Category: Nevin Manimala

J Proteome Res. 2023 Apr 28. doi: 10.1021/acs.jproteome.2c00803. Online ahead of print.

ABSTRACT

We present Meta4P (MetaProteins-Peptides-PSMs Parser), an easy-to-use bioinformatic application designed to integrate label-free quantitative metaproteomic data with taxonomic and functional annotations. Meta4P can retrieve, filter, and process identification and quantification data from three levels of inputs (proteins, peptides, PSMs) in different file formats. Abundance data can be combined with taxonomic and functional information and aggregated at different and customizable levels, including taxon-specific functions and pathways. Meta4P output tables, available in various formats, are ready to be used as inputs for downstream statistical analyses. This user-friendly tool is expected to provide a useful contribution to the field of metaproteomic data analysis, helping make it more manageable and straightforward.

PMID:37116187 | DOI:10.1021/acs.jproteome.2c00803

Global Spine J. 2023 Apr 28:21925682231173642. doi: 10.1177/21925682231173642. Online ahead of print.

ABSTRACT

STUDY DESIGN: Retrospective cohort study.

OBJECTIVES: This study aimed to (1) evaluate for any temporal trends in the rates of VTE, deep venous thrombosis (DVT), pulmonary embolism (PE), and mortality from 2011 to 2020 and (2) identify the predictors of VTE following lumbar fusion surgery.

METHODS: Annual incidences of 30-day VTE, DVT, PE, and mortality were calculated for each of the operation year groups from 2011 to 2020. Multivariable Poisson regression was utilized to test the association between operation year and primary outcomes, as well as to identify significant predictors of VTE.

RESULTS: A total of 121,205 patients were included. There were no statistically significant differences in VTE, DVT, PE, or mortality rates among the operation year groups. Multivariable regression analysis revealed that compared to 2011, operation year 2019 was associated with significantly lower rates of DVT. Age, BMI, prolonged operation time, prolonged length of stay, non-home discharge, anterior fusion, smoking status, functional dependence, and chronic steroid use were identified as independent predictors of VTE following lumbar fusion. Female sex, Hispanic ethnicity, and outpatient surgery setting were identified as protective factors from VTE in this cohort.

CONCLUSIONS: Rates of VTE after lumbar fusion have remained mostly unchanged between 2011 and 2020. Older age, higher BMI, longer operation time, prolonged length of stay, non-home discharge, anterior fusion, smoking, functional dependence, and steroid use were independent predictors of VTE after lumbar fusion, while female sex, Hispanic ethnicity, and outpatient surgery were the protective factors.

PMID:37116184 | DOI:10.1177/21925682231173642

Asian Pac J Cancer Prev. 2023 Apr 1;24(4):1413-1417. doi: 10.31557/APJCP.2023.24.4.1413.

ABSTRACT

OBJECTIVE: The aim of this study is to evaluate the expression of β-catenin and L1CAM in the type I of Endometrial Carcinoma.

MATERIAL AND METHODS: This study was an analytical study with a cross-sectional design using 49 samples of type I Endometrial Carcinoma. Immunohistochemical method was used to evaluate the expression of β-catenin and L1CAM related to two significant prognostic parameters i.e., lymphovascular space invasion (LVSI) and metastases event of type I Endometrial Carcinoma samples.

RESULTS: From all samples collected, based on the presence of LVSI, there were 17 cases (34.7%) with LVSI and 32 (65.3%) no LVSI. Among them, there were 13 cases that included lymph node or omental samples in type I Endometrial Carcinoma, 5 (38.5%) cases of metastasis, and 8 (61.5%) cases that did not metastasize. The statistical results showed that there was a significant correlation between β-catenin and L1CAM expressions examined from tumor cells with lymphovascular space invasion and the presence of metastases in the type I Endometrial Carcinoma (p <0.05).

CONCLUSION: This study suggest that the positive expression of β-catenin together with L1CAM can participate in the development of tumor cells in type I Endometrial Carcinoma, in its ability to involve lymphovascular space invasion, and metastases to other sites. Our results indicate that both of β-catenin and L1CAM are prominent biomarkers for the prognosis of type I Endometrial Carcinoma.

