Tag: nevin manimala

Behav Res Methods. 2023 Jul 19. doi: 10.3758/s13428-023-02108-2. Online ahead of print.

ABSTRACT

pyWitness is a python toolkit for recognition memory experiments, with a focus on eyewitness identification (ID) data analysis and model fitting. The current practice is for researchers to use different statistical packages to analyze a single dataset. pyWitness streamlines the process. In addition to conducting key data analyses (e.g., receiver operating characteristic analysis, confidence accuracy characteristic analysis), statistical comparisons, signal-detection-based model fits, simulated data generation, and power analyses are also possible. We describe the package implementation and provide detailed instructions and tutorials with datasets so that users can follow. There is also an online manual that is regularly updated. We developed pyWitness to be user-friendly, reduce human interaction with pre-processing and processing of data and model fits, and produce publication-ready plots. All pyWitness features align with open science practices, such that the algorithms, fits, and methods are reproducible and documented. While pyWitness is a python toolkit, it can also be used from R for users more accustomed to this environment.

PMID:37540469 | DOI:10.3758/s13428-023-02108-2

Behav Res Methods. 2023 Aug 1. doi: 10.3758/s13428-023-02117-1. Online ahead of print.

ABSTRACT

Multiple Imputation (MI) is one of the most popular approaches to addressing missing values in questionnaires and surveys. MI with multivariate imputation by chained equations (MICE) allows flexible imputation of many types of data. In MICE, for each variable under imputation, the imputer needs to specify which variables should act as predictors in the imputation model. The selection of these predictors is a difficult, but fundamental, step in the MI procedure, especially when there are many variables in a data set. In this project, we explore the use of principal component regression (PCR) as a univariate imputation method in the MICE algorithm to automatically address the many-variables problem that arises when imputing large social science data. We compare different implementations of PCR-based MICE with a correlation-thresholding strategy through two Monte Carlo simulation studies and a case study. We find the use of PCR on a variable-by-variable basis to perform best and that it can perform closely to expertly designed imputation procedures.

PMID:37540467 | DOI:10.3758/s13428-023-02117-1

Behav Res Methods. 2023 Aug 1. doi: 10.3758/s13428-023-02099-0. Online ahead of print.

ABSTRACT

Principal component analysis (PCA) is an important tool for analyzing large collections of variables. It functions both as a pre-processing tool to summarize many variables into components and as a method to reveal structure in data. Different coefficients play a central role in these two uses. One focuses on the weights when the goal is summarization, while one inspects the loadings if the goal is to reveal structure. It is well known that the solutions to the two approaches can be found by singular value decomposition; weights, loadings, and right singular vectors are mathematically equivalent. What is often overlooked, is that they are no longer equivalent in the setting of sparse PCA methods which induce zeros either in the weights or the loadings. The lack of awareness for this difference has led to questionable research practices in sparse PCA. First, in simulation studies data is generated mostly based only on structures with sparse singular vectors or sparse loadings, neglecting the structure with sparse weights. Second, reported results represent local optima as the iterative routines are often initiated with the right singular vectors. In this paper we critically re-assess sparse PCA methods by also including data generating schemes characterized by sparse weights and different initialization strategies. The results show that relying on commonly used data generating models can lead to over-optimistic conclusions. They also highlight the impact of choice between sparse weights versus sparse loadings methods and the initialization strategies. The practical consequences of this choice are illustrated with empirical datasets.

PMID:37540466 | DOI:10.3758/s13428-023-02099-0

Mol Biol Rep. 2023 Aug 4. doi: 10.1007/s11033-023-08680-2. Online ahead of print.

ABSTRACT

BACKGROUND: Acute myeloid leukemia (AML) is a type of blood cancer that affects the bone marrow and blood cells. AML is characterized by the rapid growth and accumulation of abnormal white blood cells, known as myeloblasts, which interfere with the production of normal blood cells.

AIMS: The main aim was to determine the relationship between these genetic alterations and the clinico-haematological parameters and prognostic factors with therapy for Iraqi patients with AML.

METHODS: We used Sanger Sequencing to detect the mutations in 76 AML patients. Clinical data of AML patients were retrospectively analysed to compare the prognosis of each gene mutation group.

