A Kind of Affine Weighted Moment Invariants

A new kind of geometric invariants is proposed in this paper, which is called affine weighted moment invariant (AWMI). By combination of local affine differential invariants and a framework of global integral, they can more effectively extract features of images and help to increase the number of low-order invariants and to decrease the calculating cost. The experimental results show that AWMIs have good stability and distinguishability and achieve better results in image retrieval than traditional moment invariants. An extension to 3D is straightforward

Systematic alteration of ATAC-seq for profiling open chromatin in cryopreserved nuclei preparations from livestock tissues.

The use of Assay for Transposase-Accessible Chromatin (ATAC-seq) to profile chromatin accessibility has surged over the past years, but its applicability to tissues has been very limited. With the intent of preserving nuclear architecture during long-term storage, cryopreserved nuclei preparations from chicken lung were used to optimize ATAC-seq. Sequencing data were compared with existing DNase-seq, ChIP-seq, and RNA-seq data to evaluate library quality, ultimately resulting in a modified ATAC-seq method capable of generating high quality chromatin accessibility data from cryopreserved nuclei preparations. Using this method, nucleosome-free regions (NFR) identified in chicken lung overlapped half of DNase-I hypersensitive sites, coincided with active histone modifications, and specifically marked actively expressed genes. Notably, sequencing only the subnucleosomal fraction dramatically improved signal, while separation of subnucleosomal reads post-sequencing did not improve signal or peak calling. The broader applicability of this modified ATAC-seq technique was tested using cryopreserved nuclei preparations from pig tissues, resulting in NFR that were highly consistent among biological replicates. Furthermore, tissue-specific NFR were enriched for binding motifs of transcription factors related to tissue-specific functions, and marked genes functionally enriched for tissue-specific processes. Overall, these results provide insights into the optimization of ATAC-seq and a platform for profiling open chromatin in animal tissues

Hormad1 mutation disrupts synaptonemal complex formation, recombination, and chromosome segregation in mammalian meiosis

Meiosis is unique to germ cells and essential for reproduction. During the first meiotic division, homologous chromosomes pair, recombine, and form chiasmata. The homologues connect via axial elements and numerous transverse filaments to form the synaptonemal complex. The synaptonemal complex is a critical component for chromosome pairing, segregation, and recombination. We previously identified a novel germ cell-specific HORMA domain encoding gene, Hormad1, a member of the synaptonemal complex and a mammalian counterpart to the yeast meiotic HORMA domain protein Hop1. Hormad1 is essential for mammalian gametogenesis as knockout male and female mice are infertile. Hormad1 deficient (Hormad1-/-) testes exhibit meiotic arrest in the early pachytene stage, and synaptonemal complexes cannot be visualized by electron microscopy. Hormad1 deficiency does not affect localization of other synaptonemal complex proteins, SYCP2 and SYCP3, but disrupts homologous chromosome pairing. Double stranded break formation and early recombination events are disrupted in Hormad1-/- testes and ovaries as shown by the drastic decrease in the γH2AX, DMC1, RAD51, and RPA foci. HORMAD1 co-localizes with cH2AX to the sex body during pachytene. BRCA1, ATR, and γH2AX co-localize to the sex body and participate in meiotic sex chromosome inactivation and transcriptional silencing. Hormad1 deficiency abolishes γH2AX, ATR, and BRCA1 localization to the sex chromosomes and causes transcriptional de-repression on the X chromosome. Unlike testes, Hormad1-/- ovaries have seemingly normal ovarian folliculogenesis after puberty. However, embryos generated from Hormad1-/- oocytes are hyper- and hypodiploid at the 2 cell and 8 cell stage, and they arrest at the blastocyst stage. HORMAD1 is therefore a critical component of the synaptonemal complex that affects synapsis, recombination, and meiotic sex chromosome inactivation and transcriptional silencing. © 2010 Shin et al

An energy-preserving description of nonlinear beam vibrations in modal coordinates

AbstractConserved quantities are identified in the equations describing large-amplitude free vibrations of beams projected onto their linear normal modes. This is achieved by writing the geometrically exact equations of motion in their intrinsic, or Hamiltonian, form before the modal transformation. For nonlinear free vibrations about a zero-force equilibrium, it is shown that the finite-dimensional equations of motion in modal coordinates are energy preserving, even though they only approximate the total energy of the infinite-dimensional system. For beams with constant follower forces, energy-like conserved quantities are also obtained in the finite-dimensional equations of motion via Casimir functions. The duality between space and time variables in the intrinsic description is finally carried over to the definition of a conserved quantity in space, which is identified as the local cross-sectional power. Numerical examples are used to illustrate the main results

The evolution of the actin binding NET superfamily.

