NMF-mGPU: non-negative matrix factorization on multi-GPU systems.

BACKGROUND: In the last few years, the Non-negative Matrix Factorization ( NMF ) technique has gained a great interest among the Bioinformatics community, since it is able to extract interpretable parts from high-dimensional datasets. However, the computing time required to process large data matrices may become impractical, even for a parallel application running on a multiprocessors cluster. In this paper, we present NMF-mGPU, an efficient and easy-to-use implementation of the NMF algorithm that takes advantage of the high computing performance delivered by Graphics-Processing Units ( GPUs ). Driven by the ever-growing demands from the video-games industry, graphics cards usually provided in PCs and laptops have evolved from simple graphics-drawing platforms into high-performance programmable systems that can be used as coprocessors for linear-algebra operations. However, these devices may have a limited amount of on-board memory, which is not considered by other NMF implementations on GPU. RESULTS: NMF-mGPU is based on CUDA ( Compute Unified Device Architecture ), the NVIDIA's framework for GPU computing. On devices with low memory available, large input matrices are blockwise transferred from the system's main memory to the GPU's memory, and processed accordingly. In addition, NMF-mGPU has been explicitly optimized for the different CUDA architectures. Finally, platforms with multiple GPUs can be synchronized through MPI ( Message Passing Interface ). In a four-GPU system, this implementation is about 120 times faster than a single conventional processor, and more than four times faster than a single GPU device (i.e., a super-linear speedup). CONCLUSIONS: Applications of GPUs in Bioinformatics are getting more and more attention due to their outstanding performance when compared to traditional processors. In addition, their relatively low price represents a highly cost-effective alternative to conventional clusters. In life sciences, this results in an excellent opportunity to facilitate the daily work of bioinformaticians that are trying to extract biological meaning out of hundreds of gigabytes of experimental information. NMF-mGPU can be used "out of the box" by researchers with little or no expertise in GPU programming in a variety of platforms, such as PCs, laptops, or high-end GPU clusters. NMF-mGPU is freely available at https://github.com/bioinfo-cnb/bionmf-gpu .

Offset printing plate quality sensor on a low-cost processor.

The aim of this work is to develop a microprocessor-based sensor that measures the quality of the offset printing plate through the introduction of different image analysis applications. The main features of the presented system are the low cost, the low amount of power consumption, its modularity and easy integration with other industrial modules for printing plates, and its robustness against noise environments. For the sake of clarity, a viability analysis of previous software is presented through different strategies, based on dynamic histogram and Hough transform. This paper provides performance and scalability data compared with existing costly commercial devices. Furthermore, a general overview of quality control possibilities for printing plates is presented and could be useful to a system where such controls are regularly conducted.

Biopolitics and speculative objects in Chilean health projects.

'Biopolitics' is a much-used concept in recent academic literature. One of its main fields of application is in the analysis of public health projects. This article analyses the national Explicit Health Guarantees project in Chile from that perspective. However, we criticize the standard invocation of 'biopolitics' by observing that such public health projects require technoscientific operations that establish truths and regimes of obligation for the groups involved -understanding regime both as a set of imposed orders and a set of regulated processes. Specifically, the Explicit Health Guarantees project defines what we call 'speculative objects'. These have two characteristics: (a) They relate highly diverse entities into integrated wholes that are and involve objects of knowledge and uncertainty, and (b) this integration creates regimes of obligation considered as scientific truths on many different groups. We conclude by proposing new questions about the notion of biopolitics and its relationship with uncertainty and speculation.

Government veterinarians' perceptions of routine biosecurity focused on dairy cattle farms in north-western and north-eastern Spain.

The implementation of biosecurity measures in livestock production systems can be affected by the psychosocial factors of its stakeholders, which can be observed through their knowledge, attitudes and perceptions/practices. In Spain, there are no regulations per se to promote biosecurity. Of all stakeholders, farmers and veterinarians have been addressed in previous biosecurity studies, but not veterinarians belonging specifically to the government services. This study explores this particular group's perceptions of routine biosecurity in livestock production systems in north-western and north-eastern Spain, an understanding of which could help to improve the implementation of biosecurity measures on farms. Eleven interviews were conducted with veterinarians from different levels of the government services in Galicia and Catalonia, and were analyzed through content analysis. Dairy cattle farms were considered as the reference livestock production systems. The respondents stress the limited availability of staff and time resources for biosecurity. The advisory role of government veterinarians is not well recognized among farmers, who feel that their services prioritize their sanctioning role. In fact, government veterinarians consider that farmers only implement biosecurity measures to avoid being sanctioned, and not because they are aware of the importance of biosecurity. Meanwhile, the participants comment that biosecurity regulations should be flexible and need to consider the contexts of the farms where biosecurity measures are implemented. Finally, government veterinarians are willing to attend biosecurity meetings together with all farm stakeholders, at which the government services could be informed about biosecurity issues on farms. The person who could take on the biosecurity advisory role should be defined, along with further discussion of such matters as the responsibilities of each stakeholder. Government veterinary services need to be considered in studies of biosecurity operations in order to improve their implementation. It is therefore concluded that government veterinarians are seeking to balance their own institutional perspective with that of farmers and veterinarians in the routine implementation of biosecurity measures.

MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures.

The enormous amount of data available in public gene expression repositories such as Gene Expression Omnibus (GEO) offers an inestimable resource to explore gene expression programs across several organisms and conditions. This information can be used to discover experiments that induce similar or opposite gene expression patterns to a given query, which in turn may lead to the discovery of new relationships among diseases, drugs or pathways, as well as the generation of new hypotheses. In this work, we present MARQ, a web-based application that allows researchers to compare a query set of genes, e.g. a set of over- and under-expressed genes, against a signature database built from GEO datasets for different organisms and platforms. MARQ offers an easy-to-use and integrated environment to mine GEO, in order to identify conditions that induce similar or opposite gene expression patterns to a given experimental condition. MARQ also includes additional functionalities for the exploration of the results, including a meta-analysis pipeline to find genes that are differentially expressed across different experiments. The application is freely available at http://marq.dacya.ucm.es.

A low cost matching motion estimation sensor based on the NIOS II microprocessor.

This work presents the implementation of a matching-based motion estimation sensor on a Field Programmable Gate Array (FPGA) and NIOS II microprocessor applying a C to Hardware (C2H) acceleration paradigm. The design, which involves several matching algorithms, is mapped using Very Large Scale Integration (VLSI) technology. These algorithms, as well as the hardware implementation, are presented here together with an extensive analysis of the resources needed and the throughput obtained. The developed low-cost system is practical for real-time throughput and reduced power consumption and is useful in robotic applications, such as tracking, navigation using an unmanned vehicle, or as part of a more complex system.

Contact pathway in surgical and transcatheter aortic valve replacement.

Background: Aortic valve replacement is the gold standard treatment for severe symptomatic aortic stenosis, but thrombosis of bioprosthetic valves (PVT) remains a concern. Objective: To analyze the factors involved in the contact pathway during aortic valve replacement and to assess their impact on the development of thromboembolic complications. Methods: The study was conducted in 232 consecutive patients who underwent: transcatheter aortic valve replacement (TAVR, N = 155), and surgical valve replacement (SAVR, N = 77) (MUVITAVI project). Demographic and clinical data, outcomes including a combined end point (CEP) of thrombotic events, and imaging controls were recruited. Samples were collected 24 h before and 48 h after valve replacement. FXII, FXI and (pre)kallikrein were evaluated by Western Blot and specific ELISA with nanobodies. Results: The CEP of thrombotic events was reached by 19 patients: 13 patients presented systemic embolic events and 6 patients subclinical PVT. Valve replacement did not cause FXII activation or generation of kallikrein. There was a significant reduction of FXI levels associated with the procedure, which was statistically more pronounced in SAVR than in TAVR. Cases with reductions of FXI below 80% of basal values had a lower incidence of embolic events during the procedure than patients in whom FXI increased above 150%: 2.7 vs. 16.7%; p: 0.04. Conclusion: TAVR or SAVR did not significantly activate the contact pathway. A significant reduction of FXI, was observed, particularly in SAVR, associated with lower incidence of thrombotic events. These results encourage evaluating the usefulness and safety of FXI-directed antithrombotic treatments in these patients.

GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information.

GeneCodis is a web server application for functional analysis of gene lists that integrates different sources of information and finds modular patterns of interrelated annotations. This integrative approach has proved to be useful for the interpretation of high-throughput experiments and therefore a new version of the system has been developed to expand its functionality and scope. GeneCodis now expands the functional information with regulatory patterns and user-defined annotations, offering the possibility of integrating all sources of information in the same analysis. Traditional singular enrichment is now permitted and more organisms and gene identifiers have been added to the database. The application has been re-engineered to improve performance, accessibility and scalability. In addition, GeneCodis can now be accessed through a public SOAP web services interface, enabling users to perform analysis from their own scripts and workflows. The application is freely available at http://genecodis.dacya.ucm.es.

SENT: semantic features in text.

