Phylo-mLogo: an interactive and hierarchical multiple-logo visualization tool for alignment of many sequences

BACKGROUND: When aligning several hundreds or thousands of sequences, such as epidemic virus sequences or homologous/orthologous sequences of some big gene families, to reconstruct the epidemiological history or their phylogenies, how to analyze and visualize the alignment results of many sequences has become a new challenge for computational biologists. Although there are several tools available for visualization of very long sequence alignments, few of them are applicable to the alignments of many sequences. RESULTS: A multiple-logo alignment visualization tool, called Phylo-mLogo, is presented in this paper. Phylo-mLogo calculates the variabilities and homogeneities of alignment sequences by base frequencies or entropies. Different from the traditional representations of sequence logos, Phylo-mLogo not only displays the global logo patterns of the whole alignment of multiple sequences, but also demonstrates their local homologous logos for each clade hierarchically. In addition, Phylo-mLogo also allows the user to focus only on the analysis of some important, structurally or functionally constrained sites in the alignment selected by the user or by built-in automatic calculation. CONCLUSION: With Phylo-mLogo, the user can symbolically and hierarchically visualize hundreds of aligned sequences simultaneously and easily check the changes of their amino acid sites when analyzing many homologous/orthologous or influenza virus sequences. More information of Phylo-mLogo can be found at URL

On character table of Clifford groups

Based on a presentation of $\mathcal{C}_n$ and the help of [GAP], we construct the character table of the Clifford group $\mathcal{C}_n$ for $n=1,2,3$. As an application, we can efficiently decompose the (higher power of) tensor product of the matrix representation in those cases. Our results recover some known results in [HWW, WF] and reveal some new phenomena. We prove that the trivial character is the only linear character for $\mathcal{C}_n$ and hence $\mathcal{C}_n$ equals to its commutator subgroup when $n\geq 3$. A few conjectures about $\mathcal{C}_n$ for general $n$ are proposed.Comment: 13 pages; comments and suggestions are welcom

Classification of entomological origin of honey based on its physicochemical and antioxidant properties

Physicochemical and antioxidant properties of raw honeys from Malaysia were used as markers for determining its entomological source of bee species of Apis dorsata, Apis mellifera, Apis cerana, or Heterotrigona itama. Physicochemical properties of moisture content, water activity, specific gravity, viscosity, pH, free acidity, electrical conductivity, colour (L*, a* and b*), colour intensity, and antioxidant properties including the DPPH free radical scavenging activity power (1/IC50), ascorbic acid equivalent antioxidant content (AEAC), ferric ion reducing antioxidant power (FRAP), and total phenolic content (TPC) were measured and analysed. Honeys were classified into two major groups of those from honey bees (Apis spp.) and Trigona stingless bees (Heterotrigona itama) from its physicochemical and antioxidant properties using hierarchical cluster and principal component analyses. The Kelulut honey produced by stingless bees, Heterotrigona itama was differentiable from honeys from the regular honey bee species, the Apis spp. with characteristics of high moisture content of 33.24 g/100 g, free acidity of 136.8 meq/kg, colour intensity of 990.3 mAU, AEAC of 26.64 mg/100 g, and FRAP of 41.95 mg AAE/100 g. Honey classification by its entomological origin helps in honey identification and it reduces honey fraudulence

Effect of post-thermal treatment on the density profile of rubberwood particleboard and its relation to mechanical properties

The objective of the study was to investigate the effect of heat treatment on the changes in density profile of rubberwood particleboard samples. The relationship between density profile and mechanical properties of particleboard samples was determined using regression analysis. Single layer particleboard made from rubberwood particles with dimensions of 340 mm × 340 mm × 12 mm and targeted density of 700 kg m-3 was heat-treated using oven and hot press at three different temperature levels, namely, 100, 150 and 200 °C for 30 min. All density profile attributes were significantly affected by heat treatment. Bending properties, internal bond strength and hardness were influenced by treatment temperature. However, samples treated using hot press had better mechanical properties compared with those treated using oven. Mean and peak densities exerted profound effects on mechanical properties of the samples

Properties of particleboard with oil palm trunk as core layer in comparison to three-layer rubberwood particleboard

Compaction ratio is highly dependent on the density of the wood materials used in the production of particleboard. Lower density wood materials will produce particleboard with higher compaction ratio and is believed to give better properties. The objective of this study was to evaluate the properties of threelayer particleboard made from rubberwood and oil palm trunk with different bulk density as the core layer, while the rubberwood fine particles served as surface layers for both types of particleboard. This study also investigated the effect of shelling ratios on the mechanical and physical properties of the threelayer particleboard. Melamine-fortified urea formaldehyde (UF) resin was used as the binder. The modulus of rupture (MOR), internal bond strength (IB) and thickness swelling (TS) of the particleboards were evaluated based on the Japanese Industrial Standard for particleboard (JIS A 5908:2003). The results showed that both species and shelling ratios are variables that influenced the mechanical and physical properties of the particleboard. Despite its lower compaction ratio, particleboard made from rubberwood alone had better strength properties and dimensional stability than particleboard made from a mixture of rubberwood and oil palm trunk

Thermal treatment of wood using vegetable oils: a review

Wood is an ideal building material as it is renewable and green. However, low dimensional stability and durability might restrict its usage in structural application. Therefore, modification is needed to improve the aforementioned issues. As an environmentally friendly wood modification method, heat treatment of wood using oil as a heating medium has brought to researcher’s attention to the fact that it might serve as an excellent treatment procedure in treating wood. This paper presents a review about the effects of oil heat treatment on the properties of wood such as colour stability, dimensional stability, mechanical strength and durability against termites and fungi as well as its potential to be used as construction and building materials. The pros and cons of using oil as a heating medium in wood treatment are discussed. This review shows discrepancies between the treatment methods or procedures and its resultant findings. Moreover, the effectiveness of the treatment is governed by several factors such as the type of oils used and wood species. The objective of the present paper is to conduct a review of the published literatures regarding the properties of wood modified by oil heat treatment and the results obtained were compared systematically

Thermal treatment of wood using vegetable oils: a review

Wood is an ideal building material as it is renewable and green. However, low dimensional stability and durability might restrict its usage in structural application. Therefore, modification is needed to improve the aforementioned issues. As an environmentally friendly wood modification method, heat treatment of wood using oil as a heating medium has brought to researcher’s attention to the fact that it might serve as an excellent treatment procedure in treating wood. This paper presents a review about the effects of oil heat treatment on the properties of wood such as colour stability, dimensional stability, mechanical strength and durability against termites and fungi as well as its potential to be used as construction and building materials. The pros and cons of using oil as a heating medium in wood treatment are discussed. This review shows discrepancies between the treatment methods or procedures and its resultant findings. Moreover, the effectiveness of the treatment is governed by several factors such as the type of oils used and wood species. The objective of the present paper is to conduct a review of the published literatures regarding the properties of wood modified by oil heat treatment and the results obtained were compared systematically