How many bits of information can be transferred between residues in a protein and how fast?

Time resolved Raman and infrared spectroscopy experiments show the basic features of information transfer between residues in proteins. Here, we present the theoretical basis of information transfer using a simple elastic net model and recently developed entropy transfer concept in proteins. Mutual information between two residues is a measure of communication in proteins which shows the maximum amount of information that may be transferred between two residues. However, it does not explain the actual amount of transfer nor the transfer rate of information between residues. For this, dynamic equations of the system are needed. We used the Schreiber theory of information transfer and the Gaussian network Model of proteins, together with the solution of the Langevin equation, to quantify allosteric information transfer. Results of the model are in perfect agreement with ultraviolet resonance Raman measurements. Analysis of the allosteric protein Human NAD-dependent isocitrate dehydrogenase shows that a multitude of paths contribute collectively to information transfer. While the peak values of information transferred are small relative to information content of residues, considering the estimated transfer rates, which are in the order of megabits per second, sustained transfer during the activity time-span of proteins may be significant.

Validation of a Novel Smartphone-Based Electronic Data Capture System Following Surgical Fixation of Distal Radial Fractures

Background: Large prospective institutional data provide the opportunity to conduct level II and III studies using robust methodologies and adequately powered sample-sizes, while circumventing limitations of retrospective databases. We aimed to validate a prospective data collection tool, the Orthopaedic Minimal Data Set Episode of Care (OME), implemented at a tertiary North American health care system for distal radial fracture (DRF) open reduction and internal fixation (ORIF). Methods: The first 100 DRF ORIFs performed after OME inception (February 2015) were selected for this validation study. A blinded review of the operative notes and charts was performed, and extracted data of 75 perioperative DRF ORIF procedure variables were compared with OME collected data for agreement. Outcomes included completion rates and agreement measures in OME versus electronic medical record (EMR)-based control datasets. Data counts were evaluated using raw percentages and McNemar tests. Cohen (κ) and concordance correlation coefficient analyzed categorical and numerical variable agreement, respectively. Results: Overall, OME demonstrated superior completion and agreement parameters versus EMR-based retrospective review. Nine data points (12.0%) demonstrated significantly higher completion rates within the OME dataset ( P < .05, each), and 88% (66/75) of captured variables demonstrated similar completion rates. Up to 80.0% (60/75) of variables either demonstrated an agreement proportion of ≥0.90 or were solely reported in the OME. Of 33 variables eligible for agreement analyses, 36.4% (12/33) demonstrated almost perfect agreement (κ > 0.80), and 63.6% (21/33) exhibited almost perfect or substantial agreement (κ > 0.60). Conclusions: The OME is a valid and accurate prospective data collection tool for DRF ORIF that is reliably able to match or supersede traditional retrospective chart review. Future investigations could use this tool for large-scale analyses investigating peri/intraoperative DRF ORIF variables.

A validation study of data in the National Tonsil Surgery Register in Sweden: high agreement with medical records ensures that data can be used to monitor clinical practices and outcomes

Background The ambition of the National Tonsil Surgery Register in Sweden (NTSRS) is to improve otorhinolaryngological care by monitoring trends in the clinical practices, complications, and outcomes of tonsil surgery. The NTSRS collects data from both surgeons and patients and provides the participating clinics with daily updated data on a publicly available website. On the website, national and local results can be compared and monitored. The use of NTSRS data necessitates that the data is valid, but the NTSRS has not yet been validated. With approximately half of the registered patients responding to the postoperative questionnaires, an analysis of responders and non-responders is also necessary. The aim of this study was to assess the criterion validity of NTSRS data. Another aim was to compare the characteristics and rates of complications between postoperative questionnaire responders and non-responders. Methods Data in the NTSRS were compared with data in electronic medical records. The 200 most recent surgeries, up to 31 Dec 2019, in each of 11 surgical units were included. Criterion validity was analysed in terms of observed agreement, Cohens kappa, Gwet’s AC1, and positive and negative agreement. The sign test was used to analyse systematic differences between the NTSRS and the medical records. Comparisons of rates between groups were made with Fisher’s exact test, the chi-square test, and Fisher’s non-parametric permutation test. Results A total of 1991 registrations were included in the study. All variables showed very high observed agreement ranging from 0.91 to 1.00, and all variables had AC1 values corresponding to almost perfect agreement. The analysis of questionnaire responders and non-responders showed no statistically significant differences regarding age, indication, or type of surgery. The proportion of women was higher in the responder group. The rate of reoperation due to bleeding was higher in the responder group, but there were no differences regarding other complications. Conclusions The results of this study show that data in the NTSRS have criterion validity. The NTSRS is thus well suited for monitoring the clinical practices and outcomes of tonsil surgery. The quality of the data also implies that the registry can be used in both clinical improvement projects and research.

