Tag: statistics

Nucleic Acids Res. 2023 May 11:gkad407. doi: 10.1093/nar/gkad407. Online ahead of print.

ABSTRACT

Microbiome studies have become routine in biomedical, agricultural and environmental sciences with diverse aims, including diversity profiling, functional characterization, and translational applications. The resulting complex, often multi-omics datasets demand powerful, yet user-friendly bioinformatics tools to reveal key patterns, important biomarkers, and potential activities. Here we introduce MicrobiomeAnalyst 2.0 to support comprehensive statistics, visualization, functional interpretation, and integrative analysis of data outputs commonly generated from microbiome studies. Compared to the previous version, MicrobiomeAnalyst 2.0 features three new modules: (i) a Raw Data Processing module for amplicon data processing and taxonomy annotation that connects directly with the Marker Data Profiling module for downstream statistical analysis; (ii) a Microbiome Metabolomics Profiling module to help dissect associations between community compositions and metabolic activities through joint analysis of paired microbiome and metabolomics datasets; and (iii) a Statistical Meta-Analysis module to help identify consistent signatures by integrating datasets across multiple studies. Other important improvements include added support for multi-factor differential analysis and interactive visualizations for popular graphical outputs, updated methods for functional prediction and correlation analysis, and expanded taxon set libraries based on the latest literature. These new features are demonstrated using a multi-omics dataset from a recent type 1 diabetes study. MicrobiomeAnalyst 2.0 is freely available at microbiomeanalyst.ca.

PMID:37166960 | DOI:10.1093/nar/gkad407

Psychol Addict Behav. 2023 May 11. doi: 10.1037/adb0000919. Online ahead of print.

ABSTRACT

OBJECTIVES: Problematic substance use is one of the most stigmatized health conditions leading research to examine how the labels and models used to describe it influence public stigma. Two recent studies examine whether beliefs in a disease model of addiction influence public stigma but result in equivocal findings-in line with the mixed-blessings model, Kelly et al. (2021) found that while the label “chronically relapsing brain disease” reduced blame attribution, it decreased prognostic optimism and increased perceived danger and need for continued care; however, Rundle et al. (2021) conclude absence of evidence. This study isolates the different factors used in these two studies to assess whether health condition (drug use vs. health concern), etiological label (brain disease vs. problem), and attributional judgment (low vs. high treatment stability) influence public stigma toward problematic substance use.

METHOD: Overall, 1,613 participants were assigned randomly to one of the eight vignette conditions that manipulated these factors. They completed self-report measures of discrete and general public stigma and an indirect measure of discrimination.

RESULTS: Greater social distance, danger, and public stigma but lower blame were ascribed to drug use relative to a health concern. Greater (genetic) blame was reported when drug use was labeled as a “chronically relapsing brain disease” relative to a “problem.” Findings for attributional judgment were either inconclusive or statistically equivalent.

DISCUSSION: The labels used to describe problematic substance use appear to impact discrete elements of stigma. We suggest that addiction is a functional attribution, which may explain the mixed literature on the impact of etiological labels on stigma to date. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

PMID:37166945 | DOI:10.1037/adb0000919

Psychol Methods. 2023 Apr;28(2):339-358. doi: 10.1037/met0000567.

ABSTRACT

Empirical studies often demonstrate multiple causal mechanisms potentially involving simultaneous or causally related mediators. However, researchers often use simple mediation models to understand the processes because they do not or cannot measure other theoretically relevant mediators. In such cases, another potentially relevant but unobserved mediator potentially confounds the observed mediator, thereby biasing the estimated direct and indirect effects associated with the observed mediator and threatening corresponding inferences. Additionally, researchers may not know the extent to which their measures are reliable, and accordingly, measurement error may bias estimated effects and mislead statistical inferences. Given these threats, we explore how the omission of an unobserved mediator and/or using variables with measurement error biases estimates and affects inferences associated with the observed mediator. Then, building off Frank’s impact threshold for a confounding variable (ITCV), we propose a correlation-based sensitivity analysis. Lastly, we provide an R package ConMed to assess the robustness of mediation inferences given the omission of an unobserved, confounding mediator and/or measurement error. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

PMID:37166933 | DOI:10.1037/met0000567

Georgian Med News. 2023 Mar;(336):123-125.

