scholarly journals Kaplan Meier Survival Plot

2020 ◽  
Author(s):  
Keyword(s):  
Kaplan Meier ◽  
Survival Plot

Mahalanobis distance informed by clustering

2018 ◽  
Vol 8 (2) ◽  
pp. 377-406
Author(s):  
Almog Lahav ◽  
Ronen Talmon ◽  
Yuval Kluger
Keyword(s):  
Mahalanobis Distance ◽  
High Dimensional Data ◽  
Hidden Variables ◽  
Real Data ◽  
Risk Groups ◽  
High Dimensional ◽  
Data Sets ◽  
Kaplan Meier ◽  
Data Points ◽  
Survival Plot

Abstract A fundamental question in data analysis, machine learning and signal processing is how to compare between data points. The choice of the distance metric is specifically challenging for high-dimensional data sets, where the problem of meaningfulness is more prominent (e.g. the Euclidean distance between images). In this paper, we propose to exploit a property of high-dimensional data that is usually ignored, which is the structure stemming from the relationships between the coordinates. Specifically, we show that organizing similar coordinates in clusters can be exploited for the construction of the Mahalanobis distance between samples. When the observable samples are generated by a nonlinear transformation of hidden variables, the Mahalanobis distance allows the recovery of the Euclidean distances in the hidden space. We illustrate the advantage of our approach on a synthetic example where the discovery of clusters of correlated coordinates improves the estimation of the principal directions of the samples. Our method was applied to real data of gene expression for lung adenocarcinomas (lung cancer). By using the proposed metric we found a partition of subjects to risk groups with a good separation between their Kaplan–Meier survival plot.

MCRS1 EXPRESSION MORE IN TUMOR PART AND SERVES AS A POOR PROGNOSTIC FACTOR IN EXTRAHEPATIC CHOLANGIOCARCINOMA

2021 ◽  
pp. 72-75
Author(s):  
Hung-Chune Maa ◽  
Pham van Tuyen ◽  
Yen-Lin Chen ◽  
Yao-Nan Yuan
Keyword(s):  
Prognostic Factor ◽  
Large Scale ◽  
Surgical Margin ◽  
P Value ◽  
Extrahepatic Cholangiocarcinoma ◽  
Poor Prognostic Factor ◽  
Kaplan Meier ◽  
Survival Plot

INTRODUCTION:Microporous protein 1 (MCRS1) acts as a cancer gene. MCRS1 is associated with poor prognosis in several types of cancer including colorectal cancer, hepatocellular carcinoma, glioma, and non-small cell lung cancer. In the current study, we are trying to shed light on the role of MCRS1 in the extrahepatic cholangiocarcinoma. METHODS: We retrospectively selected 13 patients who diagnosed extrahepatic cholangiocarcinoma. All clinical charts and histopathology reports were reviewed for and recoded for age, gender, tumor size, surgical margin status, lymph node metastasis, distant metastasis and TMN staging. All patients were followed for 1~10 years. The median follow-up period was 3.2 years. RESULTS: The expression level of MCRS1 showed signicantly higher in tumor part than non-tumor part. In the Kaplan-Meier survival plot , the high MCRS1 expression group showed poor survival probability with p value of 0.020. The Hazard ratio of MCRS1 showed 8.393 folds in high MCRS1 expression group when compared with low expression group with the borderline p value of 0.05. CONCLUSION:MCRS1 serves as a poor prognostic factor. Further analysis, no correlation was found in proliferation, apoptosis, angiogenesis and EMT markers. The reason may be the sample size and large-scale study in the future is mandatory

scholarly journals A Novel Cell-Free Fluorescent Assay for HDL Function: Low Apolipoprotein A1 Exchange Rate Associated with Increased Incident Cardiovascular Events

2020 ◽  
Vol 5 (3) ◽  
pp. 544-557 ◽  
Author(s):  
Shuhui Wang Lorkowski ◽  
Gregory Brubaker ◽  
Lin Li ◽  
Xinmin S Li ◽  
Stanley L Hazen ◽  
...  
Keyword(s):  
Exchange Rate ◽  
Cardiovascular Events ◽  
Hdl Cholesterol ◽  
Apolipoprotein A1 ◽  
Major Adverse Cardiovascular Events ◽  
Chromatography Analysis ◽  
Hdl Function ◽  
Kaplan Meier ◽  
Traditional Risk Factors ◽  
Survival Plot

