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1.  Diffuse pulmonary lymphangiomatosis 
Diffuse pulmonary lymphangiomatosis (DPL) is a rare disease characterized by infiltration of the lung, pleura and mediastinum with thin-walled lymphangiomas. DPL can result in mass effect from infiltrative disease, restrictive and obstructive pulmonary physiology, chylous effusions and respiratory failure. The present article discusses clinical, radiographic and pathological features, and treatment options for DPL.
PMCID: PMC3628648  PMID: 23457676
Chylous effusions; Diffuse pulmonary lymphangiomatosis; Interstitial lung disease; Lymphangiomatosis
2.  Orthobiologics and platelet rich plasma 
Orthobiologics have evolved to the extent that they significantly influence modern orthopedic surgical practice. A better understanding of the role of various growth factors and cells in the process of tendon healing, ligament repair, cartilage regeneration and bone formation has stimulated focused research in many chronic musculoskeletal ailments. Investigators have published results of laboratory as well as clinical studies, using orthobiologics like platelet rich plasma, stem cells, autologous conditioned serum etc., with variable results. However, a clear consensus over the best orthobiologic substance and the method of preparation and usage of these substances is lacking. Much of the confusion is due to the fact that studies ranging from RCTs to case reports present variable results, and the interpretations are wide-ranging. We have reviewed the available orthobiologics related data with a focus on platelet rich plasma in orthopedic conditions.
PMCID: PMC3931137  PMID: 24600055
Platelet rich plasma; orthobiologics; tendon healing; ligament repair
3.  Left Atrial Appendage Dysfunction in a Patient with Premature Ventricular Contractions - A Risk Factor for Stroke? 
A 16-year-old female with ventricular dysfunction and frequent ventricular arrhythmia presented with a cardioembolic stroke. Prior electrophysiology study and ablation was performed for ventricular tachycardia (VT). For remaining ventricular ectopy, the patient was maintained on carvedilol and mexiletine. After one year on this regimen, she presented with an acute stroke. Transesophageal echocardiography revealed no evidence of an intracardiac or ventricular thrombus but demonstrated markedly decreased left atrial appendage (LAA) flow velocity worsened during frequent premature ventricular contractions (PVC). In the absence of atrial fibrillation (AF), the LAA dysfunction was considered secondary to the frequent PVCs and was thought to be the underlying cause for the stroke. We present this case to highlight a potential under recognized association between LAA dysfunction and ventricular arrhythmia, similar to that observed with atrioventricular dyssynchronous pacing.
PMCID: PMC3775302  PMID: 24086095
PVC; left atrial appendage; stroke; risk; noncompaction cardiomyopathy
4.  Free Energetics of Carbon Nanotube Association in Pure and Aqueous Ionic Solutions 
The journal of physical chemistry. B  2012;116(28):8154-8168.
Carbon nanotubes are a promising platform across a broad spectrum of applications ranging from separations technology, drug delivery, to bio(electronic) sensors. Proper dispersion of carbon nanotube materials is important to retaining the electronic properties of nanotubes. Experimentally it has been shown that salts can regulate the dispersing properties of CNTs in aqueous system with surfactants (J. Am. Chem. Soc., 2009, 131:1144–1153); details of the physico-chemical mechanisms underlying such effects continue to be explored. We address the effects of inorganic monovalent salts (NaCl and NaI) on dispersion stability of carbon nanotubes. We perform all-atom molecular dynamics simulations using non-polarizable interaction models to compute the potential of mean force between two (10,10) single-walled carbon nanotubes (SWNTs) in the presence of NaCl/NaI and compare to the potential of mean force between SWNTs in pure water. Addition of salts enhances stability of the contact state between two SWNT’s on the order of 4 kcal/mole. The ion-specific spatial distribution of different halide anions gives rise to starkly different contributions to the free energy stability of nanotubes in the contact state. Iodide anion directly stabilizes the contact state to a much greater extent than chloride anion. The enhanced stability arises from the locally repulsive forces imposed on nanotubes by the surface-segregated iodide anion. Within the timescale of our simulations, both NaI and NaCl solutions stabilize the contact state by equivalent amounts. The marginally higher stability for contact state in salt solutions recapitulates results for small hydrophobic solutes in NaCl solutions (Athawale et al, J. Phys. Chem. B., 112, 5661. 2008) as well as single walled carbon nanotubes in NaCl and CaCl2 aqueous solutions.
