scholarly journals Quantifying the Effect of Crown Vertical Position on Individual Tree Competition: Total Overlap Index and Its Application in Sustainable Forest Management

2020 ◽  
Vol 12 (18) ◽  
pp. 7498
Author(s):  
Boheng Wang ◽  
Yuankun Bu ◽  
Guanhu Tao ◽  
Chenran Yan ◽  
Xiaolu Zhou ◽  
...  
Keyword(s):  
Survival Analysis ◽  
Forest Management ◽  
Proportional Hazards ◽  
Sustainable Forest Management ◽  
Mixed Forest ◽  
Cox Proportional Hazards ◽  
Competition Index ◽  
Individual Tree ◽  
Kaplan Meier ◽  
Competition Group

Competition is an essential driving factor that influences forest community sustainability, yet measuring it poses several challenges. To date, the Competition Index (CI) has generally been the tool of choice for quantifying actual competition. In this study, we proposed using the Total Overlap Index (TOI), a CI in which the Area Overlap (AO) index has been adapted and modified to consider the “shading” and “crowding” effects in the vertical dimension. Next, based on six mixed forest plots in Xiaolong Mountain, Gansu, China, we assessed the results to determine the TOI’s evaluation capability. Individual-tree simulation results showed that compared to the modified Area Overlap index (AOM), the TOI has superior quantification capability in the vertical direction. The results of the basal area increment (BAI) model showed that the TOI offers the best evaluation capability among the four considered CIs in mixed forest (with Akaike Information Criterion (AIC) of 1041.60 and log-likelihood (LL) of −511.80 in the model fitting test, mean relative error of −28.67%, mean absolute percent error of 117.11%, and root mean square error of 0.7993 in cross-validation). Finally, the TOI was applied in the Kaplan–Meier survival analysis and Cox proportional-hazards analysis. The Kaplan–Meier survival analysis showed a significant difference between the low- (consisting of trees with the TOI lower than 1) and high-competition (consisting of trees with the TOI higher than 1) groups’ survival and hazard curves. Moreover, the results of the Cox proportional-hazards analysis exhibited that the trees in the low-competition group only suffered 34.29% of the hazard risk that trees in the high-competition group suffered. Overall, the TOI expresses more dimensional information than other CIs and appears to be an effective competition index for evaluating individual tree competition. Thus, the competition status quantified using this method may provide new information to guide policy- and decision-makers in sustainable forest management planning projects.

scholarly journals Evaluation of Changes on World Stock Exchanges in Connection with the SARS-CoV-2 Pandemic. Survival Analysis Methods

Risks ◽  
2021 ◽  
Vol 9 (7) ◽  
pp. 121
Author(s):  
Beata Bieszk-Stolorz ◽  
Krzysztof Dmytrów
Keyword(s):  
Survival Analysis ◽  
Proportional Hazards ◽  
Proportional Hazards Model ◽  
Stock Exchange ◽  
Cox Proportional Hazards ◽  
Cox Proportional Hazards Model ◽  
Stock Exchanges ◽  
Analysis Methods ◽  
Hazards Model ◽  
Kaplan Meier

The aim of our research was to compare the intensity of decline and then increase in the value of basic stock indices during the SARS-CoV-2 coronavirus pandemic in 2020. The survival analysis methods used to assess the risk of decline and chance of rise of the indices were: Kaplan–Meier estimator, logit model, and the Cox proportional hazards model. We observed the highest intensity of decline in the European stock exchanges, followed by the American and Asian plus Australian ones (after the fourth and eighth week since the peak). The highest risk of decline was in America, then in Europe, followed by Asia and Australia. The lowest risk was in Africa. The intensity of increase was the highest in the fourth and eleventh week since the minimal value had been reached. The highest odds of increase were in the American stock exchanges, followed by the European and Asian (including Australia and Oceania), and the lowest in the African ones. The odds and intensity of increase in the stock exchange indices varied from continent to continent. The increase was faster than the initial decline.

scholarly journals A novel long non-coding RNA, AC012456.4, as a valuable and independent prognostic biomarker of survival in oral squamous cell carcinoma

