Category: Statistics

Clin Nutr. 2022 Feb 5;41(3):737-745. doi: 10.1016/j.clnu.2022.01.033. Online ahead of print.

ABSTRACT

BACKGROUND & AIMS: The current criteria for defining sarcopenic obesity (SOB) combines the threshold criteria for sarcopenia and obesity, but no consensus has been reached on the criteria. Given the variations among ethnic groups and in the prevalence of sarcopenia, the study aim was to establish sex-specific cutoff points for Chinese cancer patients and investigate the effect of SOB on clinical consequences.

METHODS: A prospective study of 2480 cancer patients was conducted. Clinical materials, bioelectrical impedance analysis measurements, and follow-up data were analyzed. The survival receiver operating characteristic curve was used to determine threshold values. The odds ratios for nutrition risk, severe malnutrition, and quality of life were calculated. The global and sex-specific survival statistics were extracted from the Kaplan-Meier curve and Cox proportional hazard regression models.

RESULTS: The cutoff points of visceral fat area to best classify patients regarding time to death were >75.6 cm² for males and >61.2 cm² for females. And the cutoff points of percent of body fat were 15% in males and 25% in females. Among all participants, the prevalence of SOB was 3.03% in males and 4.46% in females. SOB significantly increased the nutrition risk and severe malnutrition probability and worsened quality of life. Finally, SOB was significantly associated with overall cancer mortality [hazard ratio 2.772, 95% confidence interval 2.080-3.694, P < 0.001].

CONCLUSIONS: On the basis of sex-specific cutoff values, SOB was strongly associated with unfavorable clinical consequences and mortality in cancer patients. These results indicate the importance of SOB detection in routine clinical practice for improving patient assessments, cancer prognosis, and intervention.

PMID:35176638 | DOI:10.1016/j.clnu.2022.01.033

Comput Methods Programs Biomed. 2022 Feb 1;217:106668. doi: 10.1016/j.cmpb.2022.106668. Online ahead of print.

ABSTRACT

BACKGROUND AND OBJECTIVE: The Spline Reconstruction Technique (SRT) is a fast algorithm based on a novel numerical implementation of an analytic representation of the inverse Radon transform. The purpose of this study is to provide a comparison between SRT, Filtered Back-Projection (FBP), Ordered Subset Expectation Maximization 2D (2D-OSEM), and the Tera-Tomo 3D algorithm, using phantom data at various acquisition durations as well as small-animal data obtained from the Mediso nanoScan® PET/CT scanner.

METHODS: For this purpose, the “NEMA NU 4-2008 standards” protocol was employed at five different realizations and acquisition durations. In addition to the image quality metrics described by the NEMA protocol, Cold Region Contrast was also considered as a figure-of-merit. Furthermore, Cold Region Contrast was measured in the myocardial infarction region of six male Wistar rats. The volumetric defect quantification was assessed with dedicated computer software. Lastly, plots of Recovery Coefficient and Spill-Over Ratio as a function of the Percentage Standard Deviation were generated, after smoothing the phantom reconstructions with four different Gaussian filters. Statistical significance was determined by employing the Kruskal-Wallis test or One-way Analysis of Variance depending on the normality of the variable’s distribution.

RESULTS: The present study revealed that, at the expense of slightly increased noise in the reconstructed images, SRT resulted in higher Recovery Coefficient values for small hot regions of interest, when compared with FBP and 2D-OSEM at all acquisition durations. Furthermore, SRT reconstructed images exhibit higher Recovery Coefficient values, for all hot regions of interest, when compared to the other 2D algorithms at short acquisition durations. In both phantom and animal studies, SRT achieved a significant improvement over 2D-OSEM for the Spill-Over Ratio and the Cold Region Contrast. These advantages were maintained even after comparing the algorithms at equal noise levels. The Tera-Tomo 3D algorithm (4 subsets, iterations≥ 13) performed significantly better compared to the other algorithms for all figures-of-merit. No statistically significant differences regarding the myocardial defect size were observed between the algorithms investigated.

CONCLUSIONS: Overall, SRT appears that could be useful for the quantification of small hot regions of interest, cold regions of interest, as well as in low-count imaging applications.

PMID:35176596 | DOI:10.1016/j.cmpb.2022.106668

Stud Hist Philos Sci. 2022 Feb 14;92:144-151. doi: 10.1016/j.shpsa.2022.01.017. Online ahead of print.

