Tag: statistics

BMC Pulm Med. 2022 Oct 7;22(1):377. doi: 10.1186/s12890-022-02179-5.

ABSTRACT

BACKGROUND: Vasculogenic mimicry (VM) is a recently identified pattern of blood supply to tumor tissue. It has long been considered a functional element in the metastasis and prognosis of malignant tumors. Both Rho GTPase-activating protein 25 (ARHGAP25) and Ras homolog family member A (RhoA) are effective predictors of tumor metastasis. In this study, we examined the expression levels of ARHGAP25 and RhoA and the structure of VM in non-small cell lung cancer (NSCLC). At the same time, we used cytology-related experiments to explore the effect of ARHGAP25 on the migration ability of tumor cells. Furthermore, we analyzed the interaction between the three factors and their association with clinicopathological characteristics and the five-year survival time in patients using statistical tools.

METHODS: A total of 130 well-preserved NSCLC and associated paracancerous tumor-free tissues were obtained. Cell colony formation, wound healing, and cytoskeleton staining assays were used to analyze the effect of ARHGAP25 on the proliferation and migration ability of NSCLC cells. Immunohistochemical staining was used to determine the positivity rates of ARHGAP25, RhoA, and VM. Statistical software was used to examine the relationships between the three factors and clinical case characteristics, overall survival, and disease-free survival.

RESULTS: Cell colony formation, wound healing, and cytoskeleton staining assays confirmed that ARHGAP25 expression affects the proliferation and migratory abilities of NSCLC cells. ARHGAP25 positivity rates in NSCLC and paracancerous tumor-free tissues were 48.5% and 63.1%, respectively, whereas RhoA positivity rates were 62.3% and 18.5%, respectively. ARHGAP25 had a negative relationship with RhoA and VM, whereas RhoA and VM had a positive relationship (P < 0.05). ARHGAP25, RhoA, and VM affected the prognosis of patients with NSCLC (P < 0.05) according to Kaplan-Meier of survival time and Cox regression analyses. Furthermore, lowering ARHGAP25 expression increased NSCLC cell proliferation and migration.

CONCLUSIONS: ARHGAP25 and RhoA expression is associated with VM and may be of potential value in predicting tumor metastasis, prognosis, and targeted therapy.

PMID:36207695 | DOI:10.1186/s12890-022-02179-5

BMC Cancer. 2022 Oct 7;22(1):1050. doi: 10.1186/s12885-022-10129-x.

ABSTRACT

BACKGROUND: Uterine sarcomas are rare and aggressive gynaecologic malignancies, characterized by a relatively high recurrence rate and poor prognosis. The aim of this study was to investigate the clinicopathological features and explore the prognostic factors of these malignancies.

METHODS: This was a single-institution, retrospective study. We reviewed the medical records of 155 patients with pathologically confirmed uterine sarcomas including uterine leiomyosarcoma (ULMS), low-grade endometrial stromal sarcoma (LG-ESS), high-grade endometrial stromal sarcoma (HG-ESS), undifferentiated uterine sarcoma (UUS) and adenosarcoma (AS) between 2006 and 2022. A total of 112 patients who underwent surgery between January 2006 and April 2019 were included in the survival analysis. The current study recorded the clinicopathological, treatment and outcome data to determine clinical characteristics and survival.

RESULTS: The most common histopathological type was ULMS (63/155, 40.64%), followed by LG-ESS (56/155, 36.13%) and HG-ESS (16/155, 10.32%). The mean age at diagnosis of all patients was 49.27±48.50 years and 32.90% (51/155) of patients were postmenopausal. Fifteen patients underwent fast-frozen sectioning, 63(54.78%) were diagnosed with malignancy, 29(25.22%) were highly suspected of malignancy that needed further clarification and 23(14.84%) were diagnosed with benign disease. A total of 124(80%) patients underwent total hysterectomy (TH) and salpingo-oophorectomy. Multivariate analyses showed that histological type and tumour size were independent prognostic factors both for overall survival (OS) (p<0.001 and P=0.017, respectively) and progression-free survival (PFS) (p<0.001 and P=0.018, respectively). Tumour stage was only significantly associated with PFS (P=0.002). Elevated preoperative NLR, PLR and postmenopausal status were significantly correlated with shorter PFS and OS in univariate analysis, but no statistically significant difference was found in multivariate analysis.

CONCLUSIONS: In patients with uterine sarcoma, in comparison to LMS and LG-ESS, UUS and HG-ESS tend to present as more aggressive tumour with poorer outcomes. Furthermore, larger tumour (>7.5 cm) were an important predictor of shorter PFS and OS.

