The inducers 1,3-diaminopropane and spermidine cause the reprogramming of metabolism in Penicillium chrysogenum, leading to multiple vesicles and penicillin overproduction

In this article we studied the differential protein abundance of Penicillium chrysogenum in response to either 1,3-diaminopropane (1,3-DAP) or spermidine, which behave as inducers of the penicillin production process. Proteins were resolved in 2-DE gels and identified by tandem MS spectrometry. Both inducers produced largely identical changes in the proteome, suggesting that they may be interconverted and act by the same mechanism. The addition of either 1,3-DAP or spermidine led to the overrepresentation of the last enzyme of the penicillin pathway, isopenicillin N acyltransferase (IAT). A modified form of the IAT protein was newly detected in the polyamine-supplemented cultures. Both inducers produced a rearrangement of the proteome resulting in an overrepresentation of enzymes involved in the biosynthesis of valine and other precursors (e.g. coenzyme A) of penicillin. Interestingly, two enzymes of the homogentisate pathway involved in the degradation of phenylacetic acid (a well-known precursor of benzylpenicillin) were reduced following the addition of either of these two inducers, allowing an increase of the phenylacetic acid availability. Both inducers produced also an increase in the intracellular content of vesicles that derived to vacuoles in late stages and promoted sporulation of P. chrysogenum in solid medium. Biological significance The analysis of global protein changes produced in response to polyamines 1,3-DAP and spermidine provides a valuable information for the understanding of the molecular mechanisms underlying the production of penicillin. This represents useful information to improve the production of this antibiotic and many other bioactive secondary metabolites not only in P. chrysogenum, but in other filamentous fungi as well

The Servet 3.0 benchmark suite: characterization of network performance degradation

This is a post-peer-review, pre-copyedit version of an article published in Computers & Electrical Engineering. The final authenticated version is available online at: https://doi.org/10.1016/j.compeleceng.2013.08.012.[Abstract] Servet is a suite of benchmarks focused on extracting a set of parameters with high influence on the overall performance of multicore clusters. These parameters can be used to optimize the performance of parallel applications by adapting part of their behavior to the characteristics of the machine. Up to now the tool considered network bandwidth as constant and independent of the communication pattern. Nevertheless, the inter-node communication bandwidth decreases on modern large supercomputers depending on the number of cores per node that simultaneously access the network and on the distance between the communicating nodes. This paper describes two new benchmarks that improve Servet by characterizing the network performance degradation depending on these factors. This work also shows the experimental results of these benchmarks on a Cray XE6 supercomputer and some examples of how real parallel codes can be optimized by using the information about network degradation.Ministerio de Ciencia e Innovación; TIN2010-16735Ministerio de Educación; AP2008-01578Ministerio de Educación; AP2010-4348European Commision; HPC-Europa2 Programme; 22839

Automatic mapping of parallel applications on multicore architectures using the Servet benchmark suite

This is a post-peer-review, pre-copyedit version of an article published in Computers & Electrical Engineering. The final authenticated version is available online at: https://doi.org/10.1016/j.compeleceng.2011.12.007[Abstract] Servet is a suite of benchmarks focused on detecting a set of parameters with high influence on the overall performance of multicore systems. These parameters can be used for autotuning codes to increase their performance on multicore clusters. Although Servet has been proved to detect accurately cache hierarchies, bandwidths and bottlenecks in memory accesses, as well as the communication overhead among cores, up to now the impact of the use of this information on application performance optimization has not been assessed. This paper presents a novel algorithm that automatically uses Servet for mapping parallel applications on multicore systems and analyzes its impact on three testbeds using three different parallel programming models: message-passing, shared memory and partitioned global address space (PGAS). Our results show that a suitable mapping policy based on the data provided by this tool can significantly improve the performance of parallel applications without source code modification.Ministerio de Ciencia e Innovación; TIN2010-16735Ministerio de Educación; FPU; AP2008-01578Xunta de Galicia; INCITE08PXIB105161P