PMCID: PMC3562760  PMID: 22780909
single-walled nanotubes; hydrophobic effect; specific-ion effects; molecular dynamics simulation
5.  Pulmonary alveolar proteinosis 
Pulmonary alveolar proteinosis (PAP) is a disease of alveolar accumulation of phospholipoproteinaceous material that results in gas exchange impairment leading to dyspnea and alveolar infiltrates. There are three forms of PAP: congenital, acquired and idiopathic; of which the latter two are predominant in the adult population. Previous case studies have found that the acquired form can be secondary to various autoimmune, infectious, malignant and environmental etiologies. Recent advances in the understanding of the pathophysiology of PAP demonstrate that the idiopathic form is due to antigranulocyte macrophage-colony stimulating factor antibodies. Therapeutic targets that replace granulocyte macrophage colony stimulating factor or remove these antibodies are being actively developed. The current standard of care is to perform whole lung lavage on these patients to clear the alveolar space to help improve respiratory physiology. A case of PAP is reported, followed by a literature review on the diagnosis and management of this rare condition with the aim of increasing awareness among physicians when treating patients who present with alveolar infiltrates.
PMCID: PMC3411387  PMID: 22891182
Alveolar infiltrates; Crazy paving; GM-CSF; Pulmonary alveolar proteinosis
6.  Impaired coronary microvascular reactivity in women with apical ballooning syndrome (Takotsubo/stress cardiomyopathy) 
The pathophysiology of apical ballooning syndrome (ABS) remains to be elucidated. The aim of this study was to evaluate the coronary vascular reactivity of patients who were previously diagnosed with ABS.
Methods and results:
A total of 228 cases of ABS were prospectively identified, and of these, 10 patients (median age 61 years (IQR 48–75); all females) who underwent coronary vasomotion testing were included in the study. Coronary epicardial and microvascular responses to intracoronary acetylcholine (ACH; % change in diameter and % change in blood flow at doses of 10−6–10−4 mol/l), nitroglycerin (200–300 mg), and adenosine (36–60 µg) were evaluated. The median change in diameter with ACH was –9.3% (IQR –36.4, 3.2) with six patients (60%) demonstrating epicardial coronary constriction. The median increase in peak coronary blood flow in response to ACH was 13.1% (IQR –18.6, 55.0). This was markedly lower than the blood flow response seen in a reference group of 211 women from our laboratory (mean age 60 years) with normal microvascular responses to ACH: 103% (IQR 75, 149). Seven (70%) patients had <50% increase in coronary blood flow indicating abnormal microvascular response to ACH. 70% had either abnormal epicardial or microvascular response to ACH. Median coronary flow reserve was abnormal at 2.2% (IQR 2.0, 3.4; normal >2.5), and 90% had at least one abnormal measure of microvascular vasomotion.
The novel observation is that coronary microvascular dysfunction is highly prevalent in patients with ABS. Thus, chronically impaired coronary vascular reactivity, especially involving the microcirculation, may be a central feature of the pathophysiology of ABS.
PMCID: PMC3821803  PMID: 24222824
Apical ballooning syndrome; endothelium; microcirculation; stress cardiomyopathy; Tako-Tsubo cardiomyopathy
7.  How do we manage post-OLT redundant bile duct? 
AIM: To address endoscopic outcomes of post-Orthotopic liver transplantation (OLT) patients diagnosed with a “redundant bile duct” (RBD).
METHODS: Medical records of patients who underwent OLT at the Liver Transplant Center, University Texas Health Science Center at San Antonio Texas were retrospectively analyzed. Patients with suspected biliary tract complications (BTC) underwent endoscopic retrograde cholangiopancreatography (ERCP). All ERCP were performed by experienced biliary endoscopist. RBD was defined as a looped, sigmoid-shaped bile duct on cholangiogram with associated cholestatic liver biomarkers. Patients with biliary T-tube placement, biliary anastomotic strictures, bile leaks, bile-duct stones-sludge and suspected sphincter of oddi dysfunction were excluded. Therapy included single or multiple biliary stents with or without sphincterotomy. The incidence of RBD, the number of ERCP corrective sessions, and the type of endoscopic interventions were recorded. Successful response to endoscopic therapy was defined as resolution of RBD with normalization of associated cholestasis. Laboratory data and pertinent radiographic imaging noted included the pre-ERCP period and a follow up period of 6-12 mo after the last ERCP intervention.