ABSTRACT

Contamination of certain drugs and foods with one of the most potent carcinogens/mutagens- nitrosamines, remains to be an issue and unresolved at present. The increased contamination of these mutagens in the most commonly used drugs in the human population doesn’t ceases to baffle clinicians, critics, public scholars, and analysts of the nitrosamine saga. The introduction of permissive determinations of the presence of carcinogens in drugs only reinforces doubts about the powerlessness of regulatory authorities in the face of the influence of powerful pharmaceutical cartels. The FDA’s encouraging promises of 2018 for strict control of carcinogens in sartans seems to have been permanently forgotten? By 2021, it was unthinkable that these carcinogens would be present in blood drugs and affected batches were immediately removed. Following alert checks confirming their post-existence in diabetes drugs, anti-smoking drugs, a number of antibiotics, ACE inhibitors, Sartans, thiazide diuretics, ranitidine, but probably a number of others, the decision has been taken to give the green light to their permissible availability. An availability that in all likelihood has the flavour of death. A “flavour” that has been confirmed in hundreds of international publications. Or in data from scientific papers submitted to regulatory regional units for verification and which remain sadly silent to this day. The “silent confirmation” and the lack of any adequate response in favour of public health are a sufficient further indicator of the attitude and position of the regulatory authorities. A position that should be changed. Starting from the mentioned facts and the data announced already in 2016/2017 of all-American data shared originally in American scientific journals, using their statistical estimates, we present the first case in the world literature of nodular melanoma and basal cell carcinoma occurring after taking perindopril. This intake turns out to be confirmatory one with respect to the statistics presented by Beatrice Nardone dating back to 2017. The potential pro-carcinogenic effects of both nitrosamines and the generic substance of perindopril are discussed.

PMID:37166894

Georgian Med News. 2023 Mar;(336):63-65.

ABSTRACT

A comparative analysis of clinical and laboratory parameters was carried out in 49 children. The patients were divided into 3 groups depending on the type of insulin they received. Group 1 included 20 children who used Insulin human (Insulatard), group 2 included 15 children using insulin Glargine, and group 3 included 14 children using insulin Detemir. All children using Detemir and Glargine used short acting insulin Aspart. Those using Insulin human (Insulatard) used Human insulin (rDNA, Actrapid) in addition. In all children, blood glucose, glycohemoglobin and cholesterol were determined by laboratory methods. Statistical calculations were carried out using a statistical package at a confidence level of p＜0.05. A significant difference was found between the mean values of glycohemoglobin and glucose of Glargine users and patients with using Insulin human (Insulatard) (p≺0.05). These indicators were lower in Glargine users. There is a positive correlation between doses of Regular insulin and Insulin human (Insulatard) with body weight and height. There is a positive correlation between dose of Detemir and body mass. However, no such relationship between Glargine, body mass and height was recorded. It was a negative correlation between its dose Glargine with glycohemoglobin and also between glucose and cholesterol using Glargine.

PMID:37166882

Georgian Med News. 2023 Mar;(336):54-58.

ABSTRACT

The aim of study was identification of bone metastasis probability, in molecular subtypes among post-treated patients (hormone-receptor-positive breast cancer), considering statistical frequency of stages. 101 women (I, II, III stages; hormone-receptor-positive), who underwent bone scintigraphy before and after treatment, were retrospectively studied. The study was performed with radiotracer Tc99m MDP, intravenous injection. BS data were correlated with molecular subtype (Luminal-A, Luminal-B) and stage. According to the stages, molecular subtypes and bone metastasis was revealed: In the I stage – 32 (20,0%) patients: luminal A – 30 (93.7%) patients, among them with metastasis 12 (40%) cases; luminal B – 2 (6.2%) patients with metastasis 0 (0%) cases (p=0.282). II stage – 83 (51.9%) patients: luminal A = 71 (85.5%) patients, among them with metastasis – 43 (60.5%) cases; luminal B – 12 (14.4%) patients; among them with metastasis -3 (25%) cases (p=0.022) III stage =45 (28.1%) patients: Luminal A 38 (84.4%) patients, among them with metastasis – 30 (78.9%) cases; luminal B – 7 (15.5%) patients; among them with metastasis – 1 (14.2%) case (p=0.001). Among breast cancer patients’ molecular subtype luminal A has a high probability of spreading metastasis in bone, but there is more positive prognosis, rather than in luminal B type, that is much rarer and more aggressive molecular subtype. Taking into consideration molecular subtypes and stages of breast cancer is very important, as both of them are significant prognostic factors of disease, which might be helpful in the most cases.

PMID:37166880

Georgian Med News. 2023 Mar;(336):6-12.

