Microchamber Cultures of Bladder Cancer: A Platform for Characterizing Drug Responsiveness and Resistance in PDX and Primary Cancer Cells.

Precision cancer medicine seeks to target the underlying genetic alterations of cancer; however, it has been challenging to use genetic profiles of individual patients in identifying the most appropriate anti-cancer drugs. This spurred the development of patient avatars; for example, patient-derived xenografts (PDXs) established in mice and used for drug exposure studies. However, PDXs are associated with high cost, long development time and low efficiency of engraftment. Herein we explored the use of microfluidic devices or microchambers as simple and low-cost means of maintaining bladder cancer cells over extended periods of times in order to study patterns of drug responsiveness and resistance. When placed into 75 µm tall microfluidic chambers, cancer cells grew as ellipsoids reaching millimeter-scale dimeters over the course of 30 days in culture. We cultured three PDX and three clinical patient specimens with 100% success rate. The turn-around time for a typical efficacy study using microchambers was less than 10 days. Importantly, PDX-derived ellipsoids in microchambers retained patterns of drug responsiveness and resistance observed in PDX mice and also exhibited in vivo-like heterogeneity of tumor responses. Overall, this study establishes microfluidic cultures of difficult-to-maintain primary cancer cells as a useful tool for precision cancer medicine

Ionized gas outflows in infrared-bright dust-obscured galaxies selected with WISE and SDSS

We present the ionized gas properties of infrared (IR)-bright dust-obscured galaxies (DOGs) that show an extreme optical/IR color, $(i - [22])_{\rm AB} > 7.0$, selected with the Sloan Digital Sky Survey (SDSS) and Wide-field Infrared Survey Explorer (WISE). For 36 IR-bright DOGs that show [OIII]$\lambda$5007 emission in the SDSS spectra, we performed a detailed spectral analysis to investigate their ionized gas properties. In particular, we measured the velocity offset (the velocity with respect to the systemic velocity measured from the stellar absorption lines) and the velocity dispersion of the [OIII] line. We found that the derived velocity offset and dispersion of most IR-bright DOGs are larger than those of Seyfert 2 galaxies (Sy2s) at $z < 0.3$, meaning that the IR-bright DOGs show relatively strong outflows compared to Sy2s. This can be explained by the difference of IR luminosity contributed from active galactic nucleus, $L_{\rm IR}$ (AGN), because we found that (i) $L_{\rm IR}$ (AGN) correlates with the velocity offset and dispersion of [OIII] and (ii) our IR-bright DOGs sample has larger $L_{\rm IR}$ (AGN) than Sy2s. Nevertheless, the fact that about 75% IR-bright DOGs have a large ($>$ 300 km s$^{-1}$) velocity dispersion, which is a larger fraction compared to other AGN populations, suggests that IR-bright DOGs are good laboratories to investigate AGN feedback. The velocity offset and dispersion of [OIII] and [NeIII]$\lambda$3869 are larger than those of [OII]$\lambda$3727, which indicates that the highly ionized gas tends to show more stronger outflows.Comment: 19 pages, 16 figures, and 2 tables, accepted for publication in Ap

Causal graph-based analysis of genome-wide association data in rheumatoid arthritis

