Integrating impacts of climate change on aquatic environments in inter-basin water regulation: Establishing a critical threshold for best management practices

Inter-basin water diversion (IBWD) is a viable strategy to tackle water scarcity and quality degradation due to climate change and increasing water demand in headwaters regions. Nevertheless, the capacity of IBWD to mitigate the impacts of climate change on water quality has rarely been quantified, and the underlying processes are not well understood. Therefore, this study aims to elucidate how the IBWD manipulated total phosphorus (TP) loading dilution and conveying patterns under climate change and determine a critical threshold for the quantity of water entering downstream reservoirs (WIN) for operational scheduling. To resolve this issue, climate-driven hydrologic variability over a 60-year period was derived utilizing the least square fitting approach. Subsequently, six scenarios evaluating the response of in-lake TP concentrations (TPL) to increased temperatures and IBWDs of 50 %, 100 %, and 150 % from the baseline water volume in 2030 and 2050 were studied by employing a calibrated hydrological-water quality model (SWAT-YRWQM). In the next stage, three datasets derived from mathematical statistics based on the observed data, the Vollenweider formula, and modeled projections were integrated to formulate best management practices. The results revealed that elevated air temperatures would lead to reduced annual catchment runoff but increased IBWD. Additionally, our study quantified the IBWD potential for mitigating water quality degradation, indicating the adverse effects of climate change on TPL would be weakened by 4.2-14.4 %. A critical threshold for WIN was also quantified at 617 million m3, maintaining WIN at or near 617 million m3 through optimized operational scheduling of IBWD could effectively restrict external inflow TP loading to lower levels. This study clearly illustrates the intricate interactive effects of climate change and IBWD on aquatic environments. The methodology elucidated in this study for determining the critical threshold of WIN could be applied in water management for analogous watershed-receiving waterbody systems.

The Association of Time Interval between Surgery and Neoadjuvant Chemoradiation Therapy with pCR and Overall Survival for Locally Advanced Rectal Adenocarcinoma

PURPOSE/OBJECTIVE(S)

To determine the best time interval between neoadjuvant radiation therapy (RT) and surgery that is associated with the highest rate of complete pathological response (pCR) and evaluate its impact on overall survival (OS) for locally advanced rectal adenocarcinoma. We hypothesize that the longer interval the higher pCR and a higher pCR is associated with a higher OS.

MATERIALS/METHODS

The National Cancer Database (NCDB) was used to extract data on patients diagnosed with stage II and III adenocarcinoma of the anus, rectum, or rectosigmoid between 2004-2019 and who had ≤ 24 weeks' time interval between neoadjuvant RT and surgery. Multivariable logistic regression analysis was used to determine factors associated with achieving pCR and odds ratios (OR) were reported as a measure of association between the covariates of interest and the outcome of achieving pCR. Multivariable Cox regression analysis was conducted to estimate hazard ratios (HR) and their associated 95% confidence intervals. The multivariable analyses were adjusted for age at diagnosis, sex, race, income, education, facility type, insurance status, comorbidity score, place of living, chemotherapy's sequence with surgery and RT, and year of diagnosis.

RESULTS

Among 28,656 patients, 4,455 (15.6%) achieved pCR. In the multivariable logistic regression analysis, patients who received surgery between 5-8 weeks, 9-12 weeks, 13-16 weeks, 17-20 weeks, or 21-24 weeks after the completion of RT were more likely to achieve pCR compared to < = 4 weeks (ORs: 1.63, 2.16, 1.82, 1.73, 1.75, respectively, p<0.001 for all) with OR being the highest for the 9-12 weeks interval. In the multivariable Cox regression analysis, patients who achieved pCR had comparable OS regardless of when the surgery took place between < = 4 to 24 weeks after completing RT compared to < = 4 weeks after RT. Among patients who did not achieve pCR, OS was only similar if surgery was received between 5-8 weeks or 9-12 weeks after RT compared to < = 4 weeks after RT (HR: 0.90, p = 0.19 and HR: 1.02, p = 0.78 respectively). However, surgery between 13-16 weeks after RT, 71-20 weeks or 21-24 weeks after RT was associated with worse OS compared to < = 4 weeks after RT (HRs: 1.30, 1.67, 1.79, respectively, p<0.01).

CONCLUSION

In the current study, we found that among patients who achieve pCR, OS does not depend on the time interval between the completion of RT and receipt of surgery, while among patients who do not achieve pCR, delaying surgery >12 weeks is associated with reduced OS. An interval of 9-12 weeks was the best optimal time as it was associated with the highest OR of achieving pCR and better OS compared to other interval times.

Melatonin administration during the first half of pregnancy improves the reproductive performance of rabbits: Emphasis on ovarian and placental functions

This study was designed to investigate the roles of melatonin administration during different sensitive windows of the first half of pregnancy in the function and gene expression of the ovary and placenta, hormone profile, and pregnancy outcomes in rabbits. Four equal experimental groups of 20 rabbits each were used. The first (FW), second (SW), and third (F + SW) groups comprised rabbits that orally received 0.7-mg melatonin/kg body weight during the first week, second weeks, and during both weeks of pregnancy; and the fourth group served as the control group (C). The total number of visible follicles significantly increased in all melatonin-treated groups compared with that in the C group. In all melatonin-treated groups, the number of absorbed fetuses was significantly reduced, whereas the weights of embryonic sacs and fetuses were higher than in the C group. The placenta efficiency was significantly increased in the F + SW group compared with that in the C group, followed by the SW group, whereas no significant difference in the placenta efficiency was found between the FW and C groups. Melatonin treatments significantly improved the expression of antioxidants, gonadotropin receptors, and cell cycle regulatory genes in the ovary, whereas only FW treatment upregulated steroidogenic acute regulatory gene. Compared with the C and FW groups, melatonin treatments during the SW and F + SW significantly upregulated the expression of most genes in the placenta. The concentrations of estradiol were significantly higher in the SW and F + SW groups than in the FW and C groups. The concentrations of progesterone were significantly increased in the FW group compared with those in the C and SW groups, whereas the F + SW group showed intermediate values. The litter size and weight at birth significantly increased in all melatonin-treated groups compared with those in the C group. The second week of pregnancy seems to be a sensitive window for melatonin actions during pregnancy. Thus, melatonin administration during the second week of pregnancy can be effective in improving pregnancy outcomes in rabbits.

Development and validation of a nomogram model for lung cancer based on radiomics artificial intelligence score and clinical blood test data

Background

Artificial intelligence (AI) discrimination models using single radioactive variables in recognition algorithms of lung nodules cannot predict lung cancer accurately. Hence, we developed a clinical model that combines AI with blood test variables to predict lung cancer.

Methods

Between 2018 and 2021, 584 individuals (358 patients with lung cancer and 226 individuals with lung nodules other than cancer as control) were enrolled prospectively. Machine learning algorithms including lasso regression and random forest (RF) were used to select variables from blood test data, Logistic regression analysis was used to reconfirm the features to build the nomogram model. The predictive performance was assessed by performing the receiver operating characteristic (ROC) curve analysis as well as calibration, clinical decision and impact curves. A cohort of 48 patients was used to independently validate the model. The subgroup application was analyzed by pathological diagnosis.

