Microcanonical origin of the maximum entropy principle for open systems.
There are two distinct approaches for deriving the canonical ensemble. The canonical ensemble either follows as a special limit of the microcanonical ensemble or alternatively follows from the maximum entropy principle. We show the equivalence of these two approaches by applying the maximum entropy formulation to a closed universe consisting of an open system plus bath. We show that the target function for deriving the canonical distribution emerges as a natural consequence of partial maximization of the entropy over the bath degrees of freedom alone. By extending this mathematical formalism to dynamical paths rather than equilibrium ensembles, the result provides an alternative justification for the principle of path entropy maximization as well.

title: Protein structure prediction based on fragment assembly and parameter optimization.
abstract: We propose a novel method for ab-initio prediction of protein tertiary structures based on the fragment assembly and global optimization. Fifteen residue long fragment libraries are constructed using the secondary structure prediction method PREDICT, and fragments in these libraries are assembled to generate full-length chains of a query protein. Tertiary structures of 50 to 100 conformations are obtained by minimizing an energy function for proteins, using the conformational space annealing method that enables one to sample diverse low-lying local minima of the energy. Then in order to enhance the performance of the prediction method, we optimize the linear parameters of the energy function, so that the native-like conformations become energetically more favorable than the non-native ones for proteins with known structures. We test the feasibility of the parameter optimization procedure by applying it to the training set consisting of three proteins: the 10-55 residue fragment of staphylococcal protein A (PDB ID 1bdd), a designed protein betanova, and 1fsd.

title: Measures for the assessment of fuzzy predictions of protein secondary structure.
abstract: Many of the recent secondary structure prediction methods incorporate the idea of fuzzy set theory, where instead of assigning a definite secondary structure to a query residue, probability for the residue being in each of the conformational states is estimated. Moreover, continuous assignment of conformational states to the experimentally observed protein structures can be performed in order to reflect inherent flexibility. Although various measures have been developed for evaluating performances of secondary structure prediction methods, they depend only on the most probable secondary structures. They do not assess the accuracy of the probabilities produced by fuzzy prediction methods, and they cannot incorporate information contained in continuous assignments of conformational states to observed structures. Three important measures for evaluating performance of a secondary structure prediction algorithm, Q score, Segment OVerlap (SOV) measure, and the k-state correlation coefficient (Corr), are deformed into fuzzy measures F score, Fuzzy OVerlap (FOV) measure, and the fuzzy correlation coefficient (Forr), so that the new measures not only assess probabilistic outputs of fuzzy prediction methods, but also incorporate information from continuous assignments of secondary structure. As an example of application, prediction results of four fuzzy secondary structure prediction methods, PSIPRED, PROFking, SABLE, and PREDICT, are assessed using the new fuzzy measures.

title: Kinetic characterization of swelling of liquid crystalline phases of glyceryl monooleate
abstract: Research in this paper focuses on the kinetic evaluation of swelling of the liquid crystalline phases of glyceryl monooleate (GMO). Swelling of the lamellar and cubic liquid crystalline phases of GMO was studied using twoIn vitro methods, a total immersion method and a Franz cell method. The swelling of the lamellar phase and GMO having 0 %w/w initial water content was temperature dependent. The swelling ratio was greater at 20°C than 37°C. The water uptake increased dramatically with decreasing initial water content of the liquid crystalline phases. The swelling rates obtained using the Franz cell method with a moist nylon membrane to mimic buccal drug delivery situation were slower than the total immersion method. The swelling was studied by employing first-order and second-order swelling kinetics. The swelling of the liquid crystalline phases of GMO could be described by second-order swelling kinetics. The initial stage of the swelling (t < 4 h) followed the square root of time relationship, indicating that this model is also suitable for describing the water uptake by the liquid crystalline matrices. These results obtained from the current study demonstrate that the swelling strongly depends on temperature, the initial water content of the liquid crystalline phases and the methodology employed for measuring the swelling of GMO.

title: Microthermogravimetry using a microcantilever hot plate with integrated temperature-compensated piezoresistive strain sensors.
abstract: This paper reports thermogravimetric analysis of nanogram samples of paraffin using a microcantilever hot plate. The microcantilever hot plate has an integrated temperature-controlled heater and integrated temperature-compensated strain-sensing piezoresistors. The microcantilever vibration amplitude was measured using either a laser and a position sensitive photodiode, or using the piezoresistors. The cantilever resonance was measured as the cantilever was heated, such that the analyte mass could be measured as a function of temperature. Both optical and piezoresistive methods were employed to generate thermogravimetric curves for analytes in the range of 1-3 ng, and the results of the two methods compared well.

title: Target deconvolution techniques in modern phenotypic profiling.
abstract: The past decade has seen rapid growth in the use of diverse compound libraries in classical phenotypic screens to identify modulators of a given process. The subsequent process of identifying the molecular targets of active hits, also called 'target deconvolution', is an essential step for understanding compound mechanism of action and for using the identified hits as tools for further dissection of a given biological process. Recent advances in 'omics' technologies, coupled with in silico approaches and the reduced cost of whole genome sequencing, have greatly improved the workflow of target deconvolution and have contributed to a renaissance of 'modern' phenotypic profiling. In this review, we will outline how both new and old techniques are being used in the difficult process of target identification and validation as well as discuss some of the ongoing challenges remaining for phenotypic screening.

title: A shape constrained parametric active contour model for breast contour detection
abstract: Quantitative measures of breast morphology can help a breast cancer survivor to understand outcomes of reconstructive surgeries. One bottleneck of quantifying breast morphology is that there are only a few reliable automation algorithms for detecting the breast contour. This study proposes a novel approach for detecting the breast contour, which is based on a parametric active contour model. In addition to employing the traditional parametric active contour model, the proposed approach enforces a mathematical shape constraint based on the catenary curve, which has been previously shown to capture the overall shape of the breast contour reliably . The mathematical shape constraint regulates the evolution of the active contour and helps the contour evolve towards the breast, while minimizing the undesired effects of other structures such as, the nipple/areola and scars. The efficacy of the proposed approach was evaluated on anterior posterior photographs of women who underwent or were scheduled for breast reconstruction surgery including autologous tissue reconstruction. The proposed algorithm shows promising results for detecting the breast contour.

title: Effect of ultrasonic attenuation on the feasibility of acoustic tweezers.
abstract: A modified mathematical formulation for the calculation of axial radiation force was developed to incorporate the effect of ultrasonic attenuation. Axial forces, Fresnel coefficients, average internal attenuation factors and effective internal reflection coefficients were calculated. Thermal and mechanical indices were also computed to address the safety issues in the implementation of acoustic tweezers and were found to be negligible. The results show that the overall distribution of axial forces is barely affected by attenuation. Furthermore, it is found that attenuation actually works against the scattering force and may therefore reinforce the axial trapping force. For a particle size of 180 microm, the maximum trapping force increases from 29.8 x 10(-11) N to 30.3 x 10(-11) N by 1.7% when attenuation is included. In light of these results, it appears that acoustic tweezers may still be feasible beyond the focal point even under the influence of attenuation.