Tag: pubmed

Psychometrika. 2022 Oct 1. doi: 10.1007/s11336-022-09887-1. Online ahead of print.

ABSTRACT

Latent class models are powerful statistical modeling tools widely used in psychological, behavioral, and social sciences. In the modern era of data science, researchers often have access to response data collected from large-scale surveys or assessments, featuring many items (large J) and many subjects (large N). This is in contrary to the traditional regime with fixed J and large N. To analyze such large-scale data, it is important to develop methods that are both computationally efficient and theoretically valid. In terms of computation, the conventional EM algorithm for latent class models tends to have a slow algorithmic convergence rate for large-scale data and may converge to some local optima instead of the maximum likelihood estimator (MLE). Motivated by this, we introduce the tensor decomposition perspective into latent class analysis with binary responses. Methodologically, we propose to use a moment-based tensor power method in the first step and then use the obtained estimates as initialization for the EM algorithm in the second step. Theoretically, we establish the clustering consistency of the MLE in assigning subjects into latent classes when N and J both go to infinity. Simulation studies suggest that the proposed tensor-EM pipeline enjoys both good accuracy and computational efficiency for large-scale data with binary responses. We also apply the proposed method to an educational assessment dataset as an illustration.

PMID:36183034 | DOI:10.1007/s11336-022-09887-1

Eur Arch Otorhinolaryngol. 2022 Oct 1. doi: 10.1007/s00405-022-07668-1. Online ahead of print.

ABSTRACT

BACKGROUND: To create nomograms for better prediction of the oncological outcome in advanced laryngeal (LxCAs) or hypopharyngeal (HpxCAs) cancer after laryngopharyngectomy.

MATERIALS: 239 patients who underwent total laryngectomy or laryngopharyngectomy due to LxCA (52.7%) or HpxCA (47.3%) were included in this study. Based on clinical risk factors (tumor site, lymph node involvement, salvage setting), we created nomograms for prediction of disease-specific survival (DSS) and disease-free survival (DFS).

RESULTS: HpxCAs showed a higher rate of lymph node involvement (p < 0.001), a 2.47-fold higher risk of a 2nd head and neck cancer (p = 0.009) and significantly worse loco-regional control rates (p = 0.003) compared to LxCAs. Positive neck nodes and salvage procedures were associated with significantly worse outcome. Nomograms demonstrated that hypopharyngeal tumors with positive neck nodes in salvage situations had the worst oncological outcome with a 5-year DSS of 15-20%.

CONCLUSIONS: The oncological outcome is worse in hypopharyngeal carcinomas and could be easily quantified by our nomograms that are based on tumor site, lymph node involvement and salvage situation.

PMID:36183023 | DOI:10.1007/s00405-022-07668-1

Sci Rep. 2022 Oct 1;12(1):16475. doi: 10.1038/s41598-022-20872-7.

ABSTRACT

Tuberculosis is the most common opportunistic infection among HIV/AIDS patients, including those following Antiretroviral Therapy treatment. The risk of tuberculosis infection is higher in people living with HIV/AIDS than in people who are free from HIV/AIDS. Many studies focused on prevalence and determinants of tuberculosis in HIV/AIDS patients without taking into account the censoring aspects of the time to event data. Therefore, this study was undertaken with aim to model time to tuberculosis co-infection of HIV/AIDS patients under follow-up at Jimma Medical Center, Ethiopia using Bayesian parametric survival models. A data of a retrospective cohort of 421 HIV/AIDS patients under follow-up from January 2016 to December 2020 until active tuberculosis was diagnosed or until the end of the study was collected from Jimma Medical Center, Ethiopia. The analysis of the data was performed using R-INLA software package. In order to identify the risk factors which have association with tuberculosis co-infection survival time, Bayesian parametric accelerated failure time survival models were fitted to the data using Integrated Nested Laplace Approximation methodology. About 26.37% of the study subjects had been co-infected with tuberculosis during the study period. Among the parametric accelerated failure time models, the Bayesian log-logistic accelerated failure time model was found to be the best fitting model for the data. Patients who lived in urban areas had shorter tuberculosis co-infection free survival time compared to those who lived in rural areas with an acceleration factor of 0.2842. Patients who smoke and drink alcohol had also shorter tuberculosis co-infection survival time than those who do not smoke and drink alcohol respectively. Patients with advanced WHO clinical stages(Stage III and IV), bedridden functional status, low body mass index and severe anemic status had shorter tuberculosis co-infection survival time. Place of residence, smoking, drinking alcohol, larger family size, advanced clinical stages(Stage III and Stage IV), bedridden functional status, CD4 count ([Formula: see text] 200 cells/mm³ and 200-349 cells/mm³), low body mass index and low hemoglobin are the factors that lead to shorter tuberculosis co-infection survival time in HIV/AIDS patients. The findings of the study suggested us to forward the recommendations to modify patients’ life style, early screening and treatment of opportunistic diseases like anemia , as well as effective treatment and management of tuberculosis and HIV co-infection are important to prevent tuberculosis and HIV co-infection.