RESULTS: One thousand two hundred and eighty-two patient records who received OLT from 1992 through 2011 were reviewed. Two hundred and twenty-four patients underwent ERCP for suspected BTC. RBD was reported in each of the initial cholangiograms. Twenty-one out of 1282 (1.6%) were identified as having RBD. There were 12 men and 9 women, average age of 59.6 years. Primary indication for ERCP was cholestatic pattern of liver associated biomarkers. Nineteen out of 21 patients underwent endoscopic therapy and 2/21 required immediate surgical intervention. In the endoscopically managed group: 65 ERCP procedures were performed with an average of 3.4 per patient and 1.1 stent per session. Fifteen out of 19 (78.9%) patients were successfully managed with biliary stenting. All stents were plastic. Selection of stent size and length were based upon endoscopist preference. Stent size ranged from 7 to 11.5 Fr (average stent size 10 Fr); Stent length ranged from 6 to 15 cm (average length 9 cm). Concurrent biliary sphincterotomy was performed in 10/19 patients. Single ERCP session was sufficient in 6/15 (40.0%) patients, whereas 4/15 (26.7%) patients needed two ERCP sessions and 5/15 (33.3%) patients required more than two (average of 5.4 ERCP procedures). Single biliary stent was sufficient in 5 patients; the remaining patients required an average of 4.9 stents. Four out of 19 (21.1%) patients failed endotherapy (lack of resolution of RBD and recurrent cholestasis in the absence of biliary stent) and required either choledocojejunostomy (2/4) or percutaneous biliary drainage (2/4). Endoscopic complications included: 2/65 (3%) post-ERCP pancreatitis and 2/10 (20%) non-complicated post-sphincterotomy bleeding. No endoscopic related mortality was found. The medical records of the 15 successful endoscopically managed patients were reviewed for a period of one year after removal of all biliary stents. Eleven patients had continued resolution of cholestatic biomarkers (73%). One patient had recurrent hepatitis C, 2 patients suffered septic shock which was not associated with ERCP and 1 patient was transferred care to an outside provider and records were not available for our review.
CONCLUSION: Although surgical biliary reconstruction techniques have improved, RBD represents a post-OLT complication. This entity is rare however, endoscopic management of RBD represents a reasonable initial approach.
PMCID: PMC3646140  PMID: 23674851
Redundant bile duct; Orthotopic liver transplantation; Biliary complications; Biliary stent; Endoscopic retrograde cholangiopancreatography
8.  Beta3-Adrenoreceptor Stimulation Ameliorates Myocardial Ischemia-Reperfusion Injury Via Endothelial Nitric Oxide Synthase and Neuronal Nitric Oxide Synthase Activation 
This paper examined whether nebivolol protects the heart via nitric oxide (NO) synthase and NO-dependent signaling in an in vivo model of acute myocardial infarction.
Beta3-adrenergic receptor (AR) activation promotes endothelial nitric oxide synthase (eNOS) activity and NO bioavailability. We hypothesized that specific beta3-AR agonists would attenuate myocardial ischemia-reperfusion (MI/R) injury via eNOS activation and increased NO bioavailability.
Mice were subjected to 45 min of myocardial ischemia in vivo followed by 24 h of reperfusion (R). Nebivolol (500 ng/kg), CL 316243 (1 μg/kg), BRL-37344 (1 μg/kg), or vehicle (VEH) was administered at the time of R. Myocardial area-at-risk (AAR) and infarct size (INF)/AAR was measured at 24 h of R. Cardiac tissue and plasma were collected to evaluate eNOS phosphorylation, neuronal nitric oxide synthase (nNOS), inducible nitric oxide synthase expression, and nitrite and nitrosothiol levels.
Nebivolol (500 ng/kg) reduced INF/AAR by 37% (p < 0.001 vs. VEH) and serum troponin-I levels from 41 ± 4 ng/ml to 25 ± 4 ng/ml (p < 0.05 vs. VEH). CL 316243 and BRL-37344 reduced INF by 39% and 42%, respectively (p < 0.001 vs. VEH). Nebivolol and CL 316243 increased eNOS phosphorylation at Ser-1177 (p < 0.05 vs. VEH) and increased nitrite and total nitrosylated protein levels. Nebivolol and CL 316243 significantly increased myocardial nNOS expression. Nebivolol failed to reduce INF after MI/R in beta3-AR−/−, eNOS−/−, and in nNOS−/− mice.
Our results indicate that beta3-AR agonists protect against MI/R injury. Furthermore, the cardioprotective effects of beta3-AR agonists are mediated by rapid eNOS and nNOS activation and increased NO bioavailability.
PMCID: PMC3586978  PMID: 22152956
beta3 adrenergic receptor; cardiac ischemia; endothelial nitric oxide synthase; neuronal nitric oxide synthase; nitric oxide
9.  Solvation Structure and Energetics of Single Ions at the Aqueous Liquid-Vapor Interface 
Chemical physics letters  2012;527:22-26.
Potentials of mean force for single, nonpolarizable monovalent halide anions and alkali cations are computed for transversing the water-air interface (modeling using polarizable TIP4P-FQ and TIP4P-QDP). Iodide and bromide in TIP4P-FQ show interfacial stability, whereas chloride, bromide, and iodide show interfacial stability in TIP4P-QDP. A monotonic decrease in coordination number and an increasingly anisotropic distribution of solvating water molecules is shown to accompany movement of the ions towards vapor conditions; these effects are most noticeable with increases in ion size/decreases in magnitude of hydration free energy.
