Nevin Manimala

PLoS Comput Biol. 2022 May 2;18(5):e1010061. doi: 10.1371/journal.pcbi.1010061. Online ahead of print.

ABSTRACT

While hierarchical experimental designs are near-ubiquitous in neuroscience and biomedical research, researchers often do not take the structure of their datasets into account while performing statistical hypothesis tests. Resampling-based methods are a flexible strategy for performing these analyses but are difficult due to the lack of open-source software to automate test construction and execution. To address this, we present Hierarch, a Python package to perform hypothesis tests and compute confidence intervals on hierarchical experimental designs. Using a combination of permutation resampling and bootstrap aggregation, Hierarch can be used to perform hypothesis tests that maintain nominal Type I error rates and generate confidence intervals that maintain the nominal coverage probability without making distributional assumptions about the dataset of interest. Hierarch makes use of the Numba JIT compiler to reduce p-value computation times to under one second for typical datasets in biomedical research. Hierarch also enables researchers to construct user-defined resampling plans that take advantage of Hierarch’s Numba-accelerated functions.

PMID:35500032 | DOI:10.1371/journal.pcbi.1010061

PLoS Comput Biol. 2022 May 2;18(5):e1010045. doi: 10.1371/journal.pcbi.1010045. Online ahead of print.

ABSTRACT

Identifying structural differences among proteins can be a non-trivial task. When contrasting ensembles of protein structures obtained from molecular dynamics simulations, biologically-relevant features can be easily overshadowed by spurious fluctuations. Here, we present SINATRA Pro, a computational pipeline designed to robustly identify topological differences between two sets of protein structures. Algorithmically, SINATRA Pro works by first taking in the 3D atomic coordinates for each protein snapshot and summarizing them according to their underlying topology. Statistically significant topological features are then projected back onto a user-selected representative protein structure, thus facilitating the visual identification of biophysical signatures of different protein ensembles. We assess the ability of SINATRA Pro to detect minute conformational changes in five independent protein systems of varying complexities. In all test cases, SINATRA Pro identifies known structural features that have been validated by previous experimental and computational studies, as well as novel features that are also likely to be biologically-relevant according to the literature. These results highlight SINATRA Pro as a promising method for facilitating the non-trivial task of pattern recognition in trajectories resulting from molecular dynamics simulations, with substantially increased resolution.

PMID:35500014 | DOI:10.1371/journal.pcbi.1010045

PLoS One. 2022 May 2;17(5):e0267641. doi: 10.1371/journal.pone.0267641. eCollection 2022.

ABSTRACT

Ultrasound devices are common in muscle physiology laboratories due to their ease of use and validity to assess skeletal muscle characteristics. The current study assessed the reliability of ultrasound skeletal muscle image analysis across multiple raters with limited experience. Vastus lateralis (VL), rectus femoris (RF), and first dorsal interosseus (FDI) images were separately analyzed by three novice raters to determine muscle thickness (MT), cross-sectional area (CSA), and echo-intensity (EI). Separate analyses of variance (ANOVA) assessed statistical differences between and within raters. Intra-class correlation coefficients (ICC) between (inter-rater) and within (intra-rater) raters, the standard error of the measurement (SEM) and minimal difference needed to be considered real were calculated. Inter-rater reliability was high for the VL and RF (ICC: 0.984-0.999), while the FDI was lower (0.614-0.962). Further, intra-rater reliability was greater than 0.961 for each rater. SEM values calculated for inter-rater reliability expressed as a percentage of the mean ranged from 0.4-5.8% across variables. Similarly, SEM values for intra-rater reliability were between 0.8-5.8%, 0.6-3.6%, and 0.4-3.2% for Raters 1, 2 and 3, respectively. Despite this, significant differences (p<0.05) between raters were observed for RF MT and EI, VL CSA and EI, and FDI MT, suggesting that potentially more measurement trials or greater practice time may be necessary to reduce systematic error among multiple raters. Post-image acquisition processing is reliable among and within raters as determined through ICCs and SEMs. This study provided consistent results among three separate novice raters given the same training, a unique yet realistic setting in muscle physiology laboratories.