PMID:37116166 | DOI:10.31557/APJCP.2023.24.4.1413

Asian Pac J Cancer Prev. 2023 Apr 1;24(4):1379-1387. doi: 10.31557/APJCP.2023.24.4.1379.

ABSTRACT

OBJECTIVE: Fine needle aspiration cytology has higher sensitivity and predictive value for diagnosis of thyroid nodules than any other single diagnostic methods. In the Bethesda system for reporting thyroid, the category IV, encompasses both adenoma and carcinoma, but it is not possible to differentiate both lesions in the cytology practice and can be only differentiated after resection. In this work, we aim at exploring the ability of a convolutional neural network (CNN) model to sub-classifying cytological images of Bethesda category IV diagnosis into follicular adenoma and follicular carcinoma.

METHODS: We used a cohort of cytology cases n= 43 with extracted images n= 886 to train CNN model aiming to sub-classify follicular neoplasm (Bethesda category IV) into either follicular adenoma or follicular carcinoma.

RESULT: In our study, the model subclassification of follicular neoplasm into follicular adenoma (n = 28/43, images n = 527/886) from follicular carcinoma (n = 15/43, images n= 359/886), has achieved an accuracy of 78%, with a sensitivity of 88.4%, and a specificity of 64% and an area under the curve (AUC) score of 0.87 for each of follicular adenoma and follicular carcinoma.

CONCLUSION: Our CNN model has achieved high sensitivity in recognizing follicular adenoma amongest cytology smears of follciualr neoplasms, thus it can be used as an ancillary technique in the subcalssification of Bethesda Iv category cytology smears.

PMID:37116162 | DOI:10.31557/APJCP.2023.24.4.1379

Asian Pac J Cancer Prev. 2023 Apr 1;24(4):1307-1312. doi: 10.31557/APJCP.2023.24.4.1307.

ABSTRACT

Hydatid cyst is a zoonotic infestation caused by Echinococcus granulosus, and it is known that some parasites found in humans cause cancer in humans or some may have a protective effect against cancer. Cancer is one of the most serious health problems of today and it has been shown in some studies that parasites such as Echinococcus granulosus can have an inhibitory effect. The aim of this study was determined as whether Echinococcus granulosus has an inhibitory effect on exocrine pancreatic cancer with the help of the azaserine-rat model used in different cancer studies. Material and Methods: During experimental process a total of 45 male Wistar rats used, 14-day-old male Wistar rats were divided into groups according to the experimental protocol, administered azaserine injection protocol or kept as a control group without azaserine injection. Animals are grouped as Group 1, Control Group (group not treated with Azaserine and not injected with protoscolex.) (E-A-) (n=7); Group 2, Group injected with (IP) Azaserine only (30mg/kg) (E-A+) (n=8);Group 3, Group injected (IP) with protoscolex suspension of 1 cc only (E+A-) (n=15);Group 4, Group injected both Azaserine (IP) and protoscolex suspension (IP) (E+A+) (n=15). Atypical Acinar Cell Foci (AACF) load in the exocrine pancreas of each rat was measured quantitatively with the help of a video image analyzer and the AACF load was calculated with the help of a mathematical model. Results: Findings showed that the Atypical Acinar Cell Foci (AACF) burden was statistically significantly lower in the Azaserine+ protoscolex (Azaserine-injected-protoscolex-implanted) rat group compared to the other groups, suggesting that Echinococcosis in the azaserine-rat model could inhibit the development of precursor foci of neoplastic changes in the exocrine pancreas. Conclusion: The most significant aspect of our study is that it contributes new insights into the controversy that Echinococcosis suppresses pancreatic cancer.

PMID:37116153 | DOI:10.31557/APJCP.2023.24.4.1307

Asian Pac J Cancer Prev. 2023 Apr 1;24(4):1231-1237. doi: 10.31557/APJCP.2023.24.4.1231.

