Understanding the relative importance of vertical and horizontal flow in ice-wedge polygons

Ice-wedge polygons are common Arctic landforms. The future of these landforms in a warming climate depends on the bidirectional feedback between the rate of ice-wedge degradation and changes in hydrological characteristics. This work aims to better understand the relative roles of vertical and horizontal water fluxes in the subsurface of polygonal landscapes, providing new insights and data to test and calibrate hydrological models. Field-scale investigations were conducted at an intensively instrumented location on the Barrow Environmental Observatory (BEO) near Utqiagvik, AK, USA. Using a conservative tracer, we examined controls of microtopography and the frost table on subsurface flow and transport within a low-centered and a high-centered polygon. Bromide tracer was applied at both polygons in July 2015 and transport was monitored through two thaw seasons. Sampler arrays placed in polygon centers, rims, and troughs were used to monitor tracer concentrations. In both polygons, the tracer first infiltrated vertically until encountering the frost table and was then transported horizontally. Horizontal flow occurred in more locations and at higher velocities in the low-centered polygon than in the high-centered polygon. Preferential flow, influenced by frost table topography, was significant between polygon centers and troughs. Estimates of horizontal hydraulic conductivity were within the range of previous estimates of vertical conductivity, highlighting the importance of horizontal flow in these systems. This work forms a basis for understanding complexity of flow in polygonal landscapes

BibGlimpse: The case for a light-weight reprint manager in distributed literature research

Background While text-mining and distributed annotation systems both aim at capturing knowledge and presenting it in a standardized form, there have been few attempts to investigate potential synergies between these two fields. For instance, distributed annotation would be very well suited for providing topic focussed, expert knowledge enriched text corpora. A key limitation for this approach is the availability of literature annotation systems that can be routinely used by groups of collaborating researchers on a day to day basis, not distracting from the main focus of their work. Results For this purpose, we have designed BibGlimpse. Features like drop-to-file, SVM based automated retrieval of PubMed bibliography for PDF reprints, and annotation support make BibGlimpse an efficient, light-weight reprint manager that facilitates distributed literature research for work groups. Building on an established open search engine, full-text search and structured queries are supported, while at the same time making shared collections of annotated reprints accessible to literature classification and text-mining tools. Conclusion BibGlimpse offers scientists a tool that enhances their own literature management. Moreover, it may be used to create content enriched, annotated text corpora for research in text-mining

A Bayesian method for evaluating and discovering disease loci associations

Background: A genome-wide association study (GWAS) typically involves examining representative SNPs in individuals from some population. A GWAS data set can concern a million SNPs and may soon concern billions. Researchers investigate the association of each SNP individually with a disease, and it is becoming increasingly commonplace to also analyze multi-SNP associations. Techniques for handling so many hypotheses include the Bonferroni correction and recently developed Bayesian methods. These methods can encounter problems. Most importantly, they are not applicable to a complex multi-locus hypothesis which has several competing hypotheses rather than only a null hypothesis. A method that computes the posterior probability of complex hypotheses is a pressing need. Methodology/Findings: We introduce the Bayesian network posterior probability (BNPP) method which addresses the difficulties. The method represents the relationship between a disease and SNPs using a directed acyclic graph (DAG) model, and computes the likelihood of such models using a Bayesian network scoring criterion. The posterior probability of a hypothesis is computed based on the likelihoods of all competing hypotheses. The BNPP can not only be used to evaluate a hypothesis that has previously been discovered or suspected, but also to discover new disease loci associations. The results of experiments using simulated and real data sets are presented. Our results concerning simulated data sets indicate that the BNPP exhibits both better evaluation and discovery performance than does a p-value based method. For the real data sets, previous findings in the literature are confirmed and additional findings are found. Conclusions/Significance: We conclude that the BNPP resolves a pressing problem by providing a way to compute the posterior probability of complex multi-locus hypotheses. A researcher can use the BNPP to determine the expected utility of investigating a hypothesis further. Furthermore, we conclude that the BNPP is a promising method for discovering disease loci associations. © 2011 Jiang et al

Automated synthesis of transmission lines loaded with complementary split ring resonators (CSRRs) and open complementary split ring resonators (OCSRRs) through aggressive space mapping (ASM)