PMCID: PMC3488351  PMID: 23136448
Ions; Polarizable Force Fields; Molecular Dynamics; TIP4P-FQ; TIP4P-QDP; Potential of Mean Force; Solvation Structure
10.  Molecular Dynamics Simulation of Hydrated DPPC Monolayers Using Charge Equilibration Force Fields 
We present results of molecular dynamics simulations of a model DPPC-water monolayer using charge equilibration (CHEQ) force fields which explicitly account for electronic polarization in a classical treatment of intermolecular interactions. The surface pressure, determined as the difference between the monolayer and pure water surface tensions at 323 K, is predicted to be 22.92 ± 1.29 dyne/cm, just slightly below the broad range of experimental values reported for this system. The surface tension for the DPPC-water monolayer is predicted to be 42.35 ± 1.16 dyne/cm, in close agreement with the experimentally determined value of 40.9 dyne/cm. This surface tension is also consistent with the value obtained from DPPC monolayer simulations using state-of-the-art nonpolarizable force fields. The current results of simulations predict a monolayer-water potential difference relative to the pure water-air interface of 0.64 ± 0.02 Volts, an improved prediction compared to the fixed-charge CHARMM27 force field, yet still overestimating the experimental range of 0.3 to 0.45 Volts. Since the charge equilibration model is a purely charge-based model for polarization, the current results suggest that explicitly-modeled polarization effects can offer improvements in describing interfacial electrostatics in such systems.
PMCID: PMC3488352  PMID: 21997857
11.  Solvation Properties of N-acetyl-β-glucosamine: A Molecular Dynamics Study Incorporating Electrostatic Polarization 
Journal of computational chemistry  2011;32(16):3339-3353.
N-acetyl-β-glucosamine (NAG) is an important moiety of glycoproteins and is involved in many biological functions. However, conformational and dynamical properties of NAG molecules in aqueous solution, the most common biological environment, remain ambiguous due to limitations of experimental methods. Increasing efforts are made to probe structural properties of NAG and NAG-containing macromolecules, like peptidoglycans and polymeric chitin, at the atomic level using molecular dynamics simulations. In this work, we develop a polarizable carbohydrate force field for NAG and contrast simulation results of various properties using this novel force field and an analogous non-polarizable (fixed charge) model. Aqueous solutions of NAG and its oligomers are investigated; we explore conformational properties (rotatable bond geometry), electrostatic properties (dipole moment distribution), dynamical properties (self-diffusion coefficient), hydrogen bonding (water bridge structure and dynamics), and free energy of hydration. The fixed-charge carbohydrate force field exhibits deviations from the gas-phase relative rotation energy of exocyclic hydroxymethyl side-chain and of chair/boat ring distortion. The polarizable force field predicts conformational properties in agreement with corresponding first-principles results. NAG-water hydrogen bonding pattern is studied through radial distribution functions and correlation functions. Intermolecular hydrogen bonding between solute and solvent is found to stabilize NAG solution structures while intramolecular hydrogen bonds define glycosidic linkage geometry of NAG oligomers. The electrostatic component of hydration free energy is highly dependent on force field atomic partial charges, influencing a more favorable free energy of hydration in the fixed-charge model compared to the polarizable model.
PMCID: PMC3193586  PMID: 21898464
12.  Structural, Dynamic, and Electrostatic Properties of Fully Hydrated DMPC Bilayers From Molecular Dynamics Simulations Accelerated with Graphical Processing Units (GPUs) 
Journal of computational chemistry  2011;32(14):2958-2973.
We present results of molecular dynamics simulations of fully hydrated DMPC bilayers performed on graphics processing units (GPUs) using current state-of-the-art non-polarizable force fields and a local GPU-enabled molecular dynamics code named FEN ZI. We treat the conditionally convergent electrostatic interaction energy exactly using the Particle Mesh Ewald method (PME) for solution of Poisson’s Equation for the electrostatic potential under periodic boundary conditions. We discuss elements of our implementation of the PME algorithm on GPUs as well as pertinent performance issues. We proceed to show results of simulations of extended lipid bilayer systems using our program, FEN ZI. We performed simulations of DMPC bilayer systems consisting of 17004, 68484 and 273936 atoms in explicit solvent. We present bilayer structural properties (atomic number densities, electron density profiles), deuterium order parameters (SCD), electrostatic properties (dipole potential, water dipole moments), and orientational properties of water. Predicted properties demonstrate excellent agreement with experiment and previous all-atom molecular dynamics simulations. We observe no statistically significant differences in calculated structural or electrostatic properties for different system sizes, suggesting the small bilayer simulations (less than 100 lipid molecules) provide equivalent representation of structural and electrostatic properties associated with significantly larger systems (over 1000 lipid molecules). We stress that the three system size representations will have differences in other properties such as surface capillary wave dynamics or surface tension related effects that are not probed in the current study. The latter properties are inherently dependent on system size. This contribution suggests the suitability of applying emerging GPU technologies to studies of an important class of biological environments, that of lipid bilayers and their associated integral membrane proteins. We envision that this technology will push the boundaries of fully atomic-resolution modeling of these biological systems, thus enabling unprecedented exploration of meso-scale phenomena (mechanisms, kinetics, energetics) with atomic detail at commodity hardware prices.
