A generalized Markov sampler

A recent development of the Markov chain Monte Carlo (MCMC) technique is the emergence of MCMC samplers that allow transitions between different models. Such samplers make possible a range of computational tasks involving models, including model selection, model evaluation, model averaging and hypothesis testing. An example of this type of sampler is the reversible jump MCMC sampler, which is a generalization of the Metropolis-Hastings algorithm. Here, we present a new MCMC sampler of this type. The new sampler is a generalization of the Gibbs sampler, but somewhat surprisingly, it also turns out to encompass as particular cases all of the well-known MCMC samplers, including those of Metropolis, Barker, and Hastings. Moreover, the new sampler generalizes the reversible jump MCMC. It therefore appears to be a very general framework for MCMC sampling. This paper describes the new sampler and illustrates its use in three applications in Computational Biology, specifically determination of consensus sequences, phylogenetic inference and delineation of isochores via multiple change-point analysis

Stabilization of Pd3−xIn1+x polymorphs with Pd-like crystal structure and their superior performance as catalysts for semi-hydrogenation of alkynes

Selective hydrogenation (semi-hydrogenation) reactions of alkynes rely on Pd-based catalysts to provide the correct pathway to favour formation of double bonds and avoid full hydrogenation to single bonds. Here, we present the preparation and characterisation of "Pd3In"/TiO2 nanocatalysts, which show improved activity and selectivity compared to pure Pd catalysts, towards the liquid phase semi-hydrogenation of 2-methyl-3-butyn-2-ol (MBY) to 2-methyl-3-buten-2-ol (MBE), a fundamental step in the preparation of pharmaceuticals, and other industrially produced substances, as well as a model reaction for the semi-hydrogenation of alkynes. For both the supported and unsupported "Pd3In" alloys (later redefined as Pd3-xIn1+x), we stabilised two new cubic polymorphs with a Pd-like structure, instead of the tetragonal structure as reported so far in the literature. The stabilisation of these new polymorphs was made possible by using a solution-based synthesis and, thanks to the use of different solvents, the reaction was 2 carried out at different temperatures and the Pd/In ratio could be tuned. The same synthetic approach was adapted to prepare two "Pd3In"/TiO2 catalysts by adding the TiO2 support to the reaction mixture, in a practical one-step, one-pot reaction. HREM and X-Ray maps show that the cubic crystal structure of "Pd3In" is maintained when prepared in the presence of the support, however, the support seems to influence the Pd/In ratio

Arachidonic acid inhibition of the NLRP3 inflammasome is a mechanism to explain the anti-inflammatory effects of fasting.

For the purpose of open access, the author has applied a Creative Commons Attribution (CC BY) license to any author-accepted manuscript version arising from this submission.Peer reviewe

MRI T2 and T1ρ relaxation in patients at risk for knee osteoarthritis: A systematic review and meta-analysis

© 2019 The Author(s). Background: Magnetic resonance imaging (MRI) T2 and T1ρ relaxation are increasingly being proposed as imaging biomarkers potentially capable of detecting biochemical changes in articular cartilage before structural changes are evident. We aimed to: 1) summarize MRI methods of published studies investigating T2 and T1ρ relaxation time in participants at risk for but without radiographic knee OA; and 2) compare T2 and T1ρ relaxation between participants at-risk for knee OA and healthy controls. Methods: We conducted a systematic review of studies reporting T2 and T1ρ relaxation data that included both participants at risk for knee OA and healthy controls. Participant characteristics, MRI methodology, and T1ρ and T2 relaxation data were extracted. Standardized mean differences (SMDs) were calculated within each study. Pooled effect sizes were then calculated for six commonly segmented knee compartments. Results: 55 articles met eligibility criteria. There was considerable variability between scanners, coils, software, scanning protocols, pulse sequences, and post-processing. Moderate risk of bias due to lack of blinding was common. Pooled effect sizes indicated participants at risk for knee OA had lengthened T2 relaxation time in all compartments (SMDs from 0.33 to 0.74; p \u3c 0.01) and lengthened T1ρ relaxation time in the femoral compartments (SMD from 0.35 to 0.40; p \u3c 0.001). Conclusions: T2 and T1ρ relaxation distinguish participants at risk for knee OA from healthy controls. Greater standardization of MRI methods is both warranted and required for progress towards biomarker validation

Targeting OGG1 and PARG radiosensitises head and neck cancer cells to high-LET protons through complex DNA damage persistence

