Cancer tissue classification using supervised machine learning applied to maldi mass spectrometry imaging

Matrix assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) can determine the spatial distribution of analytes such as protein distributions in a tissue section according to their mass-to-charge ratio. Here, we explored the clinical potential of machine learning (ML) applied to MALDI MSI data for cancer diagnostic classification using tissue microarrays (TMAs) on 302 colorectal (CRC) and 257 endometrial cancer (EC)) patients. ML based on deep neural networks discriminated colorectal tumour from normal tissue with an overall accuracy of 98% in balanced cross-validation (98.2% sensitivity and 98.6% specificity). Moreover, our machine learning approach predicted the presence of lymph node metastasis (LNM) for primary tumours of EC with an accuracy of 80% (90% sensitivity and 69% specificity). Our results demonstrate the capability of MALDI MSI for complementing classic histopathological examination for cancer diagnostic applications.Paul Mittal, Mark R. Condina, Manuela Klingler-Hoffmann, Gurjeet Kaur, Martin K. Oehler, Oliver M. Siebe

Carrier relaxation, pseudogap, and superconducting gap in high-Tc cuprates: A Raman scattering study

We describe results of electronic Raman-scattering experiments in differently doped single crystals of Y-123 and Bi-2212. The comparison of AF insulating and metallic samples suggests that at least the low-energy part of the spectra originates predominantly from excitations of free carriers. We therefore propose an analysis of the data in terms of a memory function approach. Dynamical scattering rates and mass-enhancement factors for the carriers are obtained. In B2g symmetry the Raman data compare well to the results obtained from ordinary and optical transport. For underdoped materials the dc scattering rates in B1g symmetry become temperature independent and considerably larger than in B2g symmetry. This increasing anisotropy is accompanied by a loss of spectral weight in B2g symmetry in the range between the superconducting transition at Tc and a characteristic temperature T* of order room temperature which compares well with the pseudogap temperature found in other experiments. The energy range affected by the pseudogap is doping and temperature independent. The integrated spectral loss is approximately 25% in underdoped samples and becomes much weaker towards higher carrier concentration. In underdoped samples, superconductivity related features in the spectra can be observed only in B2g symmetry. The peak frequencies scale with Tc. We do not find a direct relation between the pseudogap and the superconducting gap.Comment: RevTeX, 21 pages, 24 gif figures. For PostScript with embedded eps figures, see http://www.wmi.badw-muenchen.de/~opel/k2.htm

Hidden polymorphism of FAPbI3 discovered by Raman spectroscopy

Formamidinium lead iodide FAPbI3 can be used in its cubic, black form as a light absorber material in single junction solar cells. It has a band gap 1.5 eV close to the maximum of the Shockley Queisser limit, and reveals a high absorption coefficient. Its high thermal stability up to 320 C has also a downside, which is the instability of the photo active form at room temperature RT . Thus, the black amp; 945; phase transforms at RT with time into a yellow non photo active amp; 948; phase. The black phase can be recovered by annealing of the yellow state. In this work, a polymorphism of the amp; 945; phase at room temperature was found as synthesized amp; 945;i , degraded amp; 945; amp; 948; and thermally recovered amp; 945;rec . They differ in the Raman spectra and PL signal, but not in the XRD patterns. Using temperature dependent Raman spectroscopy, we identified a structural change in the amp; 945;i polymorph at ca. 110 C. Above 110 C, the FAPbI3 structure has undoubtedly cubic Pm[3 with combining macron]m symmetry high temperature phase amp; 945;HT . Below that temperature, the amp; 945;i phase was suggested to have a distorted perovskite structure with Im[3 with combining macron] symmetry. Thermally recovered FAPbI3 amp; 945;rec also demonstrated the structural transition to amp; 945;HT at the same temperature ca. 110 C during its heating. The understanding of hybrid perovskites may bring additional assets in the development of new and stable structure

A Prospectively Validated Prognostic Model for Patients with Locally Advanced Squamous Cell Carcinoma of the Head and Neck Based on Radiomics of Computed Tomography Images

Background: Locoregionally advanced head and neck squamous cell carcinoma (HNSCC) patients have high relapse and mortality rates. Imaging-based decision support may improve out-comes by optimising personalised treatment, and support patient risk stratification. We propose a multifactorial prognostic model including radiomics features to improve risk stratification for advanced HNSCC, compared to TNM eighth edition, the gold standard. Patient and methods: Data of 666 retrospective-and 143 prospective-stage III-IVA/B HNSCC patients were collected. A multivar-iable Cox proportional-hazards model was trained to predict overall survival (OS) using diagnostic CT-based radiomics features extracted from the primary tumour. Separate analyses were performed using TNM8, tumour volume, clinical and biological variables, and combinations thereof with radi-omics features. Patient risk stratification in three groups was assessed through Kaplan–Meier (KM) curves. A log-rank test was performed for significance (p-value < 0.05). The prognostic accuracy was reported through the concordance index (CI). Results: A model combining an 11-feature radiomics signature, clinical and biological variables, TNM8, and volume could significantly stratify the validation cohort into three risk groups (p < 0∙01, CI of 0.79 as validation). Conclusion: A combination of radiomics features with other predictors can predict OS very accurately for advanced HNSCC patients and improves on the current gold standard of TNM8

