Long-Term Outcomes and Prognostic Factors in Periampullary Carcinoma.

PURPOSE: The aim of the study was to analyze the long-term survival and the various prognostic factors that influence overall survival in patients undergoing pancreaticoduodenectomy (PD) with non-pancreatic periampullary carcinomas. METHODS: A retrospective analysis of consecutive patients diagnosed with non-pancreatic periampullary carcinomas who underwent PD at a tertiary cancer center was performed. Univariate analysis of various prognostic factors influencing the disease-free survival (DFS) was performed using log-rank test. Factors identified to be significant in univariate analysis were included in the multivariate analysis, which was performed using the Cox proportional hazard model. The survival estimates were calculated by life-table method. Statistical significance was considered when p value was <0.05. The SPSS v16.0.1 software was used for statistical analysis. RESULTS: Between 1995 and 2010, 78 patients underwent PD with or without (Whipple's operation) pylorus preservation for non-pancreatic periampullary adenocarcinomas. Of these, eight patients received adjuvant chemotherapy. The most common subsite was ampulla (60 patients), followed by the second part duodenum (11 patients), and distal common bile duct (7 patients). The median duration of follow-up of all patients in this study was 50 months. The recurrence rate was 39.7 %. The 5-year disease-free survival and overall survival was 57 %. Patients without nodal metastasis had a non-significant trend towards better 5-year disease-free survival when compared to those with nodal metastasis (64 vs 45 %, p = 0.11). On multivariate analysis, it was found that male gender (p = 0.05) and presence of lymphovascular invasion (p = 0.04) predicted a significantly poor 5-year disease-free survival. CONCLUSION: Periampullary carcinomas have a favorable prognosis after surgery. Male gender and presence of lymphovascular invasion are independent prognostic factors in patients diagnosed with non-pancreatic periampullary carcinomas who underwent PD in this study.

Advanced techniques for constrained internal coordinate molecular dynamics.

Internal coordinate molecular dynamics (ICMD) methods provide a more natural description of a protein by using bond, angle, and torsional coordinates instead of a Cartesian coordinate representation. Freezing high-frequency bonds and angles in the ICMD model gives rise to constrained ICMD (CICMD) models. There are several theoretical aspects that need to be developed to make the CICMD method robust and widely usable. In this article, we have designed a new framework for (1) initializing velocities for nonindependent CICMD coordinates, (2) efficient computation of center of mass velocity during CICMD simulations, (3) using advanced integrators such as Runge-Kutta, Lobatto, and adaptive CVODE for CICMD simulations, and (4) cancelling out the "flying ice cube effect" that sometimes arises in Nosé-Hoover dynamics. The Generalized Newton-Euler Inverse Mass Operator (GNEIMO) method is an implementation of a CICMD method that we have developed to study protein dynamics. GNEIMO allows for a hierarchy of coarse-grained simulation models based on the ability to rigidly constrain any group of atoms. In this article, we perform tests on the Lobatto and Runge-Kutta integrators to determine optimal simulation parameters. We also implement an adaptive coarse-graining tool using the GNEIMO Python interface. This tool enables the secondary structure-guided "freezing and thawing" of degrees of freedom in the molecule on the fly during molecular dynamics simulations and is shown to fold four proteins to their native topologies. With these advancements, we envision the use of the GNEIMO method in protein structure prediction, structure refinement, and in studying domain motion.

Folding of small proteins using constrained molecular dynamics.

The focus of this paper is to examine whether conformational search using constrained molecular dynamics (MD) method is more enhanced and enriched toward "native-like" structures compared to all-atom MD for the protein folding as a model problem. Constrained MD methods provide an alternate MD tool for protein structure prediction and structure refinement. It is computationally expensive to perform all-atom simulations of protein folding because the processes occur on a time scale of microseconds. Compared to the all-atom MD simulation, constrained MD methods have the advantage that stable dynamics can be achieved for larger time steps and the number of degrees of freedom is an order of magnitude smaller, leading to a decrease in computational cost. We have developed a generalized constrained MD method that allows the user to "freeze and thaw" torsional degrees of freedom as fit for the problem studied. We have used this method to perform all-torsion constrained MD in implicit solvent coupled with the replica exchange method to study folding of small proteins with various secondary structural motifs such as, α-helix (polyalanine, WALP16), ß-turn (1E0Q), and a mixed motif protein (Trp-cage). We demonstrate that constrained MD replica exchange method exhibits a wider conformational search than all-atom MD with increased enrichment of near-native structures. "Hierarchical" constrained MD simulations, where the partially formed helical regions in the initial stretch of the all-torsion folding simulation trajectory of Trp-cage were frozen, showed a better sampling of near-native structures than all-torsion constrained MD simulations. This is in agreement with the zipping-and-assembly folding model put forth by Dill and co-workers for folding proteins. The use of hierarchical "freeze and thaw" clustering schemes in constrained MD simulation can be used to sample conformations that contribute significantly to folding of proteins.

Structural insights into conformational stability of wild-type and mutant beta1-adrenergic receptor.

Recent experiments to derive a thermally stable mutant of turkey beta-1-adrenergic receptor (beta1AR) have shown that a combination of six single point mutations resulted in a 20 degrees C increase in thermal stability in mutant beta1AR. Here we have used the all-atom force-field energy function to calculate a stability score to detect stabilizing point mutations in G-protein coupled receptors. The calculated stability score shows good correlation with the measured thermal stability for 76 single point mutations and 22 multiple mutants in beta1AR. We have demonstrated that conformational sampling of the receptor for various mutants improve the prediction of thermal stability by 50%. Point mutations Y227A5.58, V230A5.61, and F338M7.48 in the thermally stable mutant m23-beta1AR stabilizes key microdomains of the receptor in the inactive conformation. The Y227A5.58 and V230A5.61 mutations stabilize the ionic lock between R139(3.50) on transmembrane helix3 and E285(6.30) on transmembrane helix6. The mutation F338M7.48 on TM7 alters the interaction of the conserved motif NPxxY(x)5,6F with helix8 and hence modulates the interaction of TM2-TM7-helix8 microdomain. The D186-R317 salt bridge (in extracellular loops 2 and 3) is stabilized in the cyanopindolol-bound wild-type beta1AR, whereas the salt bridge between D184-R317 is preferred in the mutant m23. We propose that this could be the surrogate to a similar salt bridge found between the extracellular loop 2 and TM7 in beta2AR reported recently. We show that the binding energy difference between the inactive and active states is less in m23 compared to the wild-type, which explains the activation of m23 at higher norepinephrine concentration compared to the wild-type. Results from this work throw light into the mechanism behind stabilizing mutations. The computational scheme proposed in this work could be used to design stabilizing mutations for other G-protein coupled receptors.

Diagnostic dilemma in coinfection.

A Fifteen years girl belonging to a low socioeconomic status was admitted with peritonsillar abscess caused by methicillin resistant Staphylococcus aureus (MRSA), high fever, diarrhoea and septicaemic shock. Initial blood cultures and widal test, stool cultures and routine stool examination were non-contributory to the diagnosis. A bone marrow culture in the second week confirmed the diagnosis of Salmonella typhi infection. Examination of a fresh stool sample showed cysts of Entamoeba histolytica. She was treated with ciprofloxacin, metronidazole, augmentin and ceftriaxone. She had no clinical evidence of immunosuppression prior to this episode and her HIV test was negative. This case report highlights the presence of community acquired MRSA infection causing perititonsillar abscess, and the diagnostic dilemma of fever and diarrhoea due to coinfection with Salmonella typhi and Entamobea histolytica.