We present SENT (semantic features in text), a functional interpretation tool based on literature analysis. SENT uses Non-negative Matrix Factorization to identify topics in the scientific articles related to a collection of genes or their products, and use them to group and summarize these genes. In addition, the application allows users to rank and explore the articles that best relate to the topics found, helping put the analysis results into context. This approach is useful as an exploratory step in the workflow of interpreting and understanding experimental data, shedding some light into the complex underlying biological mechanisms. This tool provides a user-friendly interface via a web site, and a programmatic access via a SOAP web server. SENT is freely accessible at http://sent.dacya.ucm.es.

First-year health degree students in the dissection room: Analysis of adaptation to practical classes.

Human anatomy is a core subject that students of all health degrees are required to pass. Practical classes with human cadavers are a widely used educational resource in medicine, but are less frequent in other health degrees. Determining how first-year podiatry, nursing, and physiotherapy students cope with human anatomy practical classes and identifying the presence of physical reactions and possible causes of distress they experience in the dissection room are essential steps in designing a guidance plan to address students' needs. A questionnaire was distributed to 172 first-year students in non-medical health degrees immediately after their first visit to the dissection room. The questionnaire comprised 29 Yes/No questions to determine students' physical reactions, causes of distress and coping methods. The most frequent physical reactions were disgust, uneasiness and nausea. The main causes of distress were the smell of the cadavers, the smell of the dissection room and the sight of the cadavers. The coping methods used were being with friends, eating before the practical class and practicing beforehand with anatomical atlases and CDs. No significant differences were found between gender and the three variables analyzed (number of physical reactions, number of causes of distress and number of coping methods) (p-value >0.216), although differences were found between the type of health degree and the number of physical reactions and causes of distress (p-values = 0.028 and 0.001, respectively).

Influence on the implementation of biosecurity measures in dairy cattle farms: Communication between veterinarians and dairy farmers.

This study was carried out in two regions in Spain (Catalonia and Galicia) through eight focus groups; four for dairy farmers and four for veterinarians. The results showed that dairy farmers and veterinarians attributed responsibility to one another for not following biosecurity practices. The study brings to light contradictions among veterinarians and certain individual veterinary practices that participated in the study, which lead to doubt and confusion on the part of dairy farmers. Distinct perceptions were also identified of the role that government authorities should play in relation both to training and sanctions as a means of improving biosecurity on dairy farms. Additionally, the participants expressed varying opinions as to whether biosecurity measures ought to be made mandatory or remain voluntary. Results from this study highlight the need to promote initiatives through which distinct stakeholders such as veterinarians, government authorities, and dairy farmers can develop consensus-based messages on the implementation of biosecurity practices.

Dairy farmers' decision-making to implement biosecurity measures: A study of psychosocial factors.

Biosecurity measures are a set of management procedures that prevent the risk of introducing and spreading infectious diseases to a farm, although these measures are rarely implemented in dairy farms. There are some studies that have identified that the decision to implement biosecurity measures can be influenced by several psychosocial factors (attitudes and behaviours). Thus, the objective of this study was to examine the psychosocial factors (and their interactions) influencing the implementation of biosecurity measures in dairy farms in Spain, through the views of dairy farmers and veterinarians from Catalonia (northeast Spain) and Galicia (northwest Spain). Face-to-face in-depth interviews were performed with 16 dairy farmers (nine from Catalonia and seven from Galicia) and 16 veterinarians (eight from Catalonia and eight from Galicia). Grounded theory analysis was performed on the transcripts, following the subtopics of: information sources, individual factors of the farmer, social dynamics, official veterinary services and other factors. The study identified the importance of veterinarians as a source of information, including their communication skills, the individual experiences of farmers, traditions of the farms and availability of time and space in the dairy farmer's decisions making. Further, it suggests the need to deepen the knowledge of the farm workers and the obligatory biosecurity measures. This research represents a starting point to develop future strategies to improve the implementation of biosecurity measures in dairy farms.

Contributions to the study of spinocerebellar ataxia type 38 (SCA38).