Findings

A total of 584 patients were enrolled (358 lung cancers, 61.30%,226 patients for the control group) to establish the model. The integrated model identified eight potential factors including carcinoembryonic antigen (CEA), AI score, Pro-Gastrin Releasing Peptide (ProGRP), cytokeratin 19 fragment antigen21-1(CYFRA211), squamous cell carcinoma antigen(SCC), indirect bilirubin(IBIL), activated partial thromboplastin time(APTT) and age. The area under the curve (AUC) of the nomogram was 0.907 (95% CI, 0.881-0.929). The decision and clinical impact curves showed good predictive accuracy of the model. An AUC of 0.844 (95% CI, 0.710 - 0.932) was obtained for the external validation group.

Conclusion

The nomogram model integrating AI and clinical data can accurately predict lung cancer, especially for the squamous cell carcinoma subtype.

Qualitative and quantitative comparison of allergen component-specific to birch and grass analyzed by ImmunoCAP assay and Euroline immunoblot test

Summary

Background.In the diagnostic work up of allergy, determining allergen component-specific immunoglobulin E (IgE) is important for diagnosis, prognosis and choice of treatment. The purpose of this study was to evaluate the performance of the immunoblotting assay (Euroline) in detection of IgE antibodies against timothy grass and birch pollen allergen components compared to fluorescent enzyme assay (ImmunoCAP, Phadia 250). Methods. A total of 128 serum samples from patients allergic to timothy grass and birch pollen were analysed. The levels of IgE antibodies to timothy grass and birch pollen were measured using Euroline DPA-Dx pollen 1 and ImmunoCAP assay. The two methods were then compared on binary (positive vs negative), semi-quantitative (IgE classes) and quantitative (concentration) levels. The two methods were also compared to results from skin prick testing. Results. The Euroline method showed a positive percentage agreement of 93% and negative percentage agreement of 94% with an overall accuracy of 94% when compared to ImmunoCAP. Kappa analysis showed moderate strength of agreement between the methods in determining IgE classes for 7/11 components tested. All components showed a positive correlation when analysed using Spearman's rank correlation. Conclusions. Overall, we found that there is good correlation between the Euroline and ImmunoCAP methods in measuring IgE sensitization.

Teaching Medical Professionalism with a Scenario-based Approach Using Role-Playing and Reflection: A Step towards Promoting Integration of Theory and Practice

INTRODUCTION

Professionalism, as one of the core competencies of physicians, is essential for providing the patients with higher quality care. It is an abstract concept and its education and assessment need objective and operational methods. The present study aimed at teaching the concepts of professionalism based on a scenario-based approach using role-playing and reflection.

METHODS

This is a pre-experimental study (one-group pretest-posttest design) with a mixed method approach. The study was conducted on 18 medical students (by voluntary sampling method) who had enrolled in the Medical Ethics Course at Kashan University of Medical Sciences in 2020. Twelve scenarios were designed about the most prevalent issues of medical professionalism. In each session, one group of students played out their scenarios and then, the participants and instructors discussed their role-playing. Participants' knowledge about professionalism was assessed at the beginning and end of each session, and they completed a satisfaction questionnaire and a reflection form. T-tests (one-sample and paired T-test) were applied for statistical analysis. Quantitative and qualitative data were analyzed using SPSS software (version 26), and P<0.05 was considered statistically significant. Conventional content analysis was used to analyze the qualitative data.

RESULTS

The mean scores of the participants' knowledge in post-test were significantly higher than those in the pre-test (P=0.042, t=-2.074). The mean scores of the participants' role-playing quality (p<0.001) and satisfaction (p=0.001) were significantly higher than their corresponding test values. Qualitative analysis of the participants' reflections revealed their satisfaction with the study intervention.

CONCLUSION

The scenarios, role-playing, and reflection could provide an opportunity for operationalizing the concepts of professionalism and deep learning of students. Medical instructors need to improve their knowledge and skills of using active methods in teaching professionalism to medical students.

Expression of lncRNAs AK058003 and APOC1P1 in breast cancer patients

In the current study, the expression levels of two important lncRNAs, i.e., AK058003 and APOC1P1, in breast tumors were compared with adjacent non-tumor tissues to evaluate their diagnostic potential in a panel of 121 patients. Total RNA was extracted, cDNA was synthesized and expression of AK058003 and APOC1P1 was assessed using qRT-PCR. A significant overexpression and positive correlation between these two lncRNAs were observed in tumor tissues compared to marginal healthy tissues. In conclusion, the examined lncRNAs were overexpressed in tumor tissues, suggesting their significant diagnostic value in breast cancer.

Prognostic Value of LncRNA KRT18P55 in Patients with Intestinal Type of Gastric Cancer

PURPOSE

Gastric cancer (GC) is a heterogeneous disease, and this heterogeneity significantly affects survival and treatment outcomes. Identification of molecular biomarkers specific for early-stage GC can help clinicians to choose more precise and effective treatment approaches. Long non-coding RNAs (lncRNAs) have the potential to be used as biomarkers because of their tissue specificity, stability, and availability in body fluids. In this study, we aimed to investigate changes in the expression levels of lncRNA KRT18P55 and to assess its biomarker potentials in patients with GC.

METHODS

Tumor and non-tumor marginal tissues were collected from 102 patients at Noor-Nejat Hospital (Tabriz, Iran). RNA was isolated, and quantitative reverse transcriptase PCR (qRT-PCR) was performed to assess KRT18P55 expression levels in tumor and non-tumor tissue samples. The receiver operating characteristic (ROC) curve analysis was performed to evaluate potentials of KRT18P55 as a prognostic biomarker in GC. SPSS and GraphPad Prism software were used for data analysis.

RESULTS

We found that KRT18P55 is significantly overexpressed in tumor as compared to non-tumor tissues (p < 0.0001). We found a significant association between KRT18P55 overexpression and intestinal GC subtype (p < 0.0001), lymph node metastasis (p = 0.013), and Helicobacter pylori infection (p = 0.033). Based on the ROC analysis, KRT18P55 showed a sensitivity and specificity of 53.92% and 77.45%, respectively.

CONCLUSION

Overexpression of KRT18P55 in gastric tumors is suggestive of its oncogenic role in GC. In addition, KRT18P55 may be used as a potential prognosis biomarker and therapeutic target in intestinal GC subtype.

Overexpression of lncRNA AFAP1-AS1 as a diagnostic biomarker in non-small cell lung cancer

Background

Long non-coding RNAs (lncRNAs) play important roles in lung tumorigenesis. Among different lncRNAs, overexpression of the lncRNA actin filament‐associated protein 1‐antisense RNA 1 (AFAP1-AS1) in lung tumors has been reported in different studies. In the current study, we aimed to investigate the potential value of lncRNA AFAP1-AS1 as a diagnostic biomarker in lung cancer. Ninety samples from patients with lung cancer were collected from Noor-E-Nejat hospital, Tabriz, Iran. The expression of AFAP1-AS1 was assessed using quantitative reverse transcriptase-PCR (qRT-PCR), followed by the ROC curve analysis to investigate the biomarker potency of AFAP1-AS1.

Results

Our results revealed an upregulation of AFAP1-AS1 in tumor samples as compared to the adjacent non-tumor tissues. We found a significant positive association between AFAP1-AS1 expression and tumor size, as well as tumor stage.

Conclusions

Our results showed overexpression of AFAP1-AS1 and its capacity as a diagnostic biomarker in lung cancer.

