Bayesian Image Quality Transfer with CNNs: Exploring Uncertainty in dMRI Super-Resolution

In this work, we investigate the value of uncertainty modeling in 3D super-resolution with convolutional neural networks (CNNs). Deep learning has shown success in a plethora of medical image transformation problems, such as super-resolution (SR) and image synthesis. However, the highly ill-posed nature of such problems results in inevitable ambiguity in the learning of networks. We propose to account for intrinsic uncertainty through a per-patch heteroscedastic noise model and for parameter uncertainty through approximate Bayesian inference in the form of variational dropout. We show that the combined benefits of both lead to the state-of-the-art performance SR of diffusion MR brain images in terms of errors compared to ground truth. We further show that the reduced error scores produce tangible benefits in downstream tractography. In addition, the probabilistic nature of the methods naturally confers a mechanism to quantify uncertainty over the super-resolved output. We demonstrate through experiments on both healthy and pathological brains the potential utility of such an uncertainty measure in the risk assessment of the super-resolved images for subsequent clinical use.Comment: Accepted paper at MICCAI 201

An AI Approach to Identifying Novel Therapeutics for Rheumatoid Arthritis

Rheumatoid arthritis (RA) is a chronic autoimmune disorder that has a significant impact on quality of life and work capacity. Treatment of RA aims to control inflammation and alleviate pain; however, achieving remission with minimal toxicity is frequently not possible with the current suite of drugs. This review aims to summarise current treatment practices and highlight the urgent need for alternative pharmacogenomic approaches for novel drug discovery. These approaches can elucidate new relationships between drugs, genes, and diseases to identify additional effective and safe therapeutic options. This review discusses how computational approaches such as connectivity mapping offer the ability to repurpose FDA-approved drugs beyond their original treatment indication. This review also explores the concept of drug sensitisation to predict co-prescribed drugs with synergistic effects that produce enhanced anti-disease efficacy by involving multiple disease pathways. Challenges of this computational approach are discussed, including the availability of suitable high-quality datasets for comprehensive analysis and other data curation issues. The potential benefits include accelerated identification of novel drug combinations and the ability to trial and implement established treatments in a new index disease. This review underlines the huge opportunity to incorporate disease-related data and drug-related data to develop methods and algorithms that have strong potential to determine novel and effective treatment regimens

Mathematical modeling of the dynamics of the bladder cancer and the immune response applied to a patient: Evolution and short-term prediction

[EN] Bladder cancer is one of the most common malignant diseases in the urinary system and a highly aggressive neoplasm. The prognosis is not favorable usually, and its evolution for particular patients is very difficult to find out. In this paper, we propose a dynamic mathematical model that describes the bladder tumor growth and the immune response evolution. This model is customized for a single patient, determining appropriate model parameter values via model calibration. Due to the uncertainty of the tumor evolution, using the calibrated model parameters, we predict the tumor size and the immune response evolution over the next few months assuming three different scenarios: favorable, neutral, and unfavorable. In the former, it is not expected any trace of the cancer in the middle of September 2018 (after 16 mo). In the neutral scenario, at the same date, a 7- to 8-mm tumor is expected. In the worst case, a 40-mm tumor is expected. The patient was cited on 10 September 2018 to check the tumor size, and according to the doctors, there was no sign of recurrence. It seems that we are in the favorable scenario. The patient will be called again for follow-up in mid-2019.This work has been supported by the Ministerio de Economía, Industria y Competitividad grant MTM2017-89664-P.Burgos-Simon, C.; García-Medina, N.; Martínez-Rodríguez, D.; Villanueva Micó, RJ. (2019). Mathematical modeling of the dynamics of the bladder cancer and the immune response applied to a patient: Evolution and short-term prediction. Mathematical Methods in the Applied Sciences. 42(17):5746-5757. https://doi.org/10.1002/mma.5536S574657574217Official Site for Spanish Medic Oncology Society.https://www.seom.org. Accessed: 25/09/2018.Greenlee, R. T., Hill-Harmon, M. B., Murray, T., & Thun, M. (2001). Cancer Statistics, 2001. CA: A Cancer Journal for Clinicians, 51(1), 15-36. doi:10.3322/canjclin.51.1.15Holmang, S., Hedelin, H., Anderstrom, C., & Johansson, S. L. (1995). The Relationship Among Multiple Recurrences, Progression and Prognosis of Patients with Stages TA and T1 Transitional Cell Cancer of the Bladder Followed for at least 20 years. Journal of Urology, 153(6), 1823-1827. doi:10.1016/s0022-5347(01)67321-xRedelman-Sidi, G., Glickman, M. S., & Bochner, B. H. (2014). The mechanism of action of BCG therapy for bladder cancer—a current perspective. Nature Reviews Urology, 11(3), 153-162. doi:10.1038/nrurol.2014.15Bladder Cancer Treatment (PDQ)‐Health Professional Version.https://www.cancer.gov/types/bladder/hp/bladder-treatment-pdq. Accessed: 25/09/2018.Bladder Cancer Treatment (PDQ)‐Patient Version.https://www.cancer.gov/types/bladder/patient/bladder-treatment-pdq. Accessed: 25/09/2018.Official Site for Hospital Universitari i Politècnic La Fe Valencia Spain.http://www.hospital-lafe.com. Accessed: 25/09/2018.Hanahan, D., & Weinberg, R. A. (2011). Hallmarks of Cancer: The Next Generation. Cell, 144(5), 646-674. doi:10.1016/j.cell.2011.02.013Dong, H., Strome, S. E., Salomao, D. R., Tamura, H., Hirano, F., Flies, D. B., … Chen, L. (2002). Tumor-associated B7-H1 promotes T-cell apoptosis: A potential mechanism of immune evasion. Nature Medicine, 8(8), 793-800. doi:10.1038/nm730Fernandez, N. C., Lozier, A., Flament, C., Ricciardi-Castagnoli, P., Bellet, D., Suter, M., … Zitvogel, L. (1999). Dendritic cells directly trigger NK cell functions: Cross-talk relevant in innate anti-tumor immune responses in vivo. Nature Medicine, 5(4), 405-411. doi:10.1038/7403Factsheet of OncoTICE 2 − 8 × 108UFC powder for suspension intravesical (in Spanish).https://www.aemps.gob.es/cima/pdfs/es/ft/61377/61377_ft.pdf. Accessed: 25/09/2018

