ABSTRACT
MOTIVATION: Genome repositories are growing faster than our storage capacities, challenging our ability to store, transmit, process and analyze them. While genomes are not very compressible individually, those repositories usually contain myriads of genomes or genome reads of the same species, thereby creating opportunities for orders-of-magnitude compression by exploiting inter-genome similarities. A useful compression system, however, cannot be only usable for archival, but it must allow direct access to the sequences, ideally in transparent form so that applications do not need to be rewritten. RESULTS: We present a highly compressed filesystem that specializes in storing large collections of genomes and reads. The system obtains orders-of-magnitude compression by using Relative Lempel-Ziv, which exploits the high similarities between genomes of the same species. The filesystem transparently stores the files in compressed form, intervening the system calls of the applications without the need to modify them. A client/server variant of the system stores the compressed files in a server, while the client's filesystem transparently retrieves and updates the data from the server. The data between client and server are also transferred in compressed form, which saves an order of magnitude network time. AVAILABILITY AND IMPLEMENTATION: The C++ source code of our implementation is available for download in https://github.com/vsepulve/relz_fs.
Subject(s)
Data Compression , Genome , SoftwareABSTRACT
Approximate Bayesian computation (ABC) is a useful technique developed for solving Bayesian inference without explicitly requiring a likelihood function. In population genetics, it is widely used to extract part of the information about the evolutionary history of genetic data. The ABC compares the summary statistics computed on simulated and observed data sets. Typically, a forward-in-time approach is used to simulate the genetic material of a population starting from an initial ancestral population and following the evolution of the individuals by advancing generation by generation under various demographic and genetic forces. This approach is computationally expensive and requires a large number of computations making the use of high-performance computing crucial for decreasing the overall response times. In this work, we propose a fully distributed web service-oriented platform for ABC that is based on forward-in-time simulations. Our proposal is based on a client-server approach. The client enables users to define simulation scenarios. The server enables efficient and scalable population simulations and can be deployed on a distributed cluster of processors or even in the cloud. It is composed of four services: a workload generator, a simulation controller, a simulation results analyzer, and a result builder. The server performs multithread simulations by executing a simulation kernel encapsulated in a proposed libgdrift library. We present and evaluate three different libgdrift library approaches whose algorithms aim to reduce execution times and memory consumption.
Subject(s)
Genetics, Population/methods , Software , Animals , Bayes Theorem , Cloud ComputingABSTRACT
Controlled polymerizations are often used to synthesize polymers with low dispersity, which involves expensive initiators, constrained atmospheres, and multi-step purifying processes, especially with water soluble monomers. These drawbacks make the synthesis very expensive and of little industrial value. In this report, an inexpensive free radical polymerization of sodium 4-styrenesulfonate, using benzoyl peroxide as initiator in water/N,N-dimethylformamide solutions, is presented. After polymerization, an easy fiber precipitation method is implemented to extract and purify the polymer, obtaining conversions up to 99%, recoveries up to 98%, and molecular weight dispersities in the range of 1.15â»1.85, where the pseudo-controlled behavior is attributed to a thermodynamic limiting molecular weight solubility. Three different methods were used to bring the polymer to its acid form, obtaining Ion Exchange Capacities as high as 4.8 meq/g. Finally, polymeric membranes were prepared and reached conductivities up to 164 mS/cm, which makes them good candidates as proton exchange membranes in fuel cells.
ABSTRACT
El feocromocitoma es una enfermedad inusual y es causa de hipertensión arterial secundaria. Se presenta más frecuentemente como un tumor adrenal unilateral y en los mayores de 60 años. Las manifestaciones clínicas más comunes son la cefalea paroxística, las palpitaciones, la diaforesis y la hipertensión arterial paroxística o persistente. El diagnóstico se apoya en la clínica y en la determinación bioquímica, siendo el método de elección la cuantificación de metanefrinas plasmáticas. Planteado el diagnóstico es fundamental conocer la localización del tumor, lo que debe ser realizado mediante tomografía axial computada o resonancia nuclear magnética. El tratamiento consiste en el empleo de drogas antihipertensivas y la resección quirúrgica del tumor. Las drogas de elección son los antagonistas de los receptores alfa 2 adrenérgicos y/o bloqueadores de canales de calcio. La resección puede ser realizada por laparotromía clásica o por vía laparoscópica.
Subject(s)
Humans , Female , Adult , Pheochromocytoma/diagnosis , Pheochromocytoma/therapy , Pheochromocytoma/complications , Hypertension/etiologyABSTRACT
Renal artery aneurysm is a rare disease in children and usually is due to fibromuscular dysplasia. Clinical symptoms are frequently high blood pressure, abdominal pain, and hematuria. Diagnosis is carried out by means of angiography. We report the case of a 13-year-old male patient who had renovascular hypertension due to calcification and aneurysm of fibromuscular dysplasia-associated renal artery. We carried out total nephrectomy to resolve high blood pressure. We suggested that presence of discreet calcification in region of renal artery in a boy with renovascular high blood pressure should guide us toward diagnosis of fibromuscular dysplasia-related renal artery aneurysm.