ABSTRACT

BACKGROUND: The present study investigated the association of interactions between gene polymorphisms in metabolic ‘caretaker’ genes (Phase I: CYP1A1, CYP2E1; Phase II: GSTM1, GSTT1), the cell cycle regulatory gene, p53, along with its negative controller, MDM-2, and the environment variable (tobacco). A nonparametric model, multifactor dimensionality reduction (MDR), was applied to analyse these interactions.

MATERIALS AND METHODS: This case-control study was carried out on 242 subjects. Genomic DNA was extracted from peripheral blood lymphocytes.11 gene variants with an exposure variable (tobacco use) were analysed using MDR to identify the best locus model for gene-gene and gene-environment interactions. Statistical significance was evaluated using a 1000-fold permutation test using MDR permutation testing software (version 1.0 beta 2). The value of p<0.05 was considered statistically significant.

RESULTS: The best three-locus model for gene-gene interaction included two of the p53 gene polymorphisms; rs17878362 (intron 3) and rs1042522 (exon 4) and rs6413432 in the Phase I gene, CYP2E1(DraI). The three-locus model to evaluate the gene-environment interaction included two intronic polymorphisms of the p53 gene, that is, rs17878362 (intron 3) and rs1625895 (intron 6), and rs4646903 in the Phase I gene CYP1A1*2C. The interaction graphs revealed independent main effects of the tobacco and p53 polymorphism, rs1042522 (exon 4), and a significant additive interaction effect between rs17878362 (intron 3) and rs1042522 (exon 4).

CONCLUSIONS: The nonparametric approach highlighted the potential role of tobacco use and variations in the p53 gene as significant contributors to oral cancer risk. The findings of the present study will help implement preventive strategies in both tobacco use and screening using a molecular pathology approach.

PMID:37116145 | DOI:10.31557/APJCP.2023.24.4.1231

Asian Pac J Cancer Prev. 2023 Apr 1;24(4):1199-1207. doi: 10.31557/APJCP.2023.24.4.1199.

ABSTRACT

OBJECTIVE: The purpose of this study was to report quality of life of newly diagnosed breast cancer patients from India in a large cohort using the EQ-5D-5L instrument.

METHODS: The study used longitudinal data of 500 breast cancer and 200 non-cancer subjects registered at our centre, during June 2019 and March 2022. The EQ-5D-5L and EQ-VAS instruments were used to measure and compare utility scores among cancer and non-cancer subjects. Descriptive statistics were analyzed and Tobit regression model were used to confirm the predictors of the utility score.

RESULTS: The cancer subjects had a mean EQ-ED-5L utility score of 0.8703 (SD=0.121), 0.8745 (SD=0.094) and 0.8902 (SD=0.107) at the time of baseline, completion and follow up surveys respectively. EQ-5D-5L values had significantly worsened after diagnosis of cancer as compared to the non-cancer cohort (0.87 vs. 0.93, p value 0.000). EQ-5D-5L utility scores as per stage for the cancer cohort were 0.88, 0.86 and 0.83 respectively for stage I-II, III and IV. Similarly, the EQ-VAS scores for stage I-II, III and IV were 74.9, 72.6 and 73.2 respectively. Multivariate analysis confirmed strong association of age, religion and income with the utility-values.

CONCLUSION: This is the first longitudinal study reporting the utility scores derived from a large cohort of breast cancer patients demonstrating lower utility scores compared to non-cancer cohort. The utility scores also improve post treatment completion for cancer patients and decrease with higher stage at diagnosis. This information will be useful for future health economic research in India pertaining to breast cancer.

PMID:37116141 | DOI:10.31557/APJCP.2023.24.4.1199

Asian Pac J Cancer Prev. 2023 Apr 1;24(4):1131-1136. doi: 10.31557/APJCP.2023.24.4.1131.

ABSTRACT

BACKGROUND: Patients undergoing neoadjuvant chemotherapy (NC) for invasive breast cancer (IBC) need indicators to track their progress during treatment. The goal of this research is to learn how cyclin D1 works in conjunction with taxane and non-taxane therapy for people with IBC.

