Removing data and using metafounders alleviates biases for all traits in Lacaune dairy sheep predictions

Bias in dairy genetic evaluations, when it exists, has to be understood and properly addressed. The origin of biases is not always clear. We analyzed 40 yr of records from the Lacaune dairy sheep breeding program to evaluate the extent of bias, assess possible corrections, and emit hypotheses on its origin. The data set included 7 traits (milk yield, fat and protein contents, somatic cell score, teat angle, udder cleft, and udder depth) with records from 600,000 to 5 million depending on the trait,-1,900,000 animals, and-5,900 genotyped elite artificial insemination rams. For the-8% animals with missing sire, we fit 25 unknown parent groups. We used the linear regression method to compare "partial" and "whole" predictions of young rams before and after progeny testing, with 7 cut-off points, and we obtained estimates of their bias, (over)dispersion, and accuracy in early proofs. We tried (1) several scenarios as follows: multiple or single trait, the "official" (routine) evalua-tion, which is a mixture of both single and multiple trait, and "deletion" of data before 1990; and (2) sev-eral models as follows: BLUP and single-step genomic (SSG)BLUP with fixed unknown parent groups or metafounders, where, for metafounders, their relation-ship matrix gamma was estimated using either a model for inbreeding trend, or base allele frequencies esti-mated by peeling. The estimate of gamma obtained by modeling the inbreeding trend resulted in an estimated increase of inbreeding, based on markers, faster than the pedigree-based one. The estimated genetic trends were similar for most models and scenarios across all traits, but were shrunken when gamma was estimated by peeling. This was due to shrinking of the estimates of metafounders in the latter case. Across scenarios, all traits showed bias, generally as an overestimate of genetic trend for milk yield and an underestimate for the other traits. As for the slope, it showed overdisper-sion of estimated breeding values for all traits. Using multiple-trait models slightly reduced the overestimate of genetic trend and the overdispersion, as did including genomic information (i.e., SSGBLUP) when the gam-ma matrix was estimated by the model for inbreeding trend. However, only deletion of historical data before 1990 resulted in elimination of both kind of biases. The SSGBLUP resulted in more accurate early proofs than BLUP for all traits. We considered that a snowball ef-fect of small errors in each genetic evaluation, combined with selection, may have resulted in biased evaluations. Improving statistical methods reduced some bias but not all, and a simple solution for this data set was to remove historical records

Two and three-dimensional oscillons in nonlinear Faraday resonance

We study 2D and 3D localised oscillating patterns in a simple model system exhibiting nonlinear Faraday resonance. The corresponding amplitude equation is shown to have exact soliton solutions which are found to be always unstable in 3D. On the contrary, the 2D solitons are shown to be stable in a certain parameter range; hence the damping and parametric driving are capable of suppressing the nonlinear blowup and dispersive decay of solitons in two dimensions. The negative feedback loop occurs via the enslaving of the soliton's phase, coupled to the driver, to its amplitude and width.Comment: 4 pages; 1 figur

Ultraviolet photoelectron spectroscopy of Nb − 4 to Nb − 200

Abstract. We present UV (hν = 6.42 eV) photoelectron spectra of niobium cluster anions Nb − n in the size range from n = 4 to n = 200. The spectra exhibit a variety of patterns, which can be related to the geometrical structures of the clusters. The charging energies of the larger clusters are in very good agreement with the metallic sphere model. Nevertheless a strong size dependence of the work function is observed, which underlines the special properties of this transition metal. PACS. 33.60.Cv Ultraviolet and vacuum ultraviolet photoelectron spectra -36.40.Cg Electronic and magnetic properties of clusters -73.22.-f Electronic structure of nanoscale materials

Is the Unitarity of the quark-mixing-CKM-matrix violated in neutron β\beta-decay?

We report on a new measurement of neutron $\beta$-decay asymmetry. From the result \linebreak $A_0$ = -0.1189(7), we derive the ratio of the axial vector to the vector coupling constant $\lambda$ = ${\it g_A/g_V}$ = -1.2739(19). When included in the world average for the neutron lifetime $\tau$ = 885.7(7)s, this gives the first element of the Cabibbo-Kobayashi-Maskawa (CKM) matrix $V_{ud}$. With this value and the Particle Data Group values for $V_{us}$ and $V_{ub}$, we find a deviation from the unitarity condition for the first row of the CKM matrix of $\Delta$ = 0.0083(28), which is 3.0 times the stated error

Practical computational toolkits for dendrimers and dendrons structure design

Dendrimers and dendrons offer an excellent platform for developing novel drug delivery systems and medicines. The rational design and further development of these repetitively branched systems are restricted by difficulties in scalable synthesis and structural determination, which can be overcome by judicious use of molecular modelling and molecular simulations. A major difficulty to utilise in silico studies to design dendrimers lies in the laborious generation of their structures. Current modelling tools utilise automated assembly of simpler dendrimers or the inefficient manual assembly of monomer precursors to generate more complicated dendrimer structures. Herein we describe two novel graphical user interface (GUI) toolkits written in Python that provide an improved degree of automation for rapid assembly of dendrimers and generation of their 2D and 3D structures. Our first toolkit uses the RDkit library, SMILES nomenclature of monomers and SMARTS reaction nomenclature to generate SMILES and mol files of dendrimers without 3D coordinates. These files are used for simple graphical representations and storing their structures in databases. The second toolkit assembles complex topology dendrimers from monomers to construct 3D dendrimer structures to be used as starting points for simulation using existing and widely available software and force fields. Both tools were validated for ease-of-use to prototype dendrimer structure and the second toolkit was especially relevant for dendrimers of high complexity and size.Peer reviewe

