Qualitative Data Clustering to Detect Outliers

Differentiating stable and unstable protein using convolution neural network and molecular dynamics simulations

Protein stability is a critical aspect of molecular biology and biochemistry, hinges on an intricate balance of thermodynamic and structural factors. Determining protein stability is crucial for understanding and manipulating biological machineries, as it directly correlated with the protein function. Thus, this study delves into the intricacies of protein stability, highlighting its dependence on various factors, including thermodynamics, thermal conditions, and structural properties. Moreover, a notable focus is placed on the free energy change of unfolding (ΔGunfolding), change in heat capacity (ΔCp) with protein structural transition, melting temperature (Tm) and number of disulfide bonds, which are critical parameters in understanding protein stability. In this study, a machine learning (ML) predictive model was developed to estimate these four parameters using the primary sequence of the protein. The shortfall of available tools for protein stability prediction based on multiple parameters propelled the completion of this study. Convolutional Neural Network (CNN) with multiple layers was adopted to develop a more reliable ML model. Individual predictive models were prepared for each property, and all the prepared models showed results with high accuracy. The R2 (coefficient of determination) of these models were 0.79, 0.78, 0.92 and 0.92, respectively, for ΔG, ΔCp, Tm and disulfide bonds. A case study on stability analysis of two homologous proteins was presented to validate the results predicted through the developed model. The case study included in silico analysis of protein stability using molecular docking and molecular dynamic simulations. This validation study assured the accuracy of each model in predicting the stability associated properties. The alignment of physics-based principles with ML models has provided an opportunity to develop a fast machine learning solution to replace the computationally demanding physics-based calculations used to determine protein stability. Furthermore, this work provided valuable insights into the impact of mutation on protein stability, which has implications for the field of protein engineering. The source codes are available at https://github.com/Growdeatechnology.

Association of Sociodemographic Factors With Overtriage, Undertriage, and Value of Care After Major Surgery

Objective

To determine whether certain patients are vulnerable to errant triage decisions immediately after major surgery and whether there are unique sociodemographic phenotypes within overtriaged and undertriaged cohorts.

Background

In a fair system, overtriage of low-acuity patients to intensive care units (ICUs) and undertriage of high-acuity patients to general wards would affect all sociodemographic subgroups equally.

Methods

This multicenter, longitudinal cohort study of hospital admissions immediately after major surgery compared hospital mortality and value of care (risk-adjusted mortality/total costs) across 4 cohorts: overtriage (N = 660), risk-matched overtriage controls admitted to general wards (N = 3077), undertriage (N = 2335), and risk-matched undertriage controls admitted to ICUs (N = 4774). K-means clustering identified sociodemographic phenotypes within overtriage and undertriage cohorts.

Results

Compared with controls, overtriaged admissions had a predominance of male patients (56.2% vs 43.1%, P < 0.001) and commercial insurance (6.4% vs 2.5%, P < 0.001); undertriaged admissions had a predominance of Black patients (28.4% vs 24.4%, P < 0.001) and greater socioeconomic deprivation. Overtriage was associated with increased total direct costs [$16.2K ($11.4K-$23.5K) vs $14.1K ($9.1K-$20.7K), P < 0.001] and low value of care; undertriage was associated with increased hospital mortality (1.5% vs 0.7%, P = 0.002) and hospice care (2.2% vs 0.6%, P < 0.001) and low value of care. Unique sociodemographic phenotypes within both overtriage and undertriage cohorts had similar outcomes and value of care, suggesting that triage decisions, rather than patient characteristics, drive outcomes and value of care.

Conclusions

Postoperative triage decisions should ensure equality across sociodemographic groups by anchoring triage decisions to objective patient acuity assessments, circumventing cognitive shortcuts and mitigating bias.

Phenotype clustering in health care: A narrative review for clinicians

Human pathophysiology is occasionally too complex for unaided hypothetical-deductive reasoning and the isolated application of additive or linear statistical methods. Clustering algorithms use input data patterns and distributions to form groups of similar patients or diseases that share distinct properties. Although clinicians frequently perform tasks that may be enhanced by clustering, few receive formal training and clinician-centered literature in clustering is sparse. To add value to clinical care and research, optimal clustering practices require a thorough understanding of how to process and optimize data, select features, weigh strengths and weaknesses of different clustering methods, select the optimal clustering method, and apply clustering methods to solve problems. These concepts and our suggestions for implementing them are described in this narrative review of published literature. All clustering methods share the weakness of finding potential clusters even when natural clusters do not exist, underscoring the importance of applying data-driven techniques as well as clinical and statistical expertise to clustering analyses. When applied properly, patient and disease phenotype clustering can reveal obscured associations that can help clinicians understand disease pathophysiology, predict treatment response, and identify patients for clinical trial enrollment.

Acquiring, Analyzing and Interpreting Knowledge Data for Sustainable Engineering Education: An Experimental Study Using YouTube

With the immersion of a plethora of technological tools in the early post-COVID-19 era in university education, instructors around the world have been at the forefront of implementing hybrid learning spaces for knowledge delivery. The purpose of this experimental study is not only to divert the primary use of a YouTube channel into a tool to support asynchronous teaching; it also aims to provide feedback to instructors and suggest steps and actions to implement in their teaching modules to ensure students’ access to new knowledge while promoting their engagement and satisfaction, regardless of the learning environment, i.e., face-to-face, distance and hybrid. Learners’ viewing habits were analyzed in depth from the channel’s 37 instructional videos, all of which were related to the completion of a computer-aided mechanical design course. By analyzing and interpreting data directly from YouTube channel reports, six variables were identified and tested to quantify the lack of statistically significant changes in learners’ viewing habits. Two time periods were specifically studied: 2020–2021, when instruction was delivered exclusively via distance education, and 2021–2022, in a hybrid learning mode. The results of both parametric and non-parametric statistical tests showed that “Number of views” and “Number of unique viewers” are the two variables that behave the same regardless of the two time periods studied, demonstrating the relevance of the proposed concept for asynchronous instructional support regardless of the learning environment. Finally, a forthcoming instructor’s manual for learning CAD has been developed, integrating the proposed methodology into a sustainable academic educational process.

Reduction of Artifacts in Capacitive Electrocardiogram Signals of Driving Subjects

The development of smart cars with e-health services allows monitoring of the health condition of the driver. Driver comfort is preserved by the use of capacitive electrodes, but the recorded signal is characterized by large artifacts. This paper proposes a method for reducing artifacts from the ECG signal recorded by capacitive electrodes (cECG) in moving subjects. Two dominant artifact types are coarse and slow-changing artifacts. Slow-changing artifacts removal by classical filtering is not feasible as the spectral bands of artifacts and cECG overlap, mostly in the band from 0.5 to 15 Hz. We developed a method for artifact removal, based on estimating the fluctuation around linear trend, for both artifact types, including a condition for determining the presence of coarse artifacts. The method was validated on cECG recorded while driving, with the artifacts predominantly due to the movements, as well as on cECG recorded while lying, where the movements were performed according to a predefined protocol. The proposed method eliminates 96% to 100% of the coarse artifacts, while the slow-changing artifacts are completely reduced for the recorded cECG signals larger than 0.3 V. The obtained results are in accordance with the opinion of medical experts. The method is intended for reliable extraction of cardiovascular parameters to monitor driver fatigue status.