PMID:36182998 | DOI:10.1038/s41598-022-20872-7

EJNMMI Phys. 2022 Oct 1;9(1):68. doi: 10.1186/s40658-022-00496-6.

ABSTRACT

BACKGROUND: Performance assessment of positron emission tomography (PET) scanners is crucial to guide clinical practice with efficiency. Even though clinical data are the final target, their use to characterize systems response is constrained by the lack of ground truth. Phantom tests overcome this limitation by controlling the object of study, but remain simple and are not representative of patient complexity. The objective of this study is to evaluate the accuracy of a simulation method using synthetic spheres inserted into acquired raw data prior to reconstruction, simulating multiple scenarios in comparison with equivalent physical experiments.

METHODS: We defined our experimental framework using the National Electrical Manufacturers Association NU-2 2018 Image Quality standard, but replaced the standard sphere set with more appropriate sizes (4, 5, 6, 8, 10 and 13 mm) better suited to current PET scanner performance. Four experiments, with different spheres-to-background ratios (2:1, 4:1, 6:1 and 8:1), were performed. An additional dataset was acquired with a radioactive background but no activity within the spheres (water only) to establish a baseline. Then, we artificially simulated radioactive spheres to reproduce other experiments using synthetic data inserted into the original sinogram. Images were reconstructed following standard guidelines using ordered subset expectation maximization algorithm along with a Bayesian penalized likelihood algorithm. We first visually compared experimental and simulated images. Afterward, we measured the activity concentration values into the spheres to calculate the mean and maximum recovery coefficients (RC_mean and RC_max) which we used in a quantitative analysis.

RESULTS: No significant visual differences were identified between experimental and simulated series. Mann-Whitney U tests comparing simulated and experimental distributions showed no statistical differences for both RC_mean (P value = 0.611) and RC_max (P value = 0.720). Spearman tests revealed high correlation for RC_mean (ρ = 0.974, P value < 0.001) and RC_max (ρ = 0.974, P value < 0.001) between both datasets. From Bland-Altman plots, we highlighted slight shifts in RC_mean and RC_max of, respectively, 2.1 ± 16.9% and 3.3 ± 22.3%.

CONCLUSIONS: We evaluated the efficiency of our hybrid method in faithfully mimicking practical situations producing satisfactory results compared to equivalent experimental data.

PMID:36182994 | DOI:10.1186/s40658-022-00496-6

Cell Death Differ. 2022 Oct 1. doi: 10.1038/s41418-022-01069-x. Online ahead of print.

ABSTRACT

Radiation exposure of healthy cells can halt cell cycle temporarily or permanently. In this work, we analyze the time evolution of p21 and p53 from two single cell datasets of retinal pigment epithelial cells exposed to several levels of radiation, and in particular, the effect of radiation on cell cycle arrest. Employing various quantification methods from signal processing, we show how p21 levels, and to a lesser extent p53 levels, dictate whether the cells are arrested in their cell cycle and how frequently these mitosis events are likely to occur. We observed that single cells exposed to the same dose of DNA damage exhibit heterogeneity in cellular outcomes and that the frequency of cell division is a more accurate monitor of cell damage rather than just radiation level. Finally, we show how heterogeneity in DNA damage signaling is manifested early in the response to radiation exposure level and has potential to predict long-term fate.

