A derivation of the master equation from path entropy maximization.
The master equation and, more generally, Markov processes are routinely used as models for stochastic processes. They are often justified on the basis of randomization and coarse-graining assumptions. Here instead, we derive nth-order Markov processes and the master equation as unique solutions to an inverse problem. We find that when constraints are not enough to uniquely determine the stochastic model, an nth-order Markov process emerges as the unique maximum entropy solution to this otherwise underdetermined problem. This gives a rigorous alternative for justifying such models while providing a systematic recipe for generalizing widely accepted stochastic models usually assumed to follow from the first principles.

title: Exact partition function zeros of the Wako-Saitô-Muñoz-Eaton β hairpin model.
abstract: I compute exact partition function zeros of β hairpins, using both analytic and numerical methods, extending previous work  where only a restricted class of hairpins was considered. The zeros of β hairpins with an odd number of peptide bonds are computed and the difference of the distribution of zeros from those for an even number of peptide bonds is explained in terms of additional entropy of liberating the extra bond at the turn region. Upon the introduction of a hydrophobic core in the central region of the hairpin, the zeros are distributed uniformly on two concentric circles corresponding to the hydrophobic collapse and the transition to the fully folded conformation. One of the circles dissolves as the core moves toward the turn or the tip region, which is explained in terms of the similarity of the intermediate state with the folded or unfolded states. The exact partition function zeros for a hairpin with a more complex structure of native contacts, the 16 C-terminal residues of streptococcal protein G B1, are numerically computed and their loci are closely approximated by concentric circles.

title: Microcanonical origin of the maximum entropy principle for open systems.
abstract: 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: Unbiased global optimization of Lennard-Jones clusters for N < or =201 using the conformational space annealing method.
abstract: We apply the conformational space annealing method to the Lennard-Jones clusters and find all known lowest energy configurations up to 201 atoms, without using extra information of the problem such as the structures of the known global energy minima. In addition, the robustness of the algorithm with respect to the randomness of initial conditions of the problem is demonstrated by ten successful independent runs up to 183 atoms. Our results indicate that this method is a general and yet efficient global optimization algorithm applicable to many systems.

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: Surgical management of pediatric adhesive bowel obstruction.
abstract: The objective of this study was to analyze a population-based database for recent trends in surgical management of pediatric adhesive bowel obstruction and compare open versus laparoscopic lysis of adhesions (LOA).



Pediatric adhesive bowel obstruction cases were identified in the Kids' Inpatients Database from 1997, 2000, 2003, 2006, and 2009. Data analysis included patients' demographics, hospital variables, length of stay (LOS), and total hospital charges (THC). Complications analysis included postoperative shock, hemorrhage, hematoma, seroma, wound complications, infection, fistula, and pulmonary complications.



In total, 20,679 pediatric adhesive bowel obstruction cases were identified during the study period. These were characterized by a median age of 11 years old, with 59.0% of the population female. Overall treatment included 88.6% open and 11.4% laparoscopic LOA. A more than twofold increase in utilization of laparoscopy was observed from 7.2% in 1997 to 17.2% in 2009 (P<.001). Complication rates were lower for laparoscopic LOA versus open (5.6% versus 10.4%; odds ratio 0.512; 95% confidence interval 0.394-0.667; P<.001), especially accidental puncture or laceration rate (2.2% versus 3.9%; odds ratio 0.566; 95% confidence interval 0.375-0.854; P=.006). Conversion to open LOA occurred in 1.9%. Laparoscopy was associated with a shorter median LOS (6 versus 8 days; P<.001) and a lower mean THC ($38,241.11 versus $48,552.51; P<.001) compared with open LOA. Multivariate regression analysis did not find hospital bed size, location, teaching status, and regions to be statistically significant predictors for utilization of laparoscopy.



Laparoscopic LOA is a safe option for pediatric adhesive bowel obstruction with lower complication rates and a reduced economic burden. Despite the increase in utilization of laparoscopy in recent years, only a minority of patients underwent laparoscopic LOA. Further studies are needed to identify and characterize the subgroup of patients who benefit from laparoscopic LOA.

title: Vessel Diameter Measurement from Intravital Microscopy
abstract: The blood vessel diameter is often measured in microcirculation studies to quantify the effects of various stimuli. Intravital video microscopy is used to measure the change in vessel diameter by first recording the video and analyzing it using electronic calipers or by using image shearing technique. Manual measurement using electronic calipers or image shearing is time-consuming and prone to measurement error, and automated measurement can serve as an alternative that is faster and more reliable. In this paper, a new feature-based tracking algorithm is presented for automatically measuring diameter of vessels in intravital video microscopy image sequences. Our method tracks the vessel diameter throughout the entire image sequence once the diameter is marked in the first image. The parameters were calibrated using the intravital videos with manual ground truth measurements. The expriment with 10 synthetic videos and 20 intravital microscopy videos, including 10 fluorescence confocal and 10 non-confocal transmission, shows that the measurement can be performed accurately.

