Tag: statistics

Anal Chem. 2023 Jul 10. doi: 10.1021/acs.analchem.3c01864. Online ahead of print.

ABSTRACT

As the first step of metabolomic analysis in biomarker identification studies, various types of blood collection tubes are used in clinical practice. However, little attention is paid to potential contamination caused by the blank tube itself. Here, we evaluated small molecules in blank EDTA plasma tubes through LC-MS-based untargeted metabolomic analysis and identified small molecules with markedly varied levels among different production batches or specifications. Our data demonstrate possible contamination and data interference caused by blank EDTA plasma tubes when employing large clinical cohorts for biomarker identification. Therefore, we propose a workflow of filtering metabolites in blank tubes prior to statistical analysis to improve the fidelity of biomarker identification.

PMID:37428854 | DOI:10.1021/acs.analchem.3c01864

PLoS Negl Trop Dis. 2023 Jul 10;17(7):e0011432. doi: 10.1371/journal.pntd.0011432. Online ahead of print.

ABSTRACT

BACKGROUND: Nocardia species can cause local or disseminated infection. Prompt diagnosis and appropriate treatment of nocardiosis are required, because it can cause significant morbidity and mortality. Knowledge of local species distribution and susceptibility patterns is important to appropriate empiric therapy. However, knowledge on the epidemiology and antimicrobial susceptibility profiles of clinical Nocardia species remains limited in China.

METHODS: The data of isolation of Nocardia species were collected from databases such as Pubmed, Web of Science, Embase as well as Chinese databases (CNKI, Wanfang and VIP). Meta-analysis was performed using RevMan 5.3 software. Random effect models were used and tested with Cochran’s Q and I2 statistics taking into account the possibility of heterogeneity between studies.

RESULTS: In total, 791 Nocardia isolates were identified to 19 species levels among all the recruited studies. The most common species were N. farcinica (29.1%, 230/791), followed by N. cyriacigeorgica (25.3%, 200/791), N. brasiliensis (11.8%, 93/791) and N. otitidiscaviarum (7.8%, 62/791). N. farcinica and N. cyriacigeorgica are widely distributed, N. brasiliensis mainly prevalent in the Southern, N. otitidiscaviarum mainly distributed in the east coastal provinces of China. Totally, 70.4% (223/317) Nocardia were cultured from respiratory tract specimens, 16.4% (52/317) from extra-pulmonary specimens, and 13.3% (42/317) from disseminated infection. The proportion of susceptible isolates as follows: linezolid 99.5% (197/198), amikacin 96.0% (190/198), trimethoprim-sulfamethoxazole 92.9% (184/198), imipenem 64.7% (128/198). Susceptibility varied by species of Nocardia.

CONCLUSIONS: N. farcinica and N. cyriacigeorgica are the most frequently isolated species, which are widely distributed in China. Pulmonary nocardiosis is the most common type of infection. Trimethoprim-sulfamethoxazole can still be the preferred agent for initial Nocardia infection therapy due to the low resistance rate, linezolid and amikacin could be an alternative to treat nocardiosis or a choice in a combination regimen.

PMID:37428800 | DOI:10.1371/journal.pntd.0011432

PLoS One. 2023 Jul 10;18(7):e0288289. doi: 10.1371/journal.pone.0288289. eCollection 2023.

ABSTRACT

BACKGROUND: International professional organizations recommend aspirin prophylaxis to women screened high risk for preterm preeclampsia (PE) in the first trimester. The UK Fetal Medicine Foundation (FMF) screening test for preterm PE using mean arterial pressure (MAP), uterine artery pulsatility index (UTPI) and placental growth factor (PlGF) was demonstrated to have lower detection rate (DR) in Asian population studies. Additional biomarkers are therefore needed in Asian women to improve screening DRs as a significant proportion of women with preterm and term PE are currently not identified.

OBJECTIVES: To evaluate maternal serum inhibin-A at 11-13 weeks as an alternative to PlGF or as an additional biomarker within the FMF screening test for preterm PE.