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5307 ◽  
Author(s):  
Xuegang Hu ◽  
Zailing Qiu ◽  
Jianchai Zeng ◽  
Tingting Xiao ◽  
Zhihong Ke ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Survival Analysis ◽  
Oral Squamous Cell Carcinoma ◽  
Proportional Hazards ◽  
Prognostic Biomarker ◽  
Cox Proportional Hazards ◽  
Regression Analyses ◽  
Cox Proportional Hazards Regression ◽  
Proportional Hazards Regression ◽  
Kaplan Meier

Oral squamous cell carcinoma (OSCC) is a major malignant cancer of the head and neck. Long non-coding RNAs (lncRNAs) have emerged as critical regulators during the development and progression of cancers. This study aimed to identify a lncRNA-related signature with prognostic value for evaluating survival outcomes and to explore the underlying molecular mechanisms of OSCC. Associations between overall survival (OS), disease-free survival (DFS) and candidate lncRNAs were evaluated by Kaplan–Meier survival analysis and univariate and multivariate Cox proportional hazards regression analyses. The robustness of the prognostic significance was shown via the Gene Expression Omnibus (GEO) database. A total of 2,493 lncRNAs were differentially expressed between OSCC and control samples (fold change >2, p < 0.05). We used Kaplan–Meier survival analysis to identify 21 lncRNAs for which the expression levels were associated with OS and DFS of OSCC patients (p < 0.05) and found that down-expression of lncRNA AC012456.4 especially contributed to poor DFS (p = 0.00828) and OS (p = 0.00987). Furthermore, decreased expression of AC012456.4 was identified as an independent prognostic risk factor through multivariate Cox proportional hazards regression analyses (DFS: p = 0.004, hazard ratio (HR) = 0.600, 95% confidence interval(CI) [0.423–0.851]; OS: p = 0.002, HR = 0.672, 95% CI [0.523–0.863). Gene Set Enrichment Analysis (GSEA) indicated that lncRNA AC012456.4 were significantly enriched in critical biological functions and pathways and was correlated with tumorigenesis, such as regulation of cell activation, and the JAK-STAT and MAPK signal pathway. Overall, these findings were the first to evidence that AC012456.4 may be an important novel molecular target with great clinical value as a diagnostic, therapeutic and prognostic biomarker for OSCC patients.

scholarly journals Outcomes of phacoemulsification and endoscopic cyclophotocoagulation performed with dual blade ab interno trabeculectomy or trabecular micro-bypass stent insertion

Eye ◽  
2021 ◽  
Author(s):  
Emma Klug ◽  
Marika Chachanidze ◽  
Abraham Nirappel ◽  
Enchi K. Chang ◽  
Nathan Hall ◽  
...  
Keyword(s):  
Survival Analysis ◽  
Proportional Hazards ◽  
Case Series ◽  
Cox Proportional Hazards ◽  
Stent Insertion ◽  
Tertiary Referral Centre ◽  
Kaplan Meier ◽  
Ab Interno Trabeculectomy ◽  
The Mean ◽  
Ab Interno

Abstract Background/Objective To report the initial outcomes of phacoemulsification, endoscopic cyclophotocoagulation, and dual blade ab interno trabeculectomy (PEcK), and compare them to those of phacoemulsification, endoscopic cyclophotocoagulation, and trabecular micro-bypass stent insertion (ICE-1). Subjects/Methods Patients from January 2018 to December 2019 that underwent PEcK or ICE-1 at a tertiary referral centre were included in this retrospective comparative case series. Patients were excluded if they had additional concomitant procedures, less than 6 weeks (42 days) of follow-up or were not at least 18 years old. Intraocular pressure (IOP), number of glaucoma medications, and best-corrected visual acuity were collected preoperatively and postoperatively at 6 weeks, 3, 6, and 12 months. Kaplan–Meier survival analysis and Cox proportional-hazards regression were conducted to elucidate any factors associated with survival time. Results The mean preoperative IOP was 18.3 ± 5.9 mmHg in the PEcK group (53 eyes) and 14.7 ± 4.3 mmHg in the ICE-1 group (23 eyes) (p = 0.004) on 3.3 ± 1.3 and 1.7 ± 0.93 glaucoma medications (p < 0.001), respectively. Twelve months postoperatively the mean IOP reduction was 5.1 ± 4.4 mmHg and 2.3 ± 4.0 mmHg (p = 0.08), and the mean medication reduction was 1.6 ± 1.5 and 0.97 ± 0.66 (p = 0.10), in the PEcK and ICE-1 groups, respectively. Kaplan–Meier survival analysis did not reveal any differences in treatment survival. Conclusions Both PEcK and ICE-1 provide clinically relevant reductions in IOP and glaucoma medication burden, however the PEcK procedure may confer greater reductions in IOP. The procedures did not differ with regard to Kaplan–Meier survival probability.

