Biomolecular simulations are routinely used in biochemistry and molecular biology research; however, they often fail to match expectations of their impact on pharmaceutical and biotech industry. This is caused by the fact that a vast amount of computer time is required to simulate short episodes from the life of biomolecules. Several approaches have been developed to overcome this obstacle, including application of massively parallel and special purpose computers or non-conventional hardware. Methodological approaches are represented by coarse-grained models and enhanced sampling techniques. These techniques can show how the studied system behaves in long time-scales on the basis of relatively short simulations. This review presents an overview of new simulation approaches, the theory behind enhanced sampling methods and success stories of their applications with a direct impact on biotechnology or drug design.
Cíl. Cílem studie bylo stanovit diagnostickou výtěžnost kontrastní MR angiografie (MRA) s použitím paralelních akvizičních technik v diagnostice stenózy renální tepny. Metoda. Celkem bylo vyšetřeno 70 nemocných s hypertenzní chorobou a podezřením na stenózu renální tepny. Vyšetření byla prováděna na přístroji Magnetom Symphony Maestro Class 1,5 T s použitím array cívek. Průchod bolusu kontrastní látky byl monitorován metodou bolus tracking. Parametry MRA sekvence byly: TR 3,7 ms; TE 1,2 ms; flip angle 25o; akviziční doba 18 s; velikost voxelu 1,1× 1,0×1,1 mm; centrický náběr dat v k-prostoru; paralelní akviziční techniky s akceleračním faktorem 2 (GRAPPA). Za hemodynamicky významnou byla považována stenóza 60 % a více. Výsledky MRA byly porovnávány s nálezem na digitální subtrakční angiografii, která sloužila jako zlatý standard. Výsledky. Senzitivita a specificita MRA v detekci hemodynamicky významné stenózy renální tepny byla 92 %, respektive 95 %. Její prevalence v našem souboru činila 37 %. Závěr. Při splnění parametrů dostatečného geometrického rozlišení vykazuje kontrastní MR angiografie vysokou senzitivitu a specificitu v diagnostice stenózy renální tepny.
Aim. The aim of our study was to assess the diagnostic value of contrast-enhanced MR angiography (MRA) utilizing parallel acquisition techniques in the detection of renal artery stenosis. Method. Seventy hypertensive subjects with suspected renal artery stenosis were examined on a 1.5 Tesla MR system with body array coil. Bolus tracking was used to monitor the arrival of contrast agent to the abdominal aorta. The MRA sequence parameters were as follows: TR 3.7 ms; TE 1.2 ms; flip angle 25°; acquisition time 18 s; voxel size 1.1 × 1.0 × 1.1 mm; centric k-space sampling; parallel acquisition techniques with acceleration factor of 2 (GRAPPA). Renal artery stenosis of 60 % and more was considered hemodynamically significant. The results of MRA were compared to digital subtraction angiography serving as a standard of reference. Results. Sensitivity and specificity of MRA in the detection of hemodynamically significant renal artery stenosis were 92 % and 95 %, respectively. Its prevalence was 37 % in our study population. Conclusion. Contrast-enhanced MRA with high spatial resolution offers sufficient sensitivity and specificity for screening of renal artery stenosis.
- MeSH
- Diagnostic Techniques, Urological utilization MeSH
- Angiography, Digital Subtraction methods utilization MeSH
- Humans MeSH
- Magnetic Resonance Angiography methods instrumentation utilization MeSH
- Renal Artery Obstruction diagnosis etiology physiopathology MeSH
- Hypertension, Renal diagnosis MeSH
- Sensitivity and Specificity MeSH
- Check Tag
- Humans MeSH
- Publication type
- Comparative Study MeSH
Knowledge of the structure and conformational flexibility of carbohydrates in an aqueous solvent is important to improving our understanding of how carbohydrates function in biological systems. In this study, we extend a variant of the Hamiltonian replica-exchange molecular dynamics (MD) simulation to improve the conformational sampling of saccharides in an explicit solvent. During the simulations, a biasing potential along the glycosidic-dihedral linkage between the saccharide monomer units in an oligomer is applied at various levels along the replica runs to enable effective transitions between various conformations. One reference replica runs under the control of the original force field. The method was tested on disaccharide structures and further validated on biologically relevant blood group B, Lewis X and Lewis A trisaccharides. The biasing potential-based replica-exchange molecular dynamics (BP-REMD) method provided a significantly improved sampling of relevant conformational states compared with standard continuous MD simulations, with modest computational costs. Thus, the proposed BP-REMD approach adds a new dimension to existing carbohydrate conformational sampling approaches by enhancing conformational sampling in the presence of solvent molecules explicitly at relatively low computational cost.
