Project description:Bennett lesions, also known as "thrower's exostosis" of the shoulder, involve ossification of the posteroinferior glenoid and are not uncommon in overhead throwing athletes. The literature surrounding the optimal operative management of the symptomatic Bennett lesion is limited. The purpose of this article is to describe the arthroscopic surgical technique for the visualization and excision of the symptomatic extra-articular pathologic ossification involving the posteroinferior glenoid. Because many surgeons may not be familiar with this problem or procedure, we present a straightforward method that allows for identification and excision of the exostosis through an arthroscopic posterior arthrotomy.
Project description:THE RELIABILITY OF FREE ENERGY SIMULATIONS (FES) IS LIMITED BY TWO FACTORS: (a) the need for correct sampling and (b) the accuracy of the computational method employed. Classical methods (e.g., force fields) are typically used for FES and present a myriad of challenges, with parametrization being a principle one. On the other hand, parameter-free quantum mechanical (QM) methods tend to be too computationally expensive for adequate sampling. One widely used approach is a combination of methods, where the free energy difference between the two end states is computed by, e.g., molecular mechanics (MM), and the end states are corrected by more accurate methods, such as QM or hybrid QM/MM techniques. Here we report two new approaches that significantly improve the aforementioned scheme; with a focus on how to compute corrections between, e.g., the MM and the more accurate QM calculations. First, a molecular dynamics trajectory that properly samples relevant conformational degrees of freedom is generated. Next, potential energies of each trajectory frame are generated with a QM or QM/MM Hamiltonian. Free energy differences are then calculated based on the QM or QM/MM energies using either a non-Boltzmann Bennett approach (QM-NBB) or non-Boltzmann free energy perturbation (NB-FEP). Both approaches are applied to calculate relative and absolute solvation free energies in explicit and implicit solvent environments. Solvation free energy differences (relative and absolute) between ethane and methanol in explicit solvent are used as the initial test case for QM-NBB. Next, implicit solvent methods are employed in conjunction with both QM-NBB and NB-FEP to compute absolute solvation free energies for 21 compounds. These compounds range from small molecules such as ethane and methanol to fairly large, flexible solutes, such as triacetyl glycerol. Several technical aspects were investigated. Ultimately some best practices are suggested for improving methods that seek to connect MM to QM (or QM/MM) levels of theory in FES.
Project description:Hairy vetch, Vicia villosa (Roth), is a cover crop that does not exhibit a typical domestication syndrome. Pod dehiscence reduces seed yield and creates weed problems for subsequent crops. Breeding efforts aim to reduce pod dehiscence in hairy vetch. To characterize pod dehiscence in the species, we quantified visual dehiscence and force required to cause dehiscence among 606 genotypes grown among seven environments of the United States. To identify potential secondary selection traits, we correlated pod dehiscence with various morphological pod characteristics and field measurements. Genotypes of hairy vetch exhibited wide variation in pod dehiscence, from completely indehiscent to completely dehiscent ratings. Mean force to dehiscence also varied widely, from 0.279 to 8.97 N among genotypes. No morphological traits were consistently correlated with pod dehiscence among environments where plants were grown. Results indicated that visual ratings of dehiscence would efficiently screen against genotypes with high pod dehiscence early in the breeding process. Force to dehiscence may be necessary to identify the indehiscent genotypes during advanced stages of selection.
Project description:The multistate Bennett acceptance ratio method (MBAR) and unbinned weighted histogram analysis method (UWHAM) are widely employed approaches to calculate relative free energies of multiple thermodynamic states that gain statistical precision by employing free energy contributions from configurations sampled at each of the simulated ? states. With the increasing availability of high throughput computing resources, a large number of configurations can be sampled from hundreds or even thousands of states. Combining sampled configurations from all states to calculate relative free energies requires the iterative solution of large scale MBAR/UWHAM equations. In the current work, we describe the development of a fast solver to iteratively solve these large scale MBAR/UWHAM equations utilizing our previous findings that the MBAR/UWHAM equations can be derived as a Rao-Blackwell estimator. The solver is implemented and distributed as a Python module called FastMBAR. Our benchmark results show that FastMBAR is more than 2 times faster than the widely used solver pymbar, when it runs on a central processing unit (CPU) and more than 100 times faster than pymbar when it runs on a graphical processing unit (GPU). The significant speedup achieved by FastMBAR running on a GPU is useful not only for solving large scale MBAR/UWHAM equations but also for estimating uncertainty of calculated free energies using bootstrapping where the MBAR/UWHAM equations need to be solved multiple times.