<p>Abstract</p> <p>Background</p> <p>GWAS owe their popularity to the expectation that they will make a major impact on diagnosis, prognosis and management of disease by uncovering genetics underlying clinical phenotypes. The dominant paradigm in GWAS data analysis so far consists of extensive reliance on methods that emphasize contribution of individual SNPs to statistical association with phenotypes. Multivariate methods, however, can extract more information by considering associations of multiple SNPs simultaneously. Recent advances in other genomics domains pinpoint multivariate causal graph-based inference as a promising principled analysis framework for high-throughput data. Designed to discover biomarkers in the local causal pathway of the phenotype, these methods lead to accurate and highly parsimonious multivariate predictive models. In this paper, we investigate the applicability of causal graph-based method TIE* to analysis of GWAS data. To test the utility of TIE*, we focus on anti-CCP positive rheumatoid arthritis (RA) GWAS datasets, where there is a general consensus in the community about the major genetic determinants of the disease.</p> <p>Results</p> <p>Application of TIE* to the North American Rheumatoid Arthritis Cohort (NARAC) GWAS data results in six SNPs, mostly from the MHC locus. Using these SNPs we develop two predictive models that can classify cases and disease-free controls with an accuracy of 0.81 area under the ROC curve, as verified in independent testing data from the same cohort. The predictive performance of these models generalizes reasonably well to Swedish subjects from the closely related but not identical Epidemiological Investigation of Rheumatoid Arthritis (EIRA) cohort with 0.71-0.78 area under the ROC curve. Moreover, the SNPs identified by the TIE* method render many other previously known SNP associations conditionally independent of the phenotype.</p> <p>Conclusions</p> <p>Our experiments demonstrate that application of TIE* captures maximum amount of genetic information about RA in the data and recapitulates the major consensus findings about the genetic factors of this disease. In addition, TIE* yields reproducible markers and signatures of RA. This suggests that principled multivariate causal and predictive framework for GWAS analysis empowers the community with a new tool for high-quality and more efficient discovery.</p> <p>Reviewers</p> <p>This article was reviewed by Prof. Anthony Almudevar, Dr. Eugene V. Koonin, and Prof. Marianthi Markatou.</p

Study of the bivariate survival data using frailty models based on Lévy processes

Frailty models allow us to take into account the non-observable inhomogeneity of individual hazard functions. Although models with time-independent frailty have been intensively studied over the last decades and a wide range of applications in survival analysis have been found, the studies based on the models with time-dependent frailty are relatively rare. In this paper, we formulate and prove two propositions related to the identifiability of the bivariate survival models with frailty given by a nonnegative bivariate Lévy process. We discuss parametric and semiparametric procedures for estimating unknown parameters and baseline hazard functions. Numerical experiments with simulated and real data illustrate these procedures. The statements of the propositions can be easily extended to the multivariate case

A Marine Actinomycete Rescues Caenorhabditis elegans from Pseudomonas aeruginosa Infection through Restitution of Lysozyme 7

The resistance of Pseudomonas aeruginosa to conventional antimicrobial treatment is a major scourge in healthcare. Therefore, it is crucial that novel potent anti-infectives are discovered. The aim of the present study is to screen marine actinomycetes for chemical entities capable of overcoming P. aeruginosa infection through mechanisms involving anti-virulence or host immunity activities. A total of 18 actinomycetes isolates were sampled from marine sediment of Songsong Island, Kedah, Malaysia. Upon confirming that the methanolic crude extract of these isolates do not display direct bactericidal activities, they were tested for capacity to rescue Caenorhabditis elegans infected with P. aeruginosa strain PA14. A hexane partition of the extract from one isolate, designated as Streptomyces sp. CCB-PSK207, could promote the survival of PA14 infected worms by more than 60%. Partial 16S sequence analysis on this isolate showed identity of 99.79% with Streptomyces sundarbansensis. This partition did not impair feeding behavior of C. elegans worms. Tested on PA14, the partition also did not affect bacterial growth or its ability to colonize host gut. The production of biofilm, protease, and pyocyanin in PA14 were uninterrupted, although there was an increase in elastase production. In lys-7::GFP worms, this partition was shown to induce the expression of lysozyme 7, an important innate immunity defense molecule that was repressed during PA14 infection. GC-MS analysis of the bioactive fraction of Streptomyces sp. CCB-PSK207 revealed the presence of methyl esters of branched saturated fatty acids. In conclusion, this is the first report of a marine actinomycete producing metabolites capable of rescuing C. elegans from PA14 through a lys-7 mediated activity

Does empathy predict altruism in the wild?