Servet: A Benchmark Suite for Autotuning on Multicore Clusters

This is a post-peer-review, pre-copyedit version of an article published in 2010 IEEE International Symposium on Parallel & Distributed Processing (IPDPS). Proceedings. The final authenticated version is available online at: http://dx.doi.org/10.1109/IPDPS.2010.5470358.[Abstract] MapReduce is a powerful tool for processing large data sets used by many applications running in distributed environments. However, despite the increasing number of computationally intensive problems that require low-latency communications, the adoption of MapReduce in High Performance Computing (HPC) is still emerging. Here languages based on the Partitioned Global Address Space (PGAS) programming model have shown to be a good choice for implementing parallel applications, in order to take advantage of the increasing number of cores per node and the programmability benefits achieved by their global memory view, such as the transparent access to remote data. This paper presents the first PGAS-based MapReduce implementation that uses the Unified Parallel C (UPC) language, which (1) obtains programmability benefits in parallel programming, (2) offers advanced configuration options to define a customized load distribution for different codes, and (3) overcomes performance penalties and bottlenecks that have traditionally prevented the deployment of MapReduce applications in HPC. The performance evaluation of representative applications on shared and distributed memory environments assesses the scalability of the presented MapReduce framework, confirming its suitability.Xunta de Galicia; INCITE08PXIB105161PRMinisterio de Ciencia e Innovación; TIN2007-67537-C03-02Ministerio de Educación; FPU; AP2008-0157

Performance Evaluation of Sparse Matrix Products in UPC

This is a post-peer-review, pre-copyedit version of an article published in The Journal of Supercomputing. The final authenticated version is available online at: https://doi.org/10.1007/s11227-012-0796-4[Abstract] Unified Parallel C (UPC) is a Partitioned Global Address Space (PGAS) language whose popularity has increased during the last years owing to its high programmability and reasonable performance through an efficient exploitation of data locality, especially on hierarchical architectures like multicore clusters. However, the performance issues that arise in this language due to the irregular structure of sparse matrix operations have not yet been studied. Among them, the selection of an adequate storage format for the sparse matrices can significantly improve the efficiency of the parallel codes. This paper presents an evaluation, using UPC, of the most common sparse storage formats with different implementations of the matrix-vector and matrix-matrix products, which are key kernels in many scientific applications.Ministerio de Ciencia e Innovación; TIN2010-16735Ministerio de Educación; AP2008-01578Ministerio de Ciencia e Innovación; CAPAP-H3; TIN2010-12011-

Short-Term Branched-Chain Amino Acid Supplementation Does Not Enhance Vertical Jump in Professional Volleyball Players. A Double-Blind, Controlled, Randomized Study

To the best of the author's knowledge, no previous studies have described the effect of branched-chain amino acids (BCAA) on vertical performance during a week in professional volleyball players. This study assessed BCAA supplementation for a week, aiming to improve vertical jump performance in male professional volleyball players. Twelve male volleyballers were randomly assigned to a BCAA group (n = 6) or a control group (n = 6). The BCAA group ingested 21 g over a week, 7 g per day on Monday, Wednesday, and Friday, before a volleyball training session, while the control group drank a placebo drink. Participants performed 8 maximal countermovement jumps (CMJ); the 3 CMJs on Monday and Wednesday were evaluated after warm-up, after plyometric training, and at the end of the training session; and the 2 CMJs on Friday were evaluated after warm-up, and at the end of the training session. Compared with baseline, no significant differences in CMJ over the week were observed in BCAA or control group, neither between groups. The results indicated that 21 g of BCAA supplementation over a week did not improve vertical jump performance in professional volleyball players.Hasta donde los autores saben, no se han descrito estudios previos sobre el efecto de los aminoácidos ramificados (BCAA) en el rendimiento vertical durante una semana en jugadores de voleibol profesionales. Este artículo estudió la suplementación de BCAA durante una semana con el objeto de mejorar el rendimiento del salto vertical en jugadores de voleibol profesionales masculinos. Doce jugadores de voleibol masculinos se asignaron aleatoriamente a un grupo con BCAA (n = 6) o a un grupo de control (n = 6). El grupo con BCAA ingirió 21 g en una semana, 7 g por día los lunes, miércoles y viernes antes de la sesión de entrenamiento de voleibol, mientras que el grupo de control bebió una bebida placebo. Los participantes realizaron 8 saltos máximos de contramovimiento (CMJ); los 3 CMJ de lunes y miércoles se evaluaron después del calentamiento y del entrenamiento pliométrico, y al final de la sesión de entrenamiento; los 2 CMJ del viernes se evaluaron después del calentamiento y al final de la sesión de entrenamiento. En comparación con el valor inicial, no se observaron diferencias significativas en los CMJ a lo largo de la semana, ni en el grupo BCAA ni en el grupo control, tampoco hubo diferencias entre grupos. Los resultados indicaron que 21 g de BCAA administrados durante una semana no mejoraron el rendimiento del salto vertical en jugadores de voleibol profesionale

