Study of a model for the folding of a small protein

We describe the results obtained from an improved model for protein folding. We find that a good agreement with the native structure of a 46 residue long, five-letter protein segment is obtained by carefully tuning the parameters of the self-avoiding energy. In particular we find an improved free-energy profile. We also compare the efficiency of the multidimensional replica exchange method with the widely used parallel tempering.Comment: typos corrected, one figure adde

Causes of congenital corneal opacities and their management in a tertiary care center.

PURPOSE: To evaluate causes and management of congenital corneal opacities (CCO) diagnosed in a tertiary care eye center and to compare the data with a previous study at the same institution. METHODS: Computerized medical records in all patients with congenital corneal opacities diagnosed in the Cornea Service at Wills Eye Hospital (Philadelphia, PA) between January 1, 2007, and December 31, 2015, were retrospectively reviewed. Children aged 12 years and younger at the first visit were included in the study. Patients\u27 demographics, ocular diagnosis, laterality, associated ocular abnormalities, other ocular surgery performed prior or subsequent to the first visit, and their treatment were extracted from the medical records. RESULTS: A total of 77 eyes in 56 patients were examined. The mean age at presentation was 32.8 ± 44.2 months, with the mean follow-up period of 26.7 ± 30.1 months. The most frequent diagnosis was Peters anomaly (53.2%), followed by limbal dermoid (13.0%), aniridia with glaucoma and microphthalmos (6.5%), sclerocornea and congenital glaucoma (5.2%), idiopathic (3.9%), Axenfeld-Rieger anomaly and Hurler syndrome (2.6%), and microcornea (1.3%). Primary keratoplasty was performed in 26 eyes, with the outcome rate in the clear cornea of 76.0% during the follow-up. CONCLUSION: Peters anomaly is the most common cause of congenital corneal opacities encountered at our institution. Penetrating keratoplasty is the most frequent choice of corneal surgery to treat congenital corneal opacities. Additional interventions during penetrating keratoplasty were moderately positively correlated with graft failure. This study also shows the rates of some etiologies of that changed over the recent decades in our tertiary care Cornea Service. Although Peters anomaly remains the most common presenting reason for congenital corneal opacities, its rate appears to be increasing over the recent decade. Congenital corneal opacities due to birth trauma, which is one of the preventable causes, were observed in a previous study in our clinic; however, no new cases were noted in this study

Anterior Chamber Characteristics, Endothelial Parameters, and Corneal Densitometry After Descemet Stripping Automated Endothelial Keratoplasty in Patients With Fuchs Dystrophy

Purpose: To compare anterior segment parameters in patients with Fuchs endothelial dystrophy (FED) who underwent Descemet stripping automated endothelial keratoplasty (DSAEK) in one eye and no corneal surgery in the fellow eye. Methods: This prospective study was conducted on 28 eyes of 14 patients with FED who underwent DSAEK in one eye at least one year prior (DSAEK group) and no corneal surgery in the fellow eye (control group). Each eye was analyzed with the anterior segment optical coherence tomography, specular microscopy, and Scheimpflug imaging systems. Data were compared between the two groups. Results: The mean age of the patients was 76.9 ± 7.0 years. There were no statistically significant differences in the mean central corneal thickness (CCT), central anterior chamber depth, anterior chamber angle parameters, cylinder and keratometry values between two groups (all P-values > 0.05). The paracentral corneal thickness, corneal volume, endothelial cell density, and hexagonal cell ratio measurements were statistically significantly higher in the DSAEK group than the control (all P-values < 0.05), and anterior chamber volume in the DSAEK group was significantly less than the control (P = 0.046). While posterior and total corneal densitometry values in the DSAEK group were statistically significantly lower than the control (P < 0.001 and P = 0.011, respectively), there were no statistically significant differences in the anterior or middle corneal densities (P = 0.108 and P = 0.134, respectively). Conclusion: We found that total corneal densitometry value decreased in DSAEK group. Although DSAEK surgery did not affect the anterior chamber angle parameters, it reduced the anterior chamber volume and increased the corneal volume and paracentral corneal thickness due to the addition of the DSAEK graft

Light Quark Physics with Dynamical Wilson Fermions

We present results for spectroscopy, quark masses and decay constants obtained from SESAM's and TkL's large statistics simulations of QCD with two dynamical Wilson fermions.Comment: 3 pages; to appear in the proceedings of Lat.'9

Transcriptional down-regulation of ccr5 in a subset of HIV+ controllers and their family members.

