This work extends the multi-scale computational scheme for the quantum mechanics (QM) calculations of Nuclear Magnetic Resonance (NMR) chemical shifts (CSs) in proteins that lack a well-defined 3D structure. The scheme couples the sampling of an intrinsically disordered protein (IDP) by classical molecular dynamics (MD) with protein fragmentation using the adjustable density matrix assembler (ADMA) and density functional theory (DFT) calculations. In contrast to our early investigation on IDPs (Pavlíková Přecechtělová et al., J. Chem. Theory Comput., 2019, 15, 5642-5658) and the state-of-the art NMR calculations for structured proteins, a partial re-optimization was implemented on the raw MD geometries in vibrational normal mode coordinates to enhance the accuracy of the MD/ADMA/DFT computational scheme. In addition, machine-learning based cluster analysis was performed on the scheme to explore its potential in producing protein structure ensembles (CLUSTER ensembles) that yield accurate CSs at a reduced computational cost. The performance of the cluster-based calculations is validated against results obtained with conventional structural ensembles consisting of MD snapshots extracted from the MD trajectory at regular time intervals (REGULAR ensembles). CS calculations performed with the refined MD/ADMA/DFT framework employed the 6-311++G(d,p) basis set that outperformed IGLO-III calculations with the same density functional approximation (B3LYP) and both explicit and implicit solvation. The partial geometry optimization did not universally improve the agreement of computed CSs with the experiment but substantially decreased errors associated with the ensemble averaging. A CLUSTER ensemble with 50 structures yielded ensemble averages close to those obtained with a REGULAR ensemble consisting of 500 MD frames. The cluster based calculations thus required only a fraction of the computational time.

• MeSH
• Quantum Theory MeSH
• Molecular Dynamics Simulation MeSH
• Machine Learning MeSH
• Intrinsically Disordered Proteins * chemistry   MeSH
• Publication type
• Journal Article MeSH

• MeSH
• Neoplasms complications   radiotherapy   MeSH
• Radiotherapy methods   adverse effects   MeSH
• Models, Theoretical MeSH
• Dose-Response Relationship, Radiation MeSH

K detekování a měření specifických IgE protilátek jsou používány různé laboratorní testy a neexistuje standard, který by ověřil jejich analytickou kvalitu. Záměrem bylo analyzovat přesnost a správnost výsledků stanovení specifických IgE z různých laboratoří, naměřených se stejnými vzorky sér. Jako metody bylo použito 26 neoznačených vzorků sér obsahujících specifické IgE protilátky proti 17 běžným inhalačním alergenům, bylo normálním způsobem opakovaně (3x) zasláno k analýze do šesti laboratoří, které užívají 5 různých analytických testů. Šest z předložených 26 vzorků bylo dodáno v různých ředěních, jako diluční řady. Naměřené hodnoty (n = 12 708) byly analyzovány běžnou metodou nejmenších čtverců, t statistikou, standardní chybou (SE), intervalem spolehlivosti, a R2 hodnotami. Takto získané hodnoty byly porovnány s teoretickou ideální metodou, jakožto referencí. Analýza ukázala, že jeden systém užívaný ve dvou různých laboratořích pracoval téměř tak dobře jako ideální standard (0,97; rozsah 0,91 - 1,01) při hodnocení lineární regresí, (0,05; rozsah 0,02 - 0,16) při hodnocení SE, (93 %; rozsah 0,64 - 0,99) při R2 a s variačním koeficientem (10,3 %; rozsah 6 % - 14 %). Mnohem rozsáhlejší variabilita byla pozorována u zbývajících 4 testovacích systémů. Zde byly nalezeny hodnoty (0,76; rozsah 0,11 - 1,24) při hodnocení lineární regresí, (0,19; rozsah 0,03 - 0,95) při hodnocení SE, (53 %; rozsah 0,00 - 0,98) při hodnocení R2 a s variačním koeficientem (19 %; rozsah 5 % - 49 %). U některých specifických alergenů nebyly některé laboratoře schopny zachytit diluční řady. Jeden komerční systém užívaný ve dvou laboratořích poskytoval výsledky téměř shodné s metodou ideální. Zbývající čtyři metody stanovení specifického IgE poskytovaly výsledky značně vzdálené od ideálních s mnoha příklady nesprávnosti a nízké přesnosti, speciálně pro určité alergeny jako například ze skupiny plísní a plevelů.