Analytical performances of the AMPLIQUICK® Respiratory Triplex assay for simultaneous detection and differentiation of SARS-CoV-2, influenza A/B and respiratory syncytial viruses in respiratory specimens

Although patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A, influenza B and respiratory syncytial virus (RSV) show comparable or very similar manifestations, the therapeutic approaches of these respiratory viral infections are different, which requires an accurate diagnosis. Recently, the novel multiplex real-time reverse transcription-polymerase chain reaction assay AMPLIQUICK® Respiratory Triplex (BioSynex SA, Illkirch-Graffenstaden, France) allows simultaneous detection and differentiation of SARS-CoV-2, influenza A, influenza B, and RSV in respiratory tract samples. We herein evaluated the performance of the AMPLIQUICK® Respiratory Triplex for the detection of the four viruses in respiratory specimens, using Allplex™ Respiratory Panel 1 and 2019-nCoV assays (Seegene, Seoul, Korea) as reference comparator assays. A total of 359 archived predetermined respiratory samples, including 83, 145, 19 and 95 positive specimens for SARS-CoV-2, influenza A, influenza B and RSV respectively, were included. The AMPLIQUICK® Respiratory Triplex showed high concordance with the reference assays, with an overall agreement for SARS-CoV-2, influenza A, influenza B, and RSV at 97.6%, 98.8%, 98.3% and 100.0%, respectively, and high κ values ranging from 0.93 to 1.00, indicating an almost perfect agreement between assays. Furthermore, high correlations of cycle threshold (Ct) values were observed for positive samples of the four viruses between the AMPLIQUICK® Respiratory Triplex and comparator assays, with an overall high agreement between Ct values assessed by Bland-Altman analyses. In conclusion, these observations demonstrate that the multiplex AMPLIQUICK® Respiratory Triplex is a reliable assay for the qualitative detection and differentiation of SARS-CoV-2, influenza A, influenza B, and RSV in respiratory specimens, which may prove useful for streamlining diagnostics during the winter influenza-seasons.

Identification of Hydrodynamic Dispersion Tensor by Optimization Algorithm Based LBM/CMA-ES Combination

The hydrodynamic dispersion tensor (HDT) of a porous medium is a key parameter in engineering and environmental sciences. Its knowledge allows for example, to accurately predict the propagation of a pollution front induced by a surface (or subsurface) flow. This paper proposes a new mathematical model based on inverse problem-solving techniques to identify the HDT (noted D=) of the studied porous medium. We then showed that in practice, this new model can be written in the form of an integrated optimization algorithm (IOA). The IOA is based on the numerical solution of the direct problem (which solves the convection–diffusion type transport equation) and the optimization of the error function between the simulated concentration field and that observed at the application site. The partial differential equations of the direct model were solved by high resolution of (Δx=Δy=1 m) Lattice Boltzmann Method (LBM) whose computational code is named HYDRODISP-LBM (HYDRO-DISpersion by LBM). As for the optimization step, we opted for the CMA-ES (Covariance Matrix Adaptation-Evolution Strategy) algorithm. Our choice for these two methods was motivated by their excellent performance proven in the abundant literature. The paper describes in detail the operation of the coupling of the two computer codes forming the IOA that we have named HYDRODISP-LBM/CMA-ES. Finally, the IOA was applied at the Beauvais experimental site to identify the HDT D=. The geological analyzes of this site showed that the tensor identified by the IOA is in perfect agreement with the characteristics of the geological formation of the site which are connected with the mixing processes of the latter.