OBJECTIVE: To report clinical and ancillary findings in a kindred with spinocerebellar ataxia 38 (SCA38). PATIENTS AND METHODS: Five family members spanning two generations developed gait ataxia and intermittent diplopia. On examination, a cerebellar syndrome accompanied by downbeat nystagmus and a saccadic head impulse test (HIT) were found. RESULTS: Whole-exome sequencing demonstrated a heterozygous variant in ELOVL5, c.779A > G (p.Tyr260Cys), in four tested patients. Intermittent concomitant esotropia and hypertropia caused transient diplopia in one individual each. Saccadic HIT responses were found in four subjects. Sensorineural hypoacusis was present in every case. Electrophysiological studies demonstrated a sensory neuronopathy in patients from the first generation, with prolonged disease duration. Baseline serum docosahexaenoic acid (DHA) percent was diminished in four individuals. Oral 26-week dietary DHA supplementation, 650 mg/day, raised serum DHA percent and induced a statistically significant reduction in Scale for the Assessment and Rating of Ataxia (SARA) total scores, and in stance and heel-shin slide item scores. CONCLUSION: The mentioned ELOVL5 variant segregated with disease in this kindred. Downbeat nystagmus, intermittent heterotropia causing transient diplopia, vestibular impairment demonstrated by abnormal HIT, and sensory neuronopathy were part of the clinical picture in this series. DHA supplementation raised serum DHA percent in cases with diminished levels, and induced a clinical amelioration and a statistically significant reduction in SARA scores in the study group. Further studies are needed to investigate the role of these findings in SCA38, and to determine the response to prolonged DHA supplementation.

bioNMF: a versatile tool for non-negative matrix factorization in biology.

BACKGROUND: In the Bioinformatics field, a great deal of interest has been given to Non-negative matrix factorization technique (NMF), due to its capability of providing new insights and relevant information about the complex latent relationships in experimental data sets. This method, and some of its variants, has been successfully applied to gene expression, sequence analysis, functional characterization of genes and text mining. Even if the interest on this technique by the bioinformatics community has been increased during the last few years, there are not many available simple standalone tools to specifically perform these types of data analysis in an integrated environment. RESULTS: In this work we propose a versatile and user-friendly tool that implements the NMF methodology in different analysis contexts to support some of the most important reported applications of this new methodology. This includes clustering and biclustering gene expression data, protein sequence analysis, text mining of biomedical literature and sample classification using gene expression. The tool, which is named bioNMF, also contains a user-friendly graphical interface to explore results in an interactive manner and facilitate in this way the exploratory data analysis process. CONCLUSION: bioNMF is a standalone versatile application which does not require any special installation or libraries. It can be used for most of the multiple applications proposed in the bioinformatics field or to support new research using this method. This tool is publicly available at http://www.dacya.ucm.es/apascual/bioNMF.

The global condition of epidemics: Panoramas in A (H1N1) influenza and their consequences for One World One Health programme.

Among the most relevant elements contributing to define the One World One Health programme we find epidemics. The reason is that in recent decades, infectious diseases such as HIV/SIDA, SARS and Influenza have shown that we need new approaches and concepts in order to understand how biological emergencies and health alerts deploy new scales of action. Especially relevant has been the case of A(H1N1) influenza. This reached the status of global threat virtually from its onset, triggering an international response with a diffusion, visibility and rapidity unparalleled in previous health alerts. This article maintains that this global condition cannot be explained solely by the epidemiologic characteristics of the disease, such as mortality rate, severe cases, propagation capacity, etc. Resorting to the approach proposed by the Actor-Network Theory (ANT), this paper suggests that the action of certain socio-technical operators was what built a heterogeneous network of ideas, concepts and materials that turned the A (H1N1) influenza into a global-scale phenomenon with unprecedented speed. Among these operators, the most important ones were: the speaking position, a discourse about threat, the protocols and guidelines that were used and, lastly, the maps that allowed a real-time monitoring of the influenza. The paper ends with the notion of panorama, as defined by Bruno Latour: a suggestion to describe the common denominator of the aforementioned operators, and a means to foresee the development of global scales for certain health alerts. The paper will conclude by proposing that this type of analysis would allow the One World One Health to understand with greater precision the dynamic of epidemics and thus make its principles of action much more specific as well as its definition of what global health should be.

Classification of chronic obstructive pulmonary disease severity according to the new Global Initiative for Chronic Obstructive Lung Disease 2011 guidelines: COPD assessment test versus modified Medical Research Council scale.