STUDY DESIGN: This is a nested case-control study using pregnancies initially screened at 11-13 weeks for preterm PE using the FMF triple test in a non-intervention study conducted between December 2016 and June 2018. Inhibin-A levels were retrospectively measured in 1,792 singleton pregnancies, 112 (1.7%) with PE matched for time of initial screening with 1,680 unaffected pregnancies. Inhibin-A levels were transformed to multiple of the expected median (MoM). The distribution of log10 inhibin-A MoM in PE and unaffected pregnancies and the association between log10 inhibin-A MoM and gestational age (GA) at delivery in PE were assessed. The screening performance determined by area under receiver operating characteristic curves (AUC) and detection rates (DRs) at a 10% fixed false positive rate (FPR), for preterm and term PE was determined. All risks for preterm and term PE were based on the FMF competing risk model and Bayes theorem. Differences in AUC (ΔAUC) between different biomarker combinations were compared using the Delong test. McNemar’s test was used to assess the off-diagonal change in screening performance at a fixed 10% FPR after adding inhibin-A or replacing PlGF in the preterm PE adjusted risk estimation model.

RESULTS: Inhibin-A levels in unaffected pregnancies were significantly dependent on GA, maternal age and weight and were lower in parous women with no previous history of PE. Mean log10 inhibin-A MoM in any-onset PE (p<0.001), preterm (p<0.001) and term PE (p = 0.015) pregnancies were all significantly higher than that of unaffected pregnancies. Log10 inhibin-A MoM was inversely but not significantly correlated (p = 0.165) with GA at delivery in PE pregnancies. Replacing PlGF with inhibin-A in the FMF triple test reduced AUC and DR from 0.859 and 64.86% to 0.837 and 54.05%, the ΔAUC was not statistically significant. AUC and DR when adding inhibin-A to the FMF triple test were 0.814, 54.05% and the -0.045 reduction in AUC was statistically significant (p = 0.001). At a fixed 10% FPR, replacing PlGF with inhibin-A identified 1 (2.7%) additional pregnancy but missed 5 (13.5%) pregnancies which subsequently developed preterm PE identified by the FMF triple test. Adding inhibin-A missed 4 (10.8%) pregnancies and did not identify any additional pregnancies with preterm PE.

CONCLUSION: Replacing PlGF by inhibin-A or adding inhibin-A as an additional biomarker in and to the FMF triple screening test for preterm PE does not improve screening performance and will fail to identify pregnancies that are currently identified by the FMF triple test.

PMID:37428792 | DOI:10.1371/journal.pone.0288289

PLoS One. 2023 Jul 10;18(7):e0288304. doi: 10.1371/journal.pone.0288304. eCollection 2023.

ABSTRACT

We devised a surgical tape that prevents skin tears while maintaining adhesive strength. Under the assumption that microscopic damage to the skin is reflected in pain felt on the skin, we statistically analyzed skin pain when the tape was peeled off to show the skin protection effect of the mesh on the new tape. This tape has a three-layer structure consisting of a tape substrate, adhesive, and mesh. When the tape is applied to the skin, a mesh is located between the adhesive and the skin. The adhesive contacts the skin through the mesh holes and fixes the substrate to the skin; it does not come into contact with the skin at the mesh body; therefore, the adhesive-skin contact area is reduced. In this experiment, we used surgical tape with and without mesh. At 8 hours after the application of each tape to the forearm of five adult males, it was removed. All tapes were peeled off while maintaining an angle of approximately 120° between the skin and tape substrate. For the tape with mesh, the tape substrate was peeled off in two ways: peeling off the substrate together with the mesh and peeling off the substrate, leaving the mesh on the skin. A perception and pain quantification analyzer (Pain Vision™) was used to quantify pain. The data were compared and examined statistically (Friedman’s test and Wilcoxon’s coded rank test). The least pain was experienced while peeling off the tape substrate, leaving the mesh on the skin. There was a significant difference in pain levels among the three tape removal methods. There was also a significant difference between the two peeling methods in the experimental group. The skin protection effect of the mesh reduced pain when the surgical tape was removed.