RESULTS: Somatic mutations were identified in 47.4% of the enrolled patients in a core set of pathogenic genes, including FLT3 (18 patients, 23.7%), DNMT3A (14, 18.4%), NPM1 (11, 14.5%) and TP53 (5, 6.8%). As multiple mutations frequently coexisted in the same patient, we classified patients into 10 further groups. Two novel mutations were detected in FLT3-ITD, with new accession numbers deposited into NCBI GenBank (OP807465 and OP807466). These two novel mutations were computationally analysed and predicted as disease-causing mutations. We found significant differences between patients with and without the detected mutations in disease progression after induction therapy (remission, failure and death; pv = < 0.001) and statistically significant differences were reported in total leukocyte count (pv = < 0.0001).

CONCLUSION: These genes are among the most frequently mutated genes in AML patients. Understanding the molecular and clinical significance of these mutations is important for guiding treatment decisions and predicting patient outcomes.

PMID:37540457 | DOI:10.1007/s11033-023-08680-2

Environ Sci Pollut Res Int. 2023 Aug 4. doi: 10.1007/s11356-023-29038-y. Online ahead of print.

ABSTRACT

Roads and traffic are important elements of urbanization, but their spatial associations with surface water quality in watersheds have been seldom studied. In this study, the spatially varying associations of three urbanization indicators, including road density, traffic density, and percentages of urban land, with twenty water quality indicators, including dissolved oxygen (DO), specific conductance (SC), dissolved solids (DS), suspended solids (SS), biochemical oxygen demand (BOD), dissolved nutrients, dissolved ions, heavy metals, and coliform bacteria, across the watersheds in the northern part of the state of Georgia, USA, have been examined by a conventional statistical method, ordinary least squares regression (OLS), and a spatial statistical method, geographically weighted regression (GWR). The results from OLS show that the urbanization indicators all have significant positive associations with the majority of the studied water pollutants, indicating that water pollution is significantly contributed by human activities related to urbanization in northern Georgia. In contrast, GWR results show that the associations vary across the watersheds affected by their urbanization levels. Significant positive associations are found between each urbanization indicator and each of the studied water pollutants, but not in all watersheds. The associations of suspended solids, nitrogen nutrients, and coliform bacteria with all three urbanization indicators are more significant in less-urbanized watersheds, while the associations of dissolved ions, BOD, and orthophosphate (PO₄) with road density and traffic density are more significant than those with urban land in more-urbanized watersheds, indicating that those water pollutants are more contributed by human activities associated with roads and traffic than other activities in more-urbanized areas. As a pilot study to explore how and why the associations of surface water quality with roads and traffic change across watersheds with different urbanization levels, its findings suggest that the policies of watershed management, land-use planning, and transportation planning should be tailored in local areas based on the locally important water pollutants and their associated urbanization indicators.

PMID:37540414 | DOI:10.1007/s11356-023-29038-y

Clin Rheumatol. 2023 Aug 4. doi: 10.1007/s10067-023-06723-4. Online ahead of print.

ABSTRACT

OBJECTIVE: To compare the effectiveness of prolotherapy with dextrose concentrations of 5%, 10%, and 20% in patients diagnosed with knee osteoarthritis.

METHODS: This study was planned as a prospective, randomized controlled interventional trial. Prolotherapy at 5% dextrose concentration in group 1, 10% in group 2, and 20% in group 3 was applied to the knee intra-articularly and periarticularly at 0, 3, and 6 weeks, and a home exercise program was given. Group 4 received a home exercise program. All groups received hotpack therapy at weeks 0, 3, and 6. Outcome measures included the visual analog scale (VAS), Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), knee range of motion, timed up and go test, and Short Form-36.

RESULTS: A total of 128 patients were divided into 4 groups. At the 6th and 12th weeks, VAS scores were significantly lower in groups 2 and 3 than in group 4 (p < 0.05). At the 12th week, the WOMAC pain score was significantly lower in group 3 than in group 4, and WOMAC physical function and WOMAC total scores were significantly lower in groups 1, 2, and 3 than in group 4 (p < 0.05). Week 6 active and passive knee flexion and week 12 passive knee flexion were significantly higher in group 3 than in group 4 (p < 0.05).

