Tag: statistics

Nat Biotechnol. 2022 Sep 15. doi: 10.1038/s41587-022-01440-w. Online ahead of print.

ABSTRACT

Accurate identification and effective removal of unwanted variation is essential to derive meaningful biological results from RNA sequencing (RNA-seq) data, especially when the data come from large and complex studies. Using RNA-seq data from The Cancer Genome Atlas (TCGA), we examined several sources of unwanted variation and demonstrate here how these can significantly compromise various downstream analyses, including cancer subtype identification, association between gene expression and survival outcomes and gene co-expression analysis. We propose a strategy, called pseudo-replicates of pseudo-samples (PRPS), for deploying our recently developed normalization method, called removing unwanted variation III (RUV-III), to remove the variation caused by library size, tumor purity and batch effects in TCGA RNA-seq data. We illustrate the value of our approach by comparing it to the standard TCGA normalizations on several TCGA RNA-seq datasets. RUV-III with PRPS can be used to integrate and normalize other large transcriptomic datasets coming from multiple laboratories or platforms.

PMID:36109686 | DOI:10.1038/s41587-022-01440-w

Nat Methods. 2022 Sep 16. doi: 10.1038/s41592-022-01609-w. Online ahead of print.

ABSTRACT

Complex structural variants (CSVs) encompass multiple breakpoints and are often missed or misinterpreted. We developed SVision, a deep-learning-based multi-object-recognition framework, to automatically detect and haracterize CSVs from long-read sequencing data. SVision outperforms current callers at identifying the internal structure of complex events and has revealed 80 high-quality CSVs with 25 distinct structures from an individual genome. SVision directly detects CSVs without matching known structures, allowing sensitive detection of both common and previously uncharacterized complex rearrangements.

PMID:36109679 | DOI:10.1038/s41592-022-01609-w

Nat Med. 2022 Sep 15. doi: 10.1038/s41591-022-01989-8. Online ahead of print.

NO ABSTRACT

PMID:36109642 | DOI:10.1038/s41591-022-01989-8

Sci Rep. 2022 Sep 15;12(1):15515. doi: 10.1038/s41598-022-19676-6.

ABSTRACT

Anorexia nervosa (AN), a psychiatric condition defined by low body weight for age and height, is associated with numerous dermatological conditions. Yet, clinical observations report that patients with AN do not suffer from infectious skin diseases like those associated with primary malnutrition. Cell-mediated immunity appears to be amplified in AN; however, this proinflammatory state does not sufficiently explain the lower incidence of infections. Antimicrobial peptides (AMPs) are important components of the innate immune system protecting from pathogens and shaping the microbiota. In Drosophila melanogaster starvation precedes increased AMP gene expression. Here, we analyzed skin microbiota in patients with AN and age-matched, healthy-weight controls and investigated the influence of weight gain on microbial community structure. We then correlated features of the skin microbial community with psoriasin and RNase 7, two highly abundant AMPs in human skin, to clarify whether an association between AMPs and skin microbiota exists and whether such a relationship might contribute to the resistance to cutaneous infections observed in AN. We find significant statistical correlations between Shannon diversity and the highly abundant skin AMP psoriasin and bacterial load, respectively. Moreover, we reveal psoriasin significantly associates with Abiotrophia, an indicator for the healthy-weight control group. Additionally, we observe a significant correlation between an individual’s body mass index and Lactobacillus, a microbial indicator of health. Future investigation may help clarify physiological mechanisms that link nutritional intake with skin physiology.

PMID:36109548 | DOI:10.1038/s41598-022-19676-6

Sci Rep. 2022 Sep 15;12(1):15537. doi: 10.1038/s41598-022-19802-4.

ABSTRACT

In previous studies, beta-k distribution and distribution functions strongly related to that, have played important roles in representing extreme events. Among these distributions, the Beta-Singh-Maddala turned out to be adequate for modelling hydrological extreme events. Starting from this distribution, the aim of the paper is to express the model as a function of indexes of hydrological interest and simultaneously investigate on their dependence with a set of explanatory variables in such a way to explore on possible determinants of extreme hydrologic events. Finally, an application to a real hydrologic dataset is considered in order to show the potentiality of the proposed model in describing data and in understanding effects of covariates on frequently adopted hydrological indicators.