PMID:35500010 | DOI:10.1371/journal.pone.0267641

Sociol Health Illn. 2022 May 2. doi: 10.1111/1467-9566.13474. Online ahead of print.

ABSTRACT

Previous research on coronavirus disease 2019 (COVID-19) vaccine hesitancy lacks a gender perspective, and it is unclear whether gender intersects with socioeconomic status to co-produce inequalities in people’s intent to take vaccines. The current study draws on intersectionality theory and uses data from the 2021 US Household Pulse Survey (n = 50,359). Both bivariate and multivariate statistical analyses were conducted. The results suggest that American women had a higher vaccine hesitancy rate than men. Gender interacts with socioeconomic status to shape people’s vaccine hesitancy in a complex way. Specifically, women living in poverty or currently working were more vaccine-hesitant, while poverty and employment status did not affect men’s vaccine hesitancy. However, not having a college education contributed to both women’s and men’s COVID-19 vaccine hesitancy. Moreover, women were more worried about the safety of the vaccine, but men’s hesitancy tended to be driven by lower perceptions of COVID-19 dangers and belief in conspiratorial claims.

PMID:35500003 | DOI:10.1111/1467-9566.13474

PLoS One. 2022 May 2;17(5):e0266600. doi: 10.1371/journal.pone.0266600. eCollection 2022.

ABSTRACT

We take the stock prices as a dynamic system and characterize its movements by a newly derived dynamic model, called the new Price Reversion Model (nPRM), for which the solution is derived and carefully analyzed under different circumstances. We also develop a procedure of applying the nPRM to real daily closing prices of a stock index. This proposed procedure brings a different perspective to the study of stock prices based on thermodynamics, and the time varying coefficients in the nPRM offer economic meanings of the stock movements. More specifically, the average of smoothed historical data A in the nPRM, analogous to the environment temperature in the Newton’s law of cooling, represent an implied equilibrium price. The heat transfer coefficient κ is adapted to be either negative or positive, which illustrates the speed of convergence or divergence of stock prices, respectively. The empirical study of ten Asian stock indexes shows that the nPRM accurately characterizes and forecasts the market values.

PMID:35499989 | DOI:10.1371/journal.pone.0266600

Psychophysiology. 2022 May 2:e14081. doi: 10.1111/psyp.14081. Online ahead of print.

ABSTRACT

Tobacco smoking has been associated with lower cardiovascular reactivity to psychological stress in middle-aged samples, but its impact on cardiovascular reactivity to stress in young adults remains unclear. The present study examined whether young healthy adults showed differing cardiovascular stress reaction profiles depending on their smoking status. Across two laboratory studies (N = 64 and N = 114), we asked participants to complete cognitive stress-tasks while undergoing continuous hemodynamic monitoring. In both studies, there was not a statistically signification association between systolic blood pressure, diastolic blood pressure, or heart rate reactivity to stress (all ps > .05). However, examination of the underlying hemodynamic profile of the stress response suggested differences between non-smokers and smokers in both studies. In Study 1, non-smokers exhibited the expected myocardial response to the active stress-task; however, smokers exhibited a mixed hemodynamic profile. In Study 2, smokers evidenced a weaker myocardial profile to the active stress-tasks compared to non-smokers. However, the examination of the continuous hemodynamic profile score (HP) did not identify statistical differences. These results highlight that any level of the smoking habit is associated with an altered hemodynamic profile in response to stress in smokers, which may have important implications for long-term cardiovascular health. The findings also suggest that controlling for smoking behavior in reactivity research examining blood pressure and heart rate responses to stress in young adults is not necessary.

PMID:35499979 | DOI:10.1111/psyp.14081

J Chem Inf Model. 2022 May 2. doi: 10.1021/acs.jcim.1c01311. Online ahead of print.