CONCLUSIONS: Although no significant difference was observed among the dextrose prolotherapy groups, higher dextrose concentrations demonstrated a greater improvement compared to the control group. Therefore, the use of 20% dextrose is recommended due to its significant superiority. Long-term follow-up and placebo-controlled studies are needed.

TRIAL REGISTRATION: ClinicalTrial.gov Identifier: NCT05537077, registration date: 09.03.2022, retrospectively registered. Key Points • The utilization of dextrose prolotherapy has gained popularity in the management of osteoarthritis, aiming to harness its regenerative and proliferative properties. However, the comparative efficacy of various concentrations of dextrose prolotherapy in treating knee osteoarthritis remains unexplored in the literature. This study aimed to address this gap by comparing different concentrations of dextrose prolotherapy in the treatment of knee osteoarthritis. The findings revealed no statistically significant difference among the various concentrations of dextrose prolotherapy for knee osteoarthritis treatment.

PMID:37540383 | DOI:10.1007/s10067-023-06723-4

Lasers Med Sci. 2023 Aug 4;38(1):175. doi: 10.1007/s10103-023-03833-y.

ABSTRACT

Endovenous laser ablation (EVLA) is a common minimally invasive technique used to treat varicose veins. The most commonly used laser wavelengths for EVLA/EVLT of varicose veins are 810 nm and 1470 nm. The laser pulse frequency is typically set to continuous wave (CW) mode, with a pulse duration of a few milliseconds (ms) delivered in a radial mode. The energy delivered per pulse is typically set between 40 and 120 Joules, with a power setting of 10 to 30 watts and an intensity setting of 40 to 120 J/cm². The controversy exists regarding the benefits of performing saphenofemoral junction (SFJ) ligation prior to EVLA to decrease the recurrence rate of varicose veins. This meta-analysis aims to investigate the effectiveness of combining EVLA with high ligation versus using EVLA alone in treating lower extremity varicose veins. We conducted a systematic search of four databases from their inception until July 1, 2022, for randomized controlled trials and prospective controlled trials evaluating the advantages and disadvantages of EVLA with or without high ligation for the treatment of lower extremity varicose veins. In analyzing binary data, rate difference (RD) is used, while odds ratio (OR) is used for evaluating the confidence interval (CI) of binary data. A P value of less than 0.05 is deemed statistically significant. Heterogeneity is assessed using the chi-square test. If the I² statistic, which reflects statistical heterogeneity, is greater than 50%, a random-effects model should be used. In the absence of significant statistical heterogeneity, a fixed-effects model should be used if I² is less than 50%. We used the Cochrane risk-of-bias tool to assess the quality of the studies and Review Manager 5.4 for the primary and secondary outcome analysis. The meta-analysis was conducted in accordance with the Cochrane Handbook. There were no significant differences in the rate of major complications (RR = 1.63; 95% CI, 0.40-6.69; P = 0.50) or in the frequency of minor complications (RR = 1.07, 95% CI, 0.87-1.31; P = 0.52) between the EVLA with high ligation (EVLA/HL) group and the EVLA group. However, the rate of vein occlusion was significantly lower in the EVLA group than in the EVLA/HL group (RR = 1.06; 95% CI, 1.03-1.09; P = 0.0004). Our meta-analysis indicates that combining EVLA with high ligation provides stable long-term clinical efficacy in treating varicose veins of the lower extremities, although it increases the invasiveness of the surgery. The use of EVLA alone may be less effective in preventing vein occlusion.

PMID:37540336 | DOI:10.1007/s10103-023-03833-y

Ir J Med Sci. 2023 Aug 4. doi: 10.1007/s11845-023-03469-5. Online ahead of print.

ABSTRACT

BACKGROUND: Micro-RNA (miRs) targeting kinases and phosphatases regulate the hyper-phosphorylation of tau protein, which is a characteristic feature of Chronic Traumatic Encephalopathy (CTE).

PRIMARY OBJECTIVE: Identification of lead dysregulated miR expressed in CTE, and other similar tauopathies.