Cymantrene–Triazole "Click" Products: Structural Characterization and Electrochemical Properties

We report the first known examples of triazole-derivatized cymantrene complexes (η5-[4-substituted triazol-1-yl]cyclopentadienyl)tricarbonylmanganese(I), obtained via a “click” chemical synthesis, bearing a phenyl, 3-aminophenyl, or 4-aminophenyl moiety at the 4-position of the triazole ring. Structural characterization data using multinuclear NMR, UV–vis, ATR-IR, and mass spectrometric methods are provided, as well as crystallographic data for (η5-[4-phenyltriazol-1-yl]cyclopentadienyl)tricarbonylmanganese(I) and (η5-[4-(3-aminophenyl)triazol-1-yl]cyclopentadienyl)tricarbonylmanganese(I). Cyclic voltammetric characterization of the redox behavior of each of the three cymantrene–triazole complexes is presented together with digital simulations, in situ infrared spectroelectrochemistry, and DFT calculations to extract the associated kinetic and thermodynamic parameters. The trypanocidal activity of each cymantrene–triazole complex is also examined, and these complexes are found to be more active than cymantrene alone

Dendrimer-Based Fluorescent Indicators: In Vitro and In Vivo Applications

BACKGROUND: The development of fluorescent proteins and synthetic molecules whose fluorescence properties are controlled by the environment makes it possible to monitor physiological and pathological events in living systems with minimal perturbation. A large number of small organic dyes are available and routinely used to measure biologically relevant parameters. Unfortunately their application is hindered by a number of limitations stemming from the use of these small molecules in the biological environment. PRINCIPAL FINDINGS: We present a novel dendrimer-based architecture leading to multifunctional sensing elements that can overcome many of these problems. Applications in vitro, in living cells and in vivo are reported. In particular, we image for the first time extracellular pH in the brain in a mouse epilepsy model. CONCLUSION: We believe that the proposed architecture can represent a useful and novel tool in fluorescence imaging that can be widely applied in conjunction with a broad range of sensing dyes and experimental setups

Wave patterns generated by an axisymmetric obstacle in a two-layer flow

Gravity waves generated by a moving obstacle in a two-layer stratified fluid are investigated. The experimental configuration is three-dimensional with an axisymmetric obstacle which is towed in one of the two layers. The experimental method used in the present study is based on a stereoscopic technique allowing the 3D reconstruction of the interface between the two layers. Investigation into the wave pattern as a function of the Froude number, Fr, based on the relative density of the fluid layers and the velocity of the towed obstacle is presented. Specific attention is paid to the transcritical regime for which Fr is close to one. Potential energy trapped in the wave field patterns is also extracted from the experimental results and is analyzed as a function of both the Froude number, Fr, and the transcritical similarity parameter Γ. In particular, a remarkable increase in the potential energy around Fr = 1 is observed and a scaling allowing to assemble data resulting from different experimental parameters is proposed

Dendrimers in Nanoscale Confinement: The Interplay between Conformational Change and Nanopore Entrance

Hyperbranched dendrimers are nanocarriers for drugs, imaging agents, and catalysts. Their nanoscale confinement is of fundamental interest and occurs when dendrimers with bioactive payload block or pass biological nanochannels or when catalysts are entrapped in inorganic nanoporous support scaffolds. The molecular process of confinement and its effect on dendrimer conformations are, however, poorly understood. Here, we use single-molecule nanopore measurements and molecular dynamics simulations to establish an atomically detailed model of pore dendrimer interactions. We discover and explain that electrophoretic migration of polycationic PAMAM dendrimers into confined space is not dictated by the diameter of the branched molecules but by their size and generation-dependent compressibility. Differences in structural flexibility also rationalize the apparent anomaly that the experimental nanopore current read-out depends in nonlinear fashion on dendrimer size. Nanoscale confinement is inferred to reduce the protonation of the polycationic structures. Our model can likely be expanded to other dendrimers and be applied to improve the analysis of biophysical experiments, rationally design functional materials such as nanoporous filtration devices or nanoscale drug carriers that effectively pass biological pores

Squalene epoxidase, located on chromosome 8q24.1, is upregulated in 8q+ breast cancer and indicates poor clinical outcome in stage I and II disease

Gains of chromosomes 7p and 8q are associated with poor prognosis among oestrogen receptor-positive (ER+) stage I/II breast cancer. To identify transcriptional changes associated with this breast cancer subtype, we applied suppression subtractive hybridisation method to analyse differentially expressed genes among six breast tumours with and without chromosomal 7p and 8q gains. Identified mRNAs were validated by real-time RT–PCR in tissue samples obtained from 186 patients with stage I/II breast cancer. Advanced statistical methods were applied to identify associations of mRNA expression with distant metastasis-free survival (DMFS). mRNA expression of the key enzyme of cholesterol biosynthesis, squalene epoxidase (SQLE, chromosomal location 8q24.1), was associated with ER+ 7p+/8q+ breast cancer. Distant metastasis-free survival in stage I/II breast cancer cases was significantly inversely related to SQLE mRNA in multivariate Cox analysis (P<0.001) in two independent patient cohorts of 160 patients each. The clinically favourable group associated with a low SQLE mRNA expression could be further divided by mRNA expression levels of the oestrogen-regulated zinc transporter LIV-1. The data strongly support that SQLE mRNA expression might indicate high-risk ER+ stage I/II breast cancers. Further studies on tumour tissue from standardised treated patients, for example with tamoxifen, may validate the role of SQLE as a novel diagnostic parameter for ER+ early stage breast cancers