This is the final version of the article. Available from Frontiers Media via the DOI in this record.The Arabidopsis Networked (NET) superfamily are plant-specific actin binding proteins which specifically label different membrane compartments and identify specialized sites of interaction between actin and membranes unique to plants. There are 13 members of the superfamily in Arabidopsis, which group into four distinct clades or families. NET homologs are absent from the genomes of metazoa and fungi; furthermore, in plantae, NET sequences are also absent from the genome of mosses and more ancient extant plant clades. A single family of the NET proteins is found encoded in the club moss genome, an extant species of the earliest vascular plants. Gymnosperms have examples from families 4 and 3, with a hybrid form of NET1 and 2 which shows characteristics of both NET1 and NET2. In addition to NET3 and 4 families, the NET1 and pollen-expressed NET2 families are found only as independent sequences in Angiosperms. This is consistent with the divergence of reproductive actin. The four families are conserved across Monocots and Eudicots, with the numbers of members of each clade expanding at this point, due, in part, to regions of genome duplication. Since the emergence of the NET superfamily at the dawn of vascular plants, they have continued to develop and diversify in a manner which has mirrored the divergence and increasing complexity of land-plant species

Anti-inflammation activity and chemical composition of flower essential oil from Hedychium coronarium

Hedychium coronarium Koen. (Family Zingiberaceae), popularly named butterfly ginger, is widely available in tropical and subtropical regions. It has been used in folk medicine for many conditions, such as contusion inflammation, anti-rheumatic and so on. In this study, chemical compositions and anti-inflammatory activity of this flowers’ essential oil were investigated for the first time. Followed by GC–MS analysis, a total of 29 components were identified and the main constituents included -transocimenone (28.05%), linalool (18.52%), 1,8-cineole (11.35%), -terpineol (7.11%), 10-epi--eudesmol (6.06%), sabinene (4.59%) and terpinen-4-ol (3.17%). We measured the antioxidant activity of the essential oil in vitro (DPPH reduction assay and ferric reducing antioxidant power assay) and the antiinflammatory activity in vivo (carrageenan-induced hind paw edema in rats). The oil (100 mg/kg p.o.) produced significant inhibition of paw oedema, but showed poor antioxidant activity (with the DPPH IC50 value of 1091.00 g/ml and FRAP value of 0.22 mol Fe2+/mg). The results reveal that there is no direct correlation between anti-inflammatory effect and antioxidant activity of this essential oil

Tree Compression with Top Trees Revisited

We revisit tree compression with top trees (Bille et al, ICALP'13) and present several improvements to the compressor and its analysis. By significantly reducing the amount of information stored and guiding the compression step using a RePair-inspired heuristic, we obtain a fast compressor achieving good compression ratios, addressing an open problem posed by Bille et al. We show how, with relatively small overhead, the compressed file can be converted into an in-memory representation that supports basic navigation operations in worst-case logarithmic time without decompression. We also show a much improved worst-case bound on the size of the output of top-tree compression (answering an open question posed in a talk on this algorithm by Weimann in 2012).Comment: SEA 201

Factors governing microalgae harvesting efficiency by flocculation using cationic polymers.

This study aims to elucidate the mechanisms governing the harvesting efficiency of Chlorella vulgaris by flocculation using a cationic polymer. Flocculation efficiency increased as microalgae culture matured (i.e. 35-45, 75, and > 97% efficiency at early, late exponential, and stationary phase, respectively. Unlike the negative impact of phosphate on flocculation in traditional wastewater treatment; here, phosphorous residue did not influence the flocculation efficiency of C. vulgaris. The observed dependency of flocculation efficiency on growth phase was driven by changes in microalgal cell properties. Microalgal extracellular polymeric substances (EPS) in both bound and free forms at stationary phase were two and three times higher than those at late and early exponential phase, respectively. Microalgae cells also became more negatively charged as they matured. Negatively charged and high EPS content together with the addition of high molecular weight and positively charged polymer could facilitate effective flocculation via charge neutralisation and bridging