Predicting survival from colorectal cancer histology slides using deep learning: A retrospective multicenter study

BACKGROUND: For virtually every patient with colorectal cancer (CRC), hematoxylin-eosin (HE)-stained tissue slides are available. These images contain quantitative information, which is not routinely used to objectively extract prognostic biomarkers. In the present study, we investigated whether deep convolutional neural networks (CNNs) can extract prognosticators directly from these widely available images. METHODS AND FINDINGS: We hand-delineated single-tissue regions in 86 CRC tissue slides, yielding more than 100,000 HE image patches, and used these to train a CNN by transfer learning, reaching a nine-class accuracy of >94% in an independent data set of 7,180 images from 25 CRC patients. With this tool, we performed automated tissue decomposition of representative multitissue HE images from 862 HE slides in 500 stage I-IV CRC patients in the The Cancer Genome Atlas (TCGA) cohort, a large international multicenter collection of CRC tissue. Based on the output neuron activations in the CNN, we calculated a "deep stroma score," which was an independent prognostic factor for overall survival (OS) in a multivariable Cox proportional hazard model (hazard ratio [HR] with 95% confidence interval [CI]: 1.99 [1.27-3.12], p = 0.0028), while in the same cohort, manual quantification of stromal areas and a gene expression signature of cancer-associated fibroblasts (CAFs) were only prognostic in specific tumor stages. We validated these findings in an independent cohort of 409 stage I-IV CRC patients from the "Darmkrebs: Chancen der Verhütung durch Screening" (DACHS) study who were recruited between 2003 and 2007 in multiple institutions in Germany. Again, the score was an independent prognostic factor for OS (HR 1.63 [1.14-2.33], p = 0.008), CRC-specific OS (HR 2.29 [1.5-3.48], p = 0.0004), and relapse-free survival (RFS; HR 1.92 [1.34-2.76], p = 0.0004). A prospective validation is required before this biomarker can be implemented in clinical workflows. CONCLUSIONS: In our retrospective study, we show that a CNN can assess the human tumor microenvironment and predict prognosis directly from histopathological images

Large-scale database mining reveals hidden trends and future directions for cancer immunotherapy

LLC Cancer immunotherapy has fundamentally changed the landscape of oncology in recent years and significant resources are invested into immunotherapy research. It is in the interests of researchers and clinicians to identify promising and less promising trends in this field in order to rationally allocate resources. This requires a quantitative large-scale analysis of cancer immunotherapy related databases. We developed a novel tool for text mining, statistical analysis and data visualization of scientific literature data. We used this tool to analyze 72002 cancer immunotherapy publications and 1469 clinical trials from public databases. All source codes are available under an open access license. The contribution of specific topics within the cancer immunotherapy field has markedly shifted over the years. We show that the focus is moving from cell-based therapy and vaccination towards checkpoint inhibitors, with these trends reaching statistical significance. Rapidly growing subfields include the combination of chemotherapy with checkpoint blockade. Translational studies have shifted from hematological and skin neoplasms to gastrointestinal and lung cancer and from tumor antigens and angiogenesis to tumor stroma and apoptosis. This work highlights the importance of unbiased large-scale database mining to assess trends in cancer research and cancer immunotherapy in particular. Researchers, clinicians and funding agencies should be aware of quantitative trends in the immunotherapy field, allocate resources to the most promising areas and find new approaches for currently immature topics

Personalized Drug Dosage – Closing the Loop

A brief account is given of various approaches to the individualization of drug dosage, including the use of pharmacodynamic markers, therapeutic monitoring of plasma drug concentrations, genotyping, computer-guided dosage using ‘dashboards’, and automatic closed-loop control of pharmacological action. The potential for linking the real patient to his or her ‘virtual twin’ through the application of physiologically-based pharmacokinetic modeling is also discussed

On the ambiguity of 1,3,2-benzodiazaboroles as donor/acceptor functionalities in luminescent molecules

