BiOSS: A system for biomedical ontology selection

In biomedical informatics, ontologies are considered a key technology for annotating, retrieving and sharing the huge volume of publicly available data. Due to the increasing amount, complexity and variety of existing biomedical ontologies, choosing the ones to be used in a semantic annotation problem or to design a specific application is a difficult task. As a consequence, the design of approaches and tools addressed to facilitate the selection of biomedical ontologies is becoming a priority. In this paper we present BiOSS, a novel system for the selection of biomedical ontologies. BiOSS evaluates the adequacy of an ontology to a given domain according to three different criteria: (1) the extent to which the ontology covers the domain; (2) the semantic richness of the ontology in the domain; (3) the popularity of the ontology in the biomedical community. BiOSS has been applied to 5 representative problems of ontology selection. It also has been compared to existing methods and tools. Results are promising and show the usefulness of BiOSS to solve real-world ontology selection problems. BiOSS is openly available both as a web tool and a web service.     

Synthesis of SBS thermoplastic block copolymers in cyclohexane in the presence of diethylether used as a structure modifier

Diethylether (DEE) was used as a structure modifier during the synthesis of linear styrene-butadiene block copolymers of poly A-block-polyB-block-polyA type (SBS). The microstructures of synthesized polymers were analyzed, and the effect of DEE on polymerization kinetics was studied. Addition of DEE at 2 wt% concentration results in the highest styrene polymerization rate, while addition at 6 wt% concentration gives the highest butadiene polymerization rate. The vinyl content of the polybutadiene portion increases from 14 to 47% with an increase in the DEE concentration from 500 ppm to 10 wt% while thetrans- l,4 andcis-1,4 isomers decrease. For SBS polymer synthesized via a sequential method, the addition of DEE as a structure modifier minimizes the crossover deficiency which would otherwise result in a skewed molecular weight distribution with a higher polydispersity. For SBS polymers made via a coupling method, the coupling efficiency appears to be constant in a range of DEE concentration from 500 ppm to 1 wt% before declining with a further increase in DEE.     

Effects of neutral solvent addition on the body-centered cubic spheres of block copolymers

We employ self-consistent mean-field (SCMF) theory in studying the body-centered cubic (bcc) spheres of block copolymers in the presence of a neutral solvent. First we examine the accuracy of the dilution approximation then analyze the dependence of the bcc structural sizes with copolymer volume fraction ?, the interaction parameter χ_AB, and degree of copolymerization N. Our results reveal that both distribution of each component and the micro-structural length scales are greatly influenced by each parameter ?, χ_AB, and N. As expected, with decreasing ?, more solvent distributes non-uniformally in the segregated domains, therefore deviation from the dilution approximation increases. This also suggests that when the effective segregation parameter ?χ_ABN is fixed, a larger deviation is expected as χ_ABN increases (i.e. ? decreases). Although when both χ_ABN and ? are fixed, decreasing N (i.e. increasing χ_AB) enlarges the deviation from the dilution approximation. Furthermore, this solvent non-uniformity behavior is so significant that it even affects the dependence of the domain spacing L^* and the matrix length Λ^* with respect to (χ_AB)_effN=?χ_ABN near the ODT. When the systems are in molten state and/or in the concentrated regime, both L^* and Λ^* exhibit a sharp increase behavior as ODT is approached, due to many of the minority blocks being pulled from the spherical domains and swelling the matrix. With increasing solvent amount and/or χ_ABN, we observe that the increase of the degree for the minority blocks pulled from the spheres into the matrix near the ODT is not as significant as that in the melt. As such, the sharp increase behavior in L^* as well as Λ^* near the ODT smoothens and even disappears.     