Tuning the role of charge-transfer states in intramolecular singlet exciton fission through side-group engineering

Understanding the mechanism of singlet exciton fission, in which a singlet exciton separates into a pair of triplet excitons, is crucial to the development of new chromophores for efficient fission-sensitized solar cells. The challenge of controlling molecular packing and energy levels in the solid state precludes clear determination of the singlet fission pathway. Here, we circumvent this difficulty by utilizing covalent dimers of pentacene with two types of side groups. We report rapid and efficient intramolecular singlet fission in both molecules, in one case via a virtual charge-transfer state and in the other via a distinct charge-transfer intermediate. The singlet fission pathway is governed by the energy gap between singlet and charge-transfer states, which change dynamically with molecular geometry but are primarily set by the side group. These results clearly establish the role of charge-transfer states in singlet fission and highlight the importance of solubilizing groups to optimize excited-state photophysics.S.L. thanks AGS(O) Scholarship support from A*STAR Singapore. J.W. acknowledges financial support from MOE Tier 3 grant (MOE2014-T3-1-004). This work was supported by the Engineering and Physical Sciences Research Council, U.K. (Grant numbers EP/M005143/1 and EP/G060738/1). D.H.P.T. and N.D.M.H. acknowledge the Winton Programme for the Physics of Sustainability. K.C. and J.M.H. acknowledge support from a Rutherford Discovery Fellowship to J.M.H

Aquatic Hemiptera in Southwest Cameroon: Biodiversity of Potential Reservoirs of Mycobacterium ulcerans and multiple wolbachia sequence types revealed by metagenomics

Buruli ulcer (BU), caused by Mycobacterium ulcerans, is a neglected tropical disease associated with freshwater habitats. A variety of limnic organisms harbor this pathogen, including aquatic bugs (Hemiptera: Heteroptera), which have been hypothesized to be epidemiologically important reservoirs. Aquatic Hemiptera exhibit high levels of diversity in the tropics, but species identification remains challenging. In this study, we collected aquatic bugs from emerging foci of BU in the Southwest Region of Cameroon, which were identified using morphological and molecular methods. The bugs were screened for mycobacterial DNA and a selection of 20 mycobacteria-positive specimens from the families Gerridae and Veliidae were subjected to next-generation sequencing. Only one individual revealed putative M. ulcerans DNA, but all specimens contained sequences from the widespread alphaproteobacterial symbiont, Wolbachia. Phylogenetic analysis placed the Wolbachia sequences into supergroups A, B, and F. Circularized mitogenomes were obtained for seven gerrids and two veliids, the first from these families for the African continent. This study suggests that aquatic Hemiptera may have a minor role (if any) in the spread of BU in Southwest Cameroon. Our metagenomic analysis provides new insights into the incursion of Wolbachia into aquatic environments and generated valuable resources to aid molecular taxonomic studies of aquatic Hemiptera. © 2019 by the authors

