Uncertainties of predictions from temperature replica exchange simulations.

Parallel tempering molecular dynamics simulation, also known as temperature replica exchange simulation, is a popular enhanced sampling method used to study biomolecular systems. This method makes it possible to calculate the free energy differences between states of the system for a series of temperatures. We developed a method to easily calculate the errors (standard errors or confidence intervals) of these predictions using a modified version of our recently introduced JumpCount method. The number of transitions between states (e.g., protein folding events) is counted for each temperature. This number of transitions, together with the temperature, fully determines the value of the standard error or the confidence interval of the free energy difference. We also address the issue of convergence in the situation where all replicas start from one state by developing an estimator of the equilibrium constant from simulations that are not fully equilibrated. The prerequisite of the method is the Markovianity of the process studied.

Synthesis and unexpected binding of monofluorinated N,N'-diacetylchitobiose and LacdiNAc to wheat germ agglutinin.

Fluorination of carbohydrate ligands of lectins is a useful approach to examine their binding profile, improve their metabolic stability and lipophilicity, and convert them into 19F NMR-active probes. However, monofluorination of monovalent carbohydrate ligands often leads to a decreased or completely lost affinity. By chemical glycosylation, we synthesized the full series of methyl ß-glycosides of N,N'-diacetylchitobiose (GlcNAcß(1-4)GlcNAcß1-OMe) and LacdiNAc (GalNAcß(1-4)GlcNAcß1-OMe) systematically monofluorinated at all hydroxyl positions. A competitive enzyme-linked lectin assay revealed that the fluorination at the 6'-position of chitobioside resulted in an unprecedented increase in affinity to wheat germ agglutinin (WGA) by one order of magnitude. For the first time, we have characterized the binding profile of a previously underexplored WGA ligand LacdiNAc. Surprisingly, 4'-fluoro-LacdiNAc bound WGA even stronger than unmodified LacdiNAc. These observations were interpreted using molecular dynamic calculations along with STD and transferred NOESY NMR techniques, which gave evidence for the strengthening of CH/π interactions after deoxyfluorination of the side chain of the non-reducing GlcNAc. These results highlight the potential of fluorinated glycomimetics as high-affinity ligands of lectins and 19F NMR-active probes.

Pars Plana Vitrectomy in the Treatment of Rhegmatogenous Retinal Detachment.

AIM: The aim of the study is to retrospectively evaluate the anatomical success rate and functional results of 25G+ PPV in the treatment of newly diagnosed rhegmatogenous retinal detachment (RRD). MATERIAL AND METHODS: The set consists of 152 eyes of 152 patients, of which 71 (47%) were men, average age 54 years, operated on by one surgeon for RRD at the Eye Clinic of the University Hospital and Medical Faculty of Masaryk University Brno from 1.7.2019 to 4.5.2021 using the 25G+ PPV technique. 25G+ PPV with pre-equatorial cerclage was performed on 7 patients. The patients' anamnesis included blunt ocular trauma and uncomplicated cataract surgery with implantation of a posterior chamber intraocular lens. The cause of RRD was retinal tear/s, regardless of their number and location. The transparency of the anterior segment of the eye enabled reliable visualization of the posterior segment. Preoperative proliferative vitreoretinopathy (PVR) grade A-D2 was admissible. Patients with a history of penetrating ocular trauma were excluded. The postoperative findings and functional outcomes of the patients were evaluated 1-3 months after PPV. The operation was anatomically successful if the retina was fully attached. Final visual acuity (VA) was evaluated for each patient. The final visual acuity examination was carried out typically on a Snellen optotype, either without correction, with the patient's own spectacle correction or with correction according to the current values on the autorefractometer. The arithmetic average was used for the numerical expression of the attained results, and the numerical values were also expressed in percentages. Since the different groups were not compared with each other, no statistical test was necessary to analyze the results. RESULTS: In 150 (98.7%) of the 152 patients in the group, we achieved complete retinal reattachment, in 2 (1.3%) patients the retina remained detached, and we recorded anatomical failure of the treatment. Fifty (33%) patients achieved VA ≥ 4/8. CONCLUSION: In 133 (87.5%) patients, we are able to state anatomical success even without the presence of intraocular tamponade in the operated eye. These patients can be considered completely cured. 25G+ PPV has demonstrated its contribution to resolving RRD.

Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics.

The potential of molecular simulations is limited by their computational costs. There is often a need to accelerate simulations using some of the enhanced sampling methods. Metadynamics applies a history-dependent bias potential that disfavors previously visited states. To apply metadynamics, it is necessary to select a few properties of the system─collective variables (CVs) that can be used to define the bias potential. Over the past few years, there have been emerging opportunities for machine learning and, in particular, artificial neural networks within this domain. In this broad context, a specific unsupervised machine learning method was utilized, namely, parametric time-lagged t-distributed stochastic neighbor embedding (ptltSNE) to design CVs. The approach was tested on a Trp-cage trajectory (tryptophan cage) from the literature. The trajectory was used to generate a map of conformations, distinguish fast conformational changes from slow ones, and design CVs. Then, metadynamic simulations were performed. To accelerate the formation of the α-helix, we added the α-RMSD collective variable. This simulation led to one folding event in a 350 ns metadynamics simulation. To accelerate degrees of freedom not addressed by CVs, we performed parallel tempering metadynamics. This simulation led to 10 folding events in a 200 ns simulation with 32 replicas.

Free Energy Differences from Molecular Simulations: Exact Confidence Intervals from Transition Counts.

Here, we demonstrate a method to estimate the uncertainty (confidence intervals and standard errors) of free energy differences calculated by molecular simulations. The widths of confidence intervals and standard errors can be calculated solely from temperature and the number of transitions between states. Uncertainty (95% confidence interval) lower than ±1 kcal/mol can be achieved by a simulation with four forward and four reverse transitions. For a two-state Markovian system, the confidence interval is exact, regardless the number of transitions.

Clinical experience in timed arterial compression contrast-enhanced magnetic resonance angiography of the hand.

PURPOSE: A retrospective analysis of the diagnostic performance of the timed arterial compression (TAC) technique, which allows freezing of the contrast bolus during first-pass contrast-enhanced (CE) magnetic resonance angiography (MRA) to diagnose vascular pathologies in the hand. MATERIAL AND METHODS: A total of 14 consecutive CE-MRAs of the hand were acquired by using the TAC technique. By inflating a blood pressure cuff up to 200 mm Hg triggered to the arterial contrast filling of the hand, prolonged measurement times up to 144 seconds, with a spatial resolution of 0.59 × 0.59 × 0.8 mm(3), could be realized. Overall image qualities, arterial signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), and vessel conspicuity besides the final diagnosis were evaluated. RESULTS: All 14 TAC-CE-MRAs of the hand were successfully accomplished without any adverse events and yielded, in all cases, a final diagnosis with a high total number of vascular pathologies (57). High arterial SNR and CNR values exceeding the soil of 85 and 60, respectively, resulted. Thus, overall vessel visibility (>90%), vessel conspicuity (mean Δ signal intensity [SI]/mm = 1,193) and image quality on a per patient level (>60%) were rated as excellent or good. CONCLUSIONS: TAC-CE-MRA of the hand offers high diagnostic performance because of its increased spatial resolution while preserving contrast, which allowed detection of tiny stenoses of the digital arteries.