Early Stage Research Articles

The Impact of QRIS Policy on the Development of Micro Businesses in Medan City, Indonesia

This study analyzes the impact of the QRIS policy in the early stages of implementation on financial performance and expansion of the market share of micro-businesses in Medan City. Financial performance is observed through changes in turnover and net profit; meanwhile, market share is determined based on changes in the number of new customers before and after the implementation of the QRIS policy. This study employs the Difference in Differences (DiD) method. The type of data used is primary data. Purposive and random sampling was utilized with 50 samples of micro businesses for the treatment group and 50 for the control group. The time difference was found between before and after the implementation of the QRIS policy. The results of this study show that the QRIS policy has a positive and significant effect on the increase in new consumers. On the other hand, the QRIS policy has no significant impact on the net profit and turnover of micro businesses. The COVID-19 pandemic has significantly and negatively impacted micro-enterprises, sharply declining revenue and net profit. However, based on the magnitude of the decline, the control group experienced a relatively greater turnover and net profit decline than the treatment group. The implication of this study is the need for efforts to increase micro-entrepreneurs understanding of the importance of faster adaptation to advances in digital technology, one of which is adjustments to a more flexible payment system so that consumers can get a wider choice of payment schemes. In addition, payment system authorities should address various obstacles in using the system and provide more massive socialization of the products offered.

Impact of changes in root biomass on the occurrence of internal browning in radish root

The purpose of this study was to investigate the effects of root biomass during the later stage of growth on fatty acid composition and lipid peroxidation, and to clarify the physiological mechanisms by which these differences affect internal browning (IB) development in radish roots. Therefore, we controlled the enlargement of roots by changing the thinning period and generated plots composed of roots with different biomass in the latter half of growth. The earlier the radish seedlings were thinned, the more vigorous the root growth from an earlier stage was achieved. Earlier thinning caused IB from the early stage of root maturation, and IB severity progressed with subsequent age progression; however, IB damage did not occur when root size during the later growth stage was kept small by later thinning. Higher levels of hydrogen peroxide, peroxidase activity, NADPH-dependent reactive oxygen species (ROS) burst-related genes, and carbonyl compounds were detected in earlier-thinned large-sized roots compared to later-thinned small-sized ones. Compared with the latter small-sized roots, the former large-sized roots had a lower ratio of linoleic acid (18:2) and a higher ratio of α-linolenic acid (α-18:3). Furthermore, in earlier-thinned large-sized roots, higher levels of phospholipase- and/or lipoxygenase-related genes were detected compared to later-thinned small-sized ones. These facts suggest the possibility that root biomass in the later stage of growth affects the desaturation of membrane fatty acids, ROS concentration, and activity of fatty acid degrading enzymes, and controls the occurrence of IB injury through membrane oxidative degradation.

Lakeshore areas of conservation interest: Characteristics of nursery areas of the threatened lake‐dwelling grayling, Thymallus thymallus

AbstractResearch‐based knowledge is essential for effective conservation and restoration of threatened aquatic species and habitats. Here, our aim was to gather this knowledge on the lake‐dwelling grayling (Thymallus thymallus), typically a riverine fish. Such atypical populations are particularly vulnerable to anthropogenic impacts, including fishing pressure, climate change, eutrophication and waterway construction, some of which affect especially the early life stages. However, there is little information available to guide management and conservation of grayling in lakes. Accordingly, we assessed characteristics of the nursery areas in the threatened grayling population of Lake Puruvesi (eastern Finland). In particular, we used beach seines in two consecutive years to sample lakeshore sites (including islands) that were a priori presumed suitable for grayling. We assessed the occurrence of grayling fry (larvae and post‐larvae <40 mm in length) regarding depth, year, the site's exposure (fetch), bottom shear stress, substrate coarseness and shoreline's north–south orientation. Overall, we found grayling fry in low numbers at every fourth site, with the sites’ exposure and dominant substrate coarseness being most relevant variables. In particular, more exposed sites (i.e. with higher fetch values) and fine‐grained substrates dominated by sand or gravel had more grayling fry. Average depth, bottom shear stress or shoreline orientation along the north–south axis did not have a significant effect. Together, the results suggest that the most important nursery areas for lake‐dwelling grayling are lakeshore zones that are barren and exposed. Hence, the sites share characteristics with those used for reproduction by the more common riverine grayling. We hope that these findings will facilitate lake‐dwelling grayling's management and conservation efforts.