Why do people act altruistically? One theory is that empathy is a driver of morality. Experimental studies of this are often confined to laboratory settings, which often lack ecological validity. In the present study we investigated whether empathy traits predict if people will act altruistically in a real-world setting, "in the wild". We staged a situation in public that was designed to elicit helping, and subsequently measured empathic traits in those who either stopped to help or walked past and did not help. Results show that a higher number of empathic traits are a significant and positive predictor for altruistic behavior in a real-life situation. This supports the theory that the act of doing good is correlated with empathy.This work was supported by the Autism Research Trust and the Medical Research Council; Pinsent Darwin Trust, Medical Research Council and Cambridge Trust; National Institute for Health Research

Atomic layer deposited oxide films as protective interface layers for integrated graphene transfer

The transfer of chemical vapour deposited (CVD) graphene from its parent growth catalyst has become a bottleneck for many of its emerging applications. The sacrificial polymer layers that are typically deposited onto graphene for mechanical support during transfer are challenging to fully remove and hence leave graphene and subsequent device interfaces contaminated. Here, we report on the use of atomic layer deposited (ALD) oxide films as protective interface and support layers during graphene transfer. The method avoids any direct contact of the graphene with polymers and through the use of thicker ALD layers (≥100nm), polymers can be eliminated from the transfer-process altogether. The ALD film can be kept as a functional device layer, facilitating integrated device manufacturing. We demonstrate back-gated field effect devices based on single-layer graphene transferred with a protective Al2O3 film onto SiO2 that show significantly reduced charge trap and residual carrier densities. We critically discuss the advantages and challenges of processing graphene/ALD bilayer structures.We acknowledge funding from EPSRC (Grant No. EP/K016636/1, GRAPHTED) and ERC (Grant No. 279342, InsituNANO). ACV acknowledges the Conacyt Cambridge Scholarship and Roberto Rocca Fellowship. JAA-W acknowledges the support of his Research Fellowships from the Royal Commission for the Exhibition of 1851 and Churchill College, Cambridge. RSW acknowledges a Research Fellowship from St. John's College, Cambridge and a Marie Skłodowska-Curie Individual Fellowship (Global) under grant ARTIST (no. 656870) from the European Union's Horizon 2020 research and innovation programme

Graphene-passivated nickel as an efficient hole-injecting electrode for large area organic semiconductor devices

Efficient injection of charge from metal electrodes into semiconductors is of paramount importance to obtain high performance optoelectronic devices. The quality of the interface between the electrode and the semiconductor must, therefore, be carefully controlled. The case of organic semiconductors presents specific problems: ambient deposition techniques, such as solution processing, restrict the choice of electrodes to those not prone to oxidation, limiting potential applications. Additionally, damage to the semiconductor in sputter coating or high temperature thermal evaporation poses an obstacle to the use of many device-relevant metals as top electrodes in vertical metal–semiconductor–metal structures, making it preferable to use them as bottom electrodes. Here, we propose a possible solution to these problems by implementing graphene-passivated nickel as an air stable bottom electrode in vertical devices comprising organic semiconductors. We use these passivated layers as hole-injecting bottom electrodes, and we show that efficient charge injection can be achieved into standard organic semiconducting polymers, owing to an oxide free nickel/graphene/polymer interface. Crucially, we fabricate our electrodes with low roughness, which, in turn, allows us to produce large area devices (of the order of millimeter squares) without electrical shorts occurring. Our results make these graphene-passivated ferromagnetic electrodes a promising approach for large area organic optoelectronic and spintronic devices.We acknowledge funding from EPSRC (EP/P005152/1, EP/M005143/1). R.M. and K.N. acknowledges funding from the EPSRC Cambridge NanoDTC (Grant No. EP/G037221/1). J.A.-W. acknowledges the support of his Research Fellowship from the Royal Commission for the Exhibition of 1851, and Royal Society Dorothy Hodgkin Research Fellowship. R. S. W. acknowledges support from a CAMS-UK fellowship