Tag: statistics

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

PLoS One. 2022 Feb 17;17(2):e0264055. doi: 10.1371/journal.pone.0264055. eCollection 2022.

ABSTRACT

Despite research and public scrutiny over recent decades, discarding continues to be an issue for trawl fisheries. Previous research demonstrates that environmental, biological, operational, legislative and socioeconomic drivers affect a fisher’s decision to discard an organism. Therefore, the reduction of fishery discards requires a better understanding of fishery-specific drivers. Despite considerable research and mitigation, further work is required to reduce discarding to acceptable levels (currently ~ 50% in Australia). To better understand the drivers of discarding, this study used a modelling approach to determine environmental and operational factors that drive discarding in the New South Wales (NSW) ocean prawn trawl fishery (OPT). Further, the study investigated the relationship between the discarded number of individuals from all functional species groups (i.e. elasmobranchs, crustaceans and fish combined) and the retained catch weight. This model was also run on just fish partly due to their disproportionally high contribution to the discard assemblage (e.g. 76% of all species or higher taxon) and importance (e.g. to the ecosystem and fisheries). The results quantified relationships of environmental and operational drivers of discarding and the relationship of fish discarding and retained catch weight was found to be linear. However, the identified relationships appear complicated and, whilst an important first step, more work is required to identify all drivers influencing discarding practices. We, in combination with previous research, suggest implementation of effort quotas may be a suitable management initiative to reduce discarding and its impact; at least whilst more research is conducted to better understand this complex process. Furthering our understanding of discarding is urgent given its global impact and the rate of discarding in the OPT.

PMID:35176093 | DOI:10.1371/journal.pone.0264055

PLoS One. 2022 Feb 17;17(2):e0263331. doi: 10.1371/journal.pone.0263331. eCollection 2022.

ABSTRACT

This study investigates the satisfaction and adequacy of citizens through the expected quality and perceived quality in the areas of planning and territorial viability, experience in the provision of municipal services and citizen experience in environmental issues, in order to provide tools for territorial decision making for the citizens’ well-being. In our research PLS software is used for the analysis of hypotheses. A questionnaire was delivered to a sample of 521 citizens, representing the spectrum of the population, and the statistical study of the responses yielded results on citizen satisfaction and loyalty. Our research includes the study of moderating effects on the causal ratio of perceived value and satisfaction in territorial planning and viability, the perceived quality in the provision of municipal services and the perceived quality in the citizen experience in the environmental management of the territory on the value relationship perceived by the citizen and general satisfaction. A second objective of the study is to see if there are significant differences in the hypotheses raised by gender by performing a multigroup analysis. This difference has been appreciated in two of the hypotheses. The study shows that the policies exercised by the territorial managers of the different areas have a significant influence on the value perceived by citizens, satisfaction and loyalty, which shape their general well-being. Areas for improvement in territorial policies and municipal services such as citizen security, air quality, public lighting and sports services have been identified. Knowing these shortcomings allows politicians to focus their efforts on improving the quality of life in cities.

PMID:35176053 | DOI:10.1371/journal.pone.0263331

PLoS One. 2022 Feb 17;17(2):e0263584. doi: 10.1371/journal.pone.0263584. eCollection 2022.

ABSTRACT

BACKGROUND: Chronic diseases like diabetes, cardiovascular diseases and cancers are on the rise. Most of the risk factors of these diseases commence in Adolescence. Therefore, a cluster randomised controlled trial is designed to evaluate the effect of school-based health promotion intervention on the risk factors of chronic diseases.

METHODOLOGY: Considering school as a cluster, twelve schools will be randomly selected from the public schools of Chandigarh, a city in India. After baseline assessment, six schools will be randomly allocated to intervention and six to the control arm. Study participants will be students of 8th grade (age 10-16 years), their parents and teachers. A sample of 360 students (12 clusters x 30 students) has been estimated to provide statistically valid inference. The PRECEDE PROCEED Model will be used to develop health promotion interventions to prevent the use of an unbalanced diet, physical inactivity, alcohol, and tobacco. Interventions will be implemented for six-months in the school setting. For students, the intervention will comprise interactive learning sessions of 30 minutes duration per week and physical activity sessions of 30 minutes duration four times every week. Educational sessions will be conducted for parents and teachers for 30 minutes, four times during the intervention period. Primary outcomes will be changes in the prevalence of behavioural risk factors from pre- to post-intervention. Changes in anthropometric, physiological, and biochemical measures will be the secondary outcomes. The difference-in-difference (DID) method will be used to measure the net change in the outcomes.

DISCUSSION: It is essential to understand whether health promotion interventions implemented in the school setting simultaneously targeting adolescents, teachers, and parents are effective. Using the PRECEDE-PROCEED model for planning, implementing, and evaluating the intervention as part of a cluster Randomized Controlled Trial design with DID analysis, could objectively assess the impact.

PMID:35176046 | DOI:10.1371/journal.pone.0263584