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

Nanotechnology and molecular cytogenetics: the future has not yet arrived

Quantum dots (QDs) are a novel class of inorganic fluorochromes composed of nanometer-scale crystals made of a semiconductor material. They are resistant to photo-bleaching, have narrow excitation and emission wavelengths that can be controlled by particle size and thus have the potential for multiplexing experiments. Given the remarkable optical properties that quantum dots possess, they have been proposed as an ideal material for use in molecular cytogenetics, specifically the technique of fluorescent in situ hybridisation (FISH). In this review, we provide an account of the current QD-FISH literature, and speculate as to why QDs are not yet optimised for FISH in their current form

Trace doping of multiple elements enables stable battery cycling of LiCoO2 at 4.6 V

LiCoO2 is a dominant cathode material for lithium-ion (Li-ion) batteries due to its high volumetric energy density, which could potentially be further improved by charging to high voltages. However, practical adoption of high-voltage charging is hindered by LiCoO2’s structural instability at the deeply delithiated state and the associated safety concerns. Here, we achieve stable cycling of LiCoO2 at 4.6 V (versus Li/Li+) through trace Ti–Mg–Al co-doping. Using state-of-the-art synchrotron X-ray imaging and spectroscopic techniques, we report the incorporation of Mg and Al into the LiCoO2 lattice, which inhibits the undesired phase transition at voltages above 4.5 V. We also show that, even in trace amounts, Ti segregates significantly at grain boundaries and on the surface, modifying the microstructure of the particles while stabilizing the surface oxygen at high voltages. These dopants contribute through different mechanisms and synergistically promote the cycle stability of LiCoO2 at 4.6 V

Optical signature of symmetry variations and spin-valley coupling in atomically thin tungsten dichalcogenides

Motivated by the triumph and limitation of graphene for electronic applications, atomically thin layers of group VI transition metal dichalcogenides are attracting extensive interest as a class of graphene-like semiconductors with a desired band-gap in the visible frequency range. The monolayers feature a valence band spin splitting with opposite sign in the two valleys located at corners of 1st Brillouin zone. This spin-valley coupling, particularly pronounced in tungsten dichalcogenides, can benefit potential spintronics and valleytronics with the important consequences of spin-valley interplay and the suppression of spin and valley relaxations. Here we report the first optical studies of WS2 and WSe2 monolayers and multilayers. The efficiency of second harmonic generation shows a dramatic even-odd oscillation with the number of layers, consistent with the presence (absence) of inversion symmetry in even-layer (odd-layer). Photoluminescence (PL) measurements show the crossover from an indirect band gap semiconductor at mutilayers to a direct-gap one at monolayers. The PL spectra and first-principle calculations consistently reveal a spin-valley coupling of 0.4 eV which suppresses interlayer hopping and manifests as a thickness independent splitting pattern at valence band edge near K points. This giant spin-valley coupling, together with the valley dependent physical properties, may lead to rich possibilities for manipulating spin and valley degrees of freedom in these atomically thin 2D materials

Dipole Coupling Effect of Holographic Fermion in the Background of Charged Gauss-Bonnet AdS Black Hole

We investigate the holographic fermions in the charged Gauss-Bonnet $AdS_{d}$ black hole background with the dipole coupling between fermion and gauge field in the bulk. We show that in addition to the strength of the dipole coupling, the spacetime dimension and the higher curvature correction in the gravity background also influence the onset of the Fermi gap and the gap distance. We find that the higher curvature effect modifies the fermion spectral density and influences the value of the Fermi momentum for the appearance of the Fermi surface. There are richer physics in the boundary fermion system due to the modification in the bulk gravity.Comment: 16 pages, accepted for publication in JHE

Synergism of anisotropic and computational NMR methods reveals the likely configuration of phormidolide A.

Characterization of the complex molecular scaffold of the marine polyketide natural product phormidolide A represents a challenge that has persisted for nearly two decades. In light of discordant results arising from recent synthetic and biosynthetic reports, a rigorous study of the configuration of phormidolide A was necessary. This report outlines a synergistic effort employing computational and anisotropic NMR investigation, that provided orthogonal confirmation of the reassigned side chain, as well as supporting a further correction of the C7 stereocenter

Assessing mechanical integrity of spinal fusion by in situ endochondral osteoinduction in the murine model

<p>Abstract</p> <p>Background</p> <p>Historically, radiographs, micro-computed tomography (micro-CT) exams, palpation and histology have been used to assess fusions in a mouse spine. The objective of this study was to develop a faster, cheaper, reproducible test to directly quantify the mechanical integrity of spinal fusions in mice.</p> <p>Methods</p> <p>Fusions were induced in ten mice spine using a previously described technique of in situ endochondral ossification, harvested with soft tissue, and cast in radiolucent alginate material for handling. Using a validated software package and a customized mechanical apparatus that flexed and extended the spinal column, the amount of intervertebral motion between adjacent vertebral discs was determined with static flexed and extended lateral spine radiographs. Micro-CT images of the same were also blindly reviewed for fusion.</p> <p>Results</p> <p>Mean intervertebral motion between control, non-fused, spinal vertebral discs was 6.1 ± 0.2° during spine flexion/extension. In fusion samples, adjacent vertebrae with less than 3.5° intervertebral motion had fusions documented by micro-CT inspection.</p> <p>Conclusions</p> <p>Measuring the amount of intervertebral rotation between vertebrae during spine flexion/extension is a relatively simple, cheap (<$100), clinically relevant, and fast test for assessing the mechanical success of spinal fusion in mice that compared favorably to the standard, micro-CT.</p

They are not all same: variations in Asian consumers' value perceptions of luxury brands

Asian markets are steadily becoming key growth regions for luxury brands. However, despite the growth, many luxury brand firms are unable to obtain the desired economic returns through their marketing strategies in Asia. Often these firms treat consumers across Asian markets as homogenous groups, which could lead to inaccurate luxury brand management strategy. Additionally, there is limited understanding of consumer value perceptions toward luxury brands across the Asian markets. Employing impression management theory and the horizontal/vertical collectivistic cultural distinctions, this study examines differences and similarities in constituent luxury value perceptions across three prominent Asian markets, namely China, India, and Indonesia. The results of a quantitative survey conducted with 626 real luxury consumers in these three countries identify variations in perceptions of symbolic, experiential, and functional value of luxury brands. The study contributes to knowledge on constituent luxury value perceptions, along with providing theoretical explanations for the differences between consumers across Asian markets. With the emerging novel insights on Asian consumers, luxury brand firms can align their marketing strategies to respective markets by leveraging the similarities and differences in consumer value perceptions. This approach, informed by empirical evidence, will enhance luxury brands’ competitiveness and profit opportunities in the high-growth Asian markets. The study identifies a number of future research directions