Category: Nevin Manimala

Res Synth Methods. 2023 Feb 1. doi: 10.1002/jrsm.1626. Online ahead of print.

ABSTRACT

A reference interval, or an interval in which a pre-specified proportion of measurements from a healthy population are expected to fall, is used to determine whether a person’s measurement is typical of a healthy individual. For a specific biomarker, multiple published studies may provide data collected from healthy participants. A reference interval estimated by combining the data across these studies is typically more generalizable than a reference interval based on a single study. Methods for estimating reference intervals from random effects meta-analysis and fixed effects meta-analysis have been recently proposed and implemented using R software. We present an R Shiny tool, RIMeta, implementing these methods, which allows users not proficient in R to estimate a reference interval from a meta-analysis using aggregate data (mean, standard deviation, and sample size) from each study. RIMeta provides users a convenient way to estimate a reference interval from a meta-analysis and to generate the reference interval plot to visualize the results. The use of this web-based R Shiny tool does not require the installation of R or any background knowledge of programming. We explain all functions of the R Shiny tool and illustrate how to use it with a real data example. This article is protected by copyright. All rights reserved.

PMID:36725922 | DOI:10.1002/jrsm.1626

Sci Rep. 2023 Feb 1;13(1):1858. doi: 10.1038/s41598-023-28835-2.

ABSTRACT

In this paper, we study consensus behavior based on the local application of the majority consensus algorithm (a generalization of the majority rule) over four-connected bi-dimensional networks. In this context, we characterize theoretically every four-vicinity network in its capacity to reach consensus (every individual at the same opinion) for any initial configuration of binary opinions. Theoretically, we determine all regular grids with four neighbors in which consensus is reached and in which ones not. In addition, in those instances in which consensus is not reached, we characterize statistically the proportion of configurations that reach spurious fixed points from an ensemble of random initial configurations. Using numerical simulations, we also analyze two observables of the system to characterize the algorithm: (1) the quality of the achieved consensus, that is if it respects the initial majority of the network; and (2) the consensus time, measured as the average amount of steps to reach convergence.

PMID:36725907 | DOI:10.1038/s41598-023-28835-2

Sci Rep. 2023 Feb 1;13(1):1868. doi: 10.1038/s41598-023-29036-7.

ABSTRACT

Breast cancer is a global health issue affecting 2.3 million women per year, causing death in over 600,000. Mammography (and biopsy) is the gold standard for screening and diagnosis. Whilst effective, this test exposes individuals to radiation, has limitations to its sensitivity and specificity and may cause moderate to severe discomfort. Some women may also find this test culturally unacceptable. This proof-of-concept study, combining bottom-up proteomics with Matrix Assisted Laser Desorption Ionisation Mass Spectrometry (MALDI MS) detection, explores the potential for a non-invasive technique for the early detection of breast cancer from fingertip smears. A cohort of 15 women with either benign breast disease (n = 5), early breast cancer (n = 5) or metastatic breast cancer (n = 5) were recruited from a single UK breast unit. Fingertips smears were taken from each patient and from each of the ten digits, either at the time of diagnosis or, for metastatic patients, during active treatment. A number of statistical analyses and machine learning approaches were investigated and applied to the resulting mass spectral dataset. The highest performing predictive method, a 3-class Multilayer Perceptron neural network, yielded an accuracy score of 97.8% when categorising unseen MALDI MS spectra as either the benign, early or metastatic cancer classes. These findings support the need for further research into the use of sweat deposits (in the form of fingertip smears or fingerprints) for non-invasive screening of breast cancer.

PMID:36725900 | DOI:10.1038/s41598-023-29036-7

Sci Rep. 2023 Feb 1;13(1):1845. doi: 10.1038/s41598-023-29095-w.

ABSTRACT

Severe acute malnutrition (SAM) is a major global public health problem. We aimed to assess the effects of probiotic and synbiotic supplementation on rate of weight gain and change in length in young SAM infants. This study was substudy of a single-blind randomized clinical trial (NCT0366657). During nutritional rehabilitation, 67 <6 months old SAM infants were enrolled and randomized to receive either probiotic (Bifidobacterium. infantis EVC001) or synbiotic (B. infantis EVC001 + Lacto-N-neotetraose [LNnT]) or placebo (Lactose) for four weeks and were followed for four more weeks after supplementation. In multivariable linear regression model, the mean rate of weight gain in the probiotic arm compared to placebo was higher by 2.03 unit (P < 0.001), and 1.13 unit (P = 0.030) in the synbiotic arm. In linear mixed-effects model, mean WAZ was higher by 0.57 unit (P = 0.018) in probiotic arm compared to placebo. Although not statistically significant, delta length for age z score (LAZ) trended to be higher among children in probiotc (β = 0.25) and synbiotic (β = 0.26) arms compared to placebo in multivariable linear regression model. Our study describes that young SAM infants had a higher rate of weight gain when supplemented with probiotic alone, compared to their counterparts with either synbiotic or placebo.