ABSTRACT

The ACL is the primary stabilizer of the knee joint. The injury leads to instability of the knee joint, which is a trigger for the subsequent destructive changes of the intra-articular structures such as menisci and cartilage of the joint surfaces. The most affected group is people of an active age, engaged in amateur sports. Also, this pathology is an occupational hazard in the military. In this community, ACL injuries have reached 3.24% in men and 3.51% in women, with increasing trends, especially among women. This data is derived from a study by Keller Army Hospital, West Point, New York. In this study we selected 2 groups of patients – operated with autograft and operated with allograft. The groups included 25 patients followed for a period of 18 months. The tissues used for ACL reconstruction were: 1) for allograft – BTB donor tissue / allograft / 2) for autologous transplantation – mm. Semitendinosus et Gracillis / autograft /. After the operation, the patients are placed in a rehabilitation program in five interconnected phases. The way they are performed allows the principle of gradual loading and constant feedback between the patient and the physiotherapist to be observed. Each of the phases has specific goals in the rehabilitation cycle, which has a certain approximate duration. After completion of the rehabilitation process, the clinical outcomes of both groups were compared using the International Documentation Committee (IKDC), Lysholm, and three in-house diagnostic methods. Our own diagnostic methods are Power test (a strength simulator is used, which directly examines the strength of the limb in flexion and extension in real life test. The results from IKDC were in favor of the autograft group (92.82) and from Lischolm of the allograft group (92.24). In terms of the power test the results were in favor of the allograft group. The result from the Power 1 test clearly shows statistically significant difference in symmetry of power in flexion and extension which is better in the allograft group compared to the autograft group. In our research we did not come across such a test in other studies. In conclusion we proved that the development of a single strict rehabilitation protocol focusing on the principle of gradual increase in workloads achieves comparable results in the frequency of re-rupture in both the allograft and auto-graft groups.

PMID:37166871

Psychol Aging. 2023 May 11. doi: 10.1037/pag0000752. Online ahead of print.

ABSTRACT

Organizing information is beneficial to episodic memory performance. Among several possible organizational strategies, two consist of organizing the information in semantic clusters (semantic organization) or self-organizing the information based on new associations that do not exist in semantic memory (subjective organization). Here, we investigated in a single study how these two organizational behaviors were underlined by different controlled processes and whether these relations were subjected to age-related differences. We tested 123 younger adults (n = 63) and older adults (n = 60) on two episodic memory tasks, one where the words were organizable and another where the words were not organizable, allowing for semantic and subjective organization, respectively. Additionally, participants were tested on three cognitive control tasks (Wisconsin Card Sorting Test, Stroop Test and Trail Making Test) and three working memory tasks (Backward Digit Span, Alpha Span and N-back test). Results revealed well-established age-related differences in terms of recall performance and organizational strategy implementation. More importantly, we found evidence that the different cognitive tests statistically yielded two different latent factors, a cognitive control factor and a working memory factor. Based on this dissociation, we found that only cognitive control contributed to semantic organization in all age groups whereas only working memory contributed to subjective organization, also in all age groups. These results shed new lights on our understanding of how controlled processes differently contribute to organizational behaviors in episodic memory. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

PMID:37166861 | DOI:10.1037/pag0000752

Psychol Methods. 2023 May 11. doi: 10.1037/met0000559. Online ahead of print.

ABSTRACT

Researcher degrees of freedom refer to arbitrary decisions in the execution and reporting of hypothesis-testing research that allow for many possible outcomes from a single study. Selective reporting of results (p-hacking) from this “multiverse” of outcomes can inflate effect size estimates and false positive rates. We studied the effects of researcher degrees of freedom and selective reporting using empirical data from extensive multistudy projects in psychology (Registered Replication Reports) featuring 211 samples and 14 dependent variables. We used a counterfactual design to examine what biases could have emerged if the studies (and ensuing meta-analyses) had not been preregistered and could have been subjected to selective reporting based on the significance of the outcomes in the primary studies. Our results show the substantial variability in effect sizes that researcher degrees of freedom can create in relatively standard psychological studies, and how selective reporting of outcomes can alter conclusions and introduce bias in meta-analysis. Despite the typically thousands of outcomes appearing in the multiverses of the 294 included studies, only in about 30% of studies did significant effect sizes in the hypothesized direction emerge. We also observed that the effect of a particular researcher degree of freedom was inconsistent across replication studies using the same protocol, meaning multiverse analyses often fail to replicate across samples. We recommend hypothesis-testing researchers to preregister their preferred analysis and openly report multiverse analysis. We propose a descriptive index (underlying multiverse variability) that quantifies the robustness of results across alternative ways to analyze the data. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

PMID:37166859 | DOI:10.1037/met0000559

Psychol Methods. 2023 May 11. doi: 10.1037/met0000571. Online ahead of print.

ABSTRACT

R-squared measures of explained variance are easy to understand, naturally interpretable, and widely used by substantive researchers. In mediation analysis, however, despite recent advances in measures of mediation effect, few effect sizes have good statistical properties. Also, most of these measures are only available for the simplest three-variable mediation model, especially for R²-type measures. By decomposing the mediator into two parts (i.e., the part related to the predictor and the part unrelated to the predictor), this article proposes a systematic framework to develop new effect-size measures of explained variance in mediation analysis. The framework can be easily extended to more complex mediation models and provides more delicate R² measures for empirical researchers. A Monte Carlo simulation study is conducted to examine the statistical properties of the proposed R² effect-size measure. Results show that the new R2 measure performs well in approximating the true value of the explained variance of the mediation effect. The use of the proposed measure is illustrated with empirical examples together with program code for its implementation. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

PMID:37166856 | DOI:10.1037/met0000571