Abstract 7288: Evaluation of silica spin-column and bead formats for rapid promoter DNA methylation analysis by qMSP in clinical and point-of-care settings

Abstract Late-stage cancers often lack effective management and treatment options, emphasizing the importance of early diagnosis for better prognosis and lower mortality rates. Molecular markers, such as DNA methylation tests, have shown promise in predicting and detecting cancer at its earliest stages. The COVID-19 post-pandemic scenario is providing a one in one-hundred-year opportunity of utilizing the excess installed PCR capacity world-wide to develop novel Quantitative Methylation Specific PCR (qMSP) screening strategies for cervical cancer screening in low-resource settings. This study aimed to compare the use of commercial bisulfite conversion kits in cervical epithelium liquid cytology samples (liquid cytology) from cancer screening clinics in the United States. Commercially available rapid bisulfite conversion protocols using silica spin column and magnetic beads were compared with conventional DNA extraction followed by bisulfite conversion protocols to profile DNA methylation by qMSP in a panel of methylated genes we previously developed to distinguish normal and cervical cancer patient samples. The results revealed that small sample volumes are suitable for methylation studies. Comparisons among four spin-column kits showed no significant differences in β-actin Cycle Threshold (Cts) values between Abcam, Epigentek, QIAGEN and Zymo D5021 kits. Zymo The best performing spin-column kit was compared with manual and automated versions of magnetic bead kits using a 96-well plate format for higher throughput. Methylation profiling of three genes (β-actin ZNF516, and FKBP6) with manual and automated magnetic bead kits revealed that automation increases throughput without a reduction in amplification efficiency in open PCR systems. Cost analysis showed that the direct kits 96-well plate format were more affordable compared to the Gold Standard manual protocol that uses spin-columns. An optimized version of Zymo D5046 magnetic bead kit provides the fastest turnaround time with similar amplification efficiency, when compared to spin-column or other magnetic bead kits. The test cost per sample is $5.41 dollars to process 83 samples in a 96 well-plate format in less than 2 hours. Another significant finding was showing the feasibility of using as low as 12µL of liquid cytology samples for DNA methylation testing, proving that bodily fluids are a liquid biopsy alternative to plasma. Overall, this comprehensive comparison is useful in determining optimal options for efficient and cost-effective cancer DNA methylation diagnostic tests, particularly in low-resource settings. Citation Format: Fernando Zamuner, Ashley Ramos-Lopez, Amanda Garcia-Negron, Ana Purcell-Wiltz, Andrea Cortes-Ortiz, Aniris Roman, Keerthana Gosala, Eli Winkler, David Sidransky, Mariana Brait, Rafael E. Guerrero-Preston. Evaluation of silica spin-column and bead formats for rapid promoter DNA methylation analysis by qMSP in clinical and point-of-care settings [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7288.

Abstract 3774: Evaluation of FibraChek™ for non-invasive detection of hepatic fibrosis and hepatocellular carcinoma

Abstract Introduction and Objectives: The incidence of hepatocellular carcinoma (HCC) has almost tripled since the early 1980s in the United States where it is the fastest rising cause of cancer-related deaths. Advanced liver fibrosis and cirrhosis are ones of major risk factors for HCC. The recent evidence demonstrates that successfully treating the cause of early to moderate hepatic fibrosis may reverse most. For this reason, detecting hepatic fibrosis in an early stage is crucial. Liver biopsy is currently the gold standard for the assessment of hepatic fibrosis in clinical practice. Thus, there is an urgent clinical need for the development of non-invasive blood-based tests because of its ease of obtaining biological material. Previously, we developed FibraChek™, non-invasive blood-based tests. In this study, we tested the performance of FibraChek™ on detecting hepatic fibrosis and HCC in the US. Methods: The performance of FibraChek™ was evaluated in a single-institutional cohort of 14 prospectively collected subjects presenting for chronic liver disease (NAFLD/NASH) patients with hepatic fibrosis, 19 prospectively collected subjects diagnosed with HCC, and 12 prospectively collected controls from the US. The algorithm uses weighted value of the 5 biomarkers: AST, ALT, Platelet, Taurocholic Acid (TCA) & Tyrosine plus age to derive a risk score. The ability of the test to identify patients harboring hepatic fibrosis or HCC was assessed. Hepatic fibrosis status was confirmed by tissue biopsy or definitive surgery. Diagnostic performance was assessed using AUC. Results: FibraChek™ provided an AUC of 0.923 with an overall sensitivity of 93.9%, specificity of 81.8%, NPV 91.2% and PPV 81.8%. Interestingly, risk scores in HCC cohort indicated higher than those in patients with hepatic fibrosis. Thus, FibraChek™ may be also able to use for HCC detection. Conclusions: Serum levels of a biomarker panel enabled the accurate discrimination of hepatic fibrosis and controls. The FibraChek™ test can achieve the easy, efficient, and accurate detection of hepatic fibrosis and HCC in a non-invasive patient setting. Citation Format: Sunao Tanaka, Guoxiang Xie, Hideki Furuya, Wei Jia, Charles J. Rosser. Evaluation of FibraChek™ for non-invasive detection of hepatic fibrosis and hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3774.