Effects of heavy metal contamination released by petrochemical plants on marine life and water quality of coastal areas

The present study attempts to assess the threat of water contamination in Persian Gulf by heavy metals (Fe, Cr, Pb, Cu, Zn, Cd, Se, and Ni) and its subsequent effects on five fish species including Scomberomorus guttatus (S. guttatus), Lethrinus nebulosus (L. nebulosus), Brachirus orientalis (B. orientalis), Pomadasys kaakan (P. kaakan), and Scomberomorus commerson (S. commerson). Water and fish samples from fourteen monitoring stations were obtained to determine the concentrations of contaminants in water and fish. Heavy metal pollution index (HMPI) and non-carcinogenic hazard quotient (NHQI) were employed to evaluate contamination level in water and fish muscle. The Kriging geostatistical method was employed to determine the spatial distribution of different heavy metals around petrochemical plants. The highest NHQI values for P. kaakan and B. orientalis species were 1.036 and 1.046, respectively. In both cases, the NHQI values were higher than the maximum allowable value of 1, indicating that both fish species were on the verge of contamination by heavy metals, which in turn makes the consumption of these fish highly hazardous to human health. The lowest NHQI value was observed in S. commerson species at a value of 0.394, indicating its harmlessness to human health. Overall, fish species living within the top 5 m of the water column (S. commerson and S. guttatus) were found to be less contaminated by heavy metals compared to species dwelling near the seafloor (P. kaakan and B. orientalis). Results also indicated the pollution absorption rate in S. commerson and S. guttatus were 0.45 and 3.4 mg/kg-year, while the corresponding values for the B. orientalis and L. nebulosus species were 6 and 2 mg/kg-year, respectively. P. kaakan species showed a pollution absorption rate of 3.2 mg/kg-year. High heavy metal concentrations of 4.8, 10, 9.8, 5.2, 9.4, and 6.7 mg/L were obtained for Cr, Zn, Pb, Ni, Fe, Cu, and Cd, respectively, in water samples obtained from stations nearby petrochemical plants. The HMPI index for the most contaminated stations was ten times that of the maximum allowable limit. Given the intense activity of oil, gas, and petrochemical plants in the Persian Gulf, defining safe fishing areas by management practices similar to contamination zoning maps presented in this study can substantially protect the public health from heavy metal contamination.

Cancer driver gene and non-coding RNA alterations as biomarkers of brain metastasis in lung cancer: A review of the literature

Brain metastasis (BM) is the most common event in patients with lung cancer. Despite multimodal treatments and advances in systemic therapies, development of BM remains one of the main factors associated with poor prognosis and mortality in patients with lung cancer. Therefore, better understanding of mechanisms involved in lung cancer brain metastasis (LCBM) is of great importance to suppress cancer cells and to improve the overall survival of patients. Several cancer-related genes such as EGFR and KRAS have been proposed as potential predictors of LCBM. In addition, there is ample evidence supporting crucial roles of non-coding RNAs (ncRNAs) in mediating LCBM. In this review, we provide comprehensive information on risk assessment, predictive, and prognostic panels for early detection of BM in patients with lung cancer. Moreover, we present an overview of LCBM molecular mechanisms, cancer driver genes, and ncRNAs which may predict the risk of BM in lung cancer patients. Recent clinical studies have focused on determining mechanisms involved in LCBM and their association with diagnosis, prognosis, and treatment outcomes. These studies have shown that alterations in EGFR, KRAS, BRAF, and ALK, as the most frequent coding gene alterations, and dysregulation of ncRNAs such as miR-423, miR-330-3p, miR-145, piR-651, and MALAT1 can be considered as potential biomarkers of LCBM.

Key Epigenetic Events Involved in the Maintenance of Breast Cancer Stem Cells

BACKGROUND

Cancer stem cells (CSCs) are a small subpopulation of cells within tumors and play significant roles in tumorigenesis, metastasis, resistance to treatment, and relapse. They are defined by self-renewal and multi-lineage differentiation, and aggressiveness. Epigenetic modifications, including DNA methylation and acetylation, histone modifications, and non-coding. RNAs (ncRNAs), are partly responsible for CSC potentials and are involved in the modification of key components of crucial pathways such as Notch and Wnt signaling in breast cancer.

OBJECTIVE

In this review, we present an overview of the pathways and epigenetic events that lead to the transformation of mammary gland stem cells to breast CSCs (BCSCs). Based on the data presented here, important pathways such as TGF-β/SMAD2 and Wnt/β-catenin and epigenetic modifications, including histone modifications, DNA methylations, and microRNAs, play important roles in BCSC formation and maintenance.

CONCLUSION

Epigenetic events can alter the expression of genes and functional RNAs, resulting in tumor initiation and progression. Thus, a better understanding of epigenetic modifications involved in BCSC maintenance signaling pathways may help to eliminate or suppress BCSCs and overcome cancer by generating more effective and efficient therapeutic agents.

Pre-treatment allergen-specific IgE analysis and outcomes of allergen immunotherapy

Summary

Background. Patients show varied results to allergen immunotherapy (AIT. The reason for this variability is unclear. Objective. To describe the relationship between AIT efficacy and demographic characteristics, as well as pre-treatment plasma levels of specific IgE-antibodies to grass and birch pollen. Methods. A retrospective study was performed based on medical records of 128 patients who received AIT. The patients completed a questionnaire and pre-AIT plasma levels of allergen-specific IgE to grass and birch pollen were measured using EUROLINE DPA-Dx pollen 1 method. Results. Seventy percent of patients classified their allergic symptoms as less severe after AIT. Twenty-seven percent had received AIT targeting only grass pollen, 19% targeting only birch pollen, and 55% targeting both grass and birch. A total of 35 different IgE profiles were found across our study population. On comparison of the demographic characteristics and concentration of allergen-specific IgE-antibodies, no statistically significant differences could be found.Conclusions. The majority of patients rated their allergic symptoms as less severe after AIT. No clear relationship could be demonstrated between pre-treatment allergen-specific IgE concentration, or demographic characteristics, and effect of AIT. There may be other factors underlying the different responses to AIT.

Anti-Cancer Effect of Melatonin via Downregulation of Delta-like Ligand 4 in Estrogen-Responsive Breast Cancer Cells

BACKGROUND

The Notch signaling pathway has a key role in angiogenesis and Delta - Like Ligand 4 (DLL4) is one of the main ligands of Notch involved in cell proliferation in sprouting vessels.

OBJECTIVE

In this study, we aimed to evaluate the expression of DLL4 in primary breast tumors and to examine the effect of melatonin on DLL4 expression in vitro.

METHODS

Eighty-five breast tumor and paired adjacent non-tumor tissue samples were collected. Apoptosis assay was performed on breast cancer cells to evaluate melatonin effects. Western blot and quantitative RT-PCR were used to measure DLL4 expression. Then, we investigated the effect of melatonin on the expression of DLL4 in four breast cancer cell lines at RNA and protein levels. We also performed a probabilistic neural network analysis to study genes closely associated with DLL4 expression.

RESULTS

Our results showed a significantly higher expression of DLL4 in tumor tissues compared to non-tumor tissues (P = 0.027). Melatonin treatment substantially attenuated DLL4 expression in BT474 and MCF-7 cells, but not in SK-BR-3 and MDA-MB-231 cells. Also, melatonin induced apoptosis in all four cell lines. Network analysis revealed a set of 15 genes that had close association and interaction with DLL4. DLL4 was overexpressed in breast cancer tissues as compared to the non-tumor tissues.