PMID:36182991 | DOI:10.1038/s41418-022-01069-x

Arch Microbiol. 2022 Oct 1;204(10):656. doi: 10.1007/s00203-022-03272-3.

ABSTRACT

This study aims to reveal initial bacterial consortia of Ezine PDO cheeses comprehensively by following a metagenomic approach. A total of 8 artisanal Ezine cheese samples were collected from the Bayramiç and Ezine districts of Çanakkale province of Turkey. Ezine cheese was found to contain Firmicutes, Bacteroidetes, and Proteobacteria phyla dominantly. Streptococcus, Lactococcus, and Lactobacillus genera dominated the microbiota with relative abundances of 4.47-56.07%, 7.33-20.34%, and 1.21-25.12%, respectively, followed by Bacteroides and Prevotella genera. Excluding two cheese samples obtained from the Ezine district, the most dominant species was Streptococcus thermophilus (8.24-54.34%). It was also found in greater proportions in the cheeses of the Bayramiç district. Unexpectedly, Lactobacillus graminis (11.50-23.63%) was the most abundant species in two samples collected from the Ezine district. However, lower bacterial diversity was determined in the samples collected from the Bayramiç district. The lowest species richness was 129 OTU-species in the cheeses from the Bayramiç district while the highest species richness was 267 OTU-species in cheeses from the Ezine district. In addition, the Simpson index was the highest in cheeses from the Ezine district, where different species were evenly distributed. Permutational multivariate analysis of variance tests also confirmed that the differences in the structure of bacterial consortia in cheeses from two different districts were statistically significant. This study will provide pioneer data for further investigations on the role of complex bacterial composition in maintaining and improving the quality and safety of Ezine cheese.

PMID:36182984 | DOI:10.1007/s00203-022-03272-3

Arch Orthop Trauma Surg. 2022 Oct 1. doi: 10.1007/s00402-022-04625-9. Online ahead of print.

ABSTRACT

INTRODUCTION: Scaphoid fractures represent 5-10% of nonunion rate and the treatment options consist of an open reduction with correction of deformity, restoration of the scaphoid length with autologous wedge grafting and fixation. However, there is still no consensus in the literature on the best fixation method. Therefore, the purpose of the study is to compare plate fixation and screw fixation in treating scaphoid nonunion with humpback deformity and carpal instability.

METHODS: Prospective, non-randomised study comparing the treatment of two groups of patients with scaphoid nonunion. A total of 19 patients were included in the study, the first ten patients were included in group 1 (plate fixation), subsequently nine patients were included in group 2 (screw fixation). The nonunion duration was longer than 6 months and patients did not present type III Scaphoid Nonunion Advanced Collapse (SNAC). Clinical evaluations included pain intensity, range of motion, grip strength, pinch test and functional scales Disabilities of the Arm, Shoulder and Hand (DASH) and Mayo Wrist Score. Radiographic evaluations consisted of radiographs of both wrists in AP, AP with ulnar deviation, lateral and oblique views. Patients further underwent a tomography of the affected wrist for bone deformity, carpal collapse and later consolidation evaluation.

RESULTS: According to post-operative measurements, group 1 showed a significant improvement in the scapholunate angle (p = 0.011) and in the intrascaphoid angle (p = 0.002). Group 2 only showed an improvement in the scapholunate angle (p = 0.011). All patients in group 1 achieved consolidation in 8 weeks, while group 2 patients had a slower consolidation, with a mean of 14 weeks and standard deviation (SD) of 4.2, with statistical significance (p = 0.006).

CONCLUSION: Our prospective study, despite the limitations, contributes to the literature for demonstrating a better fixation using plate, with a better correction of humpback deformity and Dorsal Intercalated Segment Instability (DISI) and a faster consolidation.

LEVEL OF EVIDENCE: II, therapeutics studies; prospective comparative study.