This paper is focused on the application of space mapping optimization to the automated synthesis of transmission lines loaded with complementary split ring resonators (CSRRs) and open complementary split ring resonators (OCSRRs). These structures are of interest for the implementation of resonant-type metamaterial transmission lines and for the design of planar microwave circuits based on such complementary resonators. The paper presents a method to generate the layouts of CSRR- and OCSRR-loaded microstrip lines from the elements of their equivalent circuit models. Using the so-called aggressive space mapping, a specific implementation that uses quasi-Newton type iteration, we have developed synthesis algorithms that are able to provide the topology of these CSRR and OCSRR-loaded lines in few steps. The most relevant aspect, however, is that this synthesis process is completely automatic, i.e., it does not require any action from the designers, other than initiating the algorithm. Moreover, this technique can be translated to other electrically small planar elements described by lumped element equivalent circuit models.This work has been partially supported by MICIIN-Spain (Projects TEC2010-17512 METATRANSFER, TEC2010-21520-C04-01 AVANSAT, CONSOLIDER EMET CSD2008-00066, and Grant AP2008-04707), Generalitat de Catalunya (Project 2009SGR-421), and MITyC-Spain (Project TSI-020100-2010-169 METASINTESIS). Ferran Martin is in debt to ICREA for supporting his work through an ICREA Academia Award (calls 2008 and 2013).Selga, J.; Rodríguez Pérez, AM.; Orellana, M.; Boria Esbert, VE.; Martín, F. (2014). Automated synthesis of transmission lines loaded with complementary split ring resonators (CSRRs) and open complementary split ring resonators (OCSRRs) through aggressive space mapping (ASM). Applied Physics A. 117(2):557-565. https://doi.org/10.1007/s00339-014-8703-xS5575651172G.V. Eleftheriades, K.G. Balmain, Negative Refraction Metamaterials: Fundamental Principles and Applications (Wiley, New Jersey, 2005)C. Caloz, T. Itoh, Electromagnetic Metamaterials: Transmission Line Theory and Microwave Applications (Wiley, New Jersey, 2006)R. Marqués, F. Martín, M. Sorolla, Metamaterials with Negative Parameters: Theory, Design and Microwave Applications (Wiley, New Jersey, 2008)F. Martín, Artificial Transmission Lines for RF and Microwave Applications. (Wiley, New Jersey) (to be published)M.A. Antoniades, G.V. Eleftheriades, A broadband series power divider using zero-degree metamaterial phase shifting lines. IEEE Microw. Wirel. Compon. Lett. 15, 808–810 (2005)H. Okabe, C. Caloz, T. Itoh, A compact enhanced bandwidth hybrid ring using an artificial lumped element left handed transmission line section. IEEE Trans. Microw. Theory Tech. 52, 798–804 (2004)G. Sisó, J. Bonache, M. Gil, F. Martín, Application of resonant-type metamaterial transmission lines to the design of enhanced bandwidth components with compact dimensions. Microw. Opt. Technol. Lett. 50, 127–134 (2008)I.H. Lin, M. De Vincentis, C. Caloz, T. Itoh, Arbitrary dual-band components using composite right/left handed transmission lines. IEEE Trans. Microw. Theory Tech. 52, 1142–1149 (2004)A.C. Papanastasiou, G.E. Georghiou, G.V. Eleftheriades, A quad-band Wilkinson power divider using generalized NRI transmission lines. IEEE Microw. Wirel. Compon. Lett. 18, 521–523 (2008)M. Durán-Sindreu, G. Sisó, J. Bonache, F. Martín, Planar multi-band microwave components based on the generalized composite right/left handed transmission line concept. IEEE Trans. Microw. Theory Tech. 58(12), 3882–3891 (2010)J. Bonache, I. Gil, J. García-García, F. Martín, Novel microstrip band pass filters based on complementary split ring resonators. IEEE Trans. Microw. Theory Tech. 54, 265–271 (2006)M. Gil, J. Bonache, J. García-García, J. Martel, F. Martín, Composite right/left handed (CRLH) metamaterial transmission lines based on complementary split rings resonators (CSRRs) and their applications to very wide band and compact filter design. IEEE Trans. Microw. Theory Tech. 55, 1296–1304 (2007)S. Lim, C. Caloz, T. Itoh, Metamaterial-based