Different laboratory assays are used to detect and measure specific IgE antibodies. No standard exists to assess their analytic performance. We sought to analyze reported specific IgE results from different laboratories an the same serum samples for their accuracy and precision. Blinded serum samples (26) containing variable levels of specific IgE to 17 common aeroallergens were sent on 3 different occasions through normal channels to 6 laboratories that used 5 different test procedures. Laboratory-assays performance was assessed by analyzing the reported results (n=12,708) by using ordinary least squares regression with slope coefficients, the t statistic, SEs, confidence intervals, and R2 values. These were compared with a theoretic ideal assay as the reference. Analysis revealed that one system used in two different laboratories performed nearly as well as the ideal standard, with an overall average slope (0,97; range, 0,91-1,01), SE (0,05; range, 0,02-0,16), R2 value (93 %; range, 0,64-0,99), and coefficient of variation (10,3 %; range, 6 %-14 %). Extensive variability was observed in the other 4 laboratory-assay systems with respect to overall average slope (0,76; range, 0,11-1,24), SE (0,19; range, 0,03-0,95), R2 value (53 %; range, 0,00-0,98), and coefficient of variation (19 %; range, 5 %-49 %). For some specific allergens, some laboratories-assays were not able to detect serial dilutions of the same sample. One commercial system used two different laboratories performed nearly as well as the ideal standard. Four of the laboratories-assays for specific IgE antibodies demonstrated substandard overall performance with multiple instances of poor precision and accuracy, particularly for certain allergens, such as weeds and molds. (J Allergy Clin. Immunol 2000;105:1221-30.)

• MeSH
• Allergens immunology   MeSH
• Fungi immunology   MeSH
• Immunoglobulin E blood   MeSH
• Humans MeSH
• Reference Standards MeSH
• Plants immunology   MeSH
• Serologic Tests methods   standards   statistics & numerical data   MeSH
• Check Tag
• Humans MeSH

• MeSH
• Diagnostic Imaging methods   utilization   MeSH
• Data Compression methods   utilization   MeSH
• Humans MeSH
• Magnetic Resonance Imaging MeSH
• Tomography, X-Ray Computed MeSH
• Image Processing, Computer-Assisted methods   utilization   MeSH
• Statistics as Topic MeSH
• Models, Theoretical MeSH
• Check Tag
• Humans MeSH

Aim To verify and compare the accuracies of mortality predictions in the Intensive Care Unit (ICU) of the Internal Clinic of Central Military Hospital in Prague, Czech Republic, using model APACHE II and the newer systems of the APACHE IV, SAPS 3 and MPMo III. Methods The data were collected retrospectively between 2011 and 2012, 1000 patients were evaluated. The assessment of the overall accuracy of the mortality predictions was performed using the standardized mortality ratio (SMR), and the calibration was assessed using the Lemeshow-Hosmer "goodness-of-fit" C statistic. Discrimination was evaluated using ROC curves based on calculations of the areas under the curve (AUCs). Results The APACHE II, SAPS 3, and MPMo III systems significantly overestimated the expected mortality, whereas the APACHE IV model led to correct estimations of the overall mortality. The discrimination capabilities of the models assessed according to the constructions of the ROC curves were evaluated as good, only the APACHE II was evaluated as satisfactory. The calibrations of all models were evaluated as unsatisfactory. Conclusion The best mortality estimation for the investigated population sample was provided by the APACHE IV system. The discrimination capabilities of all models for the studied population were satisfactory, but the calibration of all of the systems was unsatisfactory. The conclusions of our study are limited by the relatively small size of the investigated sample and the fact that this study was conducted at only a single site.

• MeSH
• Intensive Care Units statistics & numerical data   MeSH
• Middle Aged MeSH
• Humans MeSH
• Hospital Mortality * MeSH
• Patient Admission statistics & numerical data   MeSH
• Retrospective Studies MeSH
• ROC Curve MeSH
• Aged, 80 and over MeSH
• Aged MeSH
• Severity of Illness Index MeSH
• Models, Theoretical MeSH
• Check Tag
• Middle Aged MeSH
• Humans MeSH
• Male MeSH
• Aged, 80 and over MeSH
• Aged MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Comparative Study MeSH
• Geographicals
• Czech Republic epidemiology   MeSH

