472 research outputs found
Signature of stripe pinning in optical conductivity
The response of charge stripes to an external electric field applied
perpendicular to the stripe direction is studied within a diagrammatic approach
for both weak and strong pinning by random impurities. The sound-like mode of
the stripes described as elastic strings moves to finite frequency due to
impurity pinning. By calculating the optical conductivity we determine this
characteristic energy scale for both a single stripe and an array of
interacting stripes. The results explain the anomalous far-infrared peak
observed recently in optical-conductivity measurements on cuprates.Comment: Revised version, to appear in Phys. Rev.
An Experimental Comparison of Hybrid Algorithms for Bayesian Network Structure Learning
International audienceWe present a novel hybrid algorithm for Bayesian network structure learning, called Hybrid HPC (H2PC). It first reconstructs the skeleton of a Bayesian network and then performs a Bayesian-scoring greedy hill-climbing search to orient the edges. It is based on a subroutine called HPC, that combines ideas from incremental and divide-and-conquer constraint-based methods to learn the parents and children of a target variable. We conduct an experimental comparison of H2PC against Max-Min Hill-Climbing (MMHC), which is currently the most powerful state-of-the-art algorithm for Bayesian network structure learning, on several benchmarks with various data sizes. Our extensive experiments show that H2PC outperforms MMHC both in terms of goodness of fit to new data and in terms of the quality of the network structure itself, which is closer to the true dependence structure of the data. The source code (in R) of H2PC as well as all data sets used for the empirical tests are publicly available
Biofilm formation behaviour of marine filamentous cyanobacterial strains in controlled hydrodynamic conditions
Marine biofouling has severe economic impacts and cyanobacteria play a significant role as early surface colonizers. Despite this fact, cyanobacterial biofilm formation studies in controlled hydrodynamic conditions are scarce. In this work, computational fluid dynamics was used to determine the shear rate field on coupons that were placed inside the wells of agitated 12-well microtiter plates. Biofilm formation by three different cyanobacterial strains was assessed at two different shear rates (4 and 40 s-1 ) which can be found in natural ecosystems and using different surfaces (glass and perspex). Biofilm formation was higher under low shear conditions, and differences obtained between surfaces were not always statistically significant. The hydrodynamic effect was more noticeable during the biofilm maturation phase rather than during initial cell adhesion and optical coherence tomography showed that different shear rates can affect biofilm architecture. This study is particularly relevant given the cosmopolitan distribution of these cyanobacterial strains and the biofouling potential of these organisms.This work was financially supported by project UID/EQU/ 00511/2019 – Laboratory for Process Engineering, Environment, Biotechnology and Energy – LEPABE funded by national funds through FCT/MCTES (PIDDAC) and by the CVMAR+i – Industrial Innovation and Marine Biotechnology Valorisation, funded by INTERREG V A Espanha Portugal (POCTEP) [0302_CVMAR_I_1_P]. The authors also acknowledge support from the EU COST Actions iPROMEDAI (TD1305) and ENBA (CA15216), and M.J.R. acknowledges a PhD grant from FCT (SFRH/BD/140080/2018)
Flux noise in high-temperature superconductors
Spontaneously created vortex-antivortex pairs are the predominant source of
flux noise in high-temperature superconductors. In principle, flux noise
measurements allow to check theoretical predictions for both the distribution
of vortex-pair sizes and for the vortex diffusivity. In this paper the
flux-noise power spectrum is calculated for the highly anisotropic
high-temperature superconductor Bi-2212, both for bulk crystals and for
ultra-thin films. The spectrum is basically given by the Fourier transform of
the temporal magnetic-field correlation function. We start from a
Berezinskii-Kosterlitz-Thouless type theory and incorporate vortex diffusion,
intra-pair vortex interaction, and annihilation of pairs by means of a
Fokker-Planck equation to determine the noise spectrum below and above the
superconducting transition temperature. We find white noise at low frequencies
omega and a spectrum proportional to 1/omega^(3/2) at high frequencies. The
cross-over frequency between these regimes strongly depends on temperature. The
results are compared with earlier results of computer simulations.Comment: 9 pages, 4 PostScript figures, to be published in Phys. Rev.