electronically-controlled transmission line structure as a novel leaky-wave antenna with tunable angle and beamwidth. IEEE Trans. Microw. Theory Tech. 52(12), 2678–2690 (2004)G. Zamora, S. Zuffanelli, F. Paredes, F. Javier Herraiz-Martínez, F. Martín, J. Bonache, Fundamental mode leaky-wave-antenna (LWA) using slot line and split-ring-resonator (SRR) based metamaterials. IEEE Antennas Wirel. Propag. Lett. 12, 1424–1427 (2013)A.K. Iyer, G.V. Eleftheriades, Negative refractive index metamaterials supporting 2-D waves. in IEEE-MTT Int’l Microwave Symposium, vol 2, Seattle, WA, pp. 412–415 (2002)A.A. Oliner, A periodic-structure negative-refractive-index medium without resonant elements. In URSI Digest, IEEE-AP-S USNC/URSI National Radio Science Meeting, San Antonio, TX, pp. 41 (2002)C. Caloz, T. Itoh, Application of the transmission line theory of left-handed (LH) materials to the realization of a microstrip LH transmission line. in Proceedings of IEEE-AP-S USNC/URSI National Radio Science Meeting, vol 2, San Antonio, TX, pp. 412–415 (2002)F. Martín, F. Falcone, J. Bonache, R. Marqués, M. Sorolla, Split ring resonator based left handed coplanar waveguide. Appl. Phys. Lett. 83, 4652–4654 (2003)F. Falcone, T. Lopetegi, M.A.G. Laso, J.D. Baena, J. Bonache, R. Marqués, F. Martín, M. Sorolla (2004) Babinet principle applied to the design of metasurfaces and metamaterials. Phys. Rev. Lett. 93, paper 197401M. Durán-Sindreu, A. Vélez, F. Aznar, G. Sisó, J. Bonache, F. Martín, Application of open split ring resonators and open complementary split ring resonators to the synthesis of artificial transmission lines and microwave passive components. IEEE Trans. Microw. Theory Tech. 57, 3395–3403 (2009)A. Vélez, F. Aznar, M. Durán-Sindreu, J. Bonache, F. Martín, Stop-band and band-pass filters in coplanar waveguide technology implemented by means of electrically small metamaterial-inspired open resonators. IET Microw. Antennas Propag. 4, 712–716 (2004)J.D. Baena, J. Bonache, F. Martín, R. Marqués, F. Falcone, T. Lopetegi, M.A.G. Laso, J. García, I. Gil, M. Flores-Portillo, M. Sorolla, Equivalent circuit models for split ring resonators and complementary split rings resonators coupled to planar transmission lines. IEEE Trans. Microw. Theory Tech. 53, 1451–1461 (2005)M. Gil, J. Bonache, J. Selga, J. García-García, F. Martín, Broadband resonant type metamaterial transmission lines. IEEE Microw. Wirel. Compon. Lett. 17, 97–99 (2007)M. Durán-Sindreu, P. Vélez, J. Bonache, F. Martín, Broadband microwave filters based on open split ring resonators (OSRRs) and open complementary split ring resonators (OCSRRs): improved models and design optimization. Radioengineering 20, 775–783 (2011)P. Vélez, J. Naqui, M. Durán-Sindreu, J. Bonache, F. Martín, Broadband microstrip bandpass filter based on open complementary split ring resonators. Int. J. Antennas Propag. 2012, 6 (2012)J.W. Bandler, R.M. Biernacki, S.H. Chen, P.A. Grobelny, R.H. Hemmers, Space mapping technique for electromagnetic optimization. IEEE Trans. Microw. Theory Tech. 42, 2536–2544 (1994)J.W. Bandler, R.M. Biernacki, S.H. Chen, R.H. Hemmers, K. Madsen, Electromagnetic optimization exploiting aggressive space mapping. IEEE Trans. Microw. Theory Tech. 43, 2874–2882 (1995)J.W. Bandler, Q.S. Cheng, S.A. Dakroury, A.S. Mohamed, M.H. Bakr, K. Madsen, J. Søndergaard, Space mapping: the state of the art. IEEE Trans. Microw. Theory Tech. 52, 337–361 (2004)C.G. Broyden, A class of methods for solving nonlinear simultaneous equations. Math. Comput. 19(92), 577–593 (1965)J. Selga, A. Rodríguez, V.E. Boria, F. Martín, Synthesis of split rings based artificial transmission lines through a new two-step, fast converging, and robust aggressive space mapping (ASM) algorithm. IEEE Trans. Microw. Theory Tech. 61(6), 2295–2308 (2013)A. Velez, F. Aznar, J. Bonache, M.C. Velázquez-Ahumada, J. Martel, F. Martín, Open complementary split ring resonators (OCSRRs) and their application to wideband CPW band pass filters. IEEE Microw. Wirel. Compon. Lett. 19, 197–199 (2009)D.M. Bates, D.G. Watts, Nonlinear Regression Analysis and Its Applications (Wiley, New York, 1998