PMID:36725893 | DOI:10.1038/s41598-023-29095-w

Sci Rep. 2023 Feb 1;13(1):1818. doi: 10.1038/s41598-023-29034-9.

ABSTRACT

Oral iron is the mainstay of treating iron deficiency anemia. Recent studies indicate better fractional iron absorption with alternate day supplementation. However, the optimal supplementation strategy is unclear. We compared effectiveness of daily versus alternate day supplementation of oral iron for treatment of iron deficiency anemia. This double blind, active control, randomized controlled trial was conducted on two hundred adults having hemoglobin 10 g/dL or less with microcytic hypochromic anemia and/or serum ferritin below 50 ng/mL. They were randomized to receive either two Ferrous sulfate tablets containing 60 mg elemental iron (120 mg total) on alternate days or single tablet of 60 mg elemental iron daily for 8 weeks. Primary outcome was mean change in hemoglobin at week 8 from baseline. Mean hemoglobin was 6.53 (± 1.89) and 6.68 (± 1.89) g/dL in the alternate day and daily arms respectively. Mean change in hemoglobin was + 1.05 ± 1.34 g/dL in alternate day arm and + 1.36 ± 1.51 g/dL in daily arm (p = 0.47) at week 8. There were no statistically significant differences between the arms with respect to any secondary outcome. There is no significant difference between alternate day and daily iron administration in improving hemoglobin. Randomized controlled trials enrolling more participants for longer periods of supplementation and evaluating clinically relevant outcomes like change in hemoglobin may be useful in identifying the ideal dosing strategy.Trial Registration: Clinical Trial Registry of India (CTRI/2019/01/017169).

PMID:36725875 | DOI:10.1038/s41598-023-29034-9

Sci Rep. 2023 Feb 1;13(1):1829. doi: 10.1038/s41598-023-28776-w.

ABSTRACT

This study developed a method for the simultaneous determination of volatile phenol, cyanide, anionic surfactant, and ammonia nitrogen in drinking water, using a continuous flow analyzer. The samples were first distilled at 145 °C. The phenol in the distillate then subsequently reacted with alkaline ferricyanide and 4-aminoantipyrine to form a red complex that was measured colorimetrically at 505 nm. Cyanide in the distillate subsequently reacted with chloramine T to form cyanogen chloride, which then formed a blue complex with pyridinecarboxylic acid that was measured colorimetrically at 630 nm. The anionic surfactant reacted with basic methylene blue to form a compound that was extracted into chloroform and washed with acidic methylene blue to remove interfering substances. The blue compound in chloroform was determined colorimetrically at 660 nm. Ammonia reacted with salicylate and chlorine from dichloroisocyanuric acid to produce indophenol blue at 37 °C in an alkaline environment that was measured at 660 nm. The relative standard deviations were 0.75-6.10% and 0.36-5.41%, respectively, and the recoveries were 96.2-103.6% and 96.0-102.4% when the mass concentration of volatile phenol and cyanide was in the range of 2-100 μg/L. The linear correlation coefficients were ≥ 0.9999, and the detection limits were1.2 μg/L and 0.9 μg/L, respectively. The relative standard deviations were 0.27-4.86% and 0.33-5.39%, and the recoveries were 93.7-107.0% and 94.4-101.7%. When the mass concentration of anionic surfactant and ammonia nitrogen was 10-1000 μg/L. The linear correlation coefficients were 0.9995 and 0.9999, and the detection limits were 10.7 μg/L and 7.3 μg/L, respectively. When compared to the national standard method, no statistically significant difference was found. This approach saves time and labor, has a lower detection limit, higher precision and accuracy, less contamination, and is more appropriate for the analysis and determination of large-volume samples.

PMID:36725871 | DOI:10.1038/s41598-023-28776-w

Nat Commun. 2023 Feb 1;14(1):544. doi: 10.1038/s41467-022-35663-x.

ABSTRACT

Immune cell function can be altered by lipids in circulation, a process potentially relevant to lipid-associated inflammatory diseases including atherosclerosis and rheumatoid arthritis. To gain further insight in the molecular changes involved, we here perform a transcriptome-wide association analysis of blood triglycerides, HDL cholesterol, and LDL cholesterol in 3229 individuals, followed by a systematic bidirectional Mendelian randomization analysis to assess the direction of effects and control for pleiotropy. Triglycerides are found to induce transcriptional changes in 55 genes and HDL cholesterol in 5 genes. The function and cell-specific expression pattern of these genes implies that triglycerides downregulate both cellular lipid metabolism and, unexpectedly, allergic response. Indeed, a Mendelian randomization approach based on GWAS summary statistics indicates that several of these genes, including interleukin-4 (IL4) and IgE receptors (FCER1A, MS4A2), affect the incidence of allergic diseases. Our findings highlight the interplay between triglycerides and immune cells in allergic disease.