PMID:36109545 | DOI:10.1038/s41598-022-19802-4

Sci Rep. 2022 Sep 15;12(1):15248. doi: 10.1038/s41598-022-18877-3.

ABSTRACT

The capability approach argues that having effective choices and fair opportunities are essential to maintain and promote one’s own health and quality of life (QoL). This study examines the determinants of QoL in four disadvantaged population groups (young people not in education, employment, or training; long-term unemployed; refugees; older people living alone) within the framework of the capabilities by tracking the direct and indirect effects of individual and structural factors and capabilities on their QoL. Cross-sectional data (N = 866) with validated scales of quality of life (physical, social, psychological, and environmental QoL) and self-reported capabilities were utilized. Individual factors included age and gender and structural factors education and income. Descriptive statistics and structural equation modelling with latent variables were used for statistical analyses. Our results suggest that capabilities have crucial direct and mediating roles in achieving good QoL in the disadvantaged population groups. Individual factors had only small effects whereas especially the structural factors affected QoL through capabilities. Our results suggest that to reduce health inequalities and to promote wellbeing, policies should focus on improving both the structural factors and the individual capabilities of people in disadvantaged positions.

PMID:36109542 | DOI:10.1038/s41598-022-18877-3

Midwifery. 2022 Aug 24;115:103468. doi: 10.1016/j.midw.2022.103468. Online ahead of print.

ABSTRACT

INTRODUCTION: Pregnancy associated osteoporosis (PAO) is a rare and complex condition. Its etiology is unclear, but possible predisposing factors include osteoporosis in a first degree relative, low body mass index, celiac or other malabsorption disorders, poor nutrition, low vitamin D and calcium intake, long-term use of medications associated with bone loss, physical inactivity, and prolonged amenorrhea. There is no standard for diagnosis or treatment. Diagnosis is typically made following reports of severe pain and imaging establishing the presence of fractures in vertebrae, pelvic structures, or the femoral neck. Research has focused on diagnosis and effective treatments. The absence of descriptive statistics and qualitative data about the presentation, recovery, and psychosocial dimensions of PAO represents a striking gap in the existing literature. The objectives for this preliminary study were to identify key features and the range of experiences of individuals with PAO to aid midwives, who are uniquely situated to identify the condition early in the postpartum course, and to inform future midwifery research on supporting recovery from this complex condition.

METHODS: A 39-47 question survey was developed in Qualtrics; questions were primarily quantitative. Members (N = 306) of a closed, international Osteoporosis and Pregnancy Facebook group were recruited with a post announcing the study and a link to the survey, followed by 2 reminders between June and August 2020. Data were analyzed in Qualtrics. Descriptive statistics were compiled. Qualitative data were analyzed using a grounded theory approach with both open and selective coding.

FINDINGS: Sixty-nine individuals (22% response rate) representing 12 countries responded to the survey, with most respondents from the United States, the United Kingdom, and Australia. Respondents frequently reported delays in diagnosis; only 4.4% of respondents were diagnosed within one month of the onset of fracture pain. Cessation of breastfeeding to reverse physiologic hypoestrogenemia and to stop calcium loss, dietary supplementation, orthopedic braces, and osteoanabolic medications or parathyroid hormone analogues were commonly reported treatment approaches. PAO has a prolonged impact on mobility and infant care. Six months from the onset of fracture pain, only 42% of respondents were physically able to care for their infants alone.

CONCLUSION: PAO is a rare and complex condition in need of further research. Dismissal of pain and lack of knowledge about PAO are frequently encountered by those seeking care, which midwives may be able to mitigate with timely referrals to appropriate specialists. PAO often has a prolonged impact on the ability to care for an infant alone. This should be considered in the development of comprehensive care plans. The core competencies of the International Confederation of Midwives include assessing health status and screening for risks, facilitating individualized decision-making about care, and recognizing conditions outside midwifery scope of practice and referring appropriately (ICM 2019). As members of diverse health care teams, midwives may have opportunities to facilitate diagnosis through timely referral, encourage collaborative decision-making on treatment and future perinatal care, and weigh in on the impact of individual social determinants of health.

