Multi-Objective Big Data Optimization with jMetal and Spark

Big Data Optimization is the term used to refer to optimization problems which have to manage very large amounts of data. In this paper, we focus on the parallelization of metaheuristics with the Apache Spark cluster computing system for solving multi-objective Big Data Optimization problems. Our purpose is to study the influence of accessing data stored in the Hadoop File System (HDFS) in each evaluation step of a metaheuristic and to provide a software tool to solve these kinds of problems. This tool combines the jMetal multi-objective optimization framework with Apache Spark. We have carried out experiments to measure the performance of the proposed parallel infrastructure in an environment based on virtual machines in a local cluster comprising up to 100 cores. We obtained interesting results for computational e ort and propose guidelines to face multi-objective Big Data Optimization problems.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

The direct evaluation of attosecond chirp from a streaking measurement

We derive an analytical expression, from classical electron trajectories in a laser field, that relates the breadth of a streaked photoelectron spectrum to the group-delay dispersion of an isolated attosecond pulse. Based on this analytical expression, we introduce a simple, efficient and robust procedure to instantly extract the attosecond pulse's chirp from the streaking measurement.Comment: 4 figure

Molecular isomerization and fragmentation of polyatomic molecules controlled by inner-valence recollision-ionization

Control over various fragmentation reactions of a series of polyatomic molecules (acetylene, ethylene, 1,3-butadiene) by the optical waveform of intense few-cycle laser pulses is demonstrated experimentally. We show both experimentally and theoretically that the responsible mechanism is inelastic ionization from inner-valence molecular orbitals by recolliding electron wave packets

Role of proton dynamics in efficient photoionization of hydrocarbon molecules

We experimentally investigate the ionizationmechanism behind the formation of remarkably high charge states observed in the laser-pulse-induced fragmentation of different hydrocarbon molecules by Roither et al. [Phys. Rev. Lett. 106, 163001 (2011)], who suggested enhanced ionization occurring at multiple C-H bonds as the underlying ionization mechanism. Using multiparticle coincidence momentum imaging we measure the yield of multiply charged fragmenting ethylene and acetylene molecules at several intensities and pulse durations ranging from the few-cycle regime to 25 fs. We observe, at constant intensity, a strong increase of the proton energy with increasing laser pulse duration. It is shown that this is caused by a strong increase in the yield of highly charged parent molecular ions with pulse duration. Based on experimental evidence we explain this increase by the necessary population of precursor states in the parent ion that feature fast C-H stretch dynamics to the critical internuclear distance, where efficient ionization via enhanced ionization takes place. For increasing pulse duration these precursor ionic states are more efficiently populated, which leads in turn to a higher enhanced-ionization probability for longer pulses. Our work provides experimental evidence for the existence of a multiple-bond version of enhanced ionization in polyatomic molecule

Role of proton dynamics in efficient photoionization of hydrocarbon molecules

We experimentally investigate the ionizationmechanism behind the formation of remarkably high charge states observed in the laser-pulse-induced fragmentation of different hydrocarbon molecules by Roither et al. [Phys. Rev. Lett. 106, 163001 (2011)], who suggested enhanced ionization occurring at multiple C-H bonds as the underlying ionization mechanism. Using multiparticle coincidence momentum imaging we measure the yield of multiply charged fragmenting ethylene and acetylene molecules at several intensities and pulse durations ranging from the few-cycle regime to 25 fs. We observe, at constant intensity, a strong increase of the proton energy with increasing laser pulse duration. It is shown that this is caused by a strong increase in the yield of highly charged parent molecular ions with pulse duration. Based on experimental evidence we explain this increase by the necessary population of precursor states in the parent ion that feature fast C-H stretch dynamics to the critical internuclear distance, where efficient ionization via enhanced ionization takes place. For increasing pulse duration these precursor ionic states are more efficiently populated, which leads in turn to a higher enhanced-ionization probability for longer pulses. Our work provides experimental evidence for the existence of a multiple-bond version of enhanced ionization in polyatomic molecule

Carbon-nitrogen interactions in European forests and semi-natural vegetation - Part 2: Untangling climatic, edaphic, management and nitrogen deposition effects on carbon sequestration potentials