Crystallization behavior of oxyethylene/oxybutylene diblock and triblock copolymers

The crystallization behavior of poly(oxyethylene)-b-poly(oxybutylene) block copolymers with different compositions, morphologies and architectures (E_mB_n diblock copolymers and E_mB_nE_m, B_nE_mB_n triblock copolymers) were investigated and the effect of volume fraction and architecture on the crystallization temperature (T_c) in non-isothermal crystallization was determined. It is found that the E_mB_n diblock copolymers having long E blocks exhibit similar crystallization temperatures, irrespective of volume fraction and morphology, but for the block copolymers with shorter E blocks the crystallization temperature increases with both the volume fraction, φ_E, and the length, m, of the E block. Some block copolymers with extremely low T_c, which fall into the temperature range normally associated with homogenous nucleation, were chosen for time-resolved small-angle X-ray scattering (SAXS) and isothermal crystallization kinetics experiments. The results show that breakout crystallization occurs in all these block copolymers. Therefore, unlike E_mB_n/B_h blends, there is no obvious relationship between T_c and crystallization behavior in neat block copolymers and homogeneous nucleation does not definitely lead to confined crystallization. The values of χ_c/χ_ODT for all the block copolymers with hex and bcc morphology were also calculated. It is found that all the block copolymers have χ_c/χ_ODT<3, in agreement with the previously reported critical value and consistent with their breakout crystallization behavior.     

Amelioration of mechanical brittleness in hyperbranched polymer. 1. Macroscopic evaluation by dynamic viscoelastic relaxation

Hyperbranched poly(ether ketone)-b-linear poly(ether ketone)-b-hyperbranched poly(ether ketone) (HLHPEK) triblock copolymers with two different block compositions were prepared as an approach to improve the mechanical brittleness of hyperbranched poly(ether ketone) (HPEK). From the time-temperature superposition of dynamic shear moduli, G′(ω) and G″(ω), of HPEK and two HLHPEKs, it was investigated that the junction points between G′(ω) and G″(ω) shifted to the higher frequencies and the rubbery plateau region spread wider over the reduced frequency axis as the linear blocks were introduced and their compositions were increased. Such changes in viscoelastic response were consequences of increase in the amount of chain entanglements additionally formed by the linear blocks. In order to verify the effect of the linear block incorporation on amelioration of the mechanical brittleness, the degree of brittleness and its improvement were evaluated from the temperature dependence of the shift factors, a_Ts, experimentally obtained during the superposition of the dynamic moduli and of the average viscoelastic relaxation times, τ_HNs, determined with empirical Havriliak-Negami distribution function. From the nonlinear curve fittings of the a_Ts and the τ_HNs by the Vogel-Tamman-Fulcher equation, the degree of brittleness for HPEK and HLHPEK triblock copolymers were quantified as values of the material parameter D, an indicative of deviation from the linear Arrhenius behavior and a measure of fragility of the given material. The tendency of increasing D values with the linear block compositions confirmed substantial improvement of the mechanical brittleness in the HLHPEK triblock copolymers compared to HPEK. Therefore, the approach to copolymerize HPEK with its chemically analogous linear counterpart was verified to be an effective strategy to impart molecular entanglements and hence ameliorate the mechanical brittleness on the basis of macroscopic rheological evaluation.     

A block copolymer nanotemplate for mechanically tunable polarized emission from a conjugated polymer

A polymer blend system consisting of polystyrene grafted onto poly (p-phenylene ethynylene) (PS-g-PPE) and poly (styrene-block-isoprene-block-styrene) triblock copolymer (SIS) yields highly polarized emission due to the unidirectional alignment of the PPE molecules. During the roll casting, the triblock copolymer microphase separates and creates unidirectionally aligned PS cylindrical microdomains in the rubbery PI matrix. PPE, a fluorescent conjugated polymer, was grafted with polystyrene (PS) side chains that enabled sequestration and alignment of these rigid backbone emitter molecules into the PS microdomains of the SIS triblock copolymer. Deforming the thermoplastic elastomer in a direction perpendicular to the orientation direction of the cylinders causes rotation of the PS cylinders and the PPE emitter molecules and affords tunable polarized emission due to re-orientation of the PPE containing PS cylinders as well as film thinning from Poisson effect.     