HIV +Elite and Viremic controllers (EC/VCs) are able to control virus infection, perhaps because of host genetic determinants. We identified 16% (21 of 131) EC/VCs with CD4 +T cells with resistance specific to R5-tropic HIV, reversed after introduction of ccr5. R5 resistance was not observed in macrophages and depended upon the method of T cell activation. CD4 +T cells of these EC/VCs had lower ccr2 and ccr5 RNA levels, reduced CCR2 and CCR5 cell-surface expression, and decreased levels of secreted chemokines. T cells had no changes in chemokine receptor mRNA half-life but instead had lower levels of active transcription of ccr2 and ccr5, despite having more accessible chromatin by ATAC-seq. Other nearby genes were also down-regulated, over a region of ~500 kb on chromosome 3p21. This same R5 resistance phenotype was observed in family members of an index VC, also associated with ccr2/ccr5 down-regulation, suggesting that the phenotype is heritable

Glueballs and string breaking from full QCD

We present results on the static potential, and torelon and glueball masses from simulations of QCD with two flavours of dynamical Wilson fermions on $16^3\times 32$ and $24^3\times 40$ lattices at $\beta=5.6$.Comment: Talk presented by Gunnar Bali at International Symposium on Lattice Field Theories (Lattice 97), Edinburgh, July 1997, 3 pages LaTeX (epscrc2.sty) with 4 eps figure

Critical Dynamics of the Hybrid Monte Carlo Algorithm

We investigate the critical dynamics of the Hybrid Monte Carlo algorithm approaching the chiral limit of standard Wilson fermions. Our observations are based on time series of lengths O(5000) for a variety of observables. The lattice sizes are 16^3 x 32 and 24^3 x 40. We work at beta=5.6, and kappa=0.156, 0.157, 0.1575, 0.158, with 0.83 > m_pi/m_rho > 0.55. We find surprisingly small integrated autocorrelation times for local and extended observables. The dynamical critical exponent $z$ of the exponential autocorrelation time is compatible with 2. We estimate the total computational effort to scale between V^2 and V^2.25 towards the chiral limit.Comment: 3 pages, Latex with espcrc2.sty and postscript figures, Talk given at Lattice 9

Expert consensus on the identification, diagnosis, and treatment of neurotrophic keratopathy

BACKGROUND: Neurotrophic keratopathy (NK) is a relatively uncommon, underdiagnosed degenerative corneal disease that is caused by damage to the ophthalmic branch of the trigeminal nerve by conditions such as herpes simplex or zoster keratitis, intracranial space-occupying lesions, diabetes, or neurosurgical procedures. Over time, epithelial breakdown, corneal ulceration, corneal melting (thinning), perforation, and loss of vision may occur. The best opportunity to reverse ocular surface damage is in the earliest stage of NK. However, patients typically experience few symptoms and diagnosis is often delayed. Increased awareness of the causes of NK, consensus on when and how to screen for NK, and recommendations for how to treat NK are needed. METHODS: An 11-member expert panel used a validated methodology (a RAND/UCLA modified Delphi panel) to develop consensus on when to screen for and how best to diagnose and treat NK. Clinicians reviewed literature on the diagnosis and management of NK then rated a detailed set of 735 scenarios. In 646 scenarios, panelists rated whether a test of corneal sensitivity was warranted; in 20 scenarios, they considered the adequacy of specific tests and examinations to diagnose and stage NK; and in 69 scenarios, they rated the appropriateness of treatments for NK. Panelist ratings were used to develop clinical recommendations. RESULTS: There was agreement on 94% of scenarios. Based on this consensus, we present distinct circumstances when we strongly recommend or may consider a test for corneal sensitivity. We also present recommendations on the diagnostic tests to be performed in patients in whom NK is suspected and treatment options for NK. CONCLUSIONS: These expert recommendations should be validated with clinical data. The recommendations represent the consensus of experts, are informed by published literature and experience, and may improve outcomes by helping improve diagnosis and treatment of patients with NK

SESAM and TXL Results for Wilson Action--A Status Report

Results from two studies of full QCD with two flavours of dynamical Wilson fermions are presented. At beta=5.6, the region 0.83 > m_pi/m_rho > 0.56 at m_pia > 0.23 L^{-1} is explored. The SESAM collaboration has generated ensembles of about 200 statistically independent configurations on a 16^3 x 32-lattice at three different kappa-values and is entering the final phase of data analysis. The TXL simulation on a 24^3 x 40-lattice at two kappa-values has reached half statistics and data analysis has started recently, hence most results presented here are preliminary. The focus of this report is fourfold: we demonstrate that algorithmic improvements like fast Krylov solvers and parallel preconditioning recently introduced can be put into practise in full QCD simulations, we present encouraging observations as to the critical dynamics of the Hybrid Monte Carlo algorithm in the approach to the chiral limit, we mention signal improvements of noisy estimator techniques for disconnected diagrams to the pi-N sigma term, and we report on SESAM's results for light hadron spectrum, light quark masses, and heavy quarkonia.Comment: 24 pages, tex + postscript figures, to appear in Proceedings of Int. Workshop "Lattice QCD on Parallel Computers", University of Tsukuba, Japa