The effects of atmospheric nitrogen deposition (N$_{dep}$) on carbon (C) sequestration in forests have often been assessed by relating differences in productivity to spatial variations of N$_{dep}$ across a large geographic domain. These correlations generally suffer from covariation of other confounding variables related to climate and other growth-limiting factors, as well as large uncertainties in total (dry+wet) reactive nitrogen (N$_{r}$) deposition.We propose a methodology for untangling the effects of N$_{dep}$ from those of meteorological variables, soil water retention capacity and stand age, using a mechanistic forest growth model in combination with eddy covariance CO$_{2}$ exchange fluxes from a Europe-wide network of 22 forest flux towers. Total N$_{r}$ deposition rates were estimated from local measurements as far as possible. The forest data were compared with data from natural or semi-natural, non-woody vegetation sites. The response of forest net ecosystem productivity to nitrogen deposition (dNEP= dN$_{dep}$) was estimated after accounting for the effects on gross primary productivity (GPP) of the co-correlates by means of a meta-modelling standardization procedure, which resulted in a reduction by a factor of about 2 of the uncorrected, apparent dGPP/dN$_{dep}$ value. This model-enhanced analysis of the C and N$_{dep}$ flux observations at the scale of the European network suggests a mean overall dNEP/dN$_{dep}$ response of forest lifetime C sequestration to N$_{dep}$ of the order of 40–50 g C per g N, which is slightly larger but not significantly different from the range of estimates published in the most recent reviews. Importantly, patterns of gross primary and net ecosystem productivity versus N$_{dep}$ were non-linear, with no further growth responses at high N$_{dep}$ levels (N$_{dep}$ >2.5–3 gNm$^{-2}$ yr$^{-1}$) but accompanied by increasingly large ecosystem N losses by leaching and gaseous emissions. The reduced increase in productivity per unit N deposited at high N$_{dep}$ levels implies that the forecast increased N$_{r}$ emissions and increased Ndep levels in large areas of Asia may not positively impact the continent’s forest CO$_{2}$ sink. The large level of unexplained variability in observed carbon sequestration efficiency (CSE) across sites further adds to the uncertainty in the dC/dN response

De novo TRIM8 variants impair its protein localization to nuclear bodies and cause developmental delay, epilepsy, and focal segmental glomerulosclerosis

Focal segmental glomerulosclerosis (FSGS) is the main pathology underlying steroid-resistant nephrotic syndrome (SRNS) and a leading cause of chronic kidney disease. Monogenic forms of pediatric SRNS are predominantly caused by recessive mutations, while the contribution of de novo variants (DNVs) to this trait is poorly understood. Using exome sequencing (ES) in a proband with FSGS/SRNS, developmental delay, and epilepsy, we discovered a nonsense DNV in TRIM8, which encodes the E3 ubiquitin ligase tripartite motif containing 8. To establish whether TRIM8 variants represent a cause of FSGS, we aggregated exome/genome-sequencing data for 2,501 pediatric FSGS/SRNS-affected individuals and 48,556 control subjects, detecting eight heterozygous TRIM8 truncating variants in affected subjects but none in control subjects (p = 3.28 × 10−11). In all six cases with available parental DNA, we demonstrated de novo inheritance (p = 2.21 × 10−15). Reverse phenotyping revealed neurodevelopmental disease in all eight families. We next analyzed ES from 9,067 individuals with epilepsy, yielding three additional families with truncating TRIM8 variants. Clinical review revealed FSGS in all. All TRIM8 variants cause protein truncation clustering within the last exon between residues 390 and 487 of the 551 amino acid protein, indicating a correlation between this syndrome and loss of the TRIM8 C-terminal region. Wild-type TRIM8 overexpressed in immortalized human podocytes and neuronal cells localized to nuclear bodies, while constructs harboring patient-specific variants mislocalized diffusely to the nucleoplasm. Co-localization studies demonstrated that Gemini and Cajal bodies frequently abut a TRIM8 nuclear body. Truncating TRIM8 DNVs cause a neuro-renal syndrome via aberrant TRIM8 localization, implicating nuclear bodies in FSGS and developmental brain disease