title: Shifting fungal reproductive mode by manipulation of mating type genes: obligatory heterothallism of Gibberella zeae.
abstract: Fungi capable of sexual reproduction use heterothallic (self-sterile) or homothallic (self-fertile) mating strategies. In most ascomycetes, a single mating type locus, MAT, with two alternative forms (MAT1-1 and MAT1-2) called idiomorphs, controls mating ability. In heterothallic ascomycetes, these alternative idiomorphs reside in different nuclei. In contrast, most homothallic ascomycetes carry both MAT1-1 and MAT1-2 in a single nucleus, usually closely linked. An example of the latter is Gibberella zeae, a species that is capable of both selfing and outcrossing. G. zeae is a devastating cereal pathogen of ubiquitous geographical distribution, and also a producer of mycotoxins that threaten human and animal health. We asked whether G. zeae could be made strictly heterothallic by manipulation of MAT. Targeted gene replacement was used to differentially delete MAT1-1 or MAT1-2 from a wild-type haploid MAT1-1; MAT1-2 strain, resulting in MAT1-1; mat1-2, mat1-1; MAT1-2 strains that were self-sterile, yet able to cross to wild-type testers and, more importantly, to each other. These results indicated that differential deletion of MAT idiomorphs eliminates selfing ability of G. zeae, but the ability to outcross is retained. They also indicated that both MAT idiomorphs are required for self-fertility. To our knowledge, this is the first report of complete conversion of fungal reproductive strategy from homothallic to heterothallic by targeted manipulation of MAT. Practically, this approach opens the door to simple and efficient procedures for obtaining sexual recombinants of G. zeae that will be useful for genetic analyses of pathogenicity and other traits, such as the ability to produce mycotoxins.

title: Evaluation of nano-technology-modified zirconia oral implants: a study in rabbits.
abstract: The objective of this study was to screen candidate nano-technology-modified, micro-structured zirconia implant surfaces relative to local bone formation and osseointegration.



Proprietary nano-technology surface-modified (calcium phosphate: CaP) micro-structured zirconia implants (A and C), control micro-structured zirconia implants (ZiUnite), and titanium porous oxide implants (TiUnite) were implanted into the femoral condyle in 40 adult male New Zealand White rabbits. Each animal received one implant in each hind leg; thus, 20 animals received A and C implants and 20 animals received ZiUnite and TiUnite implants in contralateral hind legs. Ten animals/group were euthanized at weeks 3 and 6 when biopsies of the implant sites were processed for histometric analysis using digital photomicrographs produced using backscatter scanning electron microscopy.



The TiUnite surface demonstrated significantly greater bone-implant contact (BIC) (77.6+/-2.6%) compared with the A (64.6+/-3.6%) and C (62.2+/-3.1%) surfaces at 3 weeks (p<0.05). Numerical differences between ZiUnite (70.5+/-3.1%) and A and C surfaces did not reach statistical significance (p>0.05). Similarly, there were non-significant differences between the TiUnite and the ZiUnite surfaces (p>0.05). At 6 weeks, there were no significant differences in BIC between the TiUnite (67.1+/-4.2%), ZiUnite (69.7+/-5.7%), A (68.6+/-1.9%), and C (64.5+/-4.1%) surfaces (p>0.05).



TiUnite and ZiUnite implant surfaces exhibit high levels of osseointegration that, in this model, confirm their advanced osteoconductive properties. Addition of CaP nano-technology to the ZiUnite surface does not enhance the already advanced osteoconductivity displayed by the TiUnite and ZiUnite implant surfaces.

title: Complex data analysis in high-resolution SSFP fMRI.
abstract: In transition-band steady-state free precession (SSFP) functional MRI (fMRI), functional contrast originates from a bulk frequency shift induced by a deoxygenated hemoglobin concentration change in the activated brain regions. This frequency shift causes a magnitude and/or phase-signal change depending on the off-resonance distribution of a voxel in the balanced-SSFP (bSSFP) profile. However, in early low-resolution studies, only the magnitude signal activations were shown. In this paper the task-correlated phase-signal change is presented in a high-resolution (1 x 1 x 1 mm3) study. To include this phase activation in a functional analysis, a new complex domain data analysis method is proposed. The results show statistically significant phase-signal changes in a large number of voxels comparable to that of the magnitude-activated voxels. The complex-data analysis method successfully includes these phase activations in the activation map and thus provides wider coverage compared to magnitude-data analysis results.