ABSTRACT

Bayesian approaches have long been a small minority group in scientific practice, but quickly acquired a high level of popularity since the 1990s. This paper shall describe and analyze this turn. I argue that the success of Bayesian approaches hinges on computational methods that make a class of models predictive that would otherwise lack practical relevance. Philosophically, however, this orientation toward prediction comes at a price. The new computational approaches change Bayesian rationality in an important way. Namely, they undercut the interpretation of priors, turning them from an expression of beliefs held prior to new evidence into an adjustable parameter that can be manipulated flexibly by computational machinery. Thus, in the case of Bayes, one can see a coevolution of computing technology, an exploratory-iterative mode of prediction, and the conception of rationality.

PMID:35176618 | DOI:10.1016/j.shpsa.2022.01.017

J Natl Cancer Inst. 2022 Feb 17:djac034. doi: 10.1093/jnci/djac034. Online ahead of print.

ABSTRACT

BACKGROUND: Racial and ethnic variations in attribution of cervical precancer and cancer to HPV types may result in different HPV vaccine protection, screening test coverage, and clinical management.

METHODS: Pooling data from seven U.S. studies, we calculated the proportional attribution of precancers and cancers to HPV types using HPV DNA typing from diagnosis. All statistical tests were 2-sided.

RESULTS: For all racial and ethnic groups, most cervical intraepithelial neoplasia grade 3 (CIN3) (n = 5,526) and squamous cell carcinoma (SCC) cases (n = 1,138) were attributed to types targeted by the 9-valent vaccine. A higher proportion of CIN3s were attributed to non-vaccine HPV types among non-Hispanic Black women (15.8%) compared with non-Hispanic Asian or Pacific Islander (9.7%, P=.002), non-Hispanic White (9.2%, P<.001), and Hispanic women (11.3%, P=.004). The proportion of SCCs attributed to 9-valent types was similar by race and ethnicity (90.4%-93.8%, P = .80). A higher proportion of CIN3s were attributed to non-vaccine HPV35 among non-Hispanic Black (9.0%) compared with non-Hispanic Asian or Pacific Islander (2.2%), non-Hispanic White (2.5%), and Hispanic women (3.0%, all P<.001). Compared with CIN3, the proportion of SCCs attributed to HPV35 among Non-Hispanic Black women (3.2%) was lower and closer to other groups (0.3%-2.1%, P = .70).

CONCLUSION: The 9-valent HPV vaccine will prevent nearly all cervical precancers and invasive cancers among major racial and ethnic groups in the United States. Adding HPV35 to vaccines could prevent a small percentage of CIN3s and SCCs, with greater potential impact for CIN3s among Black women. HPV screening tests target high-risk HPV types, including HPV35. Future genotyping triage strategies could consider the importance of HPV35 and other HPV16 related types.

PMID:35176161 | DOI:10.1093/jnci/djac034

Bioinformatics. 2022 Feb 17:btac096. doi: 10.1093/bioinformatics/btac096. Online ahead of print.

ABSTRACT

MOTIVATION: Cross-sectional analyses of primary cancer genomes have identified regions of recurrent somatic copy-number alteration, many of which result from positive selection during cancer formation and contain driver genes. However, no effective approach exists for identifying genomic loci under significantly different degrees of selection in cancers of different subtypes, anatomic sites, or disease stages.

RESULTS: CNGPLD is a new tool for performing case-control somatic copy-number analysis that facilitates the discovery of differentially amplified or deleted copy-number aberrations in a case group of cancer compared to a control group of cancer. This tool uses a Gaussian process statistical framework in order to account for the covariance structure of copy-number data along genomic coordinates and to control the false discovery rate at the region level.

AVAILABILITY: CNGPLD is freely available at https://bitbucket.org/djhshih/cngpld as an R package.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:35176131 | DOI:10.1093/bioinformatics/btac096

Mol Biol Evol. 2022 Feb 17:msac041. doi: 10.1093/molbev/msac041. Online ahead of print.

ABSTRACT

Significant improvements in genome sequencing and assembly technology have led to increasing numbers of high-quality genomes, revealing complex evolutionary scenarios such as multiple whole-genome duplication (WGD) events, which hinders ancestral genome reconstruction via the currently available computational frameworks. Here, we present the Inferring Ancestor Genome Structure (IAGS) framework, a novel block/endpoint matching optimization strategy with single-cut-or-join distance, to allow ancestral genome reconstruction under both simple (single-copy ancestor) and complex (multicopy ancestor) scenarios. We evaluated IAGS with two simulated datasets and applied it to four different real evolutionary scenarios to demonstrate its performance and general applicability. IAGS is available at https://github.com/xjtu-omics/IAGS.