PMCID: PMC3188664  PMID: 21793003
13.  Incorporating Phase-Dependent Polarizability in Non-Additive Electrostatic Models for Molecular Dynamics Simulations of the Aqueous Liquid-Vapor Interface 
We discuss a new classical water force field that explicitly accounts for differences in polarizability between liquid and vapor phases. The TIP4P-QDP (4-point transferable intermolecular potential with charge dependent-polarizability) force field is a modification of the original TIP4P-FQ fluctuating charge water force field of Rick et al.1 that self-consistently adjusts its atomic hardness parameters via a scaling function dependent on the M-site charge. The electronegativity (χ) parameters are also scaled in order to reproduce condensed-phase dipole moments of comparable magnitude to TIP4P-FQ. TIP4P-QDP is parameterized to reproduce experimental gas-phase and select condensed-phase properties. The TIP4P-QDP water model possesses a gas phase polarizability of 1.40 Å3 and gas-phase dipole moment of 1.85 Debye, in excellent agreement with experiment and high-level ab initio predictions. The liquid density of TIP4P-QDP is 0.9954(±0.0002) g/cm3 at 298 K and 1 atmosphere, and the enthalpy of vaporization is 10.55(±0.12) kcal/mol. Other condensed-phase properties such as the isobaric heat capacity, isothermal compressibility, and diffusion constant are also calculated within reasonable accuracy of experiment and consistent with predictions of other current state-of-the-art water force fields. The average molecular dipole moment of TIP4P-QDP in the condensed phase is 2.641(±0.001) Debye, approximately 0.02 Debye higher than TIP4P-FQ and within the range of values currently surmised for the bulk liquid. The dielectric constant, ε = 85.8 ± 1.0, is 10% higher than experiment. This is reasoned to be due to the increase in the condensed phase dipole moment over TIP4P-FQ, which estimates ε remarkably well. Radial distribution functions for TIP4P-QDP and TIP4P-FQ show similar features, with TIP4P-QDP showing slightly reduced peak heights and subtle shifts towards larger distance interactions. Since the greatest effects of the phase-dependent polarizability are anticipated in regions with both liquid and vapor character, interfacial simulations of TIP4P-QDP were performed and compared to TIP4P-FQ, a static polarizability analog. Despite similar features in density profiles such as the position of the GDS and interfacial width, enhanced dipole moments are observed for the TIP4P-QDP interface and onset of the vapor phase. Water orientational profiles show an increased preference (over TIP4P-FQ) in the orientation of the permanent dipole vector of the molecule within the interface; an enhanced z-induced dipole moment directly results from this preference. Hydrogen bond formation is lower, on average, in the bulk for TIP4P-QDP than TIP4P-FQ. However, the average number of hydrogen bonds formed by TIP4P-QDP in the interface exceeds that of TIP4P-FQ, and observed hydrogen bond networks extend further into the gaseous region. The TIP4P-QDP interfacial potential, calculated to be -11.98(±0.08) kcal/mol, is less favorable than that for TIP4P-FQ by approximately 2% as a result of a diminished quadrupole contribution. Surface tension is calculated within a 1.3% reduction from the experimental value. Results reported demonstrate TIP4P-QDP as a model comparable to the popular TIP4P-FQ while accounting for a physical effect previously neglected by other water models. Further refinements to this model, as well as future applications are discussed.
PMCID: PMC3488353  PMID: 23133341
Phase Dependent Polarizability; Molecular Dynamics; Charge Equilibration; Polarizable Force Field; Liquid-Vapor Interface; TIP4P-QDP
14.  Increases in Pediatric Antiretroviral Treatment, South Africa 2005–2010 
PLoS ONE  2012;7(9):e44914.
In South Africa in 2010, about 340,000 children under the age of 15 were infected with HIV. We describe the increase in the treatment of South African pediatric HIV-infected patients assisted by the President’s Emergency Plan for AIDS Relief (PEPFAR) from 2004 to 2010.