PMID:36207687 | DOI:10.1186/s12885-022-10129-x

BMC Geriatr. 2022 Oct 7;22(1):785. doi: 10.1186/s12877-022-03420-w.

ABSTRACT

BACKGROUND: Rehabilitation potential involves predicting who will benefit from rehabilitation. Decisions about rehabilitation potential must take into account personal, clinical and contextual factors, a process which is complicated in the presence of acute ill-health and frailty. This study aimed to evaluate the feasibility and acceptability of the Rehabilitation Potential Assessment Tool (RePAT) – a 15 item holistic, person-centred assessment tool and training package – in the acute hospital setting.

METHODS: A non-randomised feasibility study with nested semi-structured interviews explored whether RePAT was feasible and acceptable. Feasibility was tested by recruiting physiotherapy and occupational therapy participants delivering the RePAT intervention to patients alongside usual clinical care. Acceptability was tested by conducting semi-structured interviews with staff, patient and carer participants. Staff and patient characteristics were analysed using descriptive statistics. Interview data were analysed thematically. Fidelity of completed RePAT items was assessed against a priori criteria on how closely they matched tool guidance by two researchers. Mean values of the two scores were calculated. RePAT content was analysed and supported with verbatim quotes.

RESULTS: Six staff participants were recruited and trained. They assessed 26 patient participants using RePAT. Mean (SD) patient age was 86.16 (±6.39) years. 32% were vulnerable or mildly frail, 42% moderately frail and 26% severely or very severely frail using the Clinical Frailty Scale. Mean (SD) time to complete RePAT was 32.7 (±9.6) minutes. RePAT fidelity was good where 13 out of 15 items achieved a priori fidelity. RePAT was acceptable and tolerated by staff and patients. Staff participants reported RePAT enabled them to consider rehabilitation decisions in a more structured and consistent way. Patients and carer participants, although unable to comment directly on RePAT, reported being satisfied with their rehabilitation assessments which were found to embrace a person-centred approach.

CONCLUSIONS: RePAT was found to be acceptable and feasible by staff, carers and patients. It allowed clinicians to make explicit their reasoning behind rehabilitation assessments and encouraged them to become more cognisant of factors which affected their clinical decision-making.

TRIAL REGISTRATION: ID ISRCTN31938453 . Registered 05/10/2021.

PMID:36207681 | DOI:10.1186/s12877-022-03420-w

BMC Bioinformatics. 2022 Oct 7;23(1):415. doi: 10.1186/s12859-022-04972-9.

ABSTRACT

BACKGROUND: Transcriptional regulation is a fundamental mechanism underlying biological functions. In recent years, a broad array of RNA-Seq tools have been used to measure transcription levels in biological experiments, in whole organisms, tissues, and at the single cell level. Collectively, this is a vast comparative dataset on transcriptional processes across organisms. Yet, due to technical differences between the studies (sequencing, experimental design, and analysis) extracting usable comparative information and conducting meta-analyses remains challenging.

RESULTS: We introduce Comparative RNA-Seq Metadata Analysis Pipeline (CoRMAP), a meta-analysis tool to retrieve comparative gene expression data from any RNA-Seq dataset using de novo assembly, standardized gene expression tools and the implementation of OrthoMCL, a gene orthology search algorithm. It employs the use of orthogroup assignments to ensure the accurate comparison of gene expression levels between experiments and species. Here we demonstrate the use of CoRMAP on two mouse brain transcriptomes with similar scope, that were collected several years from each other using different sequencing technologies and analysis methods. We also compare the performance of CoRMAP with a functional mapping tool, previously published.

CONCLUSION: CoRMAP provides a framework for the meta-analysis of RNA-Seq data from divergent taxonomic groups. This method facilitates the retrieval and comparison of gene expression levels from published data sets using standardized assembly and analysis. CoRMAP does not rely on reference genomes and consequently facilitates direct comparison between diverse studies on a range of organisms.

PMID:36207678 | DOI:10.1186/s12859-022-04972-9

BMC Med Res Methodol. 2022 Oct 7;22(1):263. doi: 10.1186/s12874-022-01740-4.

ABSTRACT

BACKGROUND: Biotechnology in genomics, such as sequencing devices and gene quantification software, has proliferated and been applied to clinical settings. However, the lack of standards applicable to it poses practical problems in interoperability and reusability of the technology across various application domains. This study aims to visualize and identify the standard trends in clinical genomics and to suggest areas on which standardization efforts must focus.