Comparison of diagnostic accuracy of 2D and 3D measurements to determine opportunistic screening of osteoporosis using the proximal femur on abdomen-pelvic CT

Objectives To compare the osteoporosis-predicting ability of computed tomography (CT) indexes in abdomen-pelvic CT using the proximal femur and the reliability of measurements in two- and three-dimensional analyses. Methods Four hundred thirty female patients (age range, 50–96 years) who underwent dual-energy X-ray absorptiometry and abdominal-pelvic CT within 1 month were retrospectively selected. The volumes of interest (VOIs) from the femoral head to the lesser trochanter and the femoral neck were expressed as 3DFemur. Round regions of interest (ROIs) of image plane drawn over the femoral neck touching the outer cortex were determined as 2Dcoronal. In HU histogram analysis (HUHA), the percentages of HU histogram ranges related to the ROI or VOI were classified as HUHAFat (<0 HU) and HUHABone (126 HU≤). Diagnostic performance, correlation analysis and measurement reliability were analyzed by receiver operating characteristic curves, correlation coefficient and interobserver correlation coefficient (ICC), respectively. Results AUCs of each HUHA and mean-HU measurement on 2D-ROI and 3D-VOI were 0.94 or higher (P < 0.001). Both 3DFemur-Mean-HU and 3DFemur-HUHABone showed the highest AUC (0.96). The cut-off value of 3DFemur-Mean-HU was 231HU or less, (sensitivity: 94.8%; specificity: 85.0%; correlation coefficient: −0.65; P <0.001) for diagnosis of osteoporosis. There was no superiority between AUCs in 2D-ROI and 3D-VOI measurements (P > 0.05). Reliability of the 3D-VOI measurement showed perfect agreement (ICC ≥ 0.94), and 2D-ROI showed moderate to good agreement (ICC range: 0.63~0.84). Conclusions CT indexes on 3D-VOI for predicting femoral osteoporosis showed similar diagnostic accuracy with better reproducibility of measurement, compared with 2D-ROI.

Thermalization of randomly coupled SYK models

We investigate the thermalization of Sachdev–Ye–Kitaev (SYK) models coupled via random interactions following quenches from the perspective of entanglement. Previous studies have shown that when a system of two SYK models coupled by random two-body terms is quenched from the thermofield double state with sufficiently low effective temperature, the Rényi entropies do not saturate to the expected thermal values in the large-N limit. Using numerical large-N methods, we first show that the Rényi entropies in a pair SYK models coupled by two-body terms can thermalize, if quenched from a state with sufficiently high effective temperature, and hence exhibit state-dependent thermalization. In contrast, SYK models coupled by single-body terms appear to always thermalize. We provide evidence that the subthermal behavior in the former system is likely a large-N artifact by repeating the quench for finite N and finding that the saturation value of the Rényi entropy extrapolates to the expected thermal value in the N → ∞ limit. Finally, as a finer grained measure of thermalization, we compute the late-time spectral form factor of the reduced density matrix after the quench. While a single SYK dot exhibits perfect agreement with random matrix theory, both the quadratically and quartically coupled SYK models exhibit slight deviations.

