Dynamic characteristics of three-dimensional strongly coupled plasmas

The dynamic structure factor and other dynamic characteristics of strongly coupled one-component plasmas have been studied [Yu. V. Arkhipov et al., Phys. Rev. Lett. 119, 045001 (2017)PRLTAO0031-900710.1103/PhysRevLett.119.045001] using the self-consistent version of the method of moments. Within any version of the latter, the system dielectric function satisfies all involved sum rules and other exact relations automatically, and the advantage of this version is that, in addition, the dynamic characteristics (the dynamic structure factor, the dispersion, and decay parameters of the collective modes) are all expressed in terms of the static ones (the static structure factor) without any adjustment to the simulation data. The approach outlined in the aforementioned Letter is justified in detail and applied mainly to the classical Coulomb systems achieving satisfactory agreement with new numerical simulation data. It is shown how the realm of applicability of the method can be extended to partly degenerate and multicomponent systems, even to simple liquids. Some additional theoretical results are presented in the Supplemental Material.

Thrust stand based on a single point load cell for impulse measurements from plasma thrusters

We introduce a simple thrust stand for the direct measurement of the millinewton impulses or thrusts delivered by small thrusters intended for in-space electric propulsion. The thruster under test, with a weight below 1.5 kg, is disposed on a horizontal platform and its impulse is measured as an overweight by using a strain gauge cell physically protected from the ambient plasma and vacuum conditions. This system provides ten thrust readings per second with noise peak to peak amplitudes of 0.10-0.18 mN. The calibration procedures to verify its dynamic response to time dependent thrusts in the range of 0-15 mN using control weights as well as its minimum thrust sensitivity δT_s = 0.3 mN are discussed. Additionally, its simple conception permits a plain data reduction and analysis of steady state and low frequency thrust transients. This thrust stand was employed under low pressure and plasma ambient conditions to measure the steady impulses delivered by the Alternative Low Power Hybrid Ion Engine (ALPHIE) of 0.4-4.0 mN with absolute errors ΔT = ±0.3 mN. Finally, the experimental results show that a control electric voltage governs the ALPHIE thruster throttle.

Direct Determination of Dynamic Properties of Coulomb and Yukawa Classical One-Component Plasmas

Dynamic characteristics of strongly coupled classical one-component Coulomb and Yukawa plasmas are obtained within the nonperturbative model-free moment approach without any data input from simulations so that the dynamic structure factor (DSF) satisfies the first three nonvanishing sum rules automatically. The DSF, dispersion, decay, sound speed, and other characteristics of the collective modes are determined using exclusively the static structure factor calculated from various theoretical approaches including the hypernetted chain approximation. A good quantitative agreement with molecular dynamics simulation data is achieved.

Follicular lymphoma-protective HLA class II variants correlate with increased HLA-DQB1 protein expression

Multiple follicular lymphoma (FL) susceptibility single-nucleotide polymorphisms in the human leukocyte antigen (HLA) class I and II regions have been identified, including rs6457327, rs3117222, rs2647012, rs10484561, rs9268853 and rs2621416. Here we validated previous expression quantitative trait loci results with real-time reverse transcription quantitative PCR and investigated protein expression in B-lymphoblastoid cell lines and primary dendritic cells using flow cytometry, cell-based enzyme-linked immunosorbent assay and western blotting. We confirmed that FL-protective rs2647012-linked variants, in high linkage disequilibrium with the extended haplotype DRB1*15:01-DQA1*01:02-DQB1*06:02, correlate with increased HLA-DQB1 expression. This association remained significant at the protein level and was reproducible across different cell types. We also found that differences in HLA-DQB1 expression were not related to changes in activation markers or class II, major histocompatibility complex, transactivator expression, suggesting the role of an alternative regulatory mechanism. However, functional analysis using RegulomeDB did not reveal any relevant regulatory candidates. Future studies should focus on the clinical relevance of increased HLA-DQB1 protein expression facilitating tumor cell removal through increased immune surveillance.