METHODS: A search strategy was devised using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines to mine into multiple indexing databases such as Web of Science, Google Scholar, and PubMed spanning from 2005 to June 2022. Seven articles were screened out of 34,221 publications based on inclusion criteria and were categorized into two groups i.e., (1) CTE and its risk factors and (2) Age-related neurodegenerative disorders.

RESULTS: Statistical analysis [RevMan 5.4.1] results showed that the overall risk ratio (RR) of the first group is significant (RR = 0.62, 95% CI = [0.38, 1.00], z = 1.95, p = 0.05) whereas, the second group favours the control population (RR = 1.64, 95% CI = [0.85, 3.16], z = 1.14, p = 0.14).

CONCLUSION: We observed that among all other dysregulated miRs, miR-181c-5p is significantly overexpressed in Alzhimers disease (AD) and CTE. Further, we found that miR-210-3p is also upregulated notably in all groups. In sum, we conclude that these miRs can be considered as potential target and biomarker in the diagnosis and treatment of various tauopathies.

PMID:37540332 | DOI:10.1007/s11845-023-03469-5

Anthropol Anz. 2023 Aug 4. doi: 10.1127/anthranz/2023/1676. Online ahead of print.

ABSTRACT

Porotic hyperostosis and cribra orbitalia are pathological changes occurring on the human skull. These changes were observed and evaluated on skeletal remains from Dětkovice – Za zahradama and Vídeňská Street in Brno; both sites are dated back to the 10^th to 12^th centuries AD. A total of 605 subjects were assessed for age, sex, and the above-stated pathologies using standard methods. The influence of age and sex on the occurrence of these pathologies was examined statistically. Results indicated that at the site of Dětkovice – Za zahradama, porotic hyperostosis, and cribra orbitalia do not depend on sex or age. However, at Vídeňská Street in Brno, these pathologies do not depend on sex, but they depend on age so a higher incidence of pathologies in juveniles is observed. Differences between both sites could be caused by different numbers of evaluated individuals or different state of preservation of skeletal remains. The aetiology of the origin of these pathologies could not be determined by the methodology used here, but with the prevailing lower age of pathological subjects, a lack of nutrition with consequent absence of iron and developing anaemia might be the cause. Based on our statistical data, we can observe that the pathologies we studied occur more frequently in children older than newborns and younger infants. This may indicate that these studied pathologies arise only during the lifetime of the individual and do not have a prenatal occurrence.

PMID:37539649 | DOI:10.1127/anthranz/2023/1676

J Clin Sleep Med. 2023 Aug 4. doi: 10.5664/jcsm.10756. Online ahead of print.

ABSTRACT

STUDY OBJECTIVES: Chronic disruptions to sleep in childhood are associated with increased prevalence of psychiatric disease later in development. When sleep disruptions remit before adolescence, the increased prevalence of psychiatric disease is no longer observed, highlighting the importance of early detection and intervention. Clinicians typically rely on caregiver report for diagnosis and management of childhood sleep challenges. We examined if findings on polysomnogram (PSG) can offer similar insight into childhood sleep difficulties and the risk of subsequent psychiatric illness.

METHODS: A cohort was identified of 348 children ages 5 years 11 months and younger with sleep difficulties rising to the level of formal clinical workup. A retrospective review of caregiver reported sleep concerns, polysomnogram (PSG) results, and subsequent psychiatric illness was completed. PSG findings were compared to presence of psychiatric illness later in life as well as caregivers’ reported concerns. Chi-square and Fisher’s exact tests were completed to evaluate correlations and Cohen’s kappa was used to evaluate agreement.

RESULTS: With only a few exceptions, comparisons between clinician findings on PSG and subsequent psychiatric diagnoses were statistically nonsignificant. Similarly, the relationship between caregivers’ subjective complaints about sleep and clinician findings on PSG demonstrated only slight to fair agreement, suggesting reported concerns were not predictive of PSG results.

CONCLUSIONS: Parental reports of subjective sleep concerns are indicative of different sleep pathologies compared to sleep pathologies detected on PSG. The addition of PSG to caregiver reported data appears to have limited clinical utility in understanding sleep concerns associated with the risk of subsequent psychiatric illness in young children.

PMID:37539644 | DOI:10.5664/jcsm.10756