A transfer-learning approach to feature extraction from cancer transcriptomes with deep autoencoders

Publicado en Lecture Notes in Computer Science.The diagnosis and prognosis of cancer are among the more challenging tasks that oncology medicine deals with. With the main aim of fitting the more appropriate treatments, current personalized medicine focuses on using data from heterogeneous sources to estimate the evolu- tion of a given disease for the particular case of a certain patient. In recent years, next-generation sequencing data have boosted cancer prediction by supplying gene-expression information that has allowed diverse machine learning algorithms to supply valuable solutions to the problem of cancer subtype classification, which has surely contributed to better estimation of patient’s response to diverse treatments. However, the efficacy of these models is seriously affected by the existing imbalance between the high dimensionality of the gene expression feature sets and the number of sam- ples available for a particular cancer type. To counteract what is known as the curse of dimensionality, feature selection and extraction methods have been traditionally applied to reduce the number of input variables present in gene expression datasets. Although these techniques work by scaling down the input feature space, the prediction performance of tradi- tional machine learning pipelines using these feature reduction strategies remains moderate. In this work, we propose the use of the Pan-Cancer dataset to pre-train deep autoencoder architectures on a subset com- posed of thousands of gene expression samples of very diverse tumor types. The resulting architectures are subsequently fine-tuned on a col- lection of specific breast cancer samples. This transfer-learning approach aims at combining supervised and unsupervised deep learning models with traditional machine learning classification algorithms to tackle the problem of breast tumor intrinsic-subtype classification.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

A relative value method for measuring and evaluating cardiac reserve

BACKGROUND: Although a very close relationship between the amplitude of the first heart sound (S1) and the cardiac contractility have been proven by previous studies, the absolute value of S1 can not be applied for evaluating cardiac contractility. However, we were able to devise some indicators with relative values for evaluating cardiac function. METHODS: Tests were carried out on a varied group of volunteers. Four indicators were devised: (1) the increase of the amplitude of the first heart sound after accomplishing different exercise workloads, with respect to the amplitude of the first heart sound (S1)recorded at rest was defined as cardiac contractility change trend (CCCT). When the subjects completed the entire designed exercise workload (7000 J), the resulting CCCT was defined as CCCT(1); when only 1/4 of the designed exercise workload was completed, the result was defined as CCCT(1/4). (2) The ratio of S1 amplitude to S2 amplitude (S1/S2). (3) The ratio of S1 amplitude at tricuspid valve auscultation area to that at mitral auscultation area T1/M1 (4) the ratio of diastolic to systolic duration (D/S). Data were expressed as mean ± SD. RESULTS: CCCT(1/4) was 6.36 ± 3.01 (n = 67), CCCT(1) was 10.36 ± 4.2 (n = 33), S1/S2 was1.89 ± 0.94 (n = 140), T1/M1 was 1.44 ± 0.99 (n = 144), and D/S was 1.68 ± 0.27 (n = 172). CONCLUSIONS: Using indicators CCCT(1/4) and CCCT(1) may be beneficial for evaluating cardiac contractility and cardiac reserve mobilization level, S1/S2 for considering the factor for hypotension, T1/M1 for evaluating the right heart load, and D/S for evaluating diastolic cardiac blood perfusion time

Fumarate drives EMT in renal cancer

Medical Research Counci

The Paleoproterozoic Chibaisong Mafic-Ultramafic Intrusion and Cu-Ni Deposit, North China Craton: SHRIMP Zircon U-Pband Re-Os Geochronology and Geodynamic Implications