In motor functional neurological disorders (mFND), relationships between interoception (a construct of high theoretical relevance to its pathophysiology) and neuroanatomy have not been previously investigated. This study characterized white matter in mFND patients compared to healthy controls (HCs), and investigated associations between fiber bundle integrity and cardiac interoception. Voxel-based analysis and tractography quantified fractional anisotropy (FA) in 38 mFND patients compared to 38 HCs. Secondary analyses compared functional seizures (FND-seiz; n = 21) or functional movement disorders (n = 17) to HCs. Network lesion mapping identified gray matter origins of implicated fiber bundles. Within-group mFND analyses investigated relationships between FA, heartbeat tracking accuracy and interoceptive trait prediction error (discrepancies between interoceptive accuracy and self-reported bodily awareness). Results were corrected for multiple comparisons, and all findings were adjusted for depression and trait anxiety. mFND and HCs did not show any between-group interoceptive accuracy or FA differences. However, the FND-seiz subgroup compared to HCs showed decreased integrity in right-lateralized tracts: extreme capsule/inferior fronto-occipital fasciculus, arcuate fasciculus, inferior longitudinal fasciculus, and thalamic/striatum to occipital cortex projections. These alterations originated predominantly from the right temporoparietal junction and inferior temporal gyrus. In mFND patients, individual differences in interoceptive accuracy and interoceptive trait prediction error correlated with fiber bundle integrity originating from the insula, temporoparietal junction, putamen and thalamus among other regions. In this first study investigating brain-interoception relationships in mFND, individual differences in interoceptive accuracy and trait prediction error mapped onto multimodal integration-related fiber bundles. Right-lateralized limbic and associative tract disruptions distinguished FND-seiz from HCs.

• MeSH
• White Matter * diagnostic imaging   pathology   physiopathology   MeSH
• Biological Variation, Population physiology   MeSH
• Adult MeSH
• Interoception physiology   MeSH
• Middle Aged MeSH
• Humans MeSH
• Young Adult MeSH
• Cerebral Cortex MeSH
• Movement Disorders * diagnostic imaging   pathology   physiopathology   MeSH
• Anticipation, Psychological physiology   MeSH
• Gray Matter * diagnostic imaging   pathology   physiopathology   MeSH
• Heart Rate physiology   MeSH
• Diffusion Tensor Imaging * MeSH
• Check Tag
• Adult MeSH
• Middle Aged MeSH
• Humans MeSH
• Young Adult MeSH
• Male MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, N.I.H., Extramural MeSH

• MeSH
• Evaluation Studies as Topic MeSH
• Humans MeSH
• Eye anatomy & histology   MeSH
• Cornea physiology   MeSH
• Tonometry, Ocular classification   methods   instrumentation   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Book Review MeSH

Cílem této práce je shrnout současné poznatky o možnosti předpovědi léčebných změn u ortodontických pacientů a v praxi zhodnotit piresnost počítačových modelací u pacientů léčených kombinovanou metodou ortodonticko-chirurgickou pomocí modelačního programu Dolphin Imaging (verze 10.0). Do hodnoceného souboru bylo zaiřazeno 29 pacientů s kombinovanou ortodonticko-chirurgickou léčbou. Typ operace ph výběru nerozhodoval. Všichni pacienti měli ukončený růst. Byl porovnán model výsledku operace vytvořený v programu Dolphin Imaging se skutečným výsledkem léčby. Nejlepší předpověď výsledku vyšla u bimaxilárních výkonů, méně přesná byla u posunů dolní čelisti a nejméně přesná u posunů horní čelisti. Celkove lze říci, že předpověcf byla hodnocena subjektivně jako dobrá v 90% případů.

The aim of the work is to make a survey of prediction reliability and to assess the accuracy of computer simulations (performed with the Dolphin Imaging 10.0 software) in patients with a combined orthodontic-surgical treatment. The sample included 29 patients with an orthognathic surgery treatment. The type of operation was not relevant for the study. In all the patients the growth was finished. The model of the surgical result created by DoIphin Imaging software was compared with the actual therapeutic outcome. The most reliable prediction was recorded in bimaxillary operations; the prediction was less reliable in case of movements of the mandible, and the least reliable in case of the maxilla movements. The prediction was subjectively considered as good in 90% of the cases monitored.

• MeSH
• Stomatognathic System Abnormalities surgery   MeSH
• Models, Anatomic MeSH
• Jaw MeSH
• Evaluation Studies as Topic MeSH
• Cephalometry utilization   MeSH
• Humans MeSH
• Orthognathic Surgical Procedures MeSH
• Forecasting MeSH
• Oral Surgical Procedures classification   methods   MeSH
• Check Tag
• Humans MeSH

• MeSH
• Environmental Monitoring methods   standards   MeSH
• Reference Values MeSH
• Reference Standards MeSH
• Data Accuracy MeSH
• Models, Theoretical MeSH
• Legislation as Topic MeSH
• Air Pollution analysis   legislation & jurisprudence   MeSH

• MeSH
• Models, Biological MeSH
• Biomedical Engineering MeSH
• Diagnostic Imaging MeSH
• Models, Theoretical MeSH
• Publication type
• Collected Work MeSH

• Conspectus
• Lékařské vědy. Lékařství
• Biotechnologie. Genetické inženýrství
• NML Fields
• biomedicínské inženýrství