PMID:35176153 | DOI:10.1093/molbev/msac041

PLoS One. 2022 Feb 17;17(2):e0264165. doi: 10.1371/journal.pone.0264165. eCollection 2022.

ABSTRACT

BACKGROUND: Myocardial dysfunction is a major cause of poor outcomes in the post-cardiac arrest period. Omecamtiv mecarbil (OM) is a selective small molecule activator of cardiac myosin that prolongs myocardial systole and increases stroke volume without apparent effects on myocardial oxygen demand. OM administration is safe and improves cardiac function in patients with acute heart failure. Whether OM improves post-resuscitation myocardial dysfunction remains unclear. This study investigated the effect of OM treatment on post-resuscitation myocardial dysfunction and outcomes.

METHODS AND RESULTS: Adult male rats were resuscitated after 9.5 min of asphyxia-induced cardiac arrest. OM and normal saline was continuously intravenously infused after return of spontaneous circulation (ROSC) at 0.25 mg/kg/h for 4 h in the experimental group and control group, respectively (n = 20 in each group). Hemodynamic parameters were measured hourly and monitored for 4 h after cardiac arrest. Recovery of neurological function was evaluated by neurological functioning scores (0-12; favorable: 11-12) for rats 72 h after cardiac arrest. OM treatment prolonged left ventricular ejection time and improved post-resuscitation cardiac output. Post-resuscitation heart rate and left ventricular systolic function (dp/dt40) were not different between groups. Kaplan-Meier analysis showed non-statistically higher 72-h survival in the OM group (72.2% [13/18] and 58.8% [10/17], p = 0.386). The OM group had a higher chance of having favorable neurological outcomes in surviving rats 72 h after cardiac arrest (84.6% [11/13] vs. 40% [4/10], p = 0.026). The percentage of damaged neurons was lower in the OM group in a histology study at 72 h after cardiac arrest (55.5±2.3% vs. 76.2±10.2%, p = 0.004).

CONCLUSIONS: OM treatment improved post-resuscitation myocardial dysfunction and neurological outcome in an animal model. These findings support further pre-clinical studies to improve outcomes in post-cardiac arrest care.

PMID:35176110 | DOI:10.1371/journal.pone.0264165

PLoS One. 2022 Feb 17;17(2):e0264113. doi: 10.1371/journal.pone.0264113. eCollection 2022.

ABSTRACT

BACKGROUND: Visual impairment can severely affect the quality of life, with a tremendous negative impact on job performance and socioeconomic status. This substantially affects the psychological status of people with visual impairment.

OBJECTIVE: This study aimed to determine the prevalence and factors associated with psychological distress among visually impaired Ethiopian adults attending the University of Gondar Tertiary Eye Care and Training Center.

METHODS: A comparative cross-sectional study was conducted at the University of Gondar Tertiary Eye Care and Training Center in Gondar City, northwest Ethiopia. A total of 206 adults with visual impairment (a presenting VA ≤ 6/18 in at least one eye) and 206 adults with normal vision were included in the study. Psychological distress was measured using a standardized self-reporting questionnaire (SRQ-20). Chi-square and binary logistic regression analysis were performed. Variables with a P-value of less than 0.05 were considered statistically significant.

RESULTS: The overall prevalence of psychological distress in the study participants was 31.07% (95% CI: 26.2, 35.8). Psychological distress was higher (43.2%; 95% CI: 36.5, 50.5) and statistically differed (p = 0.02) in visually impaired compared to adults with normal vision (18.9%; 95% CI: 14.1, 24.3). Duration of vision loss ≥ 2 years (AOR = 8.70; 95% CI: 2.38, 31.46), sudden loss of vision (AOR = 3.50; 95% CI: 1.10, 18.30), unmarried (AOR = 5.53; 95% CI: 1.66, 18.43), living lonely (AOR = 8.40; 95% CI:1.48, 4.74), College and above educational status (AOR = 2.50; 95% CI:1.47, 10.61), and loss of vision in both eyes (AOR = 1.70; 95% CI: 2.00, 14.10) were variables with a significant association with psychological distress among visually impaired adults.