Identification of surface proteins in Enterococcus faecalis V583

<p>Abstract</p> <p>Background</p> <p>Surface proteins are a key to a deeper understanding of the behaviour of Gram-positive bacteria interacting with the human gastro-intestinal tract. Such proteins contribute to cell wall synthesis and maintenance and are important for interactions between the bacterial cell and the human host. Since they are exposed and may play roles in pathogenicity, surface proteins are interesting targets for drug design.</p> <p>Results</p> <p>Using methods based on proteolytic "shaving" of bacterial cells and subsequent mass spectrometry-based protein identification, we have identified surface-located proteins in <it>Enterococcus faecalis </it>V583. In total 69 unique proteins were identified, few of which have been identified and characterized previously. 33 of these proteins are predicted to be cytoplasmic, whereas the other 36 are predicted to have surface locations (31) or to be secreted (5). Lipid-anchored proteins were the most dominant among the identified surface proteins. The seemingly most abundant surface proteins included a membrane protein with a potentially shedded extracellular sulfatase domain that could act on the sulfate groups in mucin and a lipid-anchored fumarate reductase that could contribute to generation of reactive oxygen species.</p> <p>Conclusions</p> <p>The present proteome analysis gives an experimental impression of the protein landscape on the cell surface of the pathogenic bacterium <it>E. faecalis</it>. The 36 identified secreted (5) and surface (31) proteins included several proteins involved in cell wall synthesis, pheromone-regulated processes, and transport of solutes, as well as proteins with unknown function. These proteins stand out as interesting targets for further investigation of the interaction between <it>E. faecalis </it>and its environment.</p

Might Depression, Psychosocial Adversity, and Limited Social Assets Explain Vulnerability to and Resistance against Violent Radicalisation?

BACKGROUND: This study tests whether depression, psychosocial adversity, and limited social assets offer protection or suggest vulnerability to the process of radicalisation. METHODS: A population sample of 608 men and women of Pakistani or Bangladeshi origin, of Muslim heritage, and aged 18-45 were recruited by quota sampling. Radicalisation was measured by 16 questions asking about sympathies for violent protest and terrorism. Cluster analysis of the 16 items generated three groups: most sympathetic (or most vulnerable), most condemning (most resistant), and a large intermediary group that acted as a reference group. Associations were calculated with depression (PHQ9), anxiety (GAD7), poor health, and psychosocial adversity (adverse life events, perceived discrimination, unemployment). We also investigated protective factors such as the number social contacts, social capital (trust, satisfaction, feeling safe), political engagement and religiosity. RESULTS: Those showing the most sympathy for violent protest and terrorism were more likely to report depression (PHQ9 score of 5 or more; RR = 5.43, 1.35 to 21.84) and to report religion to be important (less often said religion was fairly rather than very important; RR = 0.08, 0.01 to 0.48). Resistance to radicalisation measured by condemnation of violent protest and terrorism was associated with larger number of social contacts (per contact: RR = 1.52, 1.26 to 1.83), less social capital (RR = 0.63, 0.50 to 0.80), unavailability for work due to housekeeping or disability (RR = 8.81, 1.06 to 37.46), and not being born in the UK (RR = 0.22, 0.08 to 0.65). CONCLUSIONS: Vulnerability to radicalisation is characterised by depression but resistance to radicalisation shows a different profile of health and psychosocial variables. The paradoxical role of social capital warrants further investigation

Preterm Birth in Caucasians Is Associated with Coagulation and Inflammation Pathway Gene Variants