Metastable States in Spin Glasses and Disordered Ferromagnets

We study analytically M-spin-flip stable states in disordered short-ranged Ising models (spin glasses and ferromagnets) in all dimensions and for all M. Our approach is primarily dynamical and is based on the convergence of a zero-temperature dynamical process with flips of lattice animals up to size M and starting from a deep quench, to a metastable limit. The results (rigorous and nonrigorous, in infinite and finite volumes) concern many aspects of metastable states: their numbers, basins of attraction, energy densities, overlaps, remanent magnetizations and relations to thermodynamic states. For example, we show that their overlap distribution is a delta-function at zero. We also define a dynamics for M=infinity, which provides a potential tool for investigating ground state structure.Comment: 34 pages (LaTeX); to appear in Physical Review

Wolbachia strain wAlbB maintains high density and dengue inhibition following introduction into a field population of Aedes aegypti

Aedes aegypti mosquitoes carrying the wAlbB Wolbachia strain show a reduced capacity to transmit dengue virus. wAlbB has been introduced into wild Ae. aegypti populations in several field sites in Kuala Lumpur, Malaysia, where it has persisted at high frequency for more than 2 years and significantly reduced dengue incidence. Although these encouraging results indicate that wAlbB releases can be an effective dengue control strategy, the long-term success depends on wAlbB maintaining high population frequencies and virus transmission inhibition, and both could be compromised by Wolbachia–host coevolution in the field. Here, wAlbB-carrying Ae. aegypti collected from the field 20 months after the cessation of releases showed no reduction in Wolbachia density or tissue distribution changes compared to a wAlbB laboratory colony. The wAlbB strain continued to induce complete unidirectional cytoplasmic incompatibility, showed perfect maternal transmission under laboratory conditions, and retained its capacity to inhibit dengue. Additionally, a field-collected wAlbB line was challenged with Malaysian dengue patient blood, and showed significant blocking of virus dissemination to the salivary glands. These results indicate that wAlbB continues to inhibit currently circulating strains of dengue in field populations of Ae. aegypti, and provides additional support for the continued scale-up of Wolbachia wAlbB releases for dengue control

Biological and geophysical feedbacks with fire in the Earth system

Roughly 3% of the Earth's land surface burns annually, representing a critical exchange of energy and matter between the land and atmosphere via combustion. Fires range from slow smouldering peat fires, to low-intensity surface fires, to intense crown fires, depending on vegetation structure, fuel moisture, prevailing climate, and weather conditions. While the links between biogeochemistry, climate and fire are widely studied within Earth system science, these relationships are also mediated by fuels—namely plants and their litter—that are the product of evolutionary and ecological processes. Fire is a powerful selective force and, over their evolutionary history, plants have evolved traits that both tolerate and promote fire numerous times and across diverse clades. Here we outline a conceptual framework of how plant traits determine the flammability of ecosystems and interact with climate and weather to influence fire regimes. We explore how these evolutionary and ecological processes scale to impact biogeochemical and Earth system processes. Finally, we outline several research challenges that, when resolved, will improve our understanding of the role of plant evolution in mediating the fire feedbacks driving Earth system processes. Understanding current patterns of fire and vegetation, as well as patterns of fire over geological time, requires research that incorporates evolutionary biology, ecology, biogeography, and the biogeosciences

Cytogenetic characterization of telomeres in the holocentric chromosomes of the lepidopteran Mamestra brassicae

Telomeres of the Mamestra brassica holocentric chromosomes were studied by Southern blotting, in-situ hybridization and Bal31 assay evidencing the presence of the telomeric (TTAGG)(n) repeat. Successively, molecular analysis of telomeres showed that TRAS1 transposable elements were present at the subtelomeric regions of autosomes but not in the NOR-bearing telomeres of the Z and W sex chromosomes. TRAS1 appeared to be transcriptionally active and non-methylated, as evaluated by RT-PCR and digestion with MspI and HpaII. Finally, dot-blotting experiments showed that the 2.8 +/- 0.5% of the M. brassicae genome consists of TRAS1

Partonic flow and ϕ\phi-meson production in Au+Au collisions at sNN\sqrt{s_{NN}} = 200 GeV

We present first measurements of the $\phi$-meson elliptic flow ($v_{2}(p_{T})$) and high statistics $p_{T}$ distributions for different centralities from $\sqrt{s_{NN}}$ = 200 GeV Au+Au collisions at RHIC. In minimum bias collisions the $v_{2}$ of the $\phi$ meson is consistent with the trend observed for mesons. The ratio of the yields of the $\Omega$ to those of the $\phi$ as a function of transverse momentum is consistent with a model based on the recombination of thermal $s$ quarks up to $p_{T}\sim 4$ GeV/$c$, but disagrees at higher momenta. The nuclear modification factor ($R_{CP}$) of $\phi$ follows the trend observed in the $K^{0}_{S}$ mesons rather than in $\Lambda$ baryons, supporting baryon-meson scaling. Since $\phi$-mesons are made via coalescence of seemingly thermalized $s$ quarks in central Au+Au collisions, the observations imply hot and dense matter with partonic collectivity has been formed at RHIC.Comment: 6 pages, 4 figures, submit to PR