PMID:37428790 | DOI:10.1371/journal.pone.0288304

PLoS One. 2023 Jul 10;18(7):e0288339. doi: 10.1371/journal.pone.0288339. eCollection 2023.

ABSTRACT

Researchers have begun studying the impact of human opioid and cannabinoid use on dog populations. These studies have used data from an animal poison control center (APCC) and there are concerns that due to the illicit nature and social stigma concerning the use of these drugs, owners may not always be forthcoming with veterinarians or APCC staff regarding pet exposures to these toxicants. As a result, models derived from APCC data that examine the predictability of opioid and cannabinoid dog poisonings using pet demographic and health disorder information may help veterinarians or APCC staff more reliably identify these toxicants when examining or responding to a call concerning a dog poisoned by an unknown toxicant. The fitting of epidemiologically informed statistical models has been useful for identifying factors associated with various health conditions and as predictive tools. However, machine learning, including lasso regression, has many useful features as predictive tools, including the ability to incorporate large numbers of independent variables. Consequently, the objectives of our study were: 1) identify pet demographic and health disorders associated with opioid and cannabinoid dog poisonings using ordinary and mixed logistic regression models; and 2) compare the predictive performance of these models to analogous lasso logistic regression models. Data were obtained from reports of dog poisoning events collected by the American Society for the Prevention of Cruelty to Animals’ (ASPCA) Animal Poisoning Control Center, from 2005-2014. We used ordinary and mixed logistic regression models as well as lasso logistic regression models with and without controlling for autocorrelation at the state level to train our models on half the dataset and test their predictive performance on the remainder. Although epidemiologically informed logistic regression models may require substantial knowledge of the disease systems being investigated, they had the same predictive abilities as lasso logistic regression models. All models had relatively high predictive parameters except for positive predictive values, due to the rare nature of calls concerning opioid and cannabinoid poisonings. Ordinary and mixed logistic regression models were also substantially more parsimonious than their lasso equivalents while still allowing for the epidemiological interpretation of model coefficients. Controlling for autocorrelation had little effect on the predictive performance of all models, but it did reduce the number of variables included in lasso models. Several disorder variables were associated with opioid and cannabinoid calls that were consistent with the acute effects of these toxicants. These models may help build diagnostic evidence concerning dog exposure to opioids and cannabinoids, saving time and resources when investigating these cases.

PMID:37428780 | DOI:10.1371/journal.pone.0288339

PLoS One. 2023 Jul 10;18(7):e0288262. doi: 10.1371/journal.pone.0288262. eCollection 2023.

ABSTRACT

Establishing links between breeding, stopover, and wintering sites for migratory species is important for their effective conservation and management. Isotopic assignment methods used to create these connections rely on the use of predictable, established relationships between the isotopic composition of environmental hydrogen and that of the non-exchangeable hydrogen in animal tissues, often in the form of a calibration equation relating feather (δ2Hf) values derived from known-origin individuals and amount-weighted long-term precipitation (δ2Hp) data. The efficacy of assigning waterfowl to moult origin using stable isotopes depends on the accuracy of these relationships and their statistical uncertainty. Most current calibrations for terrestrial species in North America are done using amount-weighted mean growing-season δ2Hp values, but the calibration relationship is less clear for aquatic and semi-aquatic species. Our objective was to critically evaluate current methods used to calibrate δ2Hp isoscapes to predicted δ2Hf values for waterfowl. Specifically, we evaluated the strength of the relationships between δ2Hp values from three commonly used isoscapes and known-origin δ2Hf values three published datasets and one collected as part of this study, also grouping these data into foraging guilds (dabbling vs diving ducks). We then evaluated the performance of assignments using these calibrations by applying a cross-validation procedure. It remains unclear if any of the tested δ2Hp isoscapes better predict surface water inputs into food webs for foraging waterfowl. We found only marginal differences in the performance of the tested known-origin datasets, where the combined foraging-guild-specific datasets showed lower assignment precision and model fit compared to data for individual species. We recommend the use of the more conservative combined foraging-guild-specific datasets to assign geographic origin for all dabbling duck species. Refining these relationships is important for improved waterfowl management and contributes to a better understanding of the limitations of assignment methods when using the isotope approach.