METHODS: Of 16,538 articles retrieved from PubMed, published from 1975 to 2020, using search keywords “genomics and standard” and “clinical genomic sequence and standard”, terms were extracted from the abstracts and titles of 15,855 articles. Our analysis includes (1) network analysis of full phases (2) period analysis with five phases; (3) statistical analysis; (4) content analysis.

RESULTS: Our research trend showed an increasing trend from 2003, years marked by the completion of the human genome project (2003). The content analysis showed that keywords related to such concepts as gene types for analysis, and analysis techniques were increased in phase 3 when US-FDA first approved the next-generation sequencer. During 2017-2019, oncology-relevant terms were clustered and contributed to the increasing trend in phase 4 of the content analysis. In the statistical analysis, all the categories showed high regression values (R² > 0.586) throughout the whole analysis period and phase-based statistical analysis showed significance only in the Genetics terminology category (P = .039^*) at phase 4.

CONCLUSIONS: Through comprehensive trend analysis from our study, we provided the trend shifts and high-demand items in standardization for clinical genetics.

PMID:36207671 | DOI:10.1186/s12874-022-01740-4

BMC Ophthalmol. 2022 Oct 7;22(1):401. doi: 10.1186/s12886-022-02622-5.

ABSTRACT

BACKGROUND: High-intensity focused ultrasound cyclo-plasty (UCP) is a recently developed glaucoma surgery. This study collected and analysed the clinical data of patients who underwent UCP to observe the efficacy and safety of this surgery in Chinese glaucoma patients.

METHODS: This was a retrospective study. The clinical data of all the patients who underwent UCP at Affiliated Foshan Hospital, Southern Medical University, were collected and analysed to evaluate the efficacy and safety of UCP. The main outcome measure was intraocular pressure, and the secondary outcome measures were best corrected visual acuity (logMAR) and complications.

RESULTS: Fifty-eight patients (61 eyes) were recruited for this study. IOP was dramatically decreased during the 12 months after UCP (p<0.05). The median IOP reduction during the 18 months post-procedure was more than 30%. The greatest reduction was at 1 month post-UCP (60.86%). The qualified success rate was more than 60% during the 18-month follow-up (Fig. 1). Poor follow up was found after 6-month post-UCP. The highest success rate was obtained at 7 days post-UCP (94.55%). No statistically significant decrease in BCVA in the vison group was observed at the follow-up visits, except for 1 day post-UCP. There was a statistically significant reduction in the use of IOP lowering medications during the 6 months post-UCP. No severe complications occurred.

CONCLUSION: UCP is a safe and effective procedure for primary and refractive glaucoma at least during the 6 months post-UCP procedure. Studies with longer follow-up time and better follow up are needed to further confirm the long-term efficacy and safety of UCP in Chinese glaucoma patients.

PMID:36207670 | DOI:10.1186/s12886-022-02622-5

Atten Percept Psychophys. 2022 Oct 7. doi: 10.3758/s13414-022-02573-5. Online ahead of print.

ABSTRACT

In dynamic environments, statistical learning of spatial and temporal regularities guides visual attention in space and time. In the current study, we explored whether and how combined spatiotemporal regularities regarding target events guide visual attention. In three experiments, participants performed the additional singleton task. They were asked to search for a target stimulus with a unique shape among five non-target distractors and respond to the orientation of a line inside the target. Unbeknownst to the participants, the moment in time that the search display was presented was predictive of the target location. Specifically, the target was more likely to be presented at one high-probability location after a short interval and at another high-probability location after a long interval. The results showed that participants’ performance was better for high-probability locations than for low-probability locations. Moreover, visual search efficiency was greater when the target appeared at the high-probability location after its associated interval than when it occurred there after its nonassociated interval, regardless of whether the distribution of intervals was uniform (Experiment 1), exponential (Experiment 2), or anti-exponential (Experiment 3). Taken together, the results indicate that implicitly learned spatiotemporal regularities dynamically guide visual attention towards the probable target location.

PMID:36207663 | DOI:10.3758/s13414-022-02573-5

Breast Cancer Res Treat. 2022 Oct 7. doi: 10.1007/s10549-022-06746-6. Online ahead of print.

ABSTRACT

PURPOSE: Findings from randomized clinical trials have shown that survival in patients with sentinel lymph node (SLN)-negative breast cancer is noninferior with SLN biopsy (SLNB) alone versus further axillary lymph node dissection (ALND). However, the long-term outcome of these two surgical approaches in pN0 breast cancer patients in real-world setting remains uncertain.