The RNA recognition motif (RRM) is the most common RNA binding domain across eukaryotic proteins. It is therefore of great value to engineer its specificity to target RNAs of arbitrary sequence. This was recently achieved for the RRM in Rbfox protein, where four mutations R118D, E147R, N151S, and E152T were designed to target the precursor to the oncogenic miRNA 21. Here, we used a variety of molecular dynamics-based approaches to predict specific interactions at the binding interface. Overall, we have run approximately 50 microseconds of enhanced sampling and plain molecular dynamics simulations on the engineered complex as well as on the wild-type Rbfox·pre-miRNA 20b from which the mutated systems were designed. Comparison with the available NMR data on the wild type molecules (protein, RNA, and their complex) served to establish the accuracy of the calculations. Free energy calculations suggest that further improvements in affinity and selectivity are achieved by the S151T replacement.
- MeSH
- Nucleic Acid Conformation MeSH
- Humans MeSH
- MicroRNAs chemistry genetics metabolism MeSH
- Models, Molecular MeSH
- RNA Recognition Motif * genetics MeSH
- Nuclear Magnetic Resonance, Biomolecular MeSH
- Protein Engineering MeSH
- RNA-Binding Proteins chemistry genetics metabolism MeSH
- RNA chemistry metabolism MeSH
- Amino Acid Sequence MeSH
- Molecular Dynamics Simulation MeSH
- RNA Stability MeSH
- Protein Binding MeSH
- Binding Sites genetics MeSH
- Computational Biology MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
The temporomandibular joint (TMJ) is typically involved in 45-87% of children with Juvenile Idiopathic Arthritis (JIA). Accurate diagnosis of JIA is difficult as various clinical tests, including MRI, disagree. The purpose of this study is to optimize the methodological aspects of Dynamic Contrast Enhanced (DCE) MRI of the TMJ in children. In this cross-sectional study, including data from 73 JIA affected children, aged 6-15 years, effects of motion correction, sampling rate and parametric modelling on DCE-MRI data is investigated. Consensus among three radiologists determined the regions of interest. Quantitative perfusion parameters were estimated using four perfusion models; the Adiabatic Approximation to Tissue Homogeneity (AATH), Distributed Capillary Adiabatic Tissue Homogeneity (DCATH), Gamma Capillary Transit Time (GCTT) and Two Compartment Exchange (2CXM) models. Effects of motion correction were evaluated by a sum of least squares between corrected raw data and the GCTT model. The effect of systematically down sampling the raw data was tested. The sum of least squares was computed across all pharmacokinetic models. Relative difference perfusion parameters between the left and right TMJ were used for an unsupervised k-means based stratification of the data based on a principal component analysis, as well as for a supervised random forest classification. Diagnostic sensitivity and specificity were computed relative to structural image scorings. Paired sample t-tests, as well as ANOVA tests, were used (significant threshold: p < 0.05) with Tukeys post hoc test. High-level elastic motion correction provides the best least square fit to the GCTT model (percental improvement: 72-84%). A 4 s sampling rate captures more of the potentially disease relevant signal variations. The various parametric models all leave comparable residues (relative standard deviation: 3.4%). In further evaluation of DCE-MRI as a potential diagnostic tool for JIA a high-level elastic motion correction scheme should be adopted, with a sampling rate of at least 4 s. Results suggest that DCE-MRI data can be a valuable part in JIA diagnostics in the TMJ.