scholarly journals RTNsurvival: an R/Bioconductor package for regulatory network survival analysis

2019 ◽  
Vol 35 (21) ◽  
pp. 4488-4489 ◽  
Author(s):  
Clarice S Groeneveld ◽  
Vinicius S Chagas ◽  
Steven J M Jones ◽  
A Gordon Robertson ◽  
Bruce A J Ponder ◽  
...  
Keyword(s):  
Survival Analysis ◽  
Proportional Hazards ◽  
Enrichment Analysis ◽  
Initial Step ◽  
Cox Proportional Hazards ◽  
Gene Set Enrichment Analysis ◽  
Supplementary Information ◽  
Transcriptional Networks ◽  
Bioconductor Package ◽  
Kaplan Meier

Abstract Motivation Transcriptional networks are models that allow the biological state of cells or tumours to be described. Such networks consist of connected regulatory units known as regulons, each comprised of a regulator and its targets. Inferring a transcriptional network can be a helpful initial step in characterizing the different phenotypes within a cohort. While the network itself provides no information on molecular differences between samples, the per-sample state of each regulon, i.e. the regulon activity, can be used for describing subtypes in a cohort. Integrating regulon activities with clinical data and outcomes would extend this characterization of differences between subtypes. Results We describe RTNsurvival, an R/Bioconductor package that calculates regulon activity profiles using transcriptional networks reconstructed by the RTN package, gene expression data, and a two-tailed Gene Set Enrichment Analysis. Given regulon activity profiles across a cohort, RTNsurvival can perform Kaplan-Meier analyses and Cox Proportional Hazards regressions, while also considering confounding variables. The Supplementary Information provides two case studies that use data from breast and liver cancer cohorts and features uni- and multivariate regulon survival analysis. Availability and implementation RTNsurvival is written in the R language, and is available from the Bioconductor project at http://bioconductor.org/packages/RTNsurvival/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Triglyceride is an independent predictor of type 2 diabetes among middle-aged and older adults: a prospective study with 8-year follow-ups in two cohorts

2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Jing Zhao ◽  
Yuan Zhang ◽  
Fengjiang Wei ◽  
Jiani Song ◽  
Zhi Cao ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Cohort Study ◽  
Survival Analysis ◽  
General Hospital ◽  
Proportional Hazards ◽  
Proportional Hazards Model ◽  
Cox Proportional Hazards ◽  
Cox Proportional Hazards Model ◽  
Kaplan Meier

Abstract Background Although there is abundant evidence indicating the connection between triglyceride and type 2 diabetes mellitus (T2DM), few reports or cohort studies confirm that high TG concentration may predict the incidence of T2DM independently. Thus, we studied the association between triglyceride (TG) and T2DM in a male-dominated, middle and older aged cohort, Tianjin General Hospital Cohort. And we further verified our results in the China Health and Retirement Longitudinal Study (CHARLS). Methods We conducted an 8-year retrospective cohort study (2009–2017) with 7241 participants who were free from T2DM at baseline. Three groups were constructed based on baseline TG levels (normal, borderline-high, and high). We used a Cox proportional hazards model to evaluate the relationship between TG and T2DM after adjusting for possible risk factors. A Kaplan–Meier survival analysis was performed to compare the incidence of T2DM among subjects in each TG group. We also tested the association between TG and T2DM in the CHARLS cohort. Results In Tianjin General Hospital Cohort, 7241 participants (male 75.8%, female 24.2%) were included, mean age was 61.49 ± 13.85 years at baseline. The cumulative incidence of T2DM in our cohort study was 8.6% (9.2% in men and 6.6% in women). Compared with the normal TG group, the hazard ratios in the borderline and high group were 1.30 (95% CI 1.04–1.62) and 1.54 (95% CI 1.24–1.90). The Kaplan–Meier survival analysis indicated that higher TG levels may predict higher onset of T2DM. These results were verified in the CHARLS cohort, the hazard ratio with T2DM (95% CI) for logTG was 3.94 (2.64–5.87). Conclusions Our findings suggest that the TG level may be an independent risk factor and predictor for T2DM.