PMID:36182974 | DOI:10.1007/s00402-022-04625-9

Stat Med. 2022 Oct 1. doi: 10.1002/sim.9582. Online ahead of print.

ABSTRACT

Over 782 000 individuals in the United States have end-stage kidney disease with about 72% of patients on dialysis, a life-sustaining treatment. Dialysis patients experience high mortality and frequent hospitalizations, at about twice per year. These poor outcomes are exacerbated at key time periods, such as the fragile period after transition to dialysis. In order to study the time-varying effects of modifiable patient and dialysis facility risk factors on hospitalization and mortality, we propose a novel Bayesian multilevel time-varying joint model. Efficient estimation and inference is achieved within the Bayesian framework using Markov chain Monte Carlo, where multilevel (patient- and dialysis facility-level) varying coefficient functions are targeted via Bayesian P-splines. Applications to the United States Renal Data System, a national database which contains data on nearly all patients on dialysis in the United States, highlight significant time-varying effects of patient- and facility-level risk factors on hospitalization risk and mortality. Finite sample performance of the proposed methodology is studied through simulations.

PMID:36181392 | DOI:10.1002/sim.9582

Anat Histol Embryol. 2022 Oct 1. doi: 10.1111/ahe.12870. Online ahead of print.

ABSTRACT

The anatomy of the sternum in birds varies according to their habitats and type of locomotion. In particular, the carina sterni manifest different shape variations. In this study, the shape of the carina sterni was investigated by means of geometric morphometrics. Birds of different types of locomotion were used in the study: flying, swimming, and terrestrial. Ducks and chickens show a wider variety of shapes. Pigeons are the species with the least differences. The margo cranialis carinae in a turkey is the flattest compared to other species. In chickens, the apex carinae is more caudally than the base of the carina sterni. The margo cranialis of the carina sterni in ducks is concave. The differences in centroid size and shape differences between species collectively are statistically significant (p < 0.0001). The most distinct shape contrast is between the duck and turkey (p: 0.0003). Form differences between the ducks and geese as well as between the chicken and turkey are statistically insignificant. There is less variation in the shape of the carina sterni among avian species representing the same type of locomotion. Although there are many comparative morphological and morphometric studies of birds, shape analysis studies revealing the interspecific differences and similarities of the sternum are very limited. Morphology of the carina sterni can be useful in taxonomic investigations.

PMID:36181376 | DOI:10.1111/ahe.12870

Clin Oral Implants Res. 2022 Oct 1. doi: 10.1111/clr.14003. Online ahead of print.

ABSTRACT

OBJECTIVES: The aim of this cross-sectional study was to evaluate the effect of brushing discomfort (BD) on peri-implant health in sites exhibiting inadequate keratinized mucosa (KM) width.

MATERIAL AND METHODS: Patients presenting with at least one implant exhibiting KM <2 mm and in function for ≥1 year were eligible for inclusion. BD was assessed with the visual analogue scale (VAS), and implants were classified into two groups: Absence (aBD; VAS = 0) or Presence (pBD; VAS > 0) of BD. Bleeding on probing (BoP), modified plaque index (mPI), probing depth (PD), clinical attachment level (CAL), suppuration (Sup), and marginal bone level (MBL) were recorded. Mann-Whitney, Chi-square test, and a multilevel model were used for analysis.

RESULTS: Fifty-nine patients with 155 dental implants were analyzed, of which 60 presented no BD, and 95 presented some level of BD. BoP, PD, CAL and MBL were significantly higher in the pBD than in the aBD group (p < 0.05). The prevalence of peri-implant diseases at implant level was also higher in the pBD group than in the aBD group. However, after controlling for confounding factors, only mPI showed an effect on BoP. In addition, difficulty to perform oral hygiene was statistically higher in the pBD group.

CONCLUSIONS: The findings of the present study suggest that although BD around implants exhibiting KM <2 mm did not influence tissue inflammation, it could represent a symptom of peri-implant diseases. Further clinical trials assessing the long-term effect of BD must be considered to better ascertain its effects on peri-implant health.

PMID:36181373 | DOI:10.1111/clr.14003