Multi-locus HLA class I and II allele and haplotype associations with follicular lymphoma

Follicular lymphoma (FL) is an indolent, sometimes, fatal disease characterized by recurrence at progressively shorter intervals and is frequently refractive to therapy. Genome-wide association studies have identified single nucleotide polymorphisms (SNPs) in the human leukocyte antigen (HLA) region on chromosome 6p21.32-33 that are statistically significantly associated with FL risk. Low to medium resolution typing of single or multiple HLA genes has provided an incomplete picture of the total genetic risk imparted by this highly variable region. To gain further insight into the role of HLA alleles in lymphomagenesis and to investigate the independence of validated SNPs and HLA alleles with FL risk, high-resolution HLA typing was conducted using next-generation sequencing in 222 non-Hispanic White FL cases and 220 matched controls from a larger San Francisco Bay Area population-based case-control study of lymphoma. A novel protective association was found between the DPB1*03:01 allele and FL risk [odds ratio (OR) = 0.39, 95% confidence interval (CI) = 0.21-0.68]. Extended haplotypes DRB1*01:01-DQA1*01:01-DQB1*05:01 (OR = 2.01, 95% CI = 1.22-3.38) and DRB1*15-DQA1*01-DQB1*06 (OR = 0.55, 95% CI = 0.36-0.82) also influenced FL risk. Moreover, DRB1*15-DQA1*01-DQB1*06 was highly correlated with an established FL risk locus, rs2647012. These results provide further insight into the critical roles of HLA alleles and SNPs in FL pathogenesis that involve multi-locus effects across the HLA region.

Langevin simulation of rf collisional multipactor breakdown of gases

The thresholds for the electron multiplication in both multipactor and the so-called collisional multipactor microwave discharges are calculated by means of an individual particle model. The simulations are restricted to low and intermediate gas pressures, where the collisional mean-free path of electrons is of the same order or larger than the characteristic dimension of the system. Thus, the charge multiplication is caused by both the electron impact ionization of the neutral gas and the secondary electron emission by electron collisions at the surfaces. The charge avalanche is simulated by the numerical integration of the trajectories of electrons up to the characteristic time for the space-charge buildup. The electron dynamics is described by the stochastic Langevin equations where the collisional scatter of electrons is incorporated by means of a random force, while the microwave electric field and the friction are deterministic forces. The physical properties of materials at the walls are considered by means of realistic models deduced from experimental data fitting, while the constant collision frequency model is used for elastic and inelastic electron collisions with neutral atoms. Previous results for low pressure electron multipactor are recovered, and for pressures corresponding to collisional multipactor the predictions of this simple model are in agreement with both the experimental results and particle in cell and Monte Carlo simulations. Finally, physical conditions under which the charge multiplication develops and the limitations for higher pressures of the proposed model are also discussed.

Friction-force model for Maxwellian drifting ions in weakly ionized plasmas

Analytical expressions for the collision frequency for momentum transfer and the friction force experienced by a Maxwellian ion population drifting with respect to the uniform neutral atom background are derived. The calculations make use of different models for the collision cross section for momentum transfer accounting for the relative speed v_{r} between the colliding particles. These results are compared with the currently used semi-empirical equations for the friction force and collision frequency in the fluid equations for weakly ionized plasmas. The kinetic model calculations are in agreement for suprathermal ion flows while they present discrepancies of orders of magnitude for subthermal ion drift speeds u_{d} . However, for the collision cross section sigma_{m} approximately 1v_{r} , the magnitude of the friction force results proportional to u_{d} and the collision frequency becomes constant regardless of the magnitude of the ion drift speed in both cases. These results are relevant for ion populations drifting in a plasma which could be approximated by shifted Maxwellian distributions, as in collisional plasma sheaths or plasma double layers.

ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling

We present the ISACGH, a web-based system that allows for the combination of genomic data with gene expression values and provides different options for functional profiling of the regions found. Several visualization options offer a convenient representation of the results. Different efficient methods for accurate estimation of genomic copy number from array-CGH hybridization data have been included in the program. Moreover, the connection to the gene expression analysis package GEPAS allows the use of different facilities for data pre-processing and analysis. A DAS server allows exporting the results to the Ensembl viewer where contextual genomic information can be obtained. The program is freely available at: http://isacgh.bioinfo.cipf.es or within http://www.gepas.org.