PMID:37428774 | DOI:10.1371/journal.pone.0288262

J Couns Psychol. 2023 Jul;70(4):340. doi: 10.1037/cou0000666.

ABSTRACT

Reports an error in “Do psychotherapists improve with time and experience? A longitudinal analysis of outcomes in a clinical setting” by Simon B. Goldberg, Tony Rousmaniere, Scott D. Miller, Jason Whipple, Stevan Lars Nielsen, William T. Hoyt and Bruce E. Wampold (Journal of Counseling Psychology, 2016[Jan], Vol 63[1], 1-11). The article (https://doi.org/10.1037/cou0000131), had an error in the Method section in the Early termination section under the Variables heading. The coding was reversed in the sentence “Patients received a code of 0 (early termination) or 1 (nonearly termination) on this dichotomous variable” and should have read “Patients received a code of 1 (early termination) or 0 (nonearly termination) on this dichotomous variable.” The online version of this article has been corrected. (The following abstract of the original article appeared in record 2015-58774-001.) Objective: Psychotherapy researchers have long questioned whether increased therapist experience is linked to improved outcomes. Despite numerous cross-sectional studies examining this question, no large-scale longitudinal study has assessed within-therapist changes in outcomes over time.

METHOD: The present study examined changes in psychotherapists’ outcomes over time using a large, longitudinal, naturalistic psychotherapy data set. The sample included 6,591 patients seen in individual psychotherapy by 170 therapists who had on average 4.73 years of data in the data set (range = 0.44 to 17.93 years). Patient-level outcomes were examined using the Outcome Questionnaire-45 and a standardized metric of change (prepost d). Two-level multilevel models (patients nested within therapist) were used to examine the relationship between therapist experience and patient prepost d and early termination. Experience was examined both as chronological time and cumulative patients seen.

RESULTS: Therapists achieved outcomes comparable with benchmarks from clinical trials. However, a very small but statistically significant change in outcome was detected indicating that on the whole, therapists’ patient prepost d tended to diminish as experience (time or cases) increases. This small reduction remained when controlling for several patient-level, caseload-level, and therapist-level characteristics, as well as when excluding several types of outliers. Further, therapists were shown to vary significantly across time, with some therapists showing improvement despite the overall tendency for outcomes to decline. In contrast, therapists showed lower rates of early termination as experience increased.

CONCLUSIONS: Implications of these findings for the development of expertise in psychotherapy are explored. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

PMID:37428762 | DOI:10.1037/cou0000666

PLoS One. 2023 Jul 10;18(7):e0274439. doi: 10.1371/journal.pone.0274439. eCollection 2023.

ABSTRACT

The relationship of food comminution and individual age in Tupaia belangeri is investigated. It is hypothesized that with increasing age the performance of the molar dentition decreases due to progressive tooth wear. While this relationship is well-documented for herbivores, age-related test series are largely lacking for insectivorous mammals. 15 individuals of Tupaia belangeri were fed exclusively with mealworms, and their faeces were analyzed for the number and size of chitin particles. The exoskeleton of a mealworm is resistant to digestive fluids in the gastrointestinal tract, and the size of individual chitin particles indicates the effectiveness of mechanical comminution that occurs in the oral cavity during mastication. It is hypothesized that a more precise occlusion of the dentition results in smaller particle size. Although individuals of all ages (juvenile, adult, and senile) were able to effectively process mealworms with their dentition prior to digestion, a larger area of very large chitin particles (98% quantile of all particles in senile animals as compared to in the same quantile in adults) in the feces of senile animals was detected. Even though the particle size of indigestible material is irrelevant for the digestive process, these findings either document somatic senescence in the functionality of the teeth, or alternatively a change in chewing behaviour with age.