PMID:36108340 | DOI:10.1016/j.midw.2022.103468

J Laparoendosc Adv Surg Tech A. 2022 Sep 14. doi: 10.1089/lap.2022.0369. Online ahead of print.

ABSTRACT

Background: To summarize and analyze the application of transvaginal natural orifice specimen extraction surgery (TV-NOSES) in the operation of renal carcinoma, upper tract urothelial carcinoma, and bladder cancer. Methods: Fifty-seven female patients who underwent 3D laparoscopic radical surgery for urinary tumors and TV-NOSES were analyzed retrospectively. The basic clinical data, perioperative-related data, postoperative complications, and related indexes of postoperative functional evaluation were analyzed and evaluated. Results: All 57 operations were successfully performed according to the original plan. One patient developed mild vaginal infection after operation, which was cured after symptomatic treatment. The visual analog scale scores at 24 and 48 hours after operation were 2.5 (1-4) and 1.1 (0-2), respectively. Patient scar assessment questionnaire scores at 3 months after operation were 37.1 (32-48). Pelvic floor distress inventory-short form 20 scores at preoperative and postoperative 3 months were 5.9 (3-9) and 6.3 (3-9), respectively, and the difference was not statistically significant (P = .48). There was no significant difference in female sexual function index scores between preoperative and postoperative 3 months (P = .82). Conclusions: TV-NOSES in urological surgery is feasible and practical. In addition, this technique further reduces wound pain and wound-related complications without affecting postoperative sexual function and pelvic floor function. The successful development of this technique has laid a solid foundation for further clinical application and promotion. Clinical Trial Registration number: 22/141-3342.

PMID:36108338 | DOI:10.1089/lap.2022.0369

J Nerv Ment Dis. 2022 Sep 13. doi: 10.1097/NMD.0000000000001591. Online ahead of print.

ABSTRACT

Since the implementation of “two-child policy” in China, the prevalence and influencing factors of postpartum depression (PPD) between women at first childbirth and second childbirth remains unclear. We aimed to compare the prevalence and the influencing factors of PPD between the two groups. Postpartum women were recruited at their 6-week postpartum checkups and invited to complete questionnaires. The prevalence rate of PPD was 42.1%. There was no statistical difference found regarding the prevalence of PPD and the total score on the Edinburgh Postnatal Depression Scale between the two groups. The median of the item “self-injury” was significantly higher among women at first childbirth. Women with gestational diabetes in pregnancy, antenatal anxiety and depression, abortion, having babies getting sick occasionally, and deteriorated relationships with partner in pregnancy had much higher risks for PPD. Both primiparous and secundiparous had a high prevalence of PPD. It provides scientific evidence for clinical preventive and nursing care for PPD.

PMID:36108287 | DOI:10.1097/NMD.0000000000001591

J Nerv Ment Dis. 2022 Sep 13. doi: 10.1097/NMD.0000000000001582. Online ahead of print.

ABSTRACT

This cross-sectional study aims to compare pre- versus post-psychiatry course stigma levels toward mental illnesses among King Saud University medical students and identify which factors could affect stigma degree. The sample included 384 randomly chosen students. The overall scores of the used scale, the 15-item Opening Minds Scale for Healthcare Providers (OMS-HC-15), indicated no statistically significant difference between the before- and the after-psychiatry-course groups. The univariate analysis for differences in OMS-HC-15 score according to the sociodemographic characteristics of the pre psychiatry course group indicated that the factors associated with the total OMS-HC-15 score were sex (p < 0.001), being diagnosed with mental illness (p < 0.001), and having a relative diagnosed with mental illness (p = 0.005). Among the post psychiatry course group, the univariate analysis indicated that the same factors, namely, sex (p = 0.001), being diagnosed with mental illness (p = 0.006), and having a relative diagnosed with mental illness (p = 0.007), were associated with the total OMS-HC-15 score. Further studies at a larger scale to confirm generalizability of the results are warranted.

PMID:36108280 | DOI:10.1097/NMD.0000000000001582