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

Single Image Super-Resolution Using Lightweight CNN with Maxout Units

Rectified linear units (ReLU) are well-known to be helpful in obtaining faster convergence and thus higher performance for many deep-learning-based applications. However, networks with ReLU tend to perform poorly when the number of filter parameters is constrained to a small number. To overcome it, in this paper, we propose a novel network utilizing maxout units (MU), and show its effectiveness on super-resolution (SR) applications. In general, the MU has been known to make the filter sizes doubled in generating the feature maps of the same sizes in classification problems. In this paper, we first reveal that the MU can even make the filter sizes halved in restoration problems thus leading to compaction of the network sizes. To show this, our SR network is designed without increasing the filter sizes with MU, which outperforms the state of the art SR methods with a smaller number of filter parameters. To the best of our knowledge, we are the first to incorporate MU into SR applications and show promising performance results. In MU, feature maps from a previous convolutional layer are divided into two parts along channels, which are then compared element-wise and only their max values are passed to a next layer. Along with some interesting properties of MU to be analyzed, we further investigate other variants of MU and their effects. In addition, while ReLU have a trouble for learning in networks with a very small number of convolutional filter parameters, MU do not. For SR applications, our MU-based network reconstructs high-resolution images with comparable quality compared to previous deep-learning-based SR methods, with lower filter parameters.Comment: ACCV201

Challenges and opportunities associated with waste management in India

India faces major environmental challenges associated with waste generation and inadequate waste collection, transport, treatment and disposal. Current systems in India cannot cope with the volumes of waste generated by an increasing urban population, and this impacts on the environment and public health. The challenges and barriers are significant, but so are the opportunities. This paper reports on an international seminar on ‘Sustainable solid waste management for cities: opportunities in South Asian Association for Regional Cooperation (SAARC) countries’ organized by the Council of Scientific and Industrial Research-National Environmental Engineering Research Institute and the Royal Society. A priority is to move from reliance on waste dumps that offer no environmental protection, to waste management systems that retain useful resources within the economy. Waste segregation at source and use of specialized waste processing facilities to separate recyclable materials has a key role. Disposal of residual waste after extraction of material resources needs engineered landfill sites and/or investment in waste-to-energy facilities. The potential for energy generation from landfill via methane extraction or thermal treatment is a major opportunity, but a key barrier is the shortage of qualified engineers and environmental professionals with the experience to deliver improved waste management systems in India

Decadal changes of the Western Arabian sea ecosystem

Historical data from oceanographic expeditions and remotely sensed data on outgoing longwave radiation, temperature, wind speed and ocean color in the western Arabian Sea (1950–2010) were used to investigate decadal trends in the physical and biochemical properties of the upper 300 m. 72 % of the 29,043 vertical profiles retrieved originated from USA and UK expeditions. Increasing outgoing longwave radiation, surface air temperatures and sea surface temperature were identified on decadal timescales. These were well correlated with decreasing wind speeds associated with a reduced Siberian High atmospheric anomaly. Shoaling of the oxycline and nitracline was observed as well as acidification of the upper 300 m. These physical and chemical changes were accompanied by declining chlorophyll-a concentrations, vertical macrofaunal habitat compression, declining sardine landings and an increase of fish kill incidents along the Omani coast

The conserved C-terminus of the PcrA/UvrD helicase interacts directly with RNA polymerase

Copyright: © 2013 Gwynn et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by a Wellcome Trust project grant to MD (Reference: 077368), an ERC starting grant to MD (Acronym: SM-DNA-REPAIR) and a BBSRC project grant to PM, NS and MD (Reference: BB/I003142/1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Hemorrhage of brain metastasis from non-small cell lung cancer post gefitinib therapy: two case reports and review of the literature

<p>Abstract</p> <p>Background</p> <p>Gefitinib is one of the small molecule inhibitors of epidermal growth factor receptor tyrosine kinase (EGFR TKIs). Clinical trials have demonstrated it is effective for treatment of a subset of patients with advanced non-small cell lung cancer (NSCLC). Gefitinib has been generally considered to be a relatively safe agent. Besides a small proportion of fatal interstitial pneumonia, the common adverse drug reactions of gefitinib include diarrhea and skin rash, which are generally mild and reversible. Herein, we report the first two cases of brain metastasis hemorrhage that might be involved with the use of gefitinib.</p> <p>Case presentation</p> <p>Two patients with brain metastasis from NSCLC developed brain hemorrhage after gefitinib therapy. The hemorrhage in one case occurred one month after gefitinib combined with whole brain radiation therapy (WBRT), and in the another case hemorrhage developed slowly within brain metastases eight months post gefitinib monotherapy for diffuse pulmonary metastasis from a lung cancer undergone surgical removal previously.</p> <p>Conclusion</p> <p>We speculate brain hemorrhage could be one of the adverse drug reactions of gefitinib treatment for NSCLC and suggest clinicians be aware of this possible rare entity. More data are needed to confirm our findings, especially when gefitinib is used in the settings of brain metastases from NSCLC or other origins.</p