INTRODUCTION: The GOLD2011 revision proposes to stratify patients with chronic obstructive pulmonary disease (COPD) by measuring the impact of the disease using the modified Medical Research Council (mMRC) scale or COPD assessment test (CAT). Our aim was to determine whether both methods are equivalent. PATIENTS AND METHODS: Observational study on a cohort of 283 patients diagnosed with COPD. We analyzed the demographic and lung function results. Patients were assessed by CAT and mMRC on the same day by the same interviewer, and divided into GOLD2011 categories according to the result of the evaluation. The degree of concordance and Spearman correlation were determined. We used ANOVA on the clinical and functional variables of the four GOLD2011 categories. RESULTS: Assessing the classification of patients according to the method used, an overall correlation ρ=0.613 and a degree of concordance κ=0.63 (moderate) were obtained. κ=0.44 was obtained for the 152 patients in categoriesA and B (moderate-low), and 0.38 for the 131 patients in categoriesC and D (low). Differences were observed between categories in terms of functional parameters. CONCLUSIONS: The classification of patients with COPD using the assessment proposed by GOLD2011 varies according to the method used (CAT or mMRC); more than 25% of patients were reclassified into different categories, implying differences in the recommended therapeutic strategy. Longitudinal studies are needed to appraise which method better classifies patients, according to its prognostic ability.

Nuevas formas de habitar la ciudad: hacia una conceptualización de la ciudadanía biovigilante / New forms to inhabit the city: towards a biowatcher citizenship

Resumen El concepto de ciudadanía es seguramente, uno de los más estudiados en la historia desde una perspectiva social: desde Aristóteles y la polis griega hasta la ciudad liberal del siglo XX. En este sentido, posteriormente han emergido una serie de estudios como los de Nikolas Rose o Kezia Barker donde el énfasis es puesto en la biociencia y la biotecnología para entender al ciudadano y donde el apego a un territorio ya no es una característica importante para la ciudadanía. En este trabajo, nos adherimos a esta línea y presentaremos el concepto de ciudadanía biovigilante para enmarcar una serie de políticas, acciones y acontecimientos que rodean a la ciudad actual en un campo donde los estudios sociales no han llegado con intensidad: la biovigilancia y las prácticas de bioseguridad en nuestra vida cotidiana. Mediante un estudio de caso de material documental sobre biovigilancia, presentaremos la novedad de nuestro trabajo frente a otras propuestas como las ya mencionadas utilizando de soporte teórico el concepto de paraskeue (equipamiento) de Michel Foucault. Finalmente, discutiremos acerca de las implicaciones biopolíticas de este nuevo tipo de ciudadanía y resaltaremos la importancia del concepto de escenario en las políticas de biovigilancia.(AU)

Abstract The citizenship concept is probably, one of the most studied along the History from a social perspective: from Aristoteles and the Greek polis until the liberal city of the 20th Century. In this sense, it has been recently emerged several studies such as the Nikolas Rose or Kezia Barker works highlighting key role of bioscience and biotechnology in order to understand the citizen without pointing out the link with a concrete territory. In this paper, we will be linked with this line and we will present the biowatcher concept in order to frame many politics, actions and events around the contemporary city in a field where the social studies has not arrive deeply: biosurveillance and biosecurity practices in our daily life. Through a study case with documentary material about biosurveillance, we will present the difference in our work with the other mentioned proposals using the paraskeue (equipment) concept given by Michel Foucault. Finally, we will discuss about the biopolitics consequences within this new kind of citizenship and we will put forward the value of the scenario concept in the biosurveillance politics.(AU)

Is a benign meningioma always an indolent tumor?

Meningiomas are considered to be slow-growing tumors that compress the brain without invading it. The development of metastases is uncommon, with a predilection for the lungs, liver, lymph nodes, and bone. We report the case of a 58-year-old man, diagnosed with a solitary pulmonary nodule in the left lower lobe that was resected through a thoracotomy. The pathology revealed lung metastases of an undiagnosed meningothelial meningioma. The evolution of the patient's case, the second case in the literature of this kind of benign tumor that has developed pleural metastases, was unsatisfactory.

[First molecular detection of Rhodococcus equi in a HIV/AIDS patient in Cuba]. / Rhodococcus equi en paciente VIH/sida: primera detección molecular en Cuba.

INTRODUCTION: Rhodococcus equi is recognized as an emerging pathogen that causes important morbidity and mortality among immunocompromised patients. OBJECTIVE: to confirm the presence of R. equi in pleural fluid through the restriction fragment length polymorphism technique. METHODS: the pleural fluid sample from one AIDS patient with respiratory symptoms was used. Microbiologic culture, staining tests, phenotypic and biochemical tests and restriction fragment length polymorphism technique for the diagnosis of microorganism were performed. RESULTS: the staining technique along with the phenotypic and biochemical tests provided the presumptive diagnosis of R. equi infection, which was further confirmed by the molecular techniques. CONCLUSIONS: this paper reported the molecular detection of R. equi from one HIV/aids patient for the first time in Cuba. The results suggested that the molecular biology techniques could be used in the diagnosis and identification of R. equi.