CONCLUSION

It can be concluded that melatonin treatment attenuated DLL4 expression only in estrogen- responsive breast cancer cells and is able to induce apoptosis in breast cancer cells.

An All-In-One Transcriptome-Based Assay to Identify Therapy-Guiding Genomic Aberrations in Nonsmall Cell Lung Cancer Patients

The number of genomic aberrations known to be relevant in making therapeutic decisions for non-small cell lung cancer patients has increased in the past decade. Multiple molecular tests are required to reliably establish the presence of these aberrations, which is challenging because available tissue specimens are generally small. To optimize diagnostic testing, we developed a transcriptome-based next-generation sequencing (NGS) assay based on single primed enrichment technology. We interrogated 11 cell lines, two patient-derived frozen biopsies, nine pleural effusion, and 29 formalin-fixed paraffin-embedded (FFPE) samples. All clinical samples were selected based on previously identified mutations at the DNA level in EGFR, KRAS, ALK, PIK3CA, BRAF, AKT1, MET, NRAS, or ROS1 at the DNA level, or fusion genes at the chromosome level, or by aberrant protein expression of ALK, ROS1, RET, and NTRK1. A successful analysis is dependent on the number of unique reads and the RNA quality, as indicated by the DV200 value. In 27 out of 51 samples with >50 K unique reads and a DV200 >30, all 19 single nucleotide variants (SNVs)/small insertions and deletions (INDELs), three MET exon 14 skipping events, and 13 fusion gene transcripts were detected at the RNA level, giving a test accuracy of 100%. In summary, this lung-cancer-specific all-in-one transcriptome-based assay for the simultaneous detection of mutations and fusion genes is highly sensitive.

Transcriptional activation of cyclin D1 via HER2/HER3 contributes to EGFR-TKI resistance in lung cancer

Several different mechanisms are implicated in the resistance of lung cancer cells to epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs), and only few have been functionally investigated. Here, using genetically knocked out EGFR and TKI-resistant lung cancer cells, we show that loss of wild-type EGFR attenuates cell proliferation, migration and 3D-spheroid formation, whereas loss of mutant EGFR or resistance to TKIs reinforces those processes. Consistently, disruption of wild-type EGFR leads to suppression of HER2/HER3, while mutant EGFR ablation or resistance to TKIs increases HER2/HER3 expression, compensating for EGFR loss. Furthermore, HER2/HER3 nuclear translocation mediates overexpression of cyclin D1, leading to tumor cell survival and drug resistance. Cyclin D1/CDK4/6 inhibition resensitizes erlotinib-resistant (ER) cells to erlotinib. Analysis of cyclin D1 expression in patients with non-small cell lung carcinoma (NSCLC) showed that its expression is negatively associated with overall survival and disease-free survival. Our results provide biological and mechanistic insights into targeting EGFR and TKI resistance.

CRISPR/Cas9 for overcoming drug resistance in solid tumors

OBJECTIVES

In this review, we focus on the application of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated nuclease 9 (Cas9), as a powerful genome editing system, in the identification of resistance mechanisms and in overcoming drug resistance in the most frequent solid tumors.

DATA ACQUISITION

Data were collected by conducting systematic searching of scientific English literature using specific keywords such as "cancer", "CRISPR" and related combinations.

RESULTS

The review findings revealed the importance of CRISPR/Cas9 system in understanding drug resistance mechanisms and identification of resistance-related genes such as PBRM1, SLFN11 and ATPE1 in different cancers. We also provided an overview of genes, including RSF1, CDK5, and SGOL1, whose disruption can synergize with the currently available drugs such as paclitaxel and sorafenib.

CONCLUSION

The data suggest CRISPR/Cas9 system as a useful tool in elucidating the molecular basis of drug resistance and improving clinical outcomes. Graphical abstract The mechanisms of CRISPR/Cas9-mediated genome editing and double-strand breaks (DSBs) repair.

Natural History of Perianal Fistulising Lesions in Patients With Elderly-onset Crohn's Disease: A Population-based Study

INTRODUCTION

Most studies of elderly-onset Crohn's disease [CD; diagnosed in patients aged 60 or over] have described a mild course. However, data on the natural history of perianal fistulising CD [pfCD] in this population are scarce. In a population-based cohort study, we described the prevalence, natural history, and treatment of pfCD in patients with elderly-onset CD vs patients with paediatric-onset CD.

METHOD

All patients diagnosed with CD at or after the age of 60 between 1988 and 2006, were included [n = 372]. Logistic regression, Cox models, and a nested case-control method were used to identify factors associated with pfCD.

RESULTS

A total of 34 elderly patients [9% of the 372] had pfCD at diagnosis. After a median follow-up of 6 years (interquartile range [IQR]: 3; 10), 59 patients [16%] had pfCD; the same prevalence [16%] was observed in paediatric-onset patients. At last follow-up, anal incontinence was more frequent in elderly patients with pfCD than in elderly patients without pfCD [22% vs 4%, respectively; p < 10-4]. Rectal CD at diagnosis was associated with pfCD: hazard ratio (95% confidence interval [CI] = 2.8 [1.6-5.0]). Although 37% of the patients received immunosuppressants and 17% received anti-tumour necrosis factor agents, 24% [14 out of 59] had a definitive stoma at last follow-up.

CONCLUSION

During the first 6 years of disease, the prevalence of pfCD was similar in elderly and paediatric patients. Rectal involvement was associated with the appearance of pfCD in elderly-onset patients. Around a quarter of patients with elderly-onset CD will have a stoma. Our results suggest that treatment with biologics should be evaluated in these patients.

CRISPR-mediated ablation of overexpressed EGFR in combination with sunitinib significantly suppresses renal cell carcinoma proliferation

Receptor tyrosine kinases, such as VEGFR, PDGFR and EGFR, play important roles in renal cancer. In this study, we investigated EGFR knockout as a therapeutic approach in renal cell carcinoma (RCC). We showed that a renal cell carcinoma cell line (RC21) has higher expression of EGFR as compared to other frequently used cell lines such as HEK293, A549, Hela and DLD1. Ablation of EGFR by CRISPR/Cas9 significantly restrained tumor cell growth and activated the MAPK (pERK1/2) pathway. The VEGFR and PDGFR inhibitor, sunitinib, attenuated the expression of MAPK (pERK1/2) and pAKT induced by EGFR loss and further inhibited EGFR-/- cell proliferation. We showed that loss of EGFR eventually leads to resistance to SAHA and cisplatin. Furthermore, EGFR loss induced G2/M phase arrest and resulted in an increased resistance to TNF-related apoptosis-inducing ligand (TRAIL) in renal cell carcinoma. Thus, ablation of overexpressed EGFR by CRISPR/Cas9 alone or in combination with sunitinib may be a new treatment option for renal cell carcinoma.