European Sea Bass (Dicentrarchus labrax) immune status and disease resistance are impaired by arginine dietary supplementation

Infectious diseases and fish feeds management are probably the major expenses in the aquaculture business. Hence, it is a priority to define sustainable strategies which simultaneously avoid therapeutic procedures and reinforce fish immunity. Currently, one preferred approach is the use of immunostimulants which can be supplemented to the fish diets. Arginine is a versatile amino acid with important mechanisms closely related to the immune response. Aiming at finding out how arginine affects the innate immune status or improve disease resistance of European seabass (Dicentrarchus labrax) against vibriosis, fish were fed two arginine-supplemented diets (1% and 2% arginine supplementation). A third diet meeting arginine requirement level for seabass served as control diet. Following 15 or 29 days of feeding, fish were sampled for blood, spleen and gut to assess cell-mediated immune parameters and immune-related gene expression. At the same time, fish from each dietary group were challenged against Vibrio anguillarum and survival was monitored. Cell-mediated immune parameters such as the extracellular superoxide and nitric oxide decreased in fish fed arginine-supplemented diets. Interleukins and immune-cell marker transcripts were down-regulated by the highest supplementation level. Disease resistance data were in accordance with a generally depressed immune status, with increased susceptibility to vibriosis in fish fed arginine supplemented diets. Altogether, these results suggest a general inhibitory effect of arginine on the immune defences and disease resistance of European seabass. Still, further research will certainly clarify arginine immunomodulation pathways thereby allowing the validation of its potential as a prophylactic strategy.European Union's Seventh Framework Programme AQUAEXCEL (Aquaculture Infrastructures for Excellence in European Fish Research) [262336]; AQUAIMPROV [NORTE-07-0124-FEDER-000038]; North Portugal Regional Operational Programme (ON. 2 - O Novo Norte) , under the National Strategic Reference Framework, through the European Regional Development Fund; North Portugal Regional Operational Programme (ON. 2 - O Novo Norte), under the National Strategic Reference Framework through the COMPETE - Operational Competitiveness Programme; Fundacao para a Ciencia e Tecnologia; Fundacao para a Ciencia e Tecnologia [SFRH/BD/89457/2012, SFRH/BPD/77210/2011]; Generalitat Valenciana through the project REVIDPAQUA [ISIC/2012/003]; [PEst-C/MAR/LA0015/2013]; [UID/Multi/04423/2013]info:eu-repo/semantics/publishedVersio

Research on information systems failures and successes: Status update and future directions

The final publication is available at Springer via http://dx.doi.org/10.1007/s10796-014-9500-yInformation systems success and failure are among the most prominent streams in IS research. Explanations of why some IS fulfill their expectations, whereas others fail, are complex and multi-factorial. Despite the efforts to understand the underlying factors, the IS failure rate remains stubbornly high. A Panel session was held at the IFIP Working Group 8.6 conference in Bangalore in 2013 which forms the subject of this Special Issue. Its aim was to reflect on the need for new perspectives and research directions, to provide insights and further guidance for managers on factors enabling IS success and avoiding IS failure. Several key issues emerged, such as the need to study problems from multiple perspectives, to move beyond narrow considerations of the IT artifact, and to venture into underexplored organizational contexts, such as the public sector. © 2014 Springer Science+Business Media New York

Entrepreneurs’ age, institutions, and social value creation goals: a multi-country study

This study explores the relationship between an entrepreneur's age and his/her social value creation goals. Building on the lifespan developmental psychology literature and institutional theory, we hypothesize a U-shaped relationship between entrepreneurs’ age and their choice to create social value through their ventures, such that younger and older entrepreneurs create more social value with their businesses while middle age entrepreneurs are relatively more economically and less socially oriented with their ventures. We further hypothesize that the quality of a country’s formal institutions in terms of economic, social, and political freedom steepen the U-shaped relationship between entrepreneurs’ age and their choice to pursue social value creation as supportive institutional environments allow entrepreneurs to follow their age-based preferences. We confirm our predictions using multilevel mixed-effects linear regressions on a sample of over 15,000 entrepreneurs (aged between 18 and 64 years) in 45 countries from Global Entrepreneurship Monitor data. The findings are robust to several alternative specifications. Based on our findings, we discuss implications for theory and practice, and we propose future research directions