A series of 1,3-bis(perfluoroaryl)-2-(hetero)aryl-1,3,2-benzodiazaboroles, 1,3-FAr2-2-Ar-1,3,2-N2BC6H4 (Ar = Ph, FAr = C6F5 5; Ar = Ph, FAr = 4-C5F4N 6; Ar = Ph, FAr = 4-NCC6F4 7; Ar = 2-C4H3S, FAr = C6F5 8; Ar = 2-C4H3S, FAr = 4-C5F4N 9; Ar = 2-C4H3S, FAr = 4-NCC6F4 10), were synthesised by cyclocondensation of the adducts PhBBr2·PPh3 or 2-thienylBBr2·PPh3 with N,N′-bis(perfluoroaryl)-o-phenylenediamines in the presence of 2,2,6,6-tetramethylpiperidine. Similar treatments of the PPh3 adducts of 4-(1′,3′-diethyl-1′,3′,2′-benzodiazaborolyl)-phenyldibromoborane with the corresponding diamines gave rise to the push–pull compounds, C6H4(NEt)2B-1,4-C6H4-B(NFAr)2C6H4 (FAr = C6F5 11; 4-C5F4N 12) and C6H4(NEt)2B-2,5-C4H2S-B(NFAr)2C6H4 (FAr = C6F5 13; 4-C5F4N 14). The X-ray structures of 8, 11, 12 and 13 were determined. Electronic structure calculations reveal that the LUMOs are located at the perfluoroaryl groups in 5–14; thus the fluorinated benzodiazaborolyl groups are considered as electron-withdrawing moieties. These moieties differ from alkylated benzodiazaborolyl groups which are regarded as donors. The emission spectra for 5–14 show charge transfer bands with significant solvatochromism and large Stokes shifts (6100–12500 cm−1 in cyclohexane and 8900–15900 cm−1 in CH2Cl2). The emissions of the benzodiazaboroles, 5–10, arise from a different charge transfer (CT) process to the local charge transfer (LCT) process typically found in many fluorescent benzodiazaboroles. This novel remote charge transfer (RCT) process involving the perfluoroaryl groups is supported by CAM-B3LYP computations. The push–pull systems 11–14 here give fluorescent emissions with moderate to high fluorescence quantum yields (65–97%) that arise from the usual LCT process only

Hf–Zr anomalies in clinopyroxene from mantle xenoliths from France and Poland: implications for Lu–Hf dating of spinel peridotite lithospheric mantle

Clinopyroxenes in some fresh anhydrous spinel peridotite mantle xenoliths from the northern Massif Central (France) and Lower Silesia (Poland), analysed for a range of incompatible trace elements by laser ablation inductively coupled plasma mass spectrometry, show unusually strong negative anomalies in Hf and Zr relative to adjacent elements Sm and Nd, on primitive mantle-normalised diagrams. Similar Zr–Hf anomalies have only rarely been reported from clinopyroxene in spinel peridotite mantle xenoliths worldwide, and most are not as strong as the examples reported here. Low Hf contents give rise to a wide range of Lu/Hf ratios, which over geological time would result in highly radiogenic εHf values, decoupling them from εNd ratios. The high 176Lu/177Hf could in theory produce an isochronous relationship with 176Hf/177Hf over time; an errorchron is shown by clinopyroxene from mantle xenoliths from the northern Massif Central. However, in a review of the literature, we show that most mantle spinel peridotites do not show such high Lu/Hf ratios in their constituent clinopyroxenes, because they lack the distinctive Zr–Hf anomaly, and this limits the usefulness of the application of the Lu–Hf system of dating to garnet-free mantle rocks. Nevertheless, some mantle xenoliths from Poland or the Czech Republic may be amenable to Hf-isotope dating in the future

Familial clustering of Leiomyomatosis peritonealis disseminata: an unknown genetic syndrome?

BACKGROUND: Leiomyomatosis peritonealis disseminata (LPD) is defined as the occurrence of multiple tumorous intraabdominal lesions, which are myomatous nodules. LPD is a rare disease with only about 100 cases reported. The usual course of LPD is benign with the majority of the patients being premenopausal females. Only two cases involving men have been reported, no syndrome or familial occurrence of LPD has been described. CASE PRESENTATION: We describe a Caucasian-American family in which six members (three men) are diagnosed with Leiomyomatosis peritonealis disseminata (LPD) and three deceased family members most likely had LPD (based on the autopsy reports). Furthermore we describe the association of LPD with Raynaud's syndrome and Prurigo nodularis. CONCLUSION: Familial clustering of Leiomyomatosis peritonealis disseminata (LPD) has not been reported so far. The etiology of LPD is unknown and no mode of inheritance is known. We discuss possible modes of inheritance in the presented case, taking into account the possibility of a genetic syndrome. Given the similarity to other genetic syndromes with leiomyomatosis and skin alterations, we describe possible similar genetic pathomechanisms