PMID:36725846 | DOI:10.1038/s41467-022-35663-x

Environ Sci Pollut Res Int. 2023 Feb 2. doi: 10.1007/s11356-023-25646-w. Online ahead of print.

ABSTRACT

The rapid rise of tourism in the karst regions has promoted the development of the local economy by relying on the unique landforms and landscapes. However, tourism development is often accompanied by land use changes and has an impact on the ecological environment. Exploring the coupling relationship between “tourism development-land use-landscape pattern” is very important for ecologically fragile karst areas. Taking the Yulong River Basin as an example, this research applied 3S technology, spatial analysis based on POIs, and regression analysis to the following: (1) identifying the process and effects of land use change, (2) determining the spatial pattern of tourism land and its correlation with land use change, (3) determining the characteristics and impacts of landscape pattern evolution. As the results suggested: (1) The significant expansion of construction land occupies a large amount of farmland, there is a balanced relationship between farmland and forest land for mutual conversion. (2) The aggregation of tourist land is affected by the trend of tourist behavior and the distribution of scenic spots. There is a significant moderate positive correlation between tourism land and construction land. (3) With the land use change, landscape heterogeneity has improved, but landscape fragmentation is serious and landscape connectivity is reduced. This research provides new evidences for the effect of the rapid development of tourism on land use change and ecological environment and as a reference to future orderly and moderate land development and ecological sustainability in karst regions.

PMID:36725804 | DOI:10.1007/s11356-023-25646-w

Psychometrika. 2023 Feb 1. doi: 10.1007/s11336-022-09899-x. Online ahead of print.

ABSTRACT

Reporting effect size index estimates with their confidence intervals (CIs) can be an excellent way to simultaneously communicate the strength and precision of the observed evidence. We recently proposed a robust effect size index (RESI) that is advantageous over common indices because it’s widely applicable to different types of data. Here, we use statistical theory and simulations to develop and evaluate RESI estimators and confidence/credible intervals that rely on different covariance estimators. Our results show (1) counter to intuition, the randomness of covariates reduces coverage for Chi-squared and F CIs; (2) when the variance of the estimators is estimated, the non-central Chi-squared and F CIs using the parametric and robust RESI estimators fail to cover the true effect size at the nominal level. Using the robust estimator along with the proposed nonparametric bootstrap or Bayesian (credible) intervals provides valid inference for the RESI, even when model assumptions may be violated. This work forms a unified effect size reporting procedure, such that effect sizes with confidence/credible intervals can be easily reported in an analysis of variance (ANOVA) table format.

PMID:36725775 | DOI:10.1007/s11336-022-09899-x

Biometals. 2023 Feb 1. doi: 10.1007/s10534-023-00491-z. Online ahead of print.

ABSTRACT

The COVID-19 pandemic has generated a major interest in designing inhibitors to prevent SARS-CoV-2 binding on host cells to protect against infection. One promising approach to such research utilizes molecular dynamics simulation to identify potential inhibitors that can prevent the interaction between spike (S) protein on the virus and angiotensin converting enzyme 2 (ACE2) receptor on the host cells. In these studies, many groups have chosen to exclude the ACE2-bound zinc (Zn) ion, which is critical for its enzymatic activity. While the relatively distant location of Zn ion from the S protein binding site (S1 domain), combined with the difficulties in modeling this ion has motivated the decision of exclusion, Zn can potentially contribute to the structural stability of the entire protein, and thus, may have implications on S protein-ACE2 interaction. In this study, the authors model both the ACE2-S1 and ACE2-inhibitor (mAb) system to investigate if there are variations in structure and the readouts due to the presence of Zn ion. Although distant from the S1 or inhibitor binding region, inclusion/exclusion of Zn has statistically significant effects on the structural stability and binding free energy in these systems. In particular, the binding free energy of the ACE2-S1 and ACE2-inhibitor structures is – 3.26 and – 14.8 kcal/mol stronger, respectively, in the Zn-bound structure than in the Zn-free structures. This finding suggests that including Zn may be important in screening potentially inhibitors and may be particularly important in modeling monoclonal antibodies, which may be more sensitive to changes in antigen structure.

PMID:36725769 | DOI:10.1007/s10534-023-00491-z