Abstract Background Cholesterol efflux capacity is a tissue culture assay for HDL function that is not amenable for high-throughput monitoring of risk assessment. Methods We devised a cell-free HDL function assay to measure the exchange rate of exogenous apoA1 into serum HDL using NBD/Alexa647 double-labeled apoA1, whose NBD/Alexa647 emission ratio increased upon exchange into HDL. ApoA1 exchange rate (AER) was assayed by incubating labeled apoA1 with human serum, and the rate of the increase of the NBD/Alexa647 ratio over time was calculated as AER. Results Fast protein liquid chromatography analysis of serum confirmed that the labeled apoA1 selectively exchanged into the HDL lipoprotein fraction. Characterization studies demonstrated that the AER assay had excellent intra- and inter-day reproducibility, was stable over 3 freeze-thaw cycles, and yielded similar results with serum or plasma. We quantified AER in serum from randomly selected stable subjects undergoing elective diagnostic coronary angiography (n = 997). AER was correlated with HDL-cholesterol (r = 0.58, P < 0.0001) and apoA1 levels (r = 0.56, P < 0.0001). Kaplan-Meier survival plot showed subjects in the lowest quartile of AER experienced a significantly higher rate of incident major adverse cardiovascular events (MACE = myocardial infarction, stroke, or death) (P < 0.0069 log rank). Moreover, compared to subjects in the lowest AER quartile, the remaining subjects showed significantly lower incident (3 year) risk for MACE, even after adjustment for traditional risk factors and apoA1 (HR 0.58; 95% CI 0.40–0.85; P = 0.005). Conclusions In a prospective cohort of stable subjects undergoing elective diagnostic cardiac evaluations, low AER was associated with increased incident risk of MACE.

scholarly journals The Multiple Sclerosis Severity Score: fluctuations and prognostic ability in a longitudinal cohort of patients with MS

2019 ◽  
Vol 5 (1) ◽  
pp. 205521731983725 ◽  
Author(s):  
RH Gross ◽  
SH Sillau ◽  
AE Miller ◽  
C Farrell ◽  
SC Krieger
Keyword(s):  
Multiple Sclerosis ◽  
Severity Score ◽  
Mixed Model ◽  
Linear Models ◽  
Longitudinal Cohort ◽  
Kaplan Meier ◽  
The Individual ◽  
Survival Plot ◽  
The Impact ◽  
Over Time

Background The Multiple Sclerosis Severity Score (MSSS), combining the Expanded Disability Status Scale (EDSS) and disease duration, attempts to stratify multiple sclerosis (MS) patients based on their rate of progression. Its prognostic ability in the individual patient remains unproven. Objectives To assess the stability of MSSS within individual persons with MS in a longitudinal cohort, to evaluate whether certain factors influence MSSS variability, and to explore the ability of MSSS to predict future ambulatory function. Methods A single-center retrospective review was performed of patients following a single provider for at least 8 years. Mixed model regression modeled MSSS over time. A Kaplan–Meier survival plot was fitted, using change of baseline MSSS by at least one decile as the event. Cox modeling assessed the influence of baseline clinical and demographic factors on the hazard of changing MSSS by at least one decile. Linear models evaluated the impact of baseline EDSS, baseline MSSS, and other factors on the Timed 25-Foot Walk (T25FW). Results Out of 122 patients, 68 (55.7%) deviated from baseline MSSS by at least one decile. Final T25FW had slightly weaker correlation to baseline MSSS than to baseline EDSS, which was moderately strongly correlated with future log T25FW. Conclusion Individual MSSS scores often vary over time. Clinicians should exercise caution when using MSSS to prognosticate.

How to read a Kaplan-Meier survival plot

BMJ ◽  
2014 ◽  
Vol 349 (sep12 4) ◽  
pp. g5608-g5608 ◽  
Author(s):  
P. Sedgwick
Keyword(s):  
Kaplan Meier ◽  
Survival Plot

scholarly journals Data mining analysis of miR-638 and key genes interaction in cisplatin resistant triple-negative breast cancer

2019 ◽  
Vol 24 (2) ◽  
pp. 65
Author(s):  
Adam Hermawan ◽  
Herwandhani Putri
Keyword(s):  
Breast Cancer ◽  
Regulatory Networks ◽  
Target Gene ◽  
Resistance Mechanism ◽  
Mrna Levels ◽  
Kaplan Meier ◽  
Gene Regulatory ◽  
Survival Plot ◽  
Geo Database

Cisplatn is one of the chemotherapy for the treatment of triple‐negatve breast cancer (TNBC), but its effectveness is limited because of the phenomenon of chemoresistance. miR‐638 was shown to regulate chemoresistance; however, it has never been validated in the cisplatn‐resistant tumor from patents. This present study aimed to identfy the key gene regulatory networks of miR‐638 and evaluate the potental role of the miR‐638 and its targets as potental prognosis biomarkers for cisplatn‐resistance triple‐negatve breast cancer patents. The miR‐638 target was obtained from the miRecords database while the mRNA of chemoresistance biomarker candidate was obtained from the GSE18864 of GEO database, which is mRNA of cisplatn‐resistance TNBC patents. CCND1 and FZD7 are potental candidates for cisplatn chemoresistance biomarkers in patents with TNBC. Moreover, a Kaplan‐Meier survival plot showed that breast cancer patents with low mRNA levels of FZD7 had signifcantly worse overall survival than those in higher mRNA expression group. Taken together, miR‐638 plays a role in cisplatn resistance mechanism through a mechanism involving its target gene CCND1 and FZD7. Overall, miR‐638, CCND1, and FZD7 are candidates for cisplatn biomarker resistance in TNBC.