Effects of lake water level fluctuation due to drought and extreme winter precipitation on mixing and water quality of an alpine lake, Case Study: Lake Arrowhead, California

Lake Arrowhead, an oligotrophic alpine lake in southern California, experienced a drought period from summer 2012 to winter 2018 followed by a season of intense storms in winter 2019 resulting in lake flooding. This study investigates the effects of seasonal variations combined with 3.5 m water level fluctuation from May 2018 to April 2019, on water quality and hydrodynamics of Lake Arrowhead. In-situ measured meteorological data and water quality profiles in five different bays were used to develop and calibrate a three-dimensional lake hydrodynamic model. The mean relative errors between simulated and measured temperature and salinity profiles were 6.1% and 4.2%, respectively. Root mean square errors between the measured and simulated water temperatures were slightly larger during the stratified period. However, no specific pattern was observed in error analysis of salinity simulations. Strong thermal stratification during summer and early-fall resulted in hypoxic hypolimnetic waters with dissolved oxygen (DO) concentrations of <1 mg L^-1. Turbulent kinetic energy (TKE) generated by convective motions in the water column due to surface heat loss was typically more than two times greater than the wind-induced mixing energy during the stratification period. The lake experienced an energetic turbulent mixing regime with TKE fluxes >1.5 m^-3 s^-3, and Lake numbers <0.1 during the winter cooling period, resulting in a complete water column turnover and resuspension of bottom sediments. Entrainment of the hypoxic hypolimnion layers and sediment resuspension resulted in decreased DO and pH in the water column from December 2018 through mid-January 2019. Comparisons of Wedderburn and Lake numbers during different stratification conditions indicated the same trends in the strong stratification period (square of buoyancy frequency >10^-4 s^-2). However, in other conditions, the Lake number, considering the lake bathymetry and density profile, could better reflect vertical mixing conditions.

Policy Analysis Of Iranian Pharmaceutical Sector; A Qualitative Study

Introduction

Improving public health through providing affordable and accessible pharmaceuticals is among the concerns of governments worldwide. This study aimed to analyze Iran’s pharmaceutical sector policies in order to identify the challenges and suggest some strategic solutions to overcome such challenges.

Methods

Top managers (15), middle managers (10), and operational managers (5) working in the Food and Drug Administration of Iranian Ministry of Health along with community pharmacists (5) participated in a qualitative study using semi-structured in-depth interviews. Data were recorded, transcribed, and then analyzed via MAXQDA 10 software.

Results

Policies for national pharmaceutical sector were divided into four groups of “research & development”, “import & export”, “pharmaceutical procurement”, and “pharmaceutical supply and distribution”. Then, the challenges faced by each sector were extracted. Considering the challenges, some policy options were recommended for growth and development of national pharmaceutical sector.

Conclusion

Iran’s pharmaceutical sector has managerial and administrative differences compared with overseas pharmaceutical sectors. These differences are the main reasons for the current status of Iran’s pharmaceutical sector and have put Iran behind foreign pharmaceutical sectors. Iran’s pharmaceutical sector has endured many critical periods during recent decades and has gained great experience during these stages. Therefore, it is believed that Iran’s pharmaceutical sector, with its experience and potential, is capable of producing world-level medicines.

Estimation of water quality profiles in deep lakes based on easily measurable constituents at the water surface using artificial neural networks coupled with stationary wavelet transform

This study proposes a novel framework to accurately estimate water quality profiles in deep lakes based on parameters measured at the water surface, considering Boulder Basin of Lake Mead as a case study. Hourly-measured meteorological data were used to compute heat exchange between lake and atmosphere. Heat fluxes combined with every 6-hour measured water temperature, conductivity, and dissolved oxygen (DO) profiles, from the water surface to a depth of 100 m over a 48-month period, were used to train seven different artificial neural network-based methods for estimating water quality profiles. Effects of different factors influencing lake water quality, including lake-atmosphere interactions, wind-induced mixing, thermocline depth, winter turnover, oxygen depletion and other factors were investigated in different methods. A method employing stationary wavelet transform with a depth-progressive estimation of temperature, conductivity, and DO generated the smallest average relative errors of 0.52%, 0.22%, and 0.62%, respectively in the water column over a 48-month period. Abrupt changes in temperature, conductivity, and DO profiles due to thermal stratification, winter turnover, and oxygen hypoxia increased estimation errors. The largest errors occurred near the interface between the epilimnion and metalimnion, where vertical mixing intensity significantly decreased.

Application of Dempster-Shafer theory and fuzzy analytic hierarchy process for evaluating the effects of geological formation units on groundwater quality

This study investigates the impacts of different geological units on groundwater quality of an aquifer in southern Iran. The Kriging interpolation technique with a Gaussian semivariogram model was employed to prepare groundwater maps for different water quality constituents. In the next stage, two different models based on fuzzy analytic hierarchy process (AHP) and Dempster-Shafer theory (DST) were used to evaluate the overall water quality index based on the World Health Organization's drinking water standard in different parts of the aquifer. The DST model was able to generate water quality maps with 99.5%, 99%, and 95% confidence levels. The water quality maps were subsequently compared with the geology map of the area to determine the effects of different soil types on the water quality of the aquifer. Both methods showed poor water quality indices in the areas with an Asmari formation containing elevated levels of chloride and sodium ions. Comparison of water quality maps generated by the fuzzy-AHP and DST model revealed that the DST could more reliably handle the uncertainty in the water quality data, and thus was able to generate more accurate water quality maps. Increasing the confidence level in the DST model yielded water quality maps with a decreased overall water quality index. Results of this study could assist water management practices to generate water quality maps for their groundwater resources with confidence levels commensurate socio-economic importance of the region.

CX Chemokine Receptor 7 Contributes to Survival of KRAS-Mutant Non-Small Cell Lung Cancer upon Loss of Epidermal Growth Factor Receptor

KRAS-driven non-small cell lung cancer (NSCLC) patients have no effective targeted treatment. In this study, we aimed to investigate targeting epidermal growth factor receptor (EGFR) as a therapeutic approach in KRAS-driven lung cancer cells. We show that ablation of EGFR significantly suppressed tumor growth in KRAS-dependent cells and induced significantly higher expression of CX chemokine receptor 7 (CXCR7) and activation of MAPK (ERK1/2). Conversely, rescue of EGFR led to CXCR7 downregulation in EGFR^−/− cells. Dual EGFR and CXCR7 inhibition led to substantial reduction of MAPK (pERK) and synergistic inhibition of cell growth. Analysis of two additional EGFR knockout NSCLC cell lines using CRISPR/Cas9 revealed genotype dependency of CXCR7 expression. In addition, treatment of different cells with gefitinib increased CXCR7 expression in EGFR^wt but decreased it in EGFR^mut cells. CXCR7 protein expression was detected in all NSCLC patient samples, with higher levels in adenocarcinoma as compared to squamous cell lung carcinoma and healthy control cases. In conclusion, EGFR and CXCR7 have a crucial interaction in NSCLC, and dual inhibition may be a potential therapeutic option for NSCLC patients.

CRISPR/Cas9: a powerful tool for identification of new targets for cancer treatment

Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated nuclease 9 (Cas9), as a powerful genome-editing tool, has revolutionized genetic engineering. It is widely used to investigate the molecular basis of different cancer types. In this review, we present an overview of recent studies in which CRISPR/Cas9 has been used for the identification of potential molecular targets. Based on the collected data, we suggest here that CRISPR/Cas9 is an effective system to distinguish between mutant and wild-type alleles in cancer. We show that several new potential therapeutic targets, such as CD38, CXCR2, MASTL, and RBX2, as well as several noncoding (nc)RNAs have been identified using CRISPR/Cas9 technology. We also discuss the obstacles and challenges that we face for using CRISPR/Cas9 as a therapeutic.

