CRBHits: From Conditional Reciprocal Best Hits toCodon Alignments and Ka/Ks in R

CRBHitsis a coding sequence (CDS) analysis pipeline inR(R Core Team, 2019). It reimple-ments the Conditional Reciprocal Best Hit (CRBH) algorithmcrb-blastand covers all necessarysteps from sequence similarity searches, codon alignments to Ka/Ks calculations and synteny.The new R package targets ecology, population and evolutionary biologists working in thefield of comparative genomics.The Reciprocal Best Hit (RBH) approach is commonly used in bioinformatics to show thattwo sequences evolved from a common ancestral gene. In other words, RBH tries to findorthologous protein sequences within and between species. These orthologous sequencescan be further analysed to evaluate protein family evolution, infer phylogenetic trees and toannotate protein function (Altenhoff et al., 2019). The initial sequence search step is classicallyperformed with the Basic Local Alignment Search Tool (blast) (Altschul et al., 1990) and dueto evolutionary constraints, in most cases protein coding sequences are compared betweentwo species. Downstream analysis use the resulting RBH to cluster sequence pairs and buildso-called orthologous groups like e.g.OrthoFinder(Emms & Kelly, 2015) and other tools.The CRBH algorithm was introduced byAubry et al.(2014) and builds upon the traditionalRBH approach to find additional orthologous sequences between two sets of sequences. Asdescribed earlier (Aubry et al., 2014;Scott, 2017), CRBH uses the sequence search results tofit an expect value (E-value) cutoff given each RBH to subsequently add sequence pairs tothe list of bona-fide orthologs given their alignment length.Unfortunately, as mentioned byScott(2017), the original implementation of CRBH (crb-blast)lag improved blast-like search algorithm to speed up the analysis. As a consequence,Scott(2017) ported CRBH to pythonshmlast, whileshmlastcannot deal with IUPAC nucleotidecode so far.CRBHitsconstitutes a new R package, which build upon previous implementations and portsCRBH into theRenvironment, which is popular among biologists.CRBHitsimprove CRBHby additional implemented filter steps (Rost, 1999) and the possibility to apply custom filtersprior E-value fitting. Further, the resulting CRBH pairs can be evaluated for the presence oftandem duplicated genes, gene order based syntenic groups and evolutionary rates

Time-resolved X-ray microscopy of nanoparticle aggregates under oscillatory shear

Of all current detection techniques with nanometer resolution, only X-ray microscopy allows imaging nanoparticles in suspension. Can it also be used to investigate structural dynamics? When studying response to mechanical stimuli, the challenge lies in applying them with precision comparable to spatial resolution. In the first shear experiments performed in an X-ray microscope, we accomplished this by inserting a piezo actuator driven shear cell into the focal plane of a scanning transmission X-ray microscope (STXM). Thus shear-induced reorganization of magnetite nanoparticle aggregates could be demonstrated in suspension. As X-ray microscopy proves suitable for studying structural change, new prospects open up in physics at small length scales.Comment: submitted to J. Synchrot. Radia

Frequency dependent deformation of liquid crystal droplets in an external electric field

Nematic drops suspended in the isotropic phase of the same substance were subjected to alternating electrical fields of varying frequency. The system was carefully kept in the isotropic-nematic coexistance region, which was broadened due to small amounts of non-mesogenic additives. Whereas the droplets remained spherical at low (order of 10 Hz) and high frequencies (in the kHz range), at intermediate frequencies, we observed a marked flattening of the droplet in the plane perpendicular to the applied field. The deformation of the liquid crystal (LC) droplets occurred both in substances with positive and negative dielectric anisotropy. The experimental data can be quantitatively modelled with a combination of the leaky dielectric model and screening of the applied electric field due to the finite conductivity.Comment: minor change

On the problem of mass-dependence of the two-point function of the real scalar free massive field on the light cone

We investigate the generally assumed inconsistency in light cone quantum field theory that the restriction of a massive, real, scalar, free field to the nullplane $\Sigma=\{x^0+x^3=0\}$ is independent of mass \cite{LKS}, but the restriction of the two-point function depends on it (see, e.g., \cite{NakYam77, Yam97}). We resolve this inconsistency by showing that the two-point function has no canonical restriction to $\Sigma$ in the sense of distribution theory. Only the so-called tame restriction of the two-point function exists which we have introduced in \cite{Ull04sub}. Furthermore, we show that this tame restriction is indeed independent of mass. Hence the inconsistency appears only by the erroneous assumption that the two-point function would have a (canonical) restriction to $\Sigma$.Comment: 10 pages, 2 figure

Five-Year NRHP Re-Evaluation of Historic Buildings Assessment

The Lawrence Livermore National Laboratory (LLNL) 'Draft Programmatic Agreement among the Department of Energy and the California State Historic Preservation Officer Regarding Operation of Lawrence Livermore National Laboratory' requires a review and re-evaluation of the eligibility of laboratory properties for the National Register of Historic Places (NRHP) every five years. The original evaluation was published in 2005; this report serves as the first five-year re-evaluation. This re-evaluation includes consideration of changes within LLNL to management, to mission, and to the built environment. it also determines the status of those buildings, objects, and districts that were recommended as NRHP-eligible in the 2005 report. Buildings that were omitted from the earlier building list, those that have reached 50 years of age since the original assessment, and new buildings are also addressed in the re-evaluation

Photoelectron spectra of anionic sodium clusters from time-dependent density-functional theory in real-time

We calculate the excitation energies of small neutral sodium clusters in the framework of time-dependent density-functional theory. In the presented calculations, we extract these energies from the power spectra of the dipole and quadrupole signals that result from a real-time and real-space propagation. For comparison with measured photoelectron spectra, we use the ionic configurations of the corresponding single-charged anions. Our calculations clearly improve on earlier results for photoelectron spectra obtained from static Kohn-Sham eigenvalues