METHODS: We included patients diagnosed with pathologically staged T1-2N0M0 breast cancer between 2000 and 2015 in surveillance, epidemiology, and end results 18-registry database. Patients were considered to have undergone SLNB alone if they had ≤ 5 examined lymph nodes (ELNs), and ALND if they had ≥ 10 ELNs. The outcomes included overall survival (OS) and breast cancer-specific survival. Propensity score analyses by weighting and matching and multivariable Cox regression analysis were performed to minimize treatment selection bias.

RESULTS: We included 309,430 patients (253,501 SLNB and 55,929 ALND). In the weighted cohort, ALND was associated with significantly lower OS (hazard ratio [HR] 1.13; 95% confidence interval [CI] 1.10-1.16) and BCSS (HR 1.16; 95% CI 1.10-1.22) compared with SLNB alone. Both the propensity score-matching model and multivariable Cox model demonstrated a survival benefit for SLNB when compared with ALND. Subgroup analyses for key variables did not change these findings.

CONCLUSION: We found statistically significant differences in OS and BCSS between SLNB and ALND, though the magnitude of these differences was small. Our findings further support that SLNB alone should be the standard of care for patients who do not have metastatic lymph nodes identified during breast cancer surgery.

PMID:36207619 | DOI:10.1007/s10549-022-06746-6

Sci Rep. 2022 Oct 7;12(1):16879. doi: 10.1038/s41598-022-21438-3.

ABSTRACT

The infant mortality rate remains unacceptably high in sub-Saharan African countries. Ethiopia has one of the highest rates of infant death. This study aimed to identify individual-and community-level factors associated with infant death in the rural part of Ethiopia. The data for the study was obtained from the 2016 Ethiopian Demographic and Health Survey. A total of 8667 newborn children were included in the analysis. The multilevel logistic regression model was considered to identify the individual and community-level factors associated with new born mortality. The random effect model found that 87.68% of the variation in infant mortality was accounted for by individual and community level variables. Multiple births (AOR = 4.35; 95%CI: 2.18, 8.69), small birth size (AOR = 1.29; 95%CI: 1.10, 1.52), unvaccinated infants (AOR = 2.03; 95%CI: 1.75, 2.37), unprotected source of water (AOR = 1.40; 95%CI: 1.09, 1.80), and non-latrine facilities (AOR = 1.62; 95%CI: 1.20) were associated with a higher risk of infant mortality. While delivery in a health facility (AOR = 0.25; 95%CI: 0.19, 0.32), maternal age 35-49 years (AOR = 0.65; 95%CI: 0.49, 0.86), mothers receiving four or more TT injections during pregnancy (AOR = 0.043, 95% CI: 0.026, 0.071), and current breast feeders (AOR = 0.33; 95% CI: 0.26, 0.42) were associated with a lower risk of infant mortality. Furthermore, Infant mortality rates were also higher in Afar, Amhara, Oromia, Somalia, and Harari than in Tigray. Infant mortality in rural Ethiopia is higher than the national average. The government and other concerned bodies should mainly focus on multiple births, unimproved breastfeeding culture, and the spacing between the orders of birth to reduce infant mortality. Furthermore, community-based outreach activities and public health interventions focused on improving the latrine facility and source of drinking water as well as the importance of health facility delivery and received TT injections during the pregnancy.

PMID:36207579 | DOI:10.1038/s41598-022-21438-3

J Behav Health Serv Res. 2022 Oct 7. doi: 10.1007/s11414-022-09813-4. Online ahead of print.

ABSTRACT

To inform the potential use of patient-reported depression symptom outcomes as measures of care quality, this study collected and analyzed longitudinal Patient Health Questionnaire (PHQ9) scores among 1,638 patients who screened positive for major depression according to a PHQ9 ≥ 10 across 29 Department of Veterans Affairs facilities. The study found baseline PHQ9, prior mental health visits, physical functioning, and treatment expectancy were consistently associated with subsequent PHQ9 outcomes. No facilities outperformed any others on PHQ9 scores at the 6-month primary endpoint, and the corresponding intra-class coefficient was ≤ .01 for the entire sample (n = 1,214) and 0.03 for the subgroup of patients with new depression episodes (n = 629). Measures of antidepressant receipt, psychotherapy, or treatment intensification were not associated with 6-month PHQ9 scores. PHQ9 outcomes are therefore unlikely to be useful as quality indicators for VA healthcare facilities due to low inter-facility variation, and new care process measures are needed to inform care for patients with chronic depression prevalent in this sample.

PMID:36207569 | DOI:10.1007/s11414-022-09813-4