scholarly journals Clinical Implication of Systemic Immune-Inflammation Index and Prognostic Nutritional Index in Skull Base Chordoma Patients

2021 ◽  
Vol 11 ◽  
Author(s):  
Mingxuan Li ◽  
Jiwei Bai ◽  
Shuai Wang ◽  
Yixuan Zhai ◽  
Shuheng Zhang ◽  
...  
Keyword(s):  
Survival Analysis ◽  
Skull Base ◽  
Proportional Hazards ◽  
Prognostic Nutritional Index ◽  
Cox Proportional Hazards ◽  
Cox Proportional Hazards Regression ◽  
Proportional Hazards Regression ◽  
Nutritional Index ◽  
Kaplan Meier ◽  
Skull Base Chordoma

Inflammation associated markers and nutritional indexes are associated with survival, and act as novel prognostic grading systems in patients with cancer, though the role of these markers in chordoma remains unclear. The current study aimed to characterize systemic immune-inflammation index (SII) and prognostic nutritional index (PNI), and their relationship with clinicopathological data and survival in skull base chordoma. Our retrospective study enrolled 183 patients with primary skull base chordoma who received surgical treatment. Clinicopathological data and preoperative blood tests including neutrophil, lymphocyte, platelet counts and albumin level were collected from medical records. Neutrophil lymphocyte ratio (NLR), platelet lymphocyte ratio (PLR), SII, PNI were calculated and the optimal cut-off values of these markers were used for further survival analysis via Kaplan–Meier survival analysis and Cox proportional hazards regression analysis. The value of NLR, PLR, SII, and PNI in skull base chordoma ranged from 0.44–6.48, 45.36–273.94, 113.37–1761.45, and 43.40–70.65, respectively. PNI was significantly correlated with patients' sex (p = 0.005) and age (p = 0.037). SII was positively correlated with NLR and PLR, but negatively correlated with PNI. The median overall survival (OS) time was 74.0 months and Kaplan–Meier survival analysis indicated that all four indexes were associated with OS. Multivariable Cox proportional hazards regression analysis identified that high SII was an independent prognostic factor for poor OS. More importantly, patients with high SII and PNI had the worst outcomes and combined use of SII and PNI increased the predictive ability for patients' survival in skull base chordoma. Our results suggest SII and PNI may be effective prognostic indicators of OS for patients with primary skull base chordoma after surgical resection.

Laryngeal Chondrosarcoma Characteristics and Survival Analysis in the National Cancer Database

2021 ◽  
pp. 019459982110045
Author(s):  
Vidit M. Talati ◽  
Matthew J. Urban ◽  
Tirth R. Patel ◽  
Christopher Wojcik ◽  
Bobby A. Tajudeen ◽  
...  
Keyword(s):  
Cohort Study ◽  
Survival Analysis ◽  
Total Laryngectomy ◽  
Proportional Hazards ◽  
Cox Proportional Hazards ◽  
National Cancer Database ◽  
Primary Surgery ◽  
White Males ◽  
Multivariate Survival ◽  
Kaplan Meier

Objective To highlight various patient, tumor, diagnostic, and treatment characteristics of laryngeal chondrosarcoma (LC) as well as elucidate factors that may independently affect overall survival (OS) for LCs. Study Design Retrospective cohort study. Setting National Cancer Database (NCDB). Methods All LC cases from 2004 to 2016 were extracted from the NCDB. Several demographic, diagnostic, and treatment variables were compared between LC subgroups using χ2 and analysis of variance tests. Univariate and multivariate survival analyses were performed for LCs using univariate Kaplan-Meier analysis and Cox proportional hazards regression models. Results There were 348 LCs included in the main cohort. LCs were predominantly non-Hispanic white males with similar rates of private and government insurance (49.4% vs 45.4%). Most LCs (81.6%) underwent primary surgery, particularly partial and total laryngectomy. The 1-, 5-, and 10-year survivals for LC were 95.7%, 88.2%, and 66.3%, respectively. On multivariate analysis, lack of insurance ( P = .019; hazard ratio [HR], 8.21; 95% CI, 1.40-48.03), high grade ( P = .001; HR, 13.51; 95% CI, 3.08-59.26), and myxoid/dedifferentiated histological subtypes ( P = .0111; HR, 10.74; 95% CI, 1.71-67.33) correlated with worse OS. No difference in OS was found between partial and total laryngectomy. Conclusion This is the first multivariate survival analysis and largest single cohort study of LCs in the literature. Overall, LCs enjoy an excellent prognosis, with insurance status, grade, and histology as the main predictors of survival.