We reviewed routine program data from PEPFAR-funded implementing partners among persons receiving antiretroviral treatment age 15 years old and less. Data quality was assessed during the reporting period by program officials through routine analysis of trends and logic checks. Based on UNAIDS estimated mortality rates of untreated HIV-infected children, we calculated the number of deaths averted and life-years gained in children under five receiving PEPFAR-assisted antiretroviral treatment.
From October 2004 through September 2010, the number of children newly initiated on antiretroviral treatment in PEPFAR-assisted programs increased from 154 to 2,641 per month resulting in an increase from 2,412 children on antiretroviral treatment in September 2005 to 79,416 children in September 2010. Of those children who initiated antiretroviral treatment before September 2009, 0–4 year olds were 1.4 (95% CI: 1.3–1.5) times as likely to transfer out of the program or die as 5–14 year olds; males were 1.3 (95% CI: 1.0–1.7) times as likely to stop treatment as females. Approximately 27,548 years of life were added to children under-five years old from PEPFAR-assisted antiretroviral treatment.
Pediatric antiretroviral treatment in South Africa has increased substantially. However, additional case-finding and a further acceleration in the implementation of pediatric care and treatment services is required to meet the current treatment need.
PMCID: PMC3441457  PMID: 23028677
15.  Valproate-induced Fanconi Syndrome in a 27-Year-old Woman 
Journal of General Internal Medicine  2011;26(9):1072-1074.
Valproate-induced Fanconi Syndrome (VFS) is a rare complication of this therapy that has been previously described only in children with epilepsy. We report the first known case of an adult with VFS. Metabolic derangements lead patients to present with fatigue, confusion, weakness, and even bone fractures. Identification and discontinuation of the offending agent is the treatment of choice and helps confirm the diagnosis. This case highlights the importance of surveillance for metabolic derangements among patients on long term therapy with this commonly prescribed medication.
PMCID: PMC3157517  PMID: 21516379
valproic acid; valproate; Fanconi syndrome; adult
16.  Water Permeation Through DMPC Lipid Bilayers using Polarizable Charge Equilibration Force Fields 
Chemical physics letters  2011;508(4-6):289-294.
We investigate permeation energetics of water entering a model dimyristoylphosphatidylcholine (DMPC) bilayer via molecular dynamics simulations using polarizable Charge Equilibration (CHEQ) models. Potentials of mean force show 4.5–5.5 kcal/mol barriers for water permeation into bilayers. Barriers are highest when water coordination within the bilayer is prevented, and also when using force fields that accurately reproduce experimental alkane hydration free energies. The magnitude of the average water dipole moment decreases from 2.6 Debye (in bulk) to 1.88 Debye (in membrane interior). This variation correlates with the change in a water molecule’s coordination number.
PMCID: PMC3107520  PMID: 21647243
17.  Phase-Transfer Energetics of Small-Molecule Alcohols Across the Water-Hexane Interface: Molecular Dynamics Simulation Using Charge Equilibration Models 
We study the water-hexane interface using molecular dynamics (MD) and polarizable charge equilibration (CHEQ) force fields. Bulk densities for TIP4P-FQ water and hexane, 1.0086±0.0002 g/cm3 and 0.6378±0.0001 g/cm3, demonstrate excellent agreement with experiment. Interfacial width and interfacial tension are consistent with previously reported values. The in-plane component of the dielectric permittivity (ε∥) for water is shown to decrease from 81.7±0.04 to unity, transitioning longitudinally from bulk water to bulk hexane. ε∥ for hexane reaches a maximum in the interface, but this term represents only a small contribution to the total dielectric constant (as expected for a non-polar species). Structurally, net orientations of the molecules arise in the interfacial region such that hexane lies slightly parallel to the interface and water reorients to maximize hydrogen bonding. Interfacial potentials due to contributions of the water and hexane are calculated to be -567.9±0.13mV and 198.7±0.01mV, respectively, giving rise to a total potential in agreement with the range of values reported from previous simulations of similar systems. Potentials of mean force (PMF) calculated for methanol, ethanol, and 1-propanol for the transfer from water to hexane indicate an interfacial free energy minimum, corresponding to the amphiphilic nature of the molecules. The magnitudes of transfer free energies were further characterized from the solvation free energies of alcohols in water and hexane using thermodynamic integration. This analysis shows that solvation free energies for alcohols in hexane are 0.2-0.3 kcal/mol too unfavorable, whereas solvation of alcohols in water is approximately 1 kcal/mol too favorable. For the pure hexane-water interfacial simulations, we observe a monotonic decrease of the water dipole moment to near-vacuum values. This suggests that the electrostatic component of the desolvation free energy is not as severe for polarizable models than for fixed-charge force fields. The implications of such behavior pertain to the modeling of polar and charged solutes in lipidic environments.