- MeSH
- Artifacts MeSH
- Child MeSH
- Arthritis, Juvenile diagnostic imaging MeSH
- Humans MeSH
- Magnetic Resonance Imaging * MeSH
- Adolescent MeSH
- Image Processing, Computer-Assisted * MeSH
- Movement * MeSH
- Child, Preschool MeSH
- Cross-Sectional Studies MeSH
- Sensitivity and Specificity MeSH
- Models, Statistical * MeSH
- Temporomandibular Joint diagnostic imaging MeSH
- Check Tag
- Child MeSH
- Humans MeSH
- Adolescent MeSH
- Male MeSH
- Child, Preschool MeSH
- Female MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Cíl: Vliv protokolu zrychlené zotavení po operaci (ERAS) na pooperační výsledky po urogynekologické operaci zatím zůstává předmětem zkoumání. Tato studie se snažila zhodnotit toto téma srovnáním pacientů, kteří měli konvenční nebo ERAS – řízenou perioperační péči, a to u několika klinických endpointů vč. chůze, délky pobytu v nemocnici (LOS), opětovné hospitalizace a pooperačních komplikací. Materiál a metody: Celkem 121 pacientů podstupujících operaci z důvodu prolapsu pánevního orgánu bylo rozděleno do dvou větví studie – protokol ERAS (skupina E) a konvenční péče (skupina C). Mezi skupinami byly porovnány proměnné zahrnující obnovení chuti k jídlu, vyprazdňování, krvácivé příhody, další komplikace, LOS a opětovné hospitalizaci. Výsledky: Pacienti skupiny C dostávali významně intenzivněji intravenózní tekutinovou léčbu ve srovnání se skupinou E (2 760 ± 656 vs. 1 045 ± 218 ml, p < 0,001). Doba potřebná k prvnímu flatusu, první defekaci, požití pevné stravy a chůzi (p < 0,001) byla také delší u první skupiny pacientů. Při použití protokolu ERAS byla významně snížena délka pobytu v nemocnici (2,5 ± 1,1 vs. 2,0 ± 0,6 dne, p < 0,001). Na druhou stranu se obě skupiny ukázaly jako srovnatelné co se týče pooperačních komplikací, včetně infekcí v místě provedení chirurgického výkonu, kardiovaskulárních komplikací, nespecifických bolestí břicha, subileu, krevních ztrát a míry opětovné hospitalizace. Závěr: V námi zkoumané populaci vedl protokol ERAS k časnému zahájení perorálního příjmu, časnému obnovení funkce střev, časné mobilizaci a dřívějšímu propuštění pacientů bez snížení bezpečnosti po urogynekologické operaci.
Objective: The impact of enhanced recovery after surgery (ERAS) protocol on postoperative outcomes after urogynecological surgery is yet to be a matter of investigation. This study sought to evaluate this issue by comparing the patients who had conventional or ERAS--guided perioperative care for several clinical end-points including ambulation, length of hospital stay (LOS), readmissions, and postoperative complications. Materials and methods: A total of 121 patients undergoing pelvic organ prolapse surgery were allocated to two study arms, ERAS protocol (Group E) or conventional care (Group C). Variables reflecting the restoration of appetite and bowel movements, bleeding events, other complications, LOS and readmissions were compared between the groups. Results: The patients in Group C significantly received a more intensive intravenous fluid treatment compared to Group E (2,760 ± 656 vs. 1,045 ± 218 mL, P < 0.001). Time required for first flatus, first defecation, eating solid food, and ambulation (P < 0.001) were also longer in the former group of patients. Moreover, LOS was significantly reduced when the ERAS protocol was applied (2.5 ± 1.1 vs. 2.0 ± 0.6 days, P < 0.001). On the other hand, the two groups were similar with respect to the frequency of the postoperative complications, including surgical site infections, cardiovascular complications, non-specific abdominal pain, sub-ileus, blood loss and readmission rate. Conclusion: In our sample population, ERAS protocol led to early initiation of oral intake, early recovery of bowel function, early mobilization, and early discharge of patients without compromise in safety concerns after urogynecological surgery.