PMID:37428732 | DOI:10.1371/journal.pone.0274439

PLoS One. 2023 Jul 10;18(7):e0283412. doi: 10.1371/journal.pone.0283412. eCollection 2023.

ABSTRACT

This study investigates the association between individuals’ concern about contracting COVID-19 and their compliance with recommended preventive and mitigation measures, namely wearing face masks, maintaining social distancing and handwashing, in the context of the Middle East and North Africa (MENA) region. The empirical analysis is based on a panel dataset from the Combined COVID-19 MENA Monitor Household Survey, which was carried out in Jordan, Morocco, Sudan, Tunisia and Egypt. Applying a probit estimation technique, a positive and statistically significant association was found between the level of COVID-19 worries and individuals’ compliance with the mitigation measures. Notably, the results revealed that this association followed a “first-up-then-down” trend, showing that compliance with the three mitigation measures rose as individuals’ worries about contracting the virus increased, and then markedly decreased after they had been infected. Socio-demographic characteristics contributing to lower levels of compliance included being male, being over 60, having lower levels of education and having a lower household income. A cross-country analysis revealed remarkable differences between the five countries, with the strongest association between COVID-19 concerns and adherence to mitigation measures observed in Tunisia and Sudan, and the weakest association seen in Jordan and Morocco. Policy implications are outlined for effective risk communication and management during disease outbreaks and public health emergencies to encourage appropriate public health behaviours.

PMID:37428731 | DOI:10.1371/journal.pone.0283412

BJS Open. 2023 Jul 10;7(4):zrad051. doi: 10.1093/bjsopen/zrad051.

ABSTRACT

BACKGROUND: Intraoperative neuromonitoring is widely used in thyroid and parathyroid surgery to prevent unilateral and especially bilateral recurrent nerve paresis. Reference values for amplitude and latency for the recurrent laryngeal nerve and vagus nerve have been published. However, data quality measures that exclude errors of the underlying intraoperative neuromonitoring (IONM) data (immanent software errors, false data labelling) before statistical analysis have not yet been implemented.

METHODS: The authors developed an easy-to-use application (the Mainz IONM Quality Assurance and Analysis tool) using the programming language R. This tool allows visualization, automated and manual correction, and statistical analysis of complete raw data sets (electromyogram signals of all stimulations) from intermittent and continuous neuromonitoring in thyroid and parathyroid surgery. The Mainz IONM Quality Assurance and Analysis tool was used to evaluate IONM data generated and exported from ‘C2’ and ‘C2 Xplore’ neuromonitoring devices (inomed Medizintechnik GmbH) after surgery. For the first time, reference values for latency and amplitude were calculated based on ‘cleaned’ IONM data.

RESULTS: Intraoperative neuromonitoring data files of 1935 patients consecutively operated on from June 2014 to May 2020 were included. Of 1921 readable files, 34 were excluded for missing data labelling. Automated plausibility checks revealed: less than 3 per cent device errors for electromyogram signal detection; 1138 files (approximately 60 per cent) contained potential labelling errors or inconsistencies necessitating manual review; and 915 files (48.5 per cent) were indeed erroneous. Mean(s.d.) reference onset latencies for the left vagus nerve, right vagus nerve, recurrent laryngeal nerve, and external branch of the superior laryngeal nerve were 6.8(1.1), 4.2(0.8), 2.5(1.1), and 2.1(0.5) ms, respectively.

CONCLUSION: Due to high error frequencies, IONM data should undergo in-depth review and multi-step cleaning processes before analysis to standardize scientific reporting. Device software calculates latencies differently; therefore reference values are device-specific (latency) and/or set-up-specific (amplitude). Novel C2-specific reference values for latency and amplitude deviate considerably from published values.

PMID:37428557 | DOI:10.1093/bjsopen/zrad051