CONCLUSION: This study revealed that the prevalence of psychological distress was significantly higher among visually impaired adults than among adults with normal vision. The effect of visual impairment on psychological distress was significantly related to marital status, living arrangements, educational status, duration of vision loss, pattern of vision loss, and laterality of vision loss.

PMID:35176097 | DOI:10.1371/journal.pone.0264113

PLoS One. 2022 Feb 17;17(2):e0264065. doi: 10.1371/journal.pone.0264065. eCollection 2022.

ABSTRACT

Polycystic liver disease (PLD) is a common extrarenal complication of autosomal dominant polycystic kidney disease (ADPKD), which causes compression-related syndrome and ultimately leads to liver dysfunction. Tolvaptan, a V2 receptor antagonist, is widely used to protect kidney function in ADPKD but its effect on PLD remains unknown. An observational cohort study was conducted to evaluate tolvaptan’s effect on patients with PLD due to ADPKD. After screening 902 patients, we found the 107 ADPKD patients with PLD who met the criteria of tolvaptan use in Japan. Among them, tolvaptan was prescribed for 62 patients (tolvaptan group), while the other was defined as the non-tolvaptan group. Compared with the non-tolvaptan group, the tolvaptan group had larger height-adjusted total kidney volume (median 994(range 450-4152) mL/m, 513 (405-1928) mL/m, p = 0.01), lower albumin level (mean 3.9±SD 0.4 g/dL, 4.3±0.4g/dL, p<0.01), and higher serum creatinine level (1.2±0.4 mg/dL, 0.9±0.2 mg/dL, p<0.01). Although the median change in annual growth rate of total liver volume (TLV) was not statistically different between the tolvaptan group (-0.8 (-15.9, 16.7) %/year) and the non-tolvaptan group (1.7 (-15.6-18.7) %/year)(p = 0.52), 20 (43.5%) patients in the tolvaptan group experienced a decrease in the growth rate of TLV (responders). A multivariable logistic regression model adjusting for related variables showed that older age (odds ratio 1.15 [95% CI 1.01-1.32]) and a higher growth rate of TLV in the non-tolvaptan period (odds 1.45 95% CI 1.10-1.90) were significantly associated with responders. In conclusion, the change in annual growth rate of TLV in ADPKD patients taking tolvaptan was not statistically different compared with that in ADPKD patients without taking tolvaptan. However, tolvaptan may have the potential to suppress the growth rate of TLV in some PLD patients due to ADPKD, especially in older patients or those that are rapid progressors of PLD. Several limitations were included in this study, therefore well-designed prospective studies were required to confirm the effect of tolvaptan on PLD.

PMID:35176098 | DOI:10.1371/journal.pone.0264065

PLoS One. 2022 Feb 17;17(2):e0263930. doi: 10.1371/journal.pone.0263930. eCollection 2022.

ABSTRACT

OBJECTIVES: This prospective study aimed to determine the association between radiographic lumbar spinal stenosis (LSS) and the quality of life (QOL) in the general Japanese population.

METHODS: The severity of radiographic LSS was qualitatively graded on axial magnetic resonance images as follows: no stenosis, mild stenosis with ≤1/3 narrowing, moderate stenosis with a narrowing between 1/3 and 2/3, and severe stenosis with > 2/3 narrowing. Patients less than 40 years of age and those who had undergone previous lumbar spine surgery were excluded from the study. The Oswestry Disability Index (ODI), which includes 10 sections, was used to assess the QOL. One-way analysis of variance was performed to determine the statistical relationship between radiographic LSS and ODI. Further, logistic regression analysis adjusted for gender, age, and body mass index was performed to detect the relationship.

RESULTS: Complete data were available for 907 patients (300 men and 607 women; mean age, 67.3±12.4 years). The prevalence of severe, moderate, and non-mild/non-radiographic were 30%, 48%, and 22%, respectively. In addition, the mean values of ODI in each group were 12.9%, 13.1%, and 11.7%, respectively, and there was no statistically significant difference between the three groups in logistic analysis (P = 0.55). In addition, no significant differences in any section of the ODI were observed among the groups. However, severe radiographic LSS was associated with low back pain in the “severe” group as determined by logistic analysis adjusted for gender, age, and body mass index (odds ratio: 1.53, confidence interval: 1.13-2.07) compared with the non-severe group.

CONCLUSION: In this general population study, severe radiographic LSS was associated with low back pain (LBP), but did not affect ODI.

PMID:35176078 | DOI:10.1371/journal.pone.0263930