ABSTRACT

Despite recent interest in deep generative models for scaffold elaboration, their applicability to fragment-to-lead campaigns has so far been limited. This is primarily due to their inability to account for local protein structure or a user’s design hypothesis. We propose a novel method for fragment elaboration, STRIFE, that overcomes these issues. STRIFE takes as input fragment hotspot maps (FHMs) extracted from a protein target and processes them to provide meaningful and interpretable structural information to its generative model, which in turn is able to rapidly generate elaborations with complementary pharmacophores to the protein. In a large-scale evaluation, STRIFE outperforms existing, structure-unaware, fragment elaboration methods in proposing highly ligand-efficient elaborations. In addition to automatically extracting pharmacophoric information from a protein target’s FHM, STRIFE optionally allows the user to specify their own design hypotheses.

PMID:35499971 | DOI:10.1021/acs.jcim.1c01311

J Clin Hypertens (Greenwich). 2022 May 2. doi: 10.1111/jch.14491. Online ahead of print.

ABSTRACT

Frequent fruit consumption has been associated with lower office blood pressure. Less is known about associations between fruit consumption and home blood pressure. Our aim was to study the correlation between consumption of specific fruits and home blood pressure in a large randomly selected study population. The main outcome was systolic home blood pressure. Home blood pressure measurements were performed with calibrated oscillometric meters during seven consecutive days. Means for all available measurements were used. Validated food frequency questionnaires were used for estimating frequency of fruit consumption. The specified fruits were bananas, apples/pears and oranges/citrus fruit. Complete case analysis regarding fruit consumption, office- and home blood pressure measurements and other relevant variables was performed in 2283 study participants out of 2603 available. Multivariable linear regression analysis was performed. There were statistically significant associations between consumption of all fruit types and lower systolic home blood pressure unadjusted (p for trend; bananas, apples/pears and oranges/citrus fruit p < .001). The numerical differences between most and least frequent consumption of fruit were for bananas -2.7 mm Hg, apples/pears -3.9 mm Hg and for oranges/citrus fruit -3.4 mm Hg. When adjusted for covariates, both consumption of apples/pears and oranges/citrus fruit had an independent statistically significant association with lower blood pressure (p = .048 resp. p = .009). Future controlled interventional studies are needed to evaluate the effect of specific fruit on home blood pressure.

PMID:35499960 | DOI:10.1111/jch.14491

Comput Methods Biomech Biomed Engin. 2022 May 2:1-14. doi: 10.1080/10255842.2022.2065631. Online ahead of print.

ABSTRACT

We formulated a Coronavirus (COVID-19) delay epidemic model with random perturbations, consisting of three different classes, namely the susceptible population, the infectious population, and the quarantine population. We studied the proposed problem to derive at least one unique solution in the positive feasweible region of the non-local solution. Sufficient conditions for the extinction and persistence of the proposed model are established. Our results show that the influence of Brownian motion and noise on the transmission of the epidemic is very large. We use the first-order stochastic Milstein scheme, taking into account the required delay of infected individuals.

PMID:35499952 | DOI:10.1080/10255842.2022.2065631

Nurs Educ Perspect. 2022 Apr 23. doi: 10.1097/01.NEP.0000000000000975. Online ahead of print.

ABSTRACT

Peer mentoring encourages relationships among novice and senior nursing students, provides emotional support, and develops leadership skills. The research design was a pretest/posttest, interventional study to evaluate a supervised peer-mentoring program among nursing students to determine socialization of mentees into the nursing discipline. The second purpose was to evaluate if financial reimbursement was an incentive for participation by mentors. The pretest mean was significantly lower than the posttest mean; the difference was statistically significant. Success was achieved for both mentors and mentees. A paid peer-mentoring program allows students to relinquish time that would otherwise be spent in outside employment.

PMID:35499949 | DOI:10.1097/01.NEP.0000000000000975