published_or_final_versio

Liquid fuel evaporation under supercritical conditions

Molecular dynamics simulations are performed to study the supercritical mixing process of the n-dodecane/nitrogen binary system. Previous studies have shown the existence of supercritical phenomenon under certain conditions in modern propulsion systems such as diesel engines. However, the physical mechanisms and internal driving forces of this phenomenon are still not well understood. In this paper, we attempt to answer this question through simulating the diffusion and evaporation of gaseous nitrogen and liquid phase n-dodecane. It addresses under what conditions the supercritical transition phenomenon happens and what features the supercritical evaporation process have. A unique configuration is constructed to mimic the evaporation of an n-dodecane thin film in an open nitrogen environment under conditions ranging from subcritical to supercritical. The detailed structure of the liquid-vapor interface during the evaporating process is described and the evaporation rate and the interface thickness are estimated, which show differences between subcritical and supercritical evaporation. Results indicate that under relatively high pressure conditions, the liquid surface transitions into supercritical state, and the liquid-vapor interface expands significantly with vanishing surface tension, leading to a diffusion like mixing process. It is shown that the supercritical evaporation would happen under conditions that correspond to the in-cylinder conditions of a turbo-charged engine

Molecular Dynamics Simulations of the Evaporation Process of a Fuel Droplet Under Supercritical Environment

The evaporation process of an n-dodecane droplet surrounded by nitrogen ambient under supercritical pressures and sub- to super-critical temperatures is studied by molecular dynamics simulation. Results show that the evaporation process under high pressures depart considerably from the theoretical prediction of D2-law. Both environmental pressure and temperature have significant inuence on the evaporation rate, and elevated pressure can greatly increase the nitrogen solubility in the liquid phase and also the liquid-vapor interface thickness. It is found that under supercritical environmental conditions, the expanded interface may enter the continuum regime, leading to a diffusion dominated mixing process, rather than a conventional evaporation

Global marine redox changes drove the rise and fall of the Ediacara biota

This is the final version. Available on open access from Wiley via the DOI in this recordThe role of O2 in the evolution of early animals, as represented by some members of the Ediacara biota, has been heavily debated because current geochemical evidence paints a conflicting picture regarding global marine O2 levels during key intervals of the rise and fall of the Ediacara biota. Fossil evidence indicates that the diversification the Ediacara biota occurred during or shortly after the Ediacaran Shuram negative C-isotope Excursion (SE), which is often interpreted to reflect ocean oxygenation. However, there is conflicting evidence regarding ocean oxygen levels during the SE and the middle Ediacaran Period. To help resolve this debate, we examined U isotope variations (δ238U) in three carbonate sections from South China, Siberia, and USA that record the SE. The δ238U data from all three sections are in excellent agreement and reveal the largest positive shift in δ238U ever reported in the geologic record (from ~ −0.74‰ to ~ −0.26‰). Quantitative modeling of these data suggests that the global ocean switched from a largely anoxic state (26%–100% of the seafloor overlain by anoxic waters) to near-modern levels of ocean oxygenation during the SE. This episode of ocean oxygenation is broadly coincident with the rise of the Ediacara biota. Following this initial radiation, the Ediacara biota persisted until the terminal Ediacaran period, when recently published U isotope data indicate a return to more widespread ocean anoxia. Taken together, it appears that global marine redox changes drove the rise and fall of the Ediacara biota.NASADanish Agency for Science, Technology and InnovationNational Science Foundation (NSF)National Key Basic Research Program of ChinaNatural Environment Research Council (NERC)Natural Science Foundation of Chin

Cancer-selective, single agent chemoradiosensitising gold nanoparticles

Two nanometre gold nanoparticles (AuNPs), bearing sugar moieties and/or thiol-polyethylene glycol-amine (PEG-amine), were synthesised and evaluated for their in vitro toxicity and ability to radiosensitise cells with 220 kV and 6 MV X-rays, using four cell lines representing normal and cancerous skin and breast tissues. Acute 3 h exposure of cells to AuNPs, bearing PEG-amine only or a 50:50 ratio of alpha-galactose derivative and PEG-amine resulted in selective uptake and toxicity towards cancer cells at unprecedentedly low nanomolar concentrations. Chemotoxicity was prevented by co-administration of N-acetyl cysteine antioxidant, or partially prevented by the caspase inhibitor Z-VAD-FMK. In addition to their intrinsic cancer-selective chemotoxicity, these AuNPs acted as radiosensitisers in combination with 220 kV or 6 MV X-rays. The ability of AuNPs bearing simple ligands to act as cancer-selective chemoradiosensitisers at low concentrations is a novel discovery that holds great promise in developing low-cost cancer nanotherapeutics