Complex DNA damage (CDD), containing two or more DNA lesions within one or two DNA helical turns, is a signature of ionising radiation (IR) and contributes significantly to the therapeutic effect through cell killing. The levels and complexity of CDD increases with linear energy transfer (LET), however, the specific cellular response to this type of DNA damage and the critical proteins essential for repair of CDD is currently unclear. We performed an siRNA screen of ~240 DNA damage response proteins to identify those specifically involved in controlling cell survival in response to high-LET protons at the Bragg peak, compared to low-LET entrance dose protons which differ in the amount of CDD produced. From this, we subsequently validated that depletion of 8-oxoguanine DNA glycosylase (OGG1) and poly(ADP-ribose) glycohydrolase (PARG) in HeLa and head and neck cancer cells leads to significantly increased cellular radiosensitivity specifically following high-LET protons, whilst no effect was observed after low-LET protons and X-rays. We subsequently confirmed that OGG1 and PARG are both required for efficient CDD repair post-irradiation with high-LET protons. Importantly, these results were also recapitulated using specific inhibitors for OGG1 (TH5487) and PARG (PDD00017273). Our results suggest OGG1 and PARG play a fundamental role in the cellular response to CDD and indicate that targeting these enzymes could represent a promising therapeutic strategy for the treatment of head and neck cancers following high-LET radiation

Machine learning active-nematic hydrodynamics

Hydrodynamic theories effectively describe many-body systems out of equilibrium in terms of a few macroscopic parameters. However, such hydrodynamic parameters are difficult to derive from microscopics. Seldom is this challenge more apparent than in active matter where the energy cascade mechanisms responsible for autonomous large-scale dynamics are poorly understood. Here, we use active nematics to demonstrate that neural networks can extract the spatio-temporal variation of hydrodynamic parameters directly from experiments. Our algorithms analyze microtubule-kinesin and actin-myosin experiments as computer vision problems. Unlike existing methods, neural networks can determine how multiple parameters such as activity and elastic constants vary with ATP and motor concentration. In addition, we can forecast the evolution of these chaotic many-body systems solely from image-sequences of their past by combining autoencoder and recurrent networks with residual architecture. Our study paves the way for artificial-intelligence characterization and control of coupled chaotic fields in diverse physical and biological systems even when no knowledge of the underlying dynamics exists.Comment: SI Movie 1: https://www.youtube.com/watch?v=9WzIT7OG9pY SI Movie 2: https://youtu.be/Trc4RyU7-dw SI Movie 3: https://youtu.be/Epm_P_EakH

Concurrent Inhibition of IGF1R and ERK Increases Pancreatic Cancer Sensitivity to Autophagy Inhibitors

The aggressive nature of pancreatic ductal adenocarcinoma (PDAC) mandates the development of improved therapies. As KRAS mutations are found in 95% of PDAC and are critical for tumor maintenance, one promising strategy involves exploiting KRAS-dependent metabolic perturbations. The macrometabolic process of autophagy is upregulated in KRAS-mutant PDAC, and PDAC growth is reliant on autophagy. However, inhibition of autophagy as monotherapy using the lysosomal inhibitor hydroxychloroquine (HCQ) has shown limited clinical efficacy. To identify strategies that can improve PDAC sensitivity to HCQ, we applied a CRISPR-Cas9 loss-of-function screen and found that a top sensitizer was the receptor tyrosine kinase (RTK) insulin-like growth factor 1 receptor (IGF1R). Additionally, reverse phase protein array pathway activation mapping profiled the signaling pathways altered by chloroquine (CQ) treatment. Activating phosphorylation of RTKs, including IGF1R, was a common compensatory increase in response to CQ. Inhibition of IGF1R increased autophagic flux and sensitivity to CQ-mediated growth suppression both in vitro and in vivo. Cotargeting both IGF1R and pathways that antagonize autophagy, such as ERK-MAPK axis, was strongly synergistic. IGF1R and ERK inhibition converged on suppression of glycolysis, leading to enhanced dependence on autophagy. Accordingly, concurrent inhibition of IGF1R, ERK, and autophagy induced cytotoxicity in PDAC cell lines and decreased viability in human PDAC organoids. In conclusion, targeting IGF1R together with ERK enhances the effectiveness of autophagy inhibitors in PDAC. Significance: Compensatory upregulation of IGF1R and ERK- MAPK signaling limits the efficacy of autophagy inhibitors chloroquine and hydroxychloroquine, and their concurrent inhibition synergistically increases autophagy dependence and chloroquine sensitivity in pancreatic ductal adenocarcinoma.Peer reviewe