The Inter-Rater and Intra-Rater Reliability of the Actual Aquatic Skills Test (AAST) for Assessing Young Children’s Motor Competence in the Water

As children’s actual aquatic skills are important for the prevention of drowning as well as their engagement in lifelong aquatic physical activity, researchers and practitioners should be able to assess this vital concept accurately and reliably. Therefore, this study aimed to investigate the inter-rater and intra-rater reliability of the Actual Aquatic Skills Test (AAST), consisting of 17 different test items for the assessment of young children’s motor competence in the water. Six raters received a training and evaluation session on scoring the AAST, after which five of them assessed four test videos (of various children (n = 38) performing the test items) twice, with one to two weeks in between (i.e., test and re-test). Inter-rater and intra-rater reliability were determined per test video and for the different AAST test items across videos using Gwet’s Agreement Coefficient 2 (Gwet’s AC2). The Gwet’s AC2 for inter-rater reliability at the test varied from 0.414 to 1.000, indicating a moderate to perfect agreement between raters. For intra-rater reliability, it ranged from 0.628 to 1.000, demonstrating a good to perfect agreement between test and re-test scoring. In conclusion, the AAST is a promising tool to reliably assess young children’s actual aquatic skills in an indoor swimming pool.

A training plan to implement lung ultrasound for diagnosing pneumonia in children

Background Lung ultrasound (LUS) for critical patients requires trained operators to perform them, though little information exists on the level of training required for independent practice. The aims were to implement a training plan for diagnosing pneumonia using LUS and to analyze the inter-observer agreement between senior radiologists (SRs) and pediatric intensive care physicians (PICPs). Methods Prospective longitudinal and interventional study conducted in the Pediatric Intensive Care Unit of a tertiary hospital. Following a theoretical and practical training plan regarding diagnosing pneumonia using LUS, the concordance between SRs and the PICPs on their LUS reports was analyzed. Results Nine PICPs were trained and tested on both theoretical and practical LUS knowledge. The mean exam mark was 13.5/15. To evaluate inter-observer agreement, a total of 483 LUS were performed. For interstitial syndrome, the global Kappa coefficient (K) was 0.51 (95% CI 0.43–0.58). Regarding the presence of consolidation, K was 0.67 (95% CI 0.53–0.78), and for the consolidation pattern, K was 0.82 (95% CI 0.79–0.85), showing almost perfect agreement. Conclusions Our training plan allowed PICPs to independently perform LUS and might improve pneumonia diagnosis. We found a high inter-observer agreement between PICPs and SRs in detecting the presence and type of consolidation on LUS. Impact Lung ultrasound (LUS) has been proposed as an alternative to diagnose pneumonia in children. However, the adoption of LUS in clinical practice has been slow, and it is not yet included in general clinical guidelines. The results of this study show that the implementation of a LUS training program may improve pneumonia diagnosis in critically ill patients. The training program’s design, implementation, and evaluation are described. The high inter-observer agreement between LUS reports from the physicians trained and expert radiologists encourage the use of LUS not only for pneumonia diagnosis, but also for discerning bacterial and viral patterns.

Parallel approach of Schrödinger-based quantum corrections for ultrascaled semiconductor devices

In the current technology node, purely classical numerical simulators lack the precision needed to obtain valid results. At the same time, the simulation of fully quantum models can be a cumbersome task in certain studies such as device variability analysis, since a single simulation can take up to weeks to compute and hundreds of device configurations need to be analyzed to obtain statistically significative results. A good compromise between fast and accurate results is to add corrections to the classical simulation that are able to reproduce the quantum nature of matter. In this context, we present a new approach of Schrödinger equation-based quantum corrections. We have implemented it using Message Passing Interface in our in-house built semiconductor simulation framework called VENDES, capable of running in distributed systems that allow for more accurate results in a reasonable time frame. Using a 12-nm-gate-length gate-all-around nanowire FET (GAA NW FET) as a benchmark device, the new implementation shows an almost perfect agreement in the output data with less than a 2% difference between the cases using 1 and 16 processes. Also, a reduction of up to 98% in the computational time has been found comparing the sequential and the 16 process simulation. For a reasonably dense mesh of 150k nodes, a variability study of 300 individual simulations can be now performed with VENDES in approximately 2.5 days instead of an estimated sequential execution of 137 days.