Viscoelastic Behavior, Thermodynamic Compatibility, and Phase Equilibria in Block Copolymer-Based Pressure-Sensitive Adhesives

The viscoelastic behavior, thermodynamic compatibility, and phase equilibria in block copolymer-based pressure-sensitive adhesives were investigated. The block copolymers investigated were: (1) polystyrene-block-polybutadiene-block-polystyrene (SBS) copolymer (KRATON® D-1102, Shell Development Company) and (2) polystyrene-block-polyisoprene-block-polystyrene (SIS) copolymer (KRATON® D-1107, Shell Development Company). The tackifying resins investigated were: (1) WINGTACK® 86 (Goodyear Tire & Rubber Company) and (2) PICCOTAC® 95BHT (Hercules Inc.). Samples of various compositions were prepared by a solution-casting method with toluene as solvent. Measurements of dynamic storage modulus (G'), dynamic loss modulus (G'), and loss tangent (tan δ) were taken, using a Rheometrics Mechanical Spectrometer. It was found that: (1) both WINGTACK 86 and PICCOTAC 95BHT were equally effective in decreasing the plateau modulus (G^O_N), and increasing the glass transition temperature (T_g) of the polyisoprene midblock of KRATON 1107; and (2) WINGTACK 86 was very effective in decreasing the G^O_N and increasing the T_g of the polybutadiene midblock of KRATON 1102, whereas PICCOTAC 95BHT was not. The observed difference between WINGTACK 86 and PICCOTAC 95BHT in decreasing the G^O_N and increasing the T_g of the polybutadiene midblock of KRATON 1102, whereas PICCOTAC 95BHT was not. The observed difference between WINGTACK 86 and PICCOTAC 95BHT in decreasing the G^O_N and increasing the T_g of the polybutadiene midblock of KRATON 1102 (perhaps to SBS block copolymers in general) is explained by the values of the interaction parameter for WINGTACK 86 and KRATON 1102, and for PICCOTAC 95BHT and KRATON 1102. The interaction parameter was determined, using the piezoelectric quartz sorption method. Phase diagrams were constructed for the four block copolymer/tackifying resin systems investigated, using information obtained from both dynamic viscoelastic measurements and optical microscopy. It was found that when mixed with KRATON 1102, PICCOTAC 95BHT formed separate domains whereas WINGTACK 86 did not over the range of concentrations and temperatures investigated. This confirms the evidence obtained from two other independent experimental techniques, namely, dynamic viscoelastic measurements and the piezo-electric sorption method. We have concluded from the present study that PICCOTAC 95BHT is not as an effective tackifying resin as WINGTACK 86, when each is mixed with KRATON 1102. It is pointed out further that information on the order-disorder transition temperature T_r, which was determined from a rheological technique proposed by us, is valuable in determining optimal processing conditions for block copolymer-based pressure-sensitive adhesives.     

Gradient orientation pattern matching with the Hamming distance

This paper presents a novel pattern matching technique that is robust to illumination changes and the occlusion problem. The technique is based on the matching of gradient orientations in place of traditional image features such as intensities or gradients. Gradient orientations depend on the texture in an image. They are known to be insensitive to changes of image intensities that are often caused by time-varying illuminations or the auto-gain control (AGC) function of the camera. Moreover,the proposed method employs a voting strategy in the process of matching gradient orientations. The method works remarkably well even when a large part of the pattern is occluded with a foreign object. Consequently, the proposed method is robust to both irregular lighting conditions and the occlusion problem.     

Ontology-based similarity for product information retrieval

Product development of today is becoming increasingly knowledge intensive. Specifically, design teams face considerable challenges in making effective use of increasing amounts of information. In order to support product information retrieval and reuse, one approach is to use case-based reasoning (CBR) in which problems are solved “by using or adapting solutions to old problems.” In CBR, a case includes both a representation of the problem and a solution to that problem. Case-based reasoning uses similarity measures to identify cases which are more relevant to the problem to be solved. However, most non-numeric similarity measures are based on syntactic grounds, which often fail to produce good matches when confronted with the meaning associated to the words they compare. To overcome this limitation, ontologies can be used to produce similarity measures that are based on semantics. This paper presents an ontology-based approach that can determine the similarity between two classes using feature-based similarity measures that replace features with attributes. The proposed approach is evaluated against other existing similarities. Finally, the effectiveness of the proposed approach is illustrated with a case study on product–service–system design problems.