scholarly journals Adapting the Default Weighted Survival Analysis Modelling Approach to Model IFRS 9 LGD

Risks ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 103
Author(s):  
Morne Joubert ◽  
Tanja Verster ◽  
Helgard Raubenheimer ◽  
Willem D. Schutte
Keyword(s):  
Survival Analysis ◽  
Financial Reporting ◽  
Proportional Hazards ◽  
Proportional Hazards Model ◽  
Survival Curve ◽  
Cox Proportional Hazards ◽  
Cox Proportional Hazards Model ◽  
Reporting Standard ◽  
International Financial Reporting Standard ◽  
Ifrs 9

Survival analysis is one of the techniques that could be used to predict loss given default (LGD) for regulatory capital (Basel) purposes. When using survival analysis to model LGD, a proposed methodology is the default weighted survival analysis (DWSA) method. This paper is aimed at adapting the DWSA method (used to model Basel LGD) to estimate the LGD for International Financial Reporting Standard (IFRS) 9 impairment requirements. The DWSA methodology allows for over recoveries, default weighting and negative cashflows. For IFRS 9, this methodology should be adapted, as the estimated LGD is a function of in the expected credit losses (ECL). Our proposed IFRS 9 LGD methodology makes use of survival analysis to estimate the LGD. The Cox proportional hazards model allows for a baseline survival curve to be adjusted to produce survival curves for different segments of the portfolio. The forward-looking LGD values are adjusted for different macro-economic scenarios and the ECL is calculated for each scenario. These ECL values are probability weighted to produce a final ECL estimate. We illustrate our proposed IFRS 9 LGD methodology and ECL estimation on a dataset from a retail portfolio of a South African bank.

PETCO2 gradient: a novel prognostic parameter in cardiopulmonary exercise testing

2020 ◽  
Vol 41 (Supplement_2) ◽  
Author(s):  
I.D Poveda Pinedo ◽  
I Marco Clement ◽  
O Gonzalez ◽  
I Ponz ◽  
A.M Iniesta ◽  
...  
Keyword(s):  
Exercise Testing ◽  
Proportional Hazards ◽  
Cardiopulmonary Exercise Testing ◽  
Cox Proportional Hazards ◽  
Prognostic Parameter ◽  
Cardiopulmonary Exercise ◽  
Proportional Hazards Regression ◽  
Kaplan Meier ◽  
Baseline Characteristics ◽  
The Difference

Abstract Background Previous parameters such as peak VO2, VE/VCO2 slope and OUES have been described to be prognostic in heart failure (HF). The aim of this study was to identify further prognostic factors of cardiopulmonary exercise testing (CPET) in HF patients. Methods A retrospective analysis of HF patients who underwent CPET from January to November 2019 in a single centre was performed. PETCO2 gradient was defined by the difference between final PETCO2 and baseline PETCO2. HF events were defined as decompensated HF requiring hospital admission or IV diuretics, or decompensated HF resulting in death. Results A total of 64 HF patients were assessed by CPET, HF events occurred in 8 (12.5%) patients. Baseline characteristics are shown in table 1. Patients having HF events had a negative PETCO2 gradient while patients not having events showed a positive PETCO2 gradient (−1.5 [IQR −4.8, 2.3] vs 3 [IQR 1, 5] mmHg; p=0.004). A multivariate Cox proportional-hazards regression analysis revealed that PETCO2 gradient was an independent predictor of HF events (HR 0.74, 95% CI [0.61–0.89]; p=0.002). Kaplan-Meier curves showed a significantly higher incidence of HF events in patients having negative gradients, p=0.002 (figure 1). Conclusion PETCO2 gradient was demonstrated to be a prognostic parameter of CPET in HF patients in our study. Patients having negative gradients had worse outcomes by having more HF events. Time to first event, decompensated heart Funding Acknowledgement Type of funding source: None

Sign in / Sign up

Export Citation Format

Share Document