PMCID: PMC3070209  PMID: 21414823
18.  Tailoring Silver Nanodots for Intracellular Staining 
Through tailored oligonucleotide scaffolds, Ag nanocluster syntheses have yielded thermally and cell culture stable silver cluster-based emitters. Optimizing ssDNA stability has enabled creation of highly concentrated and spectrally pure nanocluster emitters with strong intracellular emission. Both fixed and live-cell staining become possible, and intracellular delivery is demonstrated both through conjugation to cell penetrating peptides and via microinjection.
PMCID: PMC3142624  PMID: 21063587
19.  A 12-year-old Child with Trichinellosis, Pyomyositis and Secondary Osteomyelitis 
Trichinellosis is a parasitic infestation affecting the skeletal muscles. Cases of trichinellosis in humans have been reported from most regions of the world. However, a review of literature revealed only two reported cases of human trichinellosis in India. Further, a diagnosis of superimposed pyomyositis in trichinellosis with secondary osteomyelitis has not been reported to our knowledge. This article reports this rare case presentation in a 12-year-old child. Timely intervention helped prevent long-term morbidity in our patient. In our case report, we also discuss in detail the pathogenesis of such a condition and discuss the role of imaging modalities and an early magnetic resonance imaging (MRI) to diagnose the condition and start an early treatment.
PMCID: PMC3326967  PMID: 22529635
Osteomyelitis; Pyomyositis; Trichinella spiralis; Trichinellosis
20.  Pediatric Femoral Neck Fractures: Our 10 Years of Experience 
Clinics in Orthopedic Surgery  2011;3(4):302-308.
Femoral neck fractures are rare injuries in children, but the high incidence of long term complications make it an important clinical entity. The aim of this retrospective study was to analyze the clinical outcomes of pediatric femur neck fractures that we managed over a 10 year period.
The study included 36 children (20 boys and 16 girls) who sustained femoral neck fractures and completed a minimum follow-up of one year. The children were treated either conservatively, or by open reduction and internal fixation (ORIF), or closed reduction and internal fixation (CRIF). The outcomes were analyzed using Ratliff criteria and a detailed record of complications was kept for all patients.
The mean age of included patients was 10 years (range, 3 to 16 years) and the average follow-up was 3.2 years (range, 1.1 to 8.5 years). Based on Delbet's classification system, there were 0 type I (transepiphyseal), 16 type II, 11 type III, and 9 type IV fractures. There were 8 undisplaced fractures, 4 of which later displaced after being managed initially in a hip spica. A satisfactory outcome was obtained in 27 (75%) children. Avascular necrosis (AVN) was the most common complication. It was seen in 7 of our patients, all of whom had an unsatisfactory outcome. Other complications included three cases each of coxa vara, non-union, and arthritic changes; and one case each of infection, primary screw perforation of head, and premature epiphyseal closure. Complications were lowest in the group treated by ORIF. Only 2 patients managed exclusively by conservative treatment ultimately achieved a satisfactory outcome.
We believe that internal fixation of pediatric femoral neck fractures is preferred whenever feasible because conservative treatment carries a high risk of failure of reduction. Aggressive operative treatments aimed at anatomical reduction should be the goal and there should be no hesitation in choosing ORIF over CRIF. Outcome of patients is influenced primarily by development of AVN which occurs as an independent entity without much relation to the mode of treatment carried out.
PMCID: PMC3232358  PMID: 22162793
Pediatric femur neck fracture; Avascular necrosis; Open reduction and internal fixation; Ratliff; Delbet classification
21.  78-Year-Old Man With Nausea and Chest Pain 
Mayo Clinic Proceedings  2011;86(5):465-468.
PMCID: PMC3084649  PMID: 21531888
22.  Non-additive Empirical Force Fields for Short-Chain Linear Alcohols: Methanol to Butanol. Hydration Free Energetics and Kirkwood-Buff Analysis Using Charge Equilibration Models 
The journal of physical chemistry. B  2010;114(34):11076-11092.