scholarly journals Molecular characterization of ageratum enation virus and beta satellite associated with leaf curl disease of fenugreek in India

2019 ◽  
Vol 24 (2) ◽  
pp. 74
Author(s):  
P Swarnalatha ◽  
V Venkataravanappa ◽  
C N Lakshminarayana Reddy ◽  
M Sunil Kumar ◽  
M Krishna Reddy
Keyword(s):  
Breast Cancer ◽  
Regulatory Networks ◽  
Resistance Mechanism ◽  
Mrna Levels ◽  
Kaplan Meier ◽  
Survival Plot ◽  
Leaf Curl Disease ◽  
Geo Database

Cisplatn is one of the chemotherapy for the treatment of triple‐negatve breast cancer (TNBC), but its effectveness is limited because of the phenomenon of chemoresistance. miR‐638 was shown to regulate chemoresistance; however, it has never been validated in the cisplatn‐resistant tumor from patents. This present study aimed to identfy the key gene regulatory networks of miR‐638 and evaluate the potental role of the miR‐638 and its targets as potental prognosis biomarkers for cisplatn‐resistance triple‐negatve breast cancer patents. The miR‐638 target was obtained from the miRecords database while the mRNA of chemoresistance biomarker candidate was obtained from the GSE18864 of GEO database, which is mRNA of cisplatn‐resistance TNBC patents. CCND1 and FZD7 are potental candidates for cisplatn chemoresistance biomarkers in patents with TNBC. Moreover, a Kaplan‐Meier survival plot showed that breast cancer patents with low mRNA levels of FZD7 had signifcantly worse overall survival than those in higher mRNA expression group. Taken together, miR‐638 plays a role in cisplatn resistance mechanism through a mechanism involving its target gene CCND1 and FZD7. Overall, miR‐638, CCND1, and FZD7 are candidates for cisplatn biomarker resistance in TNBC.

Differential expression proteins in lung adenocarcinoma with bone metastasis: Correlation of ALDH2 and ENO1 with prognosis.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. e20534-e20534
Author(s):  
Mengdi Yang ◽  
Jing Sun ◽  
Zhiyu Wang ◽  
Rui Zhang ◽  
YIfeng Gu ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Differential Expression ◽  
Underlying Mechanism ◽  
The Cancer Genome Atlas ◽  
Rna Seq ◽  
Two Dimensional Gel Electrophoresis ◽  
Kaplan Meier ◽  
Cancer Genome Atlas ◽  
Survival Plot ◽  
Related Proteins

e20534 Background: The prognosis of lung adenocarcinoma (LUAD) with bone metastases (BM) is still poor. It is increasingly demanded to find key proteins to solve the problem. Methods: First, we collected three groups of bone tissues: normal, osteosarcoma, and LUAD with BM from Shanghai Sixth People's Hospital. Each group had five patients. Two-dimensional gel electrophoresis (2D-E) was used to find proteins with significant differences, then Maldi-tof-tof mass spectrometry was used to identify the proteins. Second, immunohistochemical (IHC) was used to check the expression of proteins in 28 BM patients and 9 LUAD patients. Real-Time PCR (QPCR), western boltting (WB) were further used to check the expression of para-LUAD, LUAD and BM. Last, we downloaded RNA-seq and clinical datas from the Cancer Genome Atlas(TCGA) database to further verify differentially expressed genes using ‘DESeq’ package and explored their relationship with survival using ‘survival’ package in R. Kaplan-Meier survival plot and the hazard ratio and logrankp was calculated (www.kmplot.com/lung). Results: We got 26 matched proteins from 2D-E, then selected Aldehyde Dehydrogenase 2 Family (Mitochondrial) (ALDH2) and Enolase-1 (ENO1). In IHC analysis, strong-stained ALDH2 showed OR = 0.568 (95 % confidence interval [CI], 0.317-1.019), p= 0.036, strong-stained ENO1 OR = 1.929 (95% CI, 0.915-4.066), p= 0.023, were associated with bone metastastic incidences in LUAD with statistically significantly difference. QPCR, WB validated that ALDH2 had lowest expression in BM, followed by LUAD samples, and para-LUAD highest. However, ENO1 displayed the opposite tendency . In TCGA LUAD RNA-seq, ALDH2 had low expression ( p= 3.83E-12, log2Foldchange = 1.158), and ENO1 was up-regulated ( p= 0.0004, log2Foldchange = 1.210 ). ALDH2 is correlated with better survival (HR = 0.47, 95% CI (0.37-0.61), logrankP = 6.5E-10), while ENO1 was inversely associated with better prognosis (HR = 1.67,95% CI (1.32-2.12), logrankP = 1.9E-05) in K-M Plotter. Conclusions: In this study, we discovered new differential expression and prognosis related proteins, ALDH2 and ENO1, and they are worthy of further exploration into the underlying mechanism.