Significant renal artery stenosis (RAS) is a potentially curable cause of renovascular hypertension and/or renal impairment. It is caused by either atherosclerosis or fibromuscular dysplasia. Correct and timely diagnosis remains a diagnostic challenge. MR angiography (MRA) as a minimally invasive method seems to be suitable for RAS detection, however, its diagnostic value widely differs in the literature (sensitivity 62-100% and specificity 75-100%). The aim of our prospective study was to compare the diagnostic value of contrast-enhanced MRA utilizing parallel acquisition techniques in the detection of significant RAS with digital subtraction angiography (DSA). A total of 78 hypertensive subjects with suspected renal artery stenosis were examined on a 1.5 Tesla MR system using a body array coil. Bolus tracking was used to monitor the arrival of contrast agent to the abdominal aorta. The MRA sequence parameters were as follows: TR 3.7 ms; TE 1.2 ms; flip angle 25 degrees; acquisition time 18s; voxel size 1.1 mm x1.0 mm x 1.1 mm; centric k-space sampling; parallel acquisition technique with acceleration factor of 2 (GRAPPA). Renal artery stenosis of 60% and more was considered hemodynamically significant. The results of MRA were compared to digital subtraction angiography serving as a standard of reference. Sensitivity and specificity of MRA in the detection of hemodynamically significant renal artery stenosis were 90% and 96%, respectively. Prevalence of RAS was 39% in our study population. Contrast-enhanced MRA with high spatial resolution offers sufficient sensitivity and specificity for screening of RAS.
- MeSH
- Algorithms MeSH
- Adult MeSH
- Image Interpretation, Computer-Assisted methods MeSH
- Contrast Media MeSH
- Middle Aged MeSH
- Humans MeSH
- Magnetic Resonance Angiography methods MeSH
- Young Adult MeSH
- Renal Artery Obstruction diagnosis MeSH
- Organometallic Compounds diagnostic use MeSH
- Reproducibility of Results MeSH
- Aged MeSH
- Sensitivity and Specificity MeSH
- Image Enhancement methods MeSH
- Check Tag
- Adult MeSH
- Middle Aged MeSH
- Humans MeSH
- Young Adult MeSH
- Male MeSH
- Aged MeSH
- Female MeSH
- Publication type
- Journal Article MeSH
PURPOSE: The aim of this study was to develop a simple, robust, and easy-to-use calibration procedure for correcting misalignments in rosette MRI k-space sampling, with the objective of producing images with minimal artifacts. METHODS: Quick automatic calibration scans were proposed for the beginning of the measurement to collect information on the time course of the rosette acquisition trajectory. A two-parameter model was devised to match the measured time-varying readout gradient delays and approximate the actual rosette sampling trajectory. The proposed calibration approach was implemented, and performance assessment was conducted on both phantoms and human subjects. RESULTS: The fidelity of phantom and in vivo images exhibited significant improvement compared with uncorrected rosette data. The two-parameter calibration approach also demonstrated enhanced precision and reliability, as evidenced by quantitative T2*$$ {\mathrm{T}}_2^{\ast } $$ relaxometry analyses. CONCLUSION: Adequate correction of data sampling is a crucial step in rosette MRI. The presented experimental results underscore the robustness, ease of implementation, and suitability for routine experimental use of the proposed two-parameter rosette trajectory calibration approach.
- MeSH
- Algorithms * MeSH
- Artifacts * MeSH
- Phantoms, Imaging * MeSH
- Calibration MeSH
- Humans MeSH
- Magnetic Resonance Imaging * methods MeSH
- Brain diagnostic imaging MeSH
- Image Processing, Computer-Assisted * methods MeSH
- Reproducibility of Results MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
A surface enhanced Raman scattering (SERS) spectrometry is an interesting alternative for a rapid molecular recognition of analytes at very low concentration levels. The hyphenation of this technique with advanced separation methods enhances its potential as a detection technique. Until now, it has been hyphenated mainly with common chromatographic and electrophoretic techniques. This work demonstrates for a first time a power of preparative isotachophoresis-surface enhanced Raman scattering spectrometry (pITP-SERS) combination on the analysis of model analyte (buserelin) in a complex biological sample (urine). An off-line identification of target analyte was performed using a comparison of Raman spectra of buserelin standard with spectra obtained by the analyses of the fractions from preparative isotachophoretic runs. SERS determination of buserelin was based on the method of standard addition to minimize the matrix effects. The linearity of developed method was obtained in the concentration range from 0.2 to 1.5 nmol L(-1) with coefficient of determination 0.991. The calculated limit of detection is in tens of pico mols per liter.
The extracts of a homeopathic Chamomilla vulgaris preparation and chamomile tea were analyzed by surfaceenhanced Raman scattering and surface-enhanced IR spectroscopies. The aqueous or methanolic extracts were deposited on nanostructured, electrochemically prepared Au surfaces. Only saccharose was identified reliably in homeopathic sample. The presence of other component is evident but they could not be identified.