Abstract 4166: TSPO-targeted near-infrared optical probe for early identification and localization of high-risk premalignant pancreatic lesions

Abstract Background: Pancreatic cancer is the third most prevalent cause of cancer death in the U.S. with a ~10% survival rate. Surgery represents one of the best opportunities for extending survival and potential cures. Fluorescence-guided surgery (FGS) employing near-infrared (NIR) fluorescence-based targeting agents improves resection margins, allowing removal of small lesions not visible under white light. We previously reported a targeted NIR tracer (V-1520) of translocator protein (TSPO) expression that demonstrated proof-of-principle utility in high-grade pancreatic lesions arising in Ptf1a-Cre; LSL-KrasG12D/+; Smad4flox/flox (KCS) of pancreatic cancer. The purpose of the present study is to evaluate the utility of V-1520 to identify low-grade, premalignant yet high risk lesions in KCS mice; in this scenario we attempted to model use of V-1520 to remove lesions likely to manifest as future recurrence. We compared the uptake of the tracer in these mice from weaning to adulthood to systematically evaluate the efficacy of FGS as a function of lesion grade. Experimental: The tracer, V-1520, was synthesized and KCS mice were generated as reported.1 Mice were injected with 30μg of V-1520 intravenously 24 hours before imaging. Images were acquired using the 800nm channel. KCS and WT mice were imaged as a function of from 4 to 11 weeks age. After imaging, tumor tissues and major organs were harvested for ex-vivo imaging, histopathology and Cryo-Fluorescent Tomography (CFT). Summary: We found, V-1520 prominently localized in low-grade, premalignant PanIN cystic lesions with malignancy potential, as well as pancreatic tumors with and without local invasion. In contrast, V-1520 did not accumulate in healthy pancreata of KCS or WT mice. Mice as young as 4 weeks exhibited localized accumulation of the tracer with low grade PanIN and early dysplasia. The fluorescence intensity was further enhanced in mice with higher grade disease, whereby the pathology was characterized by high-grade cyst formation, increased nuclear/cytoplasm ratio, acinar to ductal metaplasia and invasion. Low and high-grade neoplasia was characterized by high TSPO immunoreactivity, consistent with in-vivo imaging. Confocal microscopy was used to colocalize V-1520 accumulation and TSPO immunoreactivity; V-1520 was found to prominently localized to premalignant epithelia pancreatic cancer cells. CFT illustrated that the primary localization of V-1520 included the liver, kidneys, and pancreatic diseases. Conclusion: These studies suggest the utility of V-1520 to identify high-risk pancreatic lesions that could be removed with surgery. Encouragingly, the V-1520 was capable of differentiating tumors from surrounding non-tumor tissue at an early stage, which could lead to better resections and delay and/or prevent recurrence in the future. 1. Clinical Cancer Research 26(22), 15 Nov. 2020 5914-5925 Citation Format: Shilpa Sharma, Denise Hernandez, Xiaoxia Wen, Jianbo Wang, Cong-Dat Pham, Beibei Huang, Henry Charles Manning. TSPO-targeted near-infrared optical probe for early identification and localization of high-risk premalignant pancreatic lesions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4166.

Abstract 7289: PancreaAlert: Intelligent nanoengineered biosensor for pancreatic cancer

Abstract Introduction: Pancreatic cancer accounts for 3% of cancer cases and 7% of cancer deaths in the United States. It is currently in the third position with respect to cancer-related deaths, and it is expected to move to second place as of 2040. This is mainly due to its diagnosis in the later stage. If detected in the first or second stage surgery can be performed thus increasing the patient’