Self-avoiding walk on a square lattice with correlated vacancies

The self-avoiding walk on the square site-diluted correlated percolation lattice is considered. The Ising model is employed to realize the spatial correlations of the metric space. As a well-accepted result, the (generalized) Flory's mean-field relation is tested to measure the effect of correlation. After exploring a perturbative Fokker-Planck-like equation, we apply an enriched Rosenbluth Monte Carlo method to study the problem. To be more precise, the winding angle analysis is also performed from which the diffusivity parameter of Schramm-Loewner evolution theory (κ) is extracted. We find that at the critical Ising (host) system, the exponents are in agreement with Flory's approximation. For the off-critical Ising system, we find also a behavior for the fractal dimension of the walker trace in terms of the correlation length of the Ising system ξ(T), i.e., D_{F}^{SAW}(T)-D_{F}^{SAW}(T_{c})∼1/sqrt[ξ(T)].

[The Confusion Assessment Method: Transcultural adaptation of a French version]

INTRODUCTION

The Confusion Assessment Method (CAM) is a validated key tool in clinical practice and research programs to diagnose delirium and assess its severity. There is no validated French version of the CAM training manual and coding guide (Inouye SK). The aim of this study was to establish a consensual French version of the CAM and its manual.

METHODS

Cross-cultural adaptation to achieve equivalence between the original version and a French adapted version of the CAM manual.

RESULTS

A rigorous process was conducted including control of cultural adequacy of the tool's components, double forward and back translations, reconciliation, expert committee review (including bilingual translators with different nationalities, a linguist, highly qualified clinicians, methodologists) and pretesting. A consensual French version of the CAM was achieved.

CONCLUSION

Implementation of the CAM French version in daily clinical practice will enable optimal diagnosis of delirium diagnosis and enhance communication between health professionals in French speaking countries. Validity and psychometric properties are being tested in a French multicenter cohort, opening up new perspectives for improved quality of care and research programs in French speaking countries.

Investigation of kinetics and absorption isotherm models for hydroponic phytoremediation of waters contaminated with sulfate

Two common wetland plants, Pampas Grass (Cortaderia selloana) and Lucky Bamboo (Dracaena sanderiana), were used in hydroponic cultivation systems for the treatment of simulated high-sulfate wastewaters. Plants in initial experiments at pH 7.0 removed sulfate more efficiently compared to the same experimental conditions at pH 6.0. Results at sulfate concentrations of 50, 200, 300, 600, 900, 1200, 1500 and 3000 mg/L during three consecutive 7-day treatment periods with 1-day rest intervals, showed decreasing trends of both removal efficiencies and uptake rates with increasing sulfate concentrations from the first to the second to the third 7-day treatment periods. Removed sulfate masses per unit dry plant mass, calculated after 23 days, showed highest removal capacity at 600 mg/L sulfate for both plants. A Langmuir-type isotherm best described sulfate uptake capacity of both plants. Kinetic studies showed that compared to pseudo first-order kinetics, pseudo-second order kinetic models slightly better described sulfate uptake rates by both plants. The Elovich kinetic model showed faster rates of attaining equilibrium at low sulfate concentrations for both plants. The dimensionless Elovich model showed that about 80% of sulfate uptake occurred during the first four days' contact time. Application of three 4-day contact times with 2-day rest intervals at high sulfate concentrations resulted in slightly higher uptakes compared to three 7-day contact times with 1-day rest intervals, indicating that pilot-plant scale treatment systems could be sized with shorter contact times and longer rest-intervals.

Dramatic Increase in Incidence of Ulcerative Colitis and Crohn's Disease (1988-2011): A Population-Based Study of French Adolescents

OBJECTIVES

Few data are available to describe the changes in incidence of pediatric-onset inflammatory bowel disease (IBD). The aim of this study was to describe changes in incidence and phenotypic presentation of pediatric-onset IBD in northern France during a 24-year period.

METHODS

Pediatric-onset IBD (<17 years) was issued from a population-based IBD study in France between 1988 and 2011. Age groups and digestive location were defined according to the Paris classification.

RESULTS

1,350 incident cases were recorded (8.3% of all IBD) including 990 Crohn's disease (CD), 326 ulcerative colitis (UC) and 34 IBD unclassified (IBDU). Median age at diagnosis was similar in CD (14.4 years (Q1=11.8-Q3=16.0)) and UC (14.0 years (11.0-16.0)) and did not change over time. There were significantly more males with CD (females/males=0.82) than UC (females/males=1.25) (P=0.0042). Median time between onset of symptoms and IBD diagnosis was consistently 3 months (1-6). Mean incidence was 4.4/10⁵ for IBD overall (3.2 for CD, 1.1 for UC and 0.1 for IBDU). From 1988-1990 to 2009-2011, a dramatic increase in incidences of both CD and UC were observed in adolescents (10-16 years): for CD from 4.2 to 9.5/10⁵ (+126%; P<0.001) and for UC, from 1.6 to 4.1/10⁵ (+156%; P<0.001). No modification in age or location at diagnosis was observed in either CD or UC.

CONCLUSIONS

In this population-based study, CD and UC incidences increased dramatically in adolescents across a 24-year span, suggesting that one or more strong environmental factors may predispose this population to IBD.

Extra-intestinal Manifestations at Diagnosis in Paediatric- and Elderly-onset Ulcerative Colitis are Associated With a More Severe Disease Outcome: A Population-based Study

BACKGROUND AND AIMS

Data on extra-intestinal manifestations [EIM] and their impact on the disease course of ulcerative colitis [UC] in population-based cohorts are scarce, particularly in paediatric- and elderly-onset UC patients. The aims of this population-based study were to assess: 1] the occurrence of EIM in paediatric- and elderly-onset UC; 2] the factors associated with EIM; and 3] their impact on long-term disease outcome.

METHODS

Paediatric-onset [< 17 years at diagnosis] and elderly-onset UC patients [> 60 years at diagnosis] from a French prospective population-based registry [EPIMAD] were included. Data on EIM and other clinical factors at diagnosis and at maximal follow-up were collected.

RESULTS

In all, 158 paediatric- and 470 elderly-onset patients were included [median age at diagnosis 14.5 and 68.8 years, median follow-up 11.2 and 6.2 years, respectively]. EIM occurred in 8.9% of childhood- and 3% of elderly-onset patients at diagnosis and in 16.7% and 2.2% of individuals during follow-up [p < 0.01], respectively. The most frequent EIM was joint involvement [15.8% of paediatric onset and 2.6% of elderly-onset]. Presence of EIM at diagnosis was associated with more severe disease course [need for immunosuppressants or biologic therapy or colectomy] in both paediatric- and elderly-onset UC (hazard ratio [HR] = 2.0, 95% confidence interval [CI]: 1.0-4.2; and HR = 2.8, 0.9-7.9, respectively). Extensive colitis was another independent risk factor in both age groups.

CONCLUSIONS

Elderly-onset UC patients had lower risk of EIM either at diagnosis or during follow-up than paediatric-onset individuals. EIM at diagnosis predicted more severe disease outcome, including need for immunosuppressive or biologic therapy or surgery, in both paediatric- and elderly-onset UC.