Project description:The Bennett lesion is an extra-articular ossification at the posteroinferior glenoid rim that is common among overhead-throwing athletes. While the majority of these exostoses are asymptomatic, some may cause posterior shoulder pain during throwing motion and frequently have concomitant posterior labral tears. Multiple approaches to Bennett lesion resection have been described, and there is debate regarding the need for capsulotomy, posterior labral repair, and capsular repair. The purpose of this article is to describe our preferred surgical technique for arthroscopic Bennett lesion resection and posterior labral repair using knotless all-suture anchors.
Project description:Can governments increase private savings by taxing savings up front instead of in retirement? Roth 401(k) contributions are not tax-deductible in the contribution year, but withdrawals in retirement are untaxed. The more common before-tax 401(k) contribution is tax-deductible in the contribution year, but both principal and investment earnings are taxed upon withdrawal. Using administrative data from eleven companies that added a Roth contribution option to their existing 401(k) plan between 2006 and 2010, we find no evidence that total 401(k) contribution rates differ between employees hired before versus after Roth introduction, which implies that take-home pay declines and the amount of retirement consumption being purchased by 401(k) contributions increases after Roth introduction. We reject several neoclassical explanations for our null finding. Results from a survey experiment suggest two behavioral explanations: (1) employee confusion about and neglect of the tax properties of Roth balances and (2) partition dependence.
Project description:Elevated CO(2) and ozone effects were studied singly and in combination on the crown structure of two Betula pendula clones. Measurements were made at the end of the second fumigation period in an open-top-chamber experiment with 9-year-old trees. Shoot ramification (number of long and short daughter shoots), shoot length, and number of metamers, leaves and buds were measured at four positions in every tree. As a result of increased temperature, trees in chambers had longer shoots and more frequent shoot ramification than control trees not enclosed in chambers. Ozone treatment decreased shoot ramification significantly. Additionally, ozone treatment resulted in an increased number of metamers in one clone. There was no statistically significant interaction between ozone effect and crown position; however, there was a slight tendency for the lower crown to be more affected by ozone. Elevated CO(2) caused a significant increase in the number of long-shoot metamers. Therefore, 2x ambient CO(2) concentration partly ameliorated the negative effect of ozone because the increased number of leaves per shoot counteracted the decreased branching. Although the main effects of elevated ozone and CO(2) were similar in the two clones, slight, statistically insignificant, differences appeared in their responses when interactions with crown position were considered.
Project description:The dual-basin G?-model is a structural-based coarsegrained model for simulating a conformational transition between two known structures of a protein. Two parameters are required to produce a dual-basin potential mixed using two single-basin potentials, although the determination of mixing parameters is usually not straightforward. Here, we have developed an efficient scheme to determine the mixing parameters using the Multistate Bennett Acceptance Ratio (MBAR) method after short simulations with a set of parameters. In the scheme, MBAR allows us to predict observables at various unsimulated conditions, which are useful to improve the mixing parameters in the next round of iterative simulations. The number of iterations that are necessary for obtaining the converged mixing parameters are significantly reduced in the scheme. We applied the scheme to two proteins, the glutamine binding protein and the ribose binding protein, for showing the effectiveness in the parameter determination. After obtaining the converged parameters, both proteins show frequent conformational transitions between open and closed states, providing the theoretical basis to investigate structure-dynamics-function relationships of the proteins.