Investment in online self-evaluation tests: A theoretical approach

BACKGROUND: Large-scale traumatic events may burden any affected public health system with consequential charges. One major post-disaster, expense factor emerges form early psychological interventions and subsequent, posttraumatic mental health care. Due to the constant increase in mental health care costs, also post-disaster public mental health requires best possible, cost-effective care systems. Screening and monitoring the affected population might be one such area to optimize the charges. METHODS: This paper analyzes the potential cost-effectiveness of monitoring a psychologically traumatized population and to motivate individuals at risk to seek early treatment. As basis for our model served Grossman's health production function, which was modified according to fundamental concepts of cost-benefit analyzes, to match the basic conditions of online monitoring strategies. We then introduce some fundamental concepts of cost-benefit analysis. RESULTS: When performing cost-benefit analyses, policy makers have to consider both direct costs (caused by treatment) and indirect costs (due to non-productivity). Considering both costs sources we find that the use of Internet-based psychometric screening instruments may reduce the duration of future treatment, psychological burden and treatment costs. CONCLUSION: The identification of individuals at risk for PTSD following a disaster may help organizations prevent both the human and the economic costs of this disease. Consequently future research on mental health issues should put more emphasis on the importance of monitoring to detect early PTSD and focus the most effective resources within early treatment and morbidity prevention

The SAMI Galaxy Survey: A Range in S0 Properties Indicating Multiple Formation Pathways

It has been proposed that S0 galaxies are either fading spirals or the result of galaxy mergers. The relative contribution of each pathway, and the environments in which they occur remains unknown. Here we investigate stellar and gas kinematics of 219 S0s in the SAMI Survey to look for signs of multiple formation pathways occurring across the full range of environments. We identify a large range of rotational support in their stellar kinematics, which correspond to ranges in their physical structure. We find that pressure-supported S0s with $v/{\sigma}$ below 0.5 tend to be more compact and feature misaligned stellar and gas components, suggesting an external origin for their gas. We postulate that these S0s are consistent with being formed through a merger process. Meanwhile, comparisons of ellipticity, stellar mass and S\'ersic index distributions with spiral galaxies shows that the rotationally supported S0s with $v/{\sigma}$ above 0.5 are more consistent with a faded spiral origin. In addition, a simulated merger pathway involving a compact elliptical and gas-rich satellite results in an S0 that lies within the pressure-supported group. We conclude that two S0 formation pathways are active, with mergers dominating in isolated galaxies and small groups, and the faded spiral pathway being most prominent in large groups ($10^{13} < M_{halo} < 10^{14}$).Comment: 14 pages, 12 figures, accepted for publication in MNRA

The peppermint breath test benchmark for PTR-MS and SIFT-MS

18openInternationalInternational coauthor/editorA major challenge for breath research is the lack of standardization in sampling and analysis. To address this, a test that utilizes a standardized intervention and a defined study protocol has been proposed to explore disparities in breath research across different analytical platforms and to provide benchmark values for comparison. Specifically, the Peppermint Experiment involves the targeted analysis in exhaled breath of volatile constituents of peppermint oil after ingestion of the encapsulated oil. Data from the Peppermint Experiment performed by proton transfer reaction mass spectrometry (PTR-MS) and selected ion flow tube mass spectrometry (SIFT-MS) are presented and discussed herein, including the product ions associated with the key peppermint volatiles, namely limonene, α- and β-pinene, 1,8-cineole, menthol, menthone and menthofuran. The breath washout profiles of these compounds from 65 individuals were collected, comprising datasets from five PTR-MS and two SIFT-MS instruments. The washout profiles of these volatiles were evaluated by comparing the log-fold change over time of the product ion intensities associated with each volatile. Benchmark values were calculated from the lower 95% confidence interval of the linear time-to-washout regression analysis for all datasets combined. Benchmark washout values from PTR-MS analysis were 353 min for the sum of monoterpenes and 1,8-cineole (identical product ions), 173 min for menthol, 330 min for menthofuran, and 218 min for menthone; from SIFT-MS analysis values were 228 min for the sum of monoterpenes, 281 min for the sum of monoterpenes and 1,8-cineole, and 370 min for menthone plus 1,8-cineole. Large inter- and intra-dataset variations were observed, whereby the latter suggests that biological variability plays a key role in how the compounds are absorbed, metabolized and excreted from the body via breath. This variability seems large compared to the influence of sampling and analytical procedures, but further investigations are recommended to clarify the effects of these factors.openHenderson, Ben; Slingers, Gitte; Pedrotti, Michele; Pugliese, Giovanni; Malásková, Michaela; Bryant, Luke; Lomonaco, Tommaso; Ghimenti, Silvia; Moreno, Sergi; Cordell, Rebecca; Harren, Frans J M; Schubert, Jochen; Mayhew, Chris A; Wilde, Michael; Di Francesco, Fabio; Koppen, Gudrun; Beauchamp, Jonathan D; Cristescu, Simona MHenderson, B.; Slingers, G.; Pedrotti, M.; Pugliese, G.; Malásková, M.; Bryant, L.; Lomonaco, T.; Ghimenti, S.; Moreno, S.; Cordell, R.; Harren, F.J.M.; Schubert, J.; Mayhew, C.A.; Wilde, M.; Di Francesco, F.; Koppen, G.; Beauchamp, J.D.; Cristescu, S.M