METHODS: There were 31 examples divided into two groups, based on: those using a different type of NC (taxane- or non-taxane-based), and NC administration time (before or after). Tumor grade, age, PR, ER, Ki-67, HER2, and Cyclin D1 expression were among the factors considered. Using immunohistochemical labeling, we were able to categorize cyclin D1 levels according to a threshold value, and we supplemented this with data we found in our databases. To analyze the data, we used a modified linear model.

RESULTS: The expression of Cyclin D1 decreased after NC delivery (p=0.086). Cyclin D1 expression was reduced in the taxane group (p=0.792). The non-taxane group also saw no differences in outcomes (p = 0.065). There was a larger decrease in Cyclin D1 expression in the non-taxane group compared to the taxane group, but the difference was not statistically significant (p=0.200).

CONCLUSION: Cyclin D1 expression, even if the differences are not statistically significant, may be a prognostic indicator of NC reaction in IBC. The involvement of Cyclin D1 in NC warrants more research with bigger IBC sample sizes.

PMID:37116133 | DOI:10.31557/APJCP.2023.24.4.1131

Asian Pac J Cancer Prev. 2023 Apr 1;24(4):1113-1117. doi: 10.31557/APJCP.2023.24.4.1113.

ABSTRACT

BACKGROUND: Phlebitis is a severe inflammatory response in patients undergoing chemotherapy that can lead to complications and increased length of hospitalization.

OBJECTIVE: This study was conducted to examine the effects of sesame oil and nitroglycerin ointment on the incidence of chemotherapy-induced phlebitis in patients with cancer. Methods: This clinical trial study involved 138 cancer patients who were randomly assigned into three groups. The three groups received nitroglycerin ointment, sesame oil, or betadine alcoholic solution that were applied on the distal catheter area at a length of 1.5 centimeters and width of 2 × 4 cm using graded paper. The site was then dressed and fixed with anti-allergenic adhesives. The research samples were examined for 72 hours for the incidence of phlebitis.

RESULTS: No statistically significant difference was observed between the incidence of phlebitis in the sesame oil, nitroglycerin ointment and alcohol-betadine groups in the first 24 hours (p=0.2), the second 24 hours (p=0.13) and the third 24 hours (p=0.13).

CONCLUSION: External use of both sesame oil and nitroglycerin is effective in reducing chemotherapy-induced phlebitis. Due to its anti-inflammatory effect and low cost, however, using sesame oil is recommended.

PMID:37116130 | DOI:10.31557/APJCP.2023.24.4.1113

Asian Pac J Cancer Prev. 2023 Apr 1;24(4):1105-1111. doi: 10.31557/APJCP.2023.24.4.1105.

ABSTRACT

OBJECTIVE: To determine the risk factors associated the incidence of NPC, particularly in Indonesia.

METHODS: This systematic review and meta-analysis was conducted according to PRISMA statement. Database including PubMed, Scopus, Science Direct, Web of Science, and GARUDA were retrieved. Newcastle-Ottawa scale was used to assess the quality of published study and analyse the risk of bias of included study. Random-effect model and reported pooled Odds Ratio (OR) with 95%CI was carried out in our meta-analysis.

RESULTS: A pooled of 7 studies were included in our study which included 764 participants. We found that female gender was not associated with the incidences of NPC (OR 1.45, 95% CI: 0.61-3.45, p=0.40), and smoking was highly increased the incidence of NPC (OR 4.39 95% CI (0.79-24.40), but not statistically significant (p=0.09). Furthermore, salted fish consumption and some HLA alleles were associated with increased risk.

CONCLUSION: The incidence of NPC is not associated with female gender nor smoking habits. However, the risk of NPC is higher for those who consume salted fish and have some susceptible HLA alleles. Further investigations in larger studies are needed to confirm these findings.

PMID:37116129 | DOI:10.31557/APJCP.2023.24.4.1105