Building upon the nonadditive electrostatic force field for alcohols based on the CHARMM charge equilibration (CHEQ) formalism, we introduce atom-pair specific solute-solvent Lennard-Jones (LJ) parameters for alcohol-water interaction force fields targeting improved agreement with experimental hydration free energies of a series of small molecule linear alcohols as well as ab initio water-alcohol geometries and energetics. We consider short-chain, linear alcohols from methanol to butanol as they are canonical small-molecule organic model compounds to represent the hydroxyl chemical functionality for parameterizing biomolecular force fields for proteins. We discuss molecular dynamics simulations of dilute aqueous solutions of methanol and ethanol in TIP4P-FQ water, with particular discussion of solution densities, structure defined in radial distribution functions, electrostatic properties (dipole moment distributions), hydrogen bonding patterns of water, as well as a Kirkwood-Buff (KB) integral analysis. Calculation of the latter provides an assessment of how well classical force fields parameterized to at least semi-quantitatively match experimental hydration free energies capture the microscopic structures of dilute alcohol solutions; the latter translate into macroscopic thermodynamic properties through the application of KB analysis. We find that the CHEQ alcohol force fields of this work semi-quantitatively match experimental KB integrals for methanol and ethanol mole fractions of 0.1 and 0.2. The force field combination qualitatively captures the concentration dependence of the alcohol-alcohol and water-water KB integrals, but due to inadequacies in the representation of the microscopic structures in such systems (which cannot be parameterized in any systematic fashion), a priori quantitative description of alcohol-water KB integrals remains elusive.
PMCID: PMC2928884  PMID: 20687517
23.  Role of Electrostatics in Modulating Hydrophobic Interactions and Barriers to Hydrophobic Assembly 
The journal of physical chemistry. B  2010;114(24):8107-8117.
Hydrophobic effects continue to be an active area of research due to implications for a wide range of physicochemical phenomena. Molecular dynamics simulations have been used extensively in the study of such effects using various water potential models, with few studies addressing the differences between models. In particular, studies considering the explicit treatment of water polarizability are underrepresented in the literature. We present results from molecular dynamics simulations that systematically compare the dependence of large-scale hydrophobic effects on water model. We consider three common non-polarizable models (SPC/E, TIP3P, TIP4P) and two common polarizable models (TIP4P-FQ and SWM4-NDP). Results highlight the similarities and differences of the different water models in the vicinity of two large hydrophobic plates. In particular, profiles of average density, density fluctuations, orientation, and hydrogen bonding show only minor differences among the water models studied. However, the potential of mean force for the hydrophobe dimerization is significantly reduced in the polarizable water systems. TIP4P-FQ shows the deepest minimum of approximately −54(±3) kcal/mol compared to −40(±3), −40(±2), −42(±3), −45(±5) kcal/mol for TIP4P, TIP3P, SPC/E, and SWM4-NDP (all relative to the dissociated state). We discuss the relationship between hydrophobic association and the strength of water-water interactions in the liquid-phase. Results suggest models treating polarizability (both implicitly and explicitly) influence a stronger driving force towards hydrophobic assembly. Implications of these results, as well as prospectives on future work are discussed.
PMCID: PMC2916683  PMID: 20509706
24.  Successful Ablation of a Left-Sided Accessory Pathway in a Patient with Coronary Sinus Atresia and Arteriovenous Fistula: Clinical and Developmental Insights 
Background and objectives
While radiofrequency ablation catheter ablation of accessory pathways is generally safe and effective, anatomic variants can cause considerable challenges in effecting cure. Our objective was to use an unusual case where coronary sinus was absent and arterial venous fistula was present and a left-sided pathway required mapping and ablation to develop a framework to approach difficult cases.
A detailed literature search and review of contemporary cardiac embryology was undertaken to attempt and to explain a common developmental anomaly. Adjunctive approaches during the ablation procedure, including intracardiac ultrasound, were used to guide mapping and ablation despite the lack of coronary sinus access.
The accessory pathway was successfully ablated using a transseptal approach and intracardiac ultrasound guided mapping of the mitral annulus. A potential common mechanism to explain the apparently disparate anatomic variants in this patient was formulated.
Cardiac conduction development is complex and accessory pathway conduction may occur in the setting of arteriovenous anomalies thus providing insights as to the cause of WPW syndrome. Successful mapping and targeted ablation of left-sided pathways may be accomplished even when coronary sinus access is not possible.
PMCID: PMC3063614  PMID: 21468248
Coronary sinus; coronary AV fistula; accessory pathway; epicardially-derived cells; coronary atresia
25.  Revised Charge Equilibration Parameters for More Accurate Hydration Free Energies of Alkanes 
Chemical physics letters  2010;484(4-6):173.
We present a refined alkane charge equilibration (CHEQ) force field, improving our previously reported CHEQ alkane force field[1] to better reproduce experimental hydration free energies. Experimental hydration free energies of ethane, propane, butane, pentane, hexane, and heptane are reproduced to within 3.6% on average. We demonstrate that explicit polarization results in a shift in molecular dipole moment for water molecules associated with the alkane molecule. We also show that our new parameters do not have a significant effect on the alkane-water interactions as measured by the radial distribution function (RDF).
PMCID: PMC2818315  PMID: 20161648
alkanes; hydration free energy; thermodynamic integration; force field; charge equilibration

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