Discovery of distant RR Lyrae stars in the Milky Way using DECam

We report the discovery of distant RR Lyrae stars, including the most distant known in the Milky Way, using data taken in the $g-$band with the Dark Energy Camera as part of the High cadence Transient Survey (HiTS; 2014 campaign). We detect a total of 173 RR Lyrae stars over a ~120 deg^2 area, including both known RR Lyrae and new detections. The heliocentric distances d_H of the full sample range from 9 to >200 kpc, with 18 of them beyond 90 kpc. We identify three sub-groups of RR Lyrae as members of known systems: the Sextans dwarf spheroidal galaxy, for which we report 46 new discoveries, and the ultra-faint dwarf galaxies Leo IV and Leo V. Following an MCMC methodology, we fit spherical and ellipsoidal profiles of the form rho(R) ~ R^n to the radial density distribution of RR Lyrae in the Galactic halo. The best fit corresponds to the spherical case, for which we obtain a simple power-law index of n=-4.17^{+0.18}_{-0.20}, consistent with recent studies made with samples covering shorter distances. The pulsational properties of the outermost RR Lyrae in the sample (d_H>90 kpc) differ from the ones in the halo population at closer distances. The distribution of the stars in a Period-Amplitude diagram suggest they belong to Oosterhoff-intermediate or Oosterhoff II groups, similar to what is found in the ultra-faint dwarf satellites around the Milky Way. The new distant stars discovered represent an important addition to the few existing tracers of the Milky Way potential in the outer halo.Comment: Accepted for publication in The Astrophysical Journa

The application of distributed optical fiber sensors (BOTDA) to sinkhole monitoring. Review and the case of a damaging sinkhole in the Ebro Valley evaporite karst (NE Spain)

Distributed optical fiber sensors (DOFS) have been postulated as a suitable technique for long-range monitoring of sinkhole-related subsidence, and possibly for the anticipation of catastrophic collapse (early-warning systems). The strain data published in previous works refer to artificial experiments considering real and virtual cover collapse sinkholes characterized by rapid subsidence and sharp lateral deformation gradients. The influence of the subsidence mechanism (sagging, collapse, suffosion) on the capability of DOFS to satisfactorily detect active subsidence is discussed. Sagging sinkholes with poorly-defined lateral edges, low lateral deformation gradients and slow subsidence are identified as the most challenging scenario. The performance of BOTDA optical fiber for monitoring such type of sagging sinkholes is evaluated in the active Alcalá sinkhole, which affects a flood-control dike creating a high-risk and -uncertainty scenario. This sinkhole shows active subsidence in sections tens of meters long with maximum subsidence rates ranging between 5 and 35 mm/yr. The comparison of vertical displacement data measured by high-precision leveling and the strain recorded by two types of fiber optic cables shows good spatial and temporal correlation. The subsidence sections are captured in the strain profiles by: (1) troughs of negative strain (contraction) in the area affected by subsidence, with the maximum strain associated with the point of most rapid settlement; and (2) lateral ridges of positive values (extension) in the marginal zones. A subsidence acceleration phase associated with a flood is also captured by substantial increments in the strain values. In this challenging scenario, despite the reasonably good spatial and temporal correlation between the displacement and strain data, the unambiguous identification of the active subsidence area with the fiber optic data alone might be difficult. Better results could be obtained improving the monitoring system (e.g., tighter cable-ground coupling) and testing other types of sinkholes with more localized deformation zones and higher subsidence rates