Spontaneous preterm birth (<37 weeks gestation—PTB) occurs in ∼12% of pregnancies in the United States, and is the largest contributor to neonatal morbidity and mortality. PTB is a complex disease, potentially induced by several etiologic factors from multiple pathophysiologic pathways. To dissect the genetic risk factors of PTB a large-scale high-throughput candidate gene association study was performed examining 1536 SNP in 130 candidate genes from hypothesized PTB pathways. Maternal and fetal DNA from 370 US Caucasian birth-events (172 cases and 198 controls) was examined. Single locus, haplotype, and multi-locus association analyses were performed separately on maternal and fetal data. For maternal data the strongest associations were found in genes in the complement-coagulation pathway related to decidual hemorrhage in PTB. In this pathway 3 of 6 genes examined had SNPs significantly associated with PTB. These include factor V (FV) that was previously associated with PTB, factor VII (FVII), and tissue plasminogen activator (tPA). The single strongest effect was observed in tPA marker rs879293 with a significant allelic (p = 2.30×10−3) and genotypic association (p = 2.0×10−6) with PTB. The odds ratio (OR) for this SNP was 2.80 [CI 1.77–4.44] for a recessive model. Given that 6 of 8 markers in tPA were statistically significant, sliding window haplotype analyses were performed and revealed an associating 4 marker haplotype in tPA (p = 6.00×10−3). The single strongest effect in fetal DNA was observed in the inflammatory pathway at rs17121510 in the interleukin-10 receptor antagonist (IL-10RA) gene for allele (p = 0.01) and genotype (p = 3.34×10−4). The OR for the IL-10RA genotypic additive model was 1.92 [CI 1.15–3.19] (p = 2.00×10−3). Finally, exploratory multi-locus analyses in the complement and coagulation pathway were performed and revealed a potentially significant interaction between a marker in FV (rs2187952) and FVII (rs3211719) (p<0.001). These results support a role for genes in both the coagulation and inflammation pathways, and potentially different maternal and fetal genetic risks for PTB

A General Framework for Formal Tests of Interaction after Exhaustive Search Methods with Applications to MDR and MDR-PDT

The initial presentation of multifactor dimensionality reduction (MDR) featured cross-validation to mitigate over-fitting, computationally efficient searches of the epistatic model space, and variable construction with constructive induction to alleviate the curse of dimensionality. However, the method was unable to differentiate association signals arising from true interactions from those due to independent main effects at individual loci. This issue leads to problems in inference and interpretability for the results from MDR and the family-based compliment the MDR-pedigree disequilibrium test (PDT). A suggestion from previous work was to fit regression models post hoc to specifically evaluate the null hypothesis of no interaction for MDR or MDR-PDT models. We demonstrate with simulation that fitting a regression model on the same data as that analyzed by MDR or MDR-PDT is not a valid test of interaction. This is likely to be true for any other procedure that searches for models, and then performs an uncorrected test for interaction. We also show with simulation that when strong main effects are present and the null hypothesis of no interaction is true, that MDR and MDR-PDT reject at far greater than the nominal rate. We also provide a valid regression-based permutation test procedure that specifically tests the null hypothesis of no interaction, and does not reject the null when only main effects are present. The regression-based permutation test implemented here conducts a valid test of interaction after a search for multilocus models, and can be applied to any method that conducts a search to find a multilocus model representing an interaction

Role of the Functional Toll-Like Receptor-9 Promoter Polymorphism (-1237T/C) in Increased Risk of End-Stage Renal Disease:A Case-Control Study

Inflammation induced by infectious and noninfectious triggers in the kidney may lead to end stage renal disease (ESRD). Toll-like receptor 9 (TLR-9) a receptor for CpG DNA is involved in activation of immune cells in renal disease and may contribute to chronic inflammatory disease progression through an interleukin-6 (IL-6) dependent pathway. Previous studies indicate that -1237T/C confers regulatory effects on TLR-9 transcription. To date the effect of TLR-9 polymorphisms on ESRD remains unknown. We performed a case-control study and genotyped 630 ESRD patients and 415 controls for -1237T/C, -1486T/C and 1635G/A by real-time PCR assays and assessed plasma concentration of IL-6 by ELISA. Haplotype association analysis was performed using the Haploview package. A luciferase reporter assay and real-time PCR were used to test the function of the -1237T/C promoter polymorphism. A significant association between -1237T/C in TLR-9 and ESRD was identified. The TCA, TTA and CCA haplotype of TLR-9 were associated with ESRD. ESRD patients carrying -1237TC had a higher mean plasma IL-6 level when compared with -1237TT. The TLR-9 transcriptional activity of the variant -1237CC allele is higher than the -1237TT allele. The results indicate that in a Han Chinese population the presence of the C allele of -1237T/C in the TLR-9 gene increases susceptibility towards development of ESRD. In vitro studies demonstrate that -1237T/C may be involved in the development of ESRD through transcriptional modulation of TLR-9