Face and Content Validity of the MacArthur Competence Assessment Tool for the Treatment of Iranian Patients

BACKGROUND

There is not a valid Persian tool for measuring the decision-making competency of patients. The aim of this study is to evaluate the face and content validity of the MacArthur Competence Assessment Tool for the treatment of Iranian Persian-speaking patients.

METHODS

To assess the validity of the Persian version of the tool, a self-administrated questionnaire was designed. The Lawshe method was also used for assessing each item. Content validity ratio (CVR) and content validity index (CVI) were used to assess the content validity quantitatively. According to the experts' judgment, questions with a CVR ≥0.62 and CVR <0.62 were maintainable and unmaintainable, respectively.

RESULTS

The questions were designed in a manner to achieve the desirable result (CVR ≥0.62). The CVI scale (S-CVI) and CVI (S-CVI/Ave) were 0.94 (higher than 0.79). Thus, the content validity was confirmed.

CONCLUSIONS

Since capacity assessments are usually based on physician's subjective judgment, they are likely to bias and therefore, with this suitably validated tool, we can improve judgment of physicians and health-care providers in out- and in-patient cases.

Mutation patterns in small cell and non-small cell lung cancer patients suggest a different level of heterogeneity between primary and metastatic tumors

Several studies have shown heterogeneity in lung cancer, with parallel existence of multiple subclones characterized by their own specific mutational landscape. The extent to which minor clones become dominant in distinct metastasis is not clear. The aim of our study was to gain insight in the evolution pattern of lung cancer by investigating genomic heterogeneity between primary tumor and its distant metastases. Whole exome sequencing (WES) was performed on 24 tumor and five normal samples of two small cell lung carcinoma (SCLC) and three non-SCLC (NSCLC) patients. Validation of somatic variants in these 24 and screening of 33 additional samples was done by single primer enrichment technology. For each of the three NSCLC patients, about half of the mutations were shared between all tumor samples, whereas for SCLC patients, this percentage was around 95. Independent validation of the non-ubiquitous mutations confirmed the WES data for the vast majority of the variants. Phylogenetic trees indicated more distance between the tumor samples of the NSCLC patients as compared to the SCLC patients. Analysis of 30 independent DNA samples of 16 biopsies used for WES revealed a low degree of intra-tumor heterogeneity of the selected sets of mutations. In the primary tumors of all five patients, variable percentages (19-67%) of the seemingly metastases-specific mutations were present albeit at low read frequencies. Patients with advanced NSCLC have a high percentage of non-ubiquitous mutations indicative of branched evolution. In contrast, the low degree of heterogeneity in SCLC suggests a parallel and linear model of evolution.

Overall survival in EGFR mutated non-small-cell lung cancer patients treated with afatinib after EGFR TKI and resistant mechanisms upon disease progression

PURPOSE

To determine survival in afatinib-treated patients after treatment with first-generation EGFR tyrosine kinase inhibitors (TKIs) and to study resistance mechanisms in afatinib-resistant tumors.

METHODS

Characteristics and survival of patients treated with afatinib after resistance to erlotinib or gefitinib in two large Dutch centers were collected. Whole exome sequencing (WES) and pathway analysis was performed on available pre- and post-afatinib tumor biopsies and normal tissue.

RESULTS

A total of 38 patients were treated with afatinib. T790M mutations were identified in 22/29 (76%) pre-afatinib treatment tumor samples. No difference in median progression-free-survival (2.8 months (95% CI 2.3-3.3) and 2.7 months (95% CI 0.9-4.6), p = 0.55) and median overall-survival (8.8 months (95% CI 4.2-13.4) and 3.6 months (95% CI 2.3-5.0), p = 0.14) were observed in T790M+ patients compared to T790M- mutations. Somatic mutations in TP53, ADAMTS2, CNN2 and multiple genes in the Wnt and PI3K-AKT pathway were observed in post-afatinib tumors of six afatinib-responding and in one non-responding patient. No new EGFR mutations were found in the post-afatinib samples of the six responding patients. Further analyses of post-afatinib progressive tumors revealed 28 resistant specific mutations in six genes (HLA-DRB1, AQP7, FAM198A, SEC31A, CNTLN, and ESX1) in three afatinib responding patients. No known EGFR-TKI resistant-associated copy number gains were acquired in the post-afatinib samples.

CONCLUSION

No differences in survival were observed in patients with EGFR-T790M treated with afatinib compared to those without T790M. Tumors from patients who had progressive disease during afatinib treatment were enriched for mutations in genes involved in Wnt and PI3K-AKT pathways.

Life Expectancy and its Socioeconomic Determinants in Iran

INTRODUCTION

Life expectancy at birth (LEB) is closely associated with the degree of economic and social development in developed and developing countries. This study aimed to examine the socioeconomic factors affecting LEB in Iran from 1985 to 2013.

METHODS

Time series analysis was used to examine the effects of key explanatory factors (GDP per capita, number of doctors per 10,000 population, degree of urbanization, food availability, CO2 emission, total fertility rate, inflation rate, and literacy rate) on LEB in Iran from 1985 to 2013. Study data were retrieved from the Central Bank of Iran (CBI), Iranian Statistical Center (ISC), and World Bank. Augmented Dickey Fuller (ADF) and Banergy, Dolado, and Master (BDM) tests, Engle Granger approach, and an ordinary least-square (OLS) model were used to achieve the aim of the study. Data analysis was performed by Stata V.12 software.

RESULTS

Our findings indicated that GDP per capita (p=0.003), number of doctors per 10,000 population (p=0.036), literacy rate (p=0.0001), and food availability (p=0.0001) have a positive and significant statistically effect on LEB. The relationship between total fertility rate and LEB was negative and significant (p=0.023). In addition, the effect of degree urbanization (p=0.811), CO2 emission (p=0.185), and inflation rate (p=0.579) on LEB were not significant.

CONCLUSION

GDP per capita, number of doctors per 10,000 population, food availability, literacy rate, and total fertility were identified as the main factors affecting life expectancy in Iran. The study, however, suggests that life expectancy in Iran could be improved if attention is given to factors that reside outside of the health sector.

Cross-Cultural Adaptations of the MacArthur Competence Assessment Tool for Treatment in Iran

Background

According to general ethical and legal principles, valid consent must be obtained before starting any procedure.

Objectives

Due to the lack of a standard tool for assessing patients’ capacity to consent to medical treatment in Iran, the present study was carried out aiming to devise a Persian version of a cross-cultural adaptation of the MacArthur competence assessment tool.

Patients and Methods

By reviewing different methods of cultural translation and adaptation for assessment tools, and due to the lack of consensus on its processes, we selected Wild’s model as one of the most comprehensive methods in this regard. Wild’s (2005) 10-stage model includes preparation, forward translation, reconciliation of the forward translation, back translation of reconciliation, back translation review, cognitive debriefing and cognitive review, and finalization, proofreading and final reporting. Using this model, we translated the MacArthur assessment tool and made it adaptable to Iranian patients.

Results

The MacArthur assessment tool is not dependent on any specific culture and language. As a result, if translation and its scientific adaptation are done based on an integrated and detailed model, the tool can be used for every culture and language. In other words, this tool is not culture-specific; so, it is applicable in cases where a translation is needed, and it can be culturally adapted to suit different societies.

Conclusions

In the present study, we are able to focus on and prove the efficacy and benefits of this measurement tool.

