to understand perturbation of cholesterol‐dependent processes in macrophages that were shown previously by others to be necessary for their proper function in innate and adaptive immune responses

Selecting control genes for RT-QPCR using public microarray data

Background: Gene expression analysis has emerged as a major biological research area, with real-time quantitative reverse transcription PCR (RT-QPCR) being one of the most accurate and widely used techniques for expression profiling of selected genes. In order to obtain results that are comparable across assays, a stable normalization strategy is required. In general, the normalization of PCR measurements between different samples uses one to several control genes (e. g. housekeeping genes), from which a baseline reference level is constructed. Thus, the choice of the control genes is of utmost importance, yet there is not a generally accepted standard technique for screening a large number of candidates and identifying the best ones. Results: We propose a novel approach for scoring and ranking candidate genes for their suitability as control genes. Our approach relies on publicly available microarray data and allows the combination of multiple data sets originating from different platforms and/or representing different pathologies. The use of microarray data allows the screening of tens of thousands of genes, producing very comprehensive lists of candidates. We also provide two lists of candidate control genes: one which is breast cancer-specific and one with more general applicability. Two genes from the breast cancer list which had not been previously used as control genes are identified and validated by RT-QPCR. Open source R functions are available at http://www.isrec.isb-sib.ch/similar to vpopovic/research/ Conclusion: We proposed a new method for identifying candidate control genes for RT-QPCR which was able to rank thousands of genes according to some predefined suitability criteria and we applied it to the case of breast cancer. We also empirically showed that translating the results from microarray to PCR platform was achievable

Increased efficacy for in-house validation of real-time PCR GMO detection methods

To improve the efficacy of the in-house validation of GMO detection methods (DNA isolation and real-time PCR, polymerase chain reaction), a study was performed to gain insight in the contribution of the different steps of the GMO detection method to the repeatability and in-house reproducibility. In the present study, 19 methods for (GM) soy, maize canola and potato were validated in-house of which 14 on the basis of an 8-day validation scheme using eight different samples and five on the basis of a more concise validation protocol. In this way, data was obtained with respect to the detection limit, accuracy and precision. Also, decision limits were calculated for declaring non-conformance (>0.9%) with 95% reliability. In order to estimate the contribution of the different steps in the GMO analysis to the total variation variance components were estimated using REML (residual maximum likelihood method). From these components, relative standard deviations for repeatability and reproducibility (RSDr and RSDR) were calculated. The results showed that not only the PCR reaction but also the factors ‘DNA isolation’ and ‘PCR day’ are important factors for the total variance and should therefore be included in the in-house validation. It is proposed to use a statistical model to estimate these factors from a large dataset of initial validations so that for similar GMO methods in the future, only the PCR step needs to be validated. The resulting data are discussed in the light of agreed European criteria for qualified GMO detection methods

Effect of intraperitoneal chemotherapy concentration on morbidity and survival

Contains fulltext : 218098.pdf (publisher's version ) (Open Access)BACKGROUND: Selected patients with colorectal peritoneal metastases are treated with cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC). The concentration of intraperitoneal chemotherapy reflects the administered dose and perfusate volume. The aim of this study was to calculate intraperitoneal chemotherapy concentration during HIPEC and see whether this was related to clinical outcomes. METHODS: An observational multicentre study included consecutive patients with colorectal peritoneal metastases who were treated with CRS-HIPEC between 2010 and 2018 at three Dutch centres. Data were retrieved from prospectively developed databases. Chemotherapy dose and total circulating volumes of carrier solution were used to calculate chemotherapy concentrations. Postoperative complications, disease-free and overall survival were correlated with intraoperative chemotherapy concentrations. Univariable and multivariable logistic regression, Cox regression and survival analyses were performed. RESULTS: Of 320 patients, 220 received intraperitoneal mitomycin C (MMC) and 100 received oxaliplatin. Median perfusate volume for HIPEC was 5.0 (range 0.7-10.0) litres. Median intraperitoneal chemotherapy concentration was 13.3 (range 7.0-76.0) mg/l for MMC and 156.0 (91.9-377.6) mg/l in patients treated with oxaliplatin. Grade III or higher complications occurred in 75 patients (23.4 per cent). Median overall survival was 36.9 (i.q.r. 19.5-62.9) months. Intraperitoneal chemotherapy concentrations were not associated with postoperative complications or survival. CONCLUSION: CRS-HIPEC was performed with a wide variation in intraperitoneal chemotherapy concentrations that were not associated with complications or survival

Scale-free memory model for multiagent reinforcement learning. Mean field approximation and rock-paper-scissors dynamics

A continuous time model for multiagent systems governed by reinforcement learning with scale-free memory is developed. The agents are assumed to act independently of one another in optimizing their choice of possible actions via trial-and-error search. To gain awareness about the action value the agents accumulate in their memory the rewards obtained from taking a specific action at each moment of time. The contribution of the rewards in the past to the agent current perception of action value is described by an integral operator with a power-law kernel. Finally a fractional differential equation governing the system dynamics is obtained. The agents are considered to interact with one another implicitly via the reward of one agent depending on the choice of the other agents. The pairwise interaction model is adopted to describe this effect. As a specific example of systems with non-transitive interactions, a two agent and three agent systems of the rock-paper-scissors type are analyzed in detail, including the stability analysis and numerical simulation. Scale-free memory is demonstrated to cause complex dynamics of the systems at hand. In particular, it is shown that there can be simultaneously two modes of the system instability undergoing subcritical and supercritical bifurcation, with the latter one exhibiting anomalous oscillations with the amplitude and period growing with time. Besides, the instability onset via this supercritical mode may be regarded as "altruism self-organization". For the three agent system the instability dynamics is found to be rather irregular and can be composed of alternate fragments of oscillations different in their properties.Comment: 17 pages, 7 figur