Detecting Nonvolatile Life- and Nonlife-Derived Organics in a Carbonaceous Chondrite Analogue with a New Multiplex Immunoassay and Its Relevance for Planetary Exploration
Potential martian molecular targets include those supplied by meteoritic carbonaceous chondrites such as amino acids and polycyclic aromatic hydrocarbons and true biomarkers stemming from any hypothetical martian biota (organic architectures that can be directly related to once-living organisms). Heat extraction and pyrolysis-based methods currently used in planetary exploration are highly aggressive and very often modify the target molecules, making their identification a cumbersome task. We have developed and validated a mild, nondestructive, multiplex inhibitory microarray immunoassay and demonstrated its implementation in the SOLID (Signs of Life Detector) instrument for simultaneous detection of several nonvolatile life- and nonlife-derived organic molecules relevant in planetary exploration and environmental monitoring. By utilizing a set of highly specific antibodies that recognize D- or L-aromatic amino acids (Phe, Tyr, Trp), benzo[a]pyrene (B[a]P), pentachlorophenol, and sulfone-containing aromatic compounds, respectively, the assay was validated in the SOLID instrument for the analysis of carbon-rich samples used as analogues of the organic material in carbonaceous chondrites or even Mars samples. Most of the antibodies enabled sensitivities at the 1–10 ppb level and some even at the part-per-trillion level. The multiplex immunoassay allowed the detection of B[a]P as well as aromatic sulfones in a water/methanol extract of an Early Cretaceous lignite sample (ca. 140 Ma) representing type IV kerogen. No L- or D-aromatic amino acids were detected, reflecting the advanced diagenetic stage and the fossil nature of the sample. The results demonstrate the ability of the liquid extraction by ultrasonication and the versatility of the multiplex inhibitory immunoassays in the SOLID instrument to discriminate between organic matter derived from life and nonlife processes, an essential step toward life detection outside EarthThis work was supported by granted projects AYA2011-24803, ESP2014-51989-P, and ESP2015-69540-R, from the Ministry of Economy and Competitiveness (MINECO) of Spain, and by Grant No. ST/N000803/1 (United Kingdom). A. G-C was a fellow of ‘‘Plan de Formación from INTA.Peer reviewe
Normal-state conductivity in underdoped La_{2-x}Sr_xCuO_4 thin films: Search for nonlinear effects related to collective stripe motion
We report a detailed study of the electric-field dependence of the
normal-state conductivity in La_{2-x}Sr_xCuO_4 thin films for two
concentrations of doped holes, x=0.01 and 0.06, where formation of diagonal and
vertical charged stripes was recently suggested. In order to elucidate whether
high electric fields are capable of depinning the charged stripes and inducing
their collective motion, we have measured current-voltage characteristics for
various orientations of the electric field with respect to the crystallographic
axes. However, even for the highest possible fields (~1000 V/cm for x=0.01 and
\~300 V/cm for x=0.06) we observed no non-linear-conductivity features except
for those related to the conventional Joule heating of the films. Our analysis
indicates that Joule heating, rather than collective electron motion, may also
be responsible for the non-linear conductivity observed in some other 2D
transition-metal oxides as well. We discuss that a possible reason why moderate
electric fields fail to induce a collective stripe motion in layered oxides is
that fairly flexible and compressible charged stripes can adjust themselves to
the crystal lattice and individual impurities, which makes their pinning much
stronger than in the case of conventional rigid charge-density waves.Comment: 10 pages, 10 figures, accepted for publication in Phys. Rev.
From forensics to clinical research: expanding the variant calling pipeline for the precision ID mtDNA whole genome panel
Despite a multitude of methods for the sample preparation, sequencing, and data analysis of mitochondrial DNA (mtDNA), the demand for innovation remains, particularly in comparison with nuclear DNA (nDNA) research. The Applied Biosystems™ Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific, USA) is an innovative library preparation kit suitable for degraded samples and low DNA input. However, its bioinformatic processing occurs in the enterprise Ion Torrent Suite™ Software (TSS), yielding BAM files aligned to an unorthodox version of the revised Cambridge Reference Sequence (rCRS), with a heteroplasmy threshold level of 10%. Here, we present an alternative customizable pipeline, the PrecisionCallerPipeline (PCP), for processing samples with the correct rCRS output after Ion Torrent sequencing with the Precision ID library kit. Using 18 samples (3 original samples and 15 mixtures) derived from the 1000 Genomes Project, we achieved overall improved performance metrics in comparison with the proprietary TSS, with optimal performance at a 2.5% heteroplasmy threshold. We further validated our findings with 50 samples from an ongoing independent cohort of stroke patients, with PCP finding 98.31% of TSS’s variants (TSS found 57.92% of PCP’s variants), with a significant correlation between the variant levels of variants found with both pipelines
Stripes and holes in a two-dimensional model of spinless fermions and hardcore bosons
We consider a Hubbard-like model of strongly-interacting spinless fermions
and hardcore bosons on a square lattice, such that nearest neighbor occupation
is forbidden. Stripes (lines of holes across the lattice forming antiphase
walls between ordered domains) are a favorable way to dope this system below
half-filling. The problem of a single stripe can be mapped to a spin-1/2 chain,
which allows understanding of its elementary excitations and calculation of the
stripe's effective mass for transverse vibrations. Using Lanczos exact
diagonalization, we investigate the excitation gap and dispersion of a hole on
a stripe, and the interaction of two holes. We also study the interaction of
two, three, and four stripes, finding that they repel, and the interaction
energy decays with stripe separation as if they are hardcore particles moving
in one (transverse) direction. To determine the stability of an array of
stripes against phase separation into particle-rich phase and hole-rich liquid,
we evaluate the liquid's equation of state, finding the stripe-array is not
stable for bosons but is possibly stable for fermions.Comment: 24 pages, 18 figure
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