Genomic Aberrations in Crizotinib Resistant Lung Adenocarcinoma Samples Identified by Transcriptome Sequencing

ALK-break positive non-small cell lung cancer (NSCLC) patients initially respond to crizotinib, but resistance occurs inevitably. In this study we aimed to identify fusion genes in crizotinib resistant tumor samples. Re-biopsies of three patients were subjected to paired-end RNA sequencing to identify fusion genes using deFuse and EricScript. The IGV browser was used to determine presence of known resistance-associated mutations. Sanger sequencing was used to validate fusion genes and digital droplet PCR to validate mutations. ALK fusion genes were detected in all three patients with EML4 being the fusion partner. One patient had no additional fusion genes. Another patient had one additional fusion gene, but without a predicted open reading frame (ORF). The third patient had three additional fusion genes, of which two were derived from the same chromosomal region as the EML4-ALK. A predicted ORF was identified only in the CLIP4-VSNL1 fusion product. The fusion genes validated in the post-treatment sample were also present in the biopsy before crizotinib. ALK mutations (p.C1156Y and p.G1269A) detected in the re-biopsies of two patients, were not detected in pre-treatment biopsies. In conclusion, fusion genes identified in our study are unlikely to be involved in crizotinib resistance based on presence in pre-treatment biopsies. The detection of ALK mutations in post-treatment tumor samples of two patients underlines their role in crizotinib resistance.

Chronic Obstructive Pulmonary Disease Is Not Associated with KRAS Mutations in Non-Small Cell Lung Cancer

Mutations in epithelial growth factor receptor (EGFR), as well as in the EGFR downstream target KRAS are frequently observed in non-small cell lung cancer (NSCLC). Chronic obstructive pulmonary disease (COPD), an independent risk factor for developing NSCLC, is associated with an increased activation of EGFR. In this study we determined presence of EGFR and KRAS hotspot mutations in 325 consecutive NSCLC patients subjected to EGFR and KRAS mutation analysis in the diagnostic setting and for whom the pulmonary function has been determined at time of NSCLC diagnosis. Information about age at diagnosis, sex, smoking status, forced vital capacity (FVC) and forced expiratory volume in 1 sec (FEV₁) was collected. Chronic obstructive pulmonary disease(COPD) was defined according to 2013 GOLD criteria. Chi-Square, student t-test and multivariate logistic regression were used to analyze the data. A total of 325 NSCLC patients were included, 193 with COPD and 132 without COPD. COPD was not associated with presence of KRAS hotspot mutations, while EGFR mutations were significantly higher in non-COPD NSCLC patients. Both female gender (HR 2.61; 95% CI: 1.56–4.39; p<0.001) and smoking (HR 4.10; 95% CI: 1.14–14.79; p = 0.03) were associated with KRAS mutational status. In contrast, only smoking (HR 0.11; 95% CI: 0.04–0.32; p<0.001) was inversely associated with EGFR mutational status. Smoking related G>T and G>C transversions were significantly more frequent in females (86.2%) than in males (61.5%) (p = 0.008). The exon 19del mutation was more frequent in non-smokers (90%) compared to current or past smokers (36.8%). In conclusion, KRAS mutations are more common in females and smokers, but are not associated with COPD-status in NSCLC patients. EGFR mutations are more common in non-smoking NSCLC patients.

Abstract 4757: Whole exome sequencing reveals a distinct mutation pattern in metastatic small cell lung cancer compared to non-small cell lung cancer

Purpose: Lung cancer is divided into two main groups, small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC), the latter subdivided in squamous, large cell and adenocarcinoma. Many studies have shown intra-tumor heterogeneity in lung cancer with multiple minor clones characterized by their own specific mutational landscape. These minor clones can become predominant under selective pressure caused by therapy. Aim of our study is to investigate the relation between primary lung cancer and multiple distant metastases using whole exome sequencing.

Materials and methods: Normal tissue, primary lung tumor, and multiple metastases were obtained from 2 SCLC and 3 NSCLC patients resulting in a total of 29 samples (Table 1). DNA was isolated from total, macro-dissected, or laser micro-dissected tissue to obtain a purity of at least 80% tumor cells. Library preparation was based on the SureSelect All Exon V5 bait (Agilent) and paired-end sequencing was done using Illumina® HiSeq2000. Genome analysis toolkit (GATK) was used to analyze data and the 1000-Genome database was used to remove single nucleotide polymorphisms.

Patients' characteristics and overview of sequenced metastases samplesSubtypeSexAge at diagnosisCOPDSmokingPack yearTime interval between diagnosis and death (days)No. of somatic mutationsMetastasesLarge cell carcinomaMale65YesYes302308446Lymph node (1x)Adrenal gland (1x)Squamous cell carcinomaMale68YesYes&gt;100111306Liver (1x)Spleen (1x)Heart (1x)AdenocarcinomaFemale51NoNo02579Liver (1x)Lymph nodes (2x)Ovary (1x)Vertebra (1x)Jejunum (1x)Small cell carcinoma-1Female79YesYes&gt;508347Liver (1x)Adrenal gland (1x)Small cell carcinoma-2Female58YesYes406260Liver (1x)Lymph nodes (4x)

Results: In four patients more than 70% of the observed variants were true somatic mutations. In the adenocarcinoma patient, only 32% of the variants were called as true somatic mutations. After excluding personal variants, 79 to 446 true somatic mutations were observed in any of the tumor samples of the five lung cancer patients (Table 1). Comparison of the mutations observed in the primary and metastatic samples revealed that around 50% of the mutations were shared between all tumor samples of the three NSCLC patients, whereas more than 95% of mutations were shared in all samples of the two SCLC patients.

Conclusion: We found a high percentage of metastasis specific mutations in NSCLC patients. In contrast, SCLC patients show a limited number of metastasis specific mutations, consistent with the aggressiveness of these tumor and the very poor prognosis.

Citation Format: Ali Saber, Klaas Kok, Martijn M. Terpstra, Wim Timens, Sijmen Aukema, T. Jeroen Hiltermann, Harry J. M. Groen, Anke van den Berg. Whole exome sequencing reveals a distinct mutation pattern in metastatic small cell lung cancer compared to non-small cell lung cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4757. doi:10.1158/1538-7445.AM2015-4757

Laparoscopic elective cholecystectomy with and without drain: A controlled randomised trial

BACKGROUND:

Laparoscopic cholecystectomy is the main method of treatment of symptomatic gallstones. Routine drainage after laparoscopic cholecystectomy is an issue of considerable debate. Therefore, a controlled randomised trial was designed to assess the value of drains in elective laparoscopic cholecystectomy.

MATERIALS AND METHODS:

During a two-year period (From April 2008 to January 2010), 80 patients were simply randomised to have a drain placed (group A), an 8-mm pentose tube drain was retained below the liver bed, whereas 80 patients were randomised not to have a drain (group B) placed in the subhepatic space. End points of this trial were to detect any differences in morbidity, postoperative pain, wound infection and hospital stay between the two groups.

RESULTS:

There was no mortality in either group and no statistically significant difference in postoperative pain, nausea and vomiting, wound infection or abdominal collection between the two groups. However, hospital stay was longer in the drain group than in group without drain and it is appearing that the use of drain delays hospital discharge.

CONCLUSION:

The routine use of a drain in non-complicated laparoscopic cholecystectomy has nothing to offer; in contrast, it is associated with longer hospital stay.