Tourmaline Reference Materials for the In Situ Analysis of Oxygen and Lithium Isotope Ratio Compositions

Three tourmaline reference materials sourced from the Harvard Mineralogical and Geological Museum (schorl 112566, dravite 108796 and elbaite 98144), which are already widely used for the calibration of in situ boron isotope measurements, are characterised here for their oxygen and lithium isotope compositions. Homogeneity tests by secondary ion mass spectrometry (SIMS) showed that at sub‐nanogram test portion masses their 18O/16O and 7Li/6Li isotope ratios are constant within ± 0.27‰ and ± 2.2‰ (1s), respectively. The lithium mass fractions of the three materials vary over three orders of magnitude. SIMS homogeneity tests showed variations in 7Li/28Si between 8% and 14% (1s), which provides a measure of the heterogeneity of the Li contents in these three materials. Here we provide recommended values for δ18O, Δ’17O and δ7Li for the three Harvard tourmaline reference materials based on results from bulk mineral analyses from multiple, independent laboratories using laser‐ and stepwise fluorination gas mass spectrometry (for O), and solution multi‐collector inductively coupled plasma‐mass spectroscopy (for Li). These bulk data also allow us to assess the degree of inter‐laboratory data that might be present in such datasets. This work also re‐evaluates the major element chemical composition of the materials by electron probe microanalysis and investigates the presence of a chemical matrix effect on SIMS instrumental mass fractionation with regards to δ18O determinations, which was found to be < 1.6‰ between these three materials. The final table presented here provides a summary of the isotope ratio values that we have determined for these three materials. Depending on their starting mass either 128 or 256 splits have been produced of each material, assuring their availability for many years into the future

200-GeV ISA with room temperature magnets

A conceptual design study of 200-GeV proton intersecting storage accclerators with room temperature magnets is presented. The key to this study was thc desire to keep the electric power consumptiom to an acceptable level (40 MW). The design has been optimized by choosing small-gap (4 cm) aluminum coil dipoles operating at about 15 kG. The luminosity of this machine is limited to about 10/sup 32/ cm-/sup -2/ sec/sup -1/ by transverse space-charg e effects. An order of magnitude higher luminositics can be obtained by adding a booster of modest cost. A novel vacuum system using distributed Ti-sublimation pumps results in considerable savings. A cost comparison with a high-luminosity superconducting machine is given. (auth

Characterization of exercise-induced hemolysis in endurance horses

Exercise-induced hemolysis occurs as the result of intense physical exercise and is caused by metabolic and mechanical factors including repeated muscle contractions leading to capillary vessels compression, vasoconstriction of internal organs and foot strike among others. We hypothesized that exercise-induced hemolysis occurred in endurance racehorses and its severity was associated with the intensity of exercise. To provide further insight into the hemolysis of endurance horses, the aim of the study was to deployed a strategy for small molecules (metabolites) profiling, beyond standard molecular methods. The study included 47 Arabian endurance horses competing for either 80, 100, or 120 km distances. Blood plasma was collected before and after the competition and analyzed macroscopically, by ELISA and non-targeted metabolomics with liquid chromatography–mass spectrometry. A significant increase in all hemolysis parameters was observed after the race, and an association was found between the measured parameters, average speed, and distance completed. Levels of hemolysis markers were highest in horses eliminated for metabolic reasons in comparison to finishers and horses eliminated for lameness (gait abnormality), which may suggest a connection between the intensity of exercise, metabolic challenges, and hemolysis. Utilization of omics methods alongside conventional methods revealed a broader insight into the exercise-induced hemolysis process by displaying, apart from commonly measured hemoglobin and haptoglobin, levels of hemoglobin degradation metabolites. Obtained results emphasized the importance of respecting horse limitations in regard to speed and distance which, if underestimated, may lead to severe damages