A shape constrained parametric active contour model for breast contour detection
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: Analysis of Breast Contour using Rotated Catenary.
abstract: Surgical reconstruction of natural-appearing breasts is a challenging task. Currently, surgical planning is limited to the surgeon's subjective assessment of breast morphology. Therefore, it is useful to develop objective measurements of breast contour. In this paper, a novel quantitative measure of the breast contour based on catenary theory is introduced. A catenary curve is fitted on the breast contour (lateral and inferior) and the key parameter determining the shape of the curve is extracted. The new catenary analysis was applied to pre- and post-operative clinical photographs of women who underwent tissue expander/implant (TE/Implant) reconstruction. A logistic regression model was developed to predict the probability that the observed contour is that of a TE/Implant reconstruction from the catenary parameter, patient age, and patient body mass index. It was demonstrated that the parameters contain useful information for distinguishing TE/Implant reconstructed breasts from pre-operative breasts.

title: Quantitative measures of facial expression for patients with head and neck cancer
abstract: In addition to changes in facial morphology, head and neck cancer treatment can impact the facial expression. Quantification of changes in facial expression, particularly of smiling, would enable a deeper understanding of the relationship between physical changes and psychosocial adjustment in patients being treated for facial cancer. This study proposes 48 quantitative facial expression measures, which consist of the length normalized distances and slopes between 27 manually annotated fiducial points on standard 2D clinical photographs of patients with head and neck cancer. Using the proposed measures, the maximum intensity of smiling for patients with head and neck cancer prior to their treatments was compared to that of a sample from a healthy population. A total of 7 facial expression measures captured statistically significant differences between patients with head and neck cancer and healthy individuals. These measures suggest that patients with head and neck cancer are less expressive than people without head and neck cancer. This study is the first attempt to quantify the facial expression of patients with head and neck cancer and to build a foundation for studying how surgical interventions may affect their facial expressions. Moreover, this study lays the groundwork for future investigation of the relationship between facial expression and psychosocial adjustment in cancer patients.

title: Chicoric acid: chemistry, distribution, and production
abstract: Though chicoric acid was first identified in 1958, it was largely ignored until recent popular media coverage cited potential health beneficial properties from consuming food and dietary supplements containing this compound. To date, plants from at least 63 genera and species have been found to contain chicoric acid, and while the compound is used as a processing quality indicator, it may also have useful health benefits. This review of chicoric acid summarizes research findings and highlights gaps in research knowledge for investigators, industry stakeholders, and consumers alike. Additionally, chicoric acid identification, and quantification methods, biosynthesis, processing improvements to increase chicoric acid retention, and potential areas for future research are discussed.

title: Spectrum measurement of fast optical signal of neural activity in brain tissue and its theoretical origin
abstract: Functional brain imaging technologies have enabled recent advances in understanding human brain function. In particular, a noninvasive and fast optical technique will become one of the most promising tools for future studies. As a fundamental ex vivo study for the development of such a technique, this paper demonstrates the spectral measurement of fast optical changes associated with neural activity in bulk brain tissue. For this purpose, a high-speed confocal near-infrared spectrometer was built and used. The results verified that observed transient optical responses (tORs) are associated with neural activity by showing that the following: tORs were concurrent and correlated with local field potentials (LFPs); tORs disappeared following tetrodotoxin application; and tORs were reproducibly observed across preparations. In addition, the amplitude of tORs was statistically significantly larger in longer wavelengths (approximately 1200 nm). The time course of tORs, however, is quite different from that of LFPs. Since this difference implies that tORs may originate not directly from the electric potential variation but from other neurophysiological events accompanying excitation, this paper tested the hypothesis that tORs are attributed to transient cellular volume changes (tCVCs). With no previous dynamic equation to elucidate such different temporal dynamics of the optical responses, a novel mathematical neuron model to describe tCVCs was developed. This neuron model, along with finite-difference time-domain simulations, showed that tCVCs and tORs were similar in the temporal dynamics, order of magnitude, response direction, and detectability in the bulk tissue; thus supporting the hypothesis.

title: Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing.
abstract: A novel method for ab initio prediction of protein tertiary structures, PROFESY (PROFile Enumerating SYstem), is proposed. This method utilizes the secondary structure prediction information of a query sequence and the fragment assembly procedure based on 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. We apply PROFESY for benchmark tests to proteins with known structures to demonstrate its feasibility. In addition, we participated in CASP5 and applied PROFESY to four new-fold targets for blind prediction. The results are quite promising, despite the fact that PROFESY was in its early stages of development. In particular, PROFESY successfully provided us the best model-one structure for the target T0161.

title: Erasing genomic imprinting memory in mouse clone embryos produced from day 11.5 primordial germ cells.
abstract: Genomic imprinting is an epigenetic mechanism that causes functional differences between paternal and maternal genomes, and plays an essential role in mammalian development. Stage-specific changes in the DNA methylation patterns of imprinted genes suggest that their imprints are erased some time during the primordial germ cell (PGC) stage, before their gametic patterns are re-established during gametogenesis according to the sex of individuals. To define the exact timing and pattern of the erasure process, we have analyzed parental-origin-specific expression of imprinted genes and DNA methylation patterns of differentially methylated regions (DMRs) in embryos, each derived from a single day 11.5 to day 13.5 PGC by nuclear transfer. Cloned embryos produced from day 12.5 to day 13.5 PGCs showed growth retardation and early embryonic lethality around day 9.5. Imprinted genes lost their parental-origin-specific expression patterns completely and became biallelic or silenced. We confirmed that clones derived from both male and female PGCs gave the same result, demonstrating the existence of a common default state of genomic imprinting to male and female germlines. When we produced clone embryos from day 11.5 PGCs, their development was significantly improved, allowing them to survive until at least the day 11.5 embryonic stage. Interestingly, several intermediate states of genomic imprinting between somatic cell states and the default states were seen in these embryos. Loss of the monoallelic expression of imprinted genes proceeded in a step-wise manner coordinated specifically for each imprinted gene. DNA demethylation of the DMRs of the imprinted genes in exact accordance with the loss of their imprinted monoallelic expression was also observed. Analysis of DNA methylation in day 10.5 to day 12.5 PGCs demonstrated that PGC clones represented the DNA methylation status of donor PGCs well. These findings provide strong evidence that the erasure process of genomic imprinting memory proceeds in the day 10.5 to day 11.5 PGCs, with the timing precisely controlled for each imprinted gene. The nuclear transfer technique enabled us to analyze the imprinting status of each PGC and clearly demonstrated a close relationship between expression and DNA methylation patterns and the ability of imprinted genes to support development.

title: Receptor-activity modifying protein 1 expression is increased in the striatum following repeated L-DOPA administration in a 6-hydroxydopamine lesioned rat model of Parkinson's disease.
abstract: Abnormalities in signaling by G-protein coupled receptors (GPCRs) within the striatum are involved in the pathophysiology of Parkinson's disease (PD) and L-DOPA induced dyskinesia (LID). Receptor activity modifying proteins (RAMPs) are single transmembrane accessory proteins crucial for both trafficking and defining the phenotype of GPCRs. In the CNS, RAMP1 mRNA is predominantly expressed in striatum, cortex, and olfactory tubercles. In the present study, expression of RAMP1 mRNA is increased in the striatum (68-77%), following repeated L-DOPA administration, in the 6-hydroxydopamine-lesioned rat. These data are the first to describe regulation of RAMP1 expression in the CNS and suggest that changes in RAMP1 activity are involved in the pathophysiology of LID.