Co3O4 Nanocrystals on Graphene as a Synergistic Catalyst for Oxygen Reduction Reaction

Catalysts for oxygen reduction and evolution reactions are at the heart of key renewable energy technologies including fuel cells and water splitting. Despite tremendous efforts, developing oxygen electrode catalysts with high activity at low costs remains a grand challenge. Here, we report a hybrid material of Co3O4 nanocrystals grown on reduced graphene oxide (GO) as a high-performance bi-functional catalyst for oxygen reduction reaction (ORR) and oxygen evolution reaction (OER). While Co3O4 or graphene oxide alone has little catalytic activity, their hybrid exhibits an unexpected, surprisingly high ORR activity that is further enhanced by nitrogen-doping of graphene. The Co3O4/N-doped graphene hybrid exhibits similar catalytic activity but superior stability to Pt in alkaline solutions. The same hybrid is also highly active for OER, making it a high performance non-precious metal based bi-catalyst for both ORR and OER. The unusual catalytic activity arises from synergetic chemical coupling effects between Co3O4 and graphene.Comment: published in Nature Material

Species Boundaries and Parapatric Speciation in the Complex of Alpine Shrubs, Rosa sericea (Rosaceae), Based on Population Genetics and Ecological Tolerances

Discerning species boundaries among closely related taxa is fundamental to studying evolution and biodiversity. However, species boundaries can be difficult to access in plants because ongoing divergence and speciation may leave an evolutionary footprint similar to introgression, which occurs frequently among species and genera. In this study, we sought to determine species boundaries between two closely related alpine shrubs, Rosa sericea and Rosa omeiensis, using population genetics, environmental data and ecological niche modeling, and morphological traits. We analyzed populations of R. sericea and R. omeiensis using genetic markers comprising a fragment of the single-copy nuclear gene, LEAFY, micro-satellites (EST-SSR), and plastid DNA sequences. The DNA sequence data suggested clusters of populations consistent with geography but not with previously proposed species boundaries based on morphology. Nevertheless, we found that the ecological niches of the previously proposed species only partially overlap. Thus, we suspect that these species are in the process of parapatric speciation; that is, differentiating along an ecological gradient, so that they exhibit differing morphology. Morphology has previously been the basis of recognizing the species R.sericea and R. omeiensis, which are the most widely distributed species within a broader R. sericea complex that includes several other narrow endemics. Here, we recognize R.sericea and R. omeiensis as independent species based on morphological and ecological data under the unified species concept, which emphasizes that these data types are of equal value to DNA for determining species boundaries and refining taxonomic treatments. While the DNA data did not delimit species within the R.sericea complex, we expect to develop and utilize new, robust DNA tools for understanding speciation within this group in future studies

Electron Accumulation Induces Efficiency Bottleneck for Hydrogen Production in Carbon Nitride Photocatalysts.

This study addresses the light intensity dependence of charge accumulation in a photocatalyst suspension, and its impact on both charge recombination kinetics and steady-state H2 evolution efficiency. Cyanamide surface functionalized melon-type carbon nitride (NCNCNx) has been selected as an example of emerging carbon nitrides photocatalysts because of its excellent charge storage ability. Transient spectroscopic studies (from ps to s) show that the bimolecular recombination of photogenerated electrons and holes in NCNCNx can be well described by a random walk model. Remarkably, the addition of hole scavengers such as 4-methylbenzyl alcohol can lead to ∼400-fold faster recombination kinetics (lifetime shortening to ∼10 ps). We show that this acceleration is not the direct result of ultrafast hole extraction by the scavenger, but is rather caused by long-lived electron accumulation in NCNCNx after hole extraction. The dispersive pseudo-first order recombination kinetics become controlled by the density of accumulated electrons. H2 production and steady-state spectroscopic measurements indicate that the accelerated recombination caused by electron accumulation limits the H2 generation efficiency. The addition of a reversible electron acceptor and mediator, methyl viologen (MV2+), accelerates the extraction of electrons from the NCNCNx and increases the H2 production efficiency under one sun irradiation by more than 30%. These results demonstrate quantitatively that while long-lived electrons are essential to drive photoinduced H2 generation in many photocatalysts, excessive electron accumulation may result in accelerated recombination losses and lower performance, and thus highlight the importance of efficient electron and hole extraction in enabling efficient water splitting photocatalysts.ERC AdG Intersolar grant (Grant No. 291482), The Christian Doppler Research Association The OMV Grou