scholarly journals The Survival Of All Ceramic Crowns With A Zirconia Core (Lava™)

2019 ◽  
Vol 2 (1) ◽  
pp. 01-04
Author(s):  
Gang wei ◽  
Jiang Dai ◽  
Ling Xiao ◽  
Chen Dong ◽  
Fei Liu
Keyword(s):  
Survival Time ◽  
Hospital Setting ◽  
Clinical Situation ◽  
Convenience Sample ◽  
Mean Survival Time ◽  
Anterior Teeth ◽  
Kaplan Meier ◽  
Increased Risk ◽  
The Mean ◽  
Survival Plot

Background: Few studies have assessed the survival of restorations and particularly zirconia based crowns in the restoration of the severely worn dentition. This study aimed to determine survival and factors associated with failure in anterior teeth worn through to dentine restored with Lava™ crowns. Methods: A convenience sample of 30 participants (27 male, 3 female) had 161 Lava™ crowns placed by one specialist clinician in a hospital setting. Follow-up was over a median 72 month period. Results: Of the 161 Lava™ crowns only 25 failed (15.5%) in 15 individuals up to 84 months for the longest case. Major failures were total debond (N=7) or minor delamination chips within the veneer ceramic layer (N=18). The mean time to first failure was 25.23 months. The Kaplan Meier survival plot estimated the Mean Survival Time for the crowns to be 74 months (95%CI 70.4, 77.3). Failures by subject were not associated with an increase in Occlusal Vertical Dimension using a Dahl approach but were associated with an edge-to-edge incisal relation (p<0.05), attrition (p<0.05) and bruxism (p<0.005). Conclusion: The Kaplan Meier survival plot estimated the Mean Survival Time for the crowns to be 74 months. The high loads in bruxism result in increased risk of fracture or debond. Clinical relevance: A protective bi-laminar splint is thus advisable. Nonetheless, application of zirconia based crowns in a difficult clinical situation such as bruxism can be a successful treatment modality.

scholarly journals Convalescent Plasma Therapy for COVID-19: A Graphical Mosaic of the Worldwide Evidence

2021 ◽  
Vol 8 ◽  
Author(s):  
Stephen A. Klassen ◽  
Jonathon W. Senefeld ◽  
Katherine A. Senese ◽  
Patrick W. Johnson ◽  
Chad C. Wiggins ◽  
...  
Keyword(s):  
Survival Data ◽  
Survival Benefit ◽  
Patient Survival ◽  
Disease Outbreaks ◽  
Disease Course ◽  
Plasma Transfusion ◽  
Plasma Therapy ◽  
Kaplan Meier ◽  
Multiple Levels ◽  
Survival Plot

Convalescent plasma has been used worldwide to treat patients hospitalized with coronavirus disease 2019 (COVID-19) and prevent disease progression. Despite global usage, uncertainty remains regarding plasma efficacy, as randomized controlled trials (RCTs) have provided divergent evidence regarding the survival benefit of convalescent plasma. Here, we argue that during a global health emergency, the mosaic of evidence originating from multiple levels of the epistemic hierarchy should inform contemporary policy and healthcare decisions. Indeed, worldwide matched-control studies have generally found convalescent plasma to improve COVID-19 patient survival, and RCTs have demonstrated a survival benefit when transfused early in the disease course but limited or no benefit later in the disease course when patients required greater supportive therapies. RCTs have also revealed that convalescent plasma transfusion contributes to improved symptomatology and viral clearance. To further investigate the effect of convalescent plasma on patient mortality, we performed a meta-analytical approach to pool daily survival data from all controlled studies that reported Kaplan–Meier survival plots. Qualitative inspection of all available Kaplan–Meier survival data and an aggregate Kaplan–Meier survival plot revealed a directionally consistent pattern among studies arising from multiple levels of the epistemic hierarchy, whereby convalescent plasma transfusion was generally associated with greater patient survival. Given that convalescent plasma has a similar safety profile as standard plasma, convalescent plasma should be implemented within weeks of the onset of future infectious disease outbreaks.

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