Functional profiling and gene expression analysis of chromosomal copy number alterations

Contrarily to the traditional view in which only one or a few key genes were supposed to be the causative factors of diseases, we discuss the importance of considering groups of functionally related genes in the study of pathologies characterised by chromosomal copy number alterations. Recent observations have reported the existence of regions in higher eukaryotic chromosomes (including humans) containing genes of related function that show a high degree of coregulation. Copy number alterations will consequently affect to clusters of functionally related genes, which will be the final causative agents of the diseased phenotype, in many cases. Therefore, we propose that the functional profiling of the regions affected by copy number alterations must be an important aspect to take into account in the understanding of this type of pathologies. To illustrate this, we present an integrated study of DNA copy number variations, gene expression along with the functional profiling of chromosomal regions in a case of multiple myeloma.

BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments

We present a new version of Babelomics, a complete suite of web tools for functional analysis of genome-scale experiments, with new and improved tools. New functionally relevant terms have been included such as CisRed motifs or bioentities obtained by text-mining procedures. An improved indexing has considerably speeded up several of the modules. An improved version of the FatiScan method for studying the coordinate behaviour of groups of functionally related genes is presented, along with a similar tool, the Gene Set Enrichment Analysis. Babelomics is now more oriented to test systems biology inspired hypotheses. Babelomics can be found at .

PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes

We have developed a web tool, PupaSuite, for the selection of single nucleotide polymorphisms (SNPs) with potential phenotypic effect, specifically oriented to help in the design of large-scale genotyping projects. PupaSuite uses a collection of data on SNPs from heterogeneous sources and a large number of pre-calculated predictions to offer a flexible and intuitive interface for selecting an optimal set of SNPs. It improves the functionality of PupaSNP and PupasView programs and implements new facilities such as the analysis of user's data to derive haplotypes with functional information. A new estimator of putative effect of polymorphisms has been included that uses evolutionary information. Also SNPeffect database predictions have been included. The PupaSuite web interface is accessible through and through .

Next station in microarray data analysis: GEPAS

The Gene Expression Profile Analysis Suite (GEPAS) has been running for more than four years. During this time it has evolved to keep pace with the new interests and trends in the still changing world of microarray data analysis. GEPAS has been designed to provide an intuitive although powerful web-based interface that offers diverse analysis options from the early step of preprocessing (normalization of Affymetrix and two-colour microarray experiments and other preprocessing options), to the final step of the functional annotation of the experiment (using Gene Ontology, pathways, PubMed abstracts etc.), and include different possibilities for clustering, gene selection, class prediction and array-comparative genomic hybridization management. GEPAS is extensively used by researchers of many countries and its records indicate an average usage rate of 400 experiments per day. The web-based pipeline for microarray gene expression data, GEPAS, is available at http://www.gepas.org.

PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes

We have developed a web tool, PupasView, for the selection of single nucleotide polymorphisms (SNPs) with potential phenotypic effect. PupasView constitutes an interactive environment in which functional information and population frequency data can be used as sequential filters over linkage disequilibrium parameters to obtain a final list of SNPs optimal for genotyping purposes. PupasView is the first resource that integrates phenotypic effects caused by SNPs at both the translational and the transcriptional level. PupasView retrieves SNPs that could affect conserved regions that the cellular machinery uses for the correct processing of genes (intron/exon boundaries or exonic splicing enhancers), predicted transcription factor binding sites and changes in amino acids in the proteins for which a putative pathological effect is calculated. The program uses the mapping of SNPs in the genome provided by Ensembl. PupasView will be of much help in studies of multifactorial disorders, where the use of functional SNPs will increase the sensitivity of the identification of the genes responsible for the disease. The PupasView web interface is accessible through http://pupasview.ochoa.fib.es and through http://www.pupasnp.org.

BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments

We present Babelomics, a complete suite of web tools for the functional analysis of groups of genes in high-throughput experiments, which includes the use of information on Gene Ontology terms, interpro motifs, KEGG pathways, Swiss-Prot keywords, analysis of predicted transcription factor binding sites, chromosomal positions and presence in tissues with determined histological characteristics, through five integrated modules: FatiGO (fast assignment and transference of information), FatiWise, transcription factor association test, GenomeGO and tissues mining tool, respectively. Additionally, another module, FatiScan, provides a new procedure that integrates biological information in combination with experimental results in order to find groups of genes with modest but coordinate significant differential behaviour. FatiScan is highly sensitive and is capable of finding significant asymmetries in the distribution of genes of common function across a list of ordered genes even if these asymmetries were not extreme. The strong multiple-testing nature of the contrasts made by the tools is taken into account. All the tools are integrated in the gene expression analysis package GEPAS. Babelomics is the natural evolution of our tool FatiGO (which analysed almost 22 000 experiments during the last year) to include more sources on information and new modes of using it. Babelomics can be found at .

GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data

The Gene Expression Profile Analysis Suite, GEPAS, has been running for more than three years. With >76,000 experiments analysed during the last year and a daily average of almost 300 analyses, GEPAS can be considered a well-established and widely used platform for gene expression microarray data analysis. GEPAS is oriented to the analysis of whole series of experiments. Its design and development have been driven by the demands of the biomedical community, probably the most active collective in the field of microarray users. Although clustering methods have obviously been implemented in GEPAS, our interest has focused more on methods for finding genes differentially expressed among distinct classes of experiments or correlated to diverse clinical outcomes, as well as on building predictors. There is also a great interest in CGH-arrays which fostered the development of the corresponding tool in GEPAS: InSilicoCGH. Much effort has been invested in GEPAS for developing and implementing efficient methods for functional annotation of experiments in the proper statistical framework. Thus, the popular FatiGO has expanded to a suite of programs for functional annotation of experiments, including information on transcription factor binding sites, chromosomal location and tissues. The web-based pipeline for microarray gene expression data, GEPAS, is available at http://www.gepas.org.

PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level

We have developed a web tool, PupaSNP Finder (PupaSNP for short), for high-throughput searching for single nucleotide polymorphisms (SNPs) with potential phenotypic effect. PupaSNP takes as its input lists of genes (or generates them from chromosomal coordinates) and retrieves SNPs that could affect the conserved regions that the cellular machinery uses for the correct processing of genes (intron/exon boundaries or exonic splicing enhancers), predicted transcription factor binding sites (TFBS) and changes in amino acids in the proteins. The program uses the mapping of SNPs in the genome provided by Ensembl. Additionally, user-defined SNPs (not yet mapped in the genome) can be easily provided to the program. Also, additional functional information from Gene Ontology, OMIM and homologies in other model organisms is provided. In contrast to other programs already available, which focus only on SNPs with possible effect in the protein, PupaSNP includes SNPs with possible transcriptional effect. PupaSNP will be of significant help in studies of multifactorial disorders, where the use of functional SNPs will increase the sensitivity of identification of the genes responsible for the disease. The PupaSNP web interface is accessible through http://pupasnp.bioinfo.cnio.es.

New challenges in gene expression data analysis and the extended GEPAS

Since the first papers published in the late nineties, including, for the first time, a comprehensive analysis of microarray data, the number of questions that have been addressed through this technique have both increased and diversified. Initially, interest focussed on genes coexpressing across sets of experimental conditions, implying, essentially, the use of clustering techniques. Recently, however, interest has focussed more on finding genes differentially expressed among distinct classes of experiments, or correlated to diverse clinical outcomes, as well as in building predictors. In addition to this, the availability of accurate genomic data and the recent implementation of CGH arrays has made mapping expression and genomic data on the chromosomes possible. There is also a clear demand for methods that allow the automatic transfer of biological information to the results of microarray experiments. Different initiatives, such as the Gene Ontology (GO) consortium, pathways databases, protein functional motifs, etc., provide curated annotations for genes. Whereas many resources on the web focus mainly on clustering methods, GEPAS has evolved to cope with the aforementioned new challenges that have recently arisen in the field of microarray data analysis. The web-based pipeline for microarray gene expression data, GEPAS, is available at http://gepas.bioinfo.cnio.es.

Electron impact ionization by drifting electrons in weakly ionized plasmas

The expression for electron impact ionization rate by a Maxwellian electron population drifting with respect to a uniform neutral atom background is derived. Depending on electron temperature, drift speeds between one to five times electron thermal velocity produce increments in the ionization rate from two to seven orders of magnitude. Local ionization takes place over shorter distances than predicted for nondrifting electron populations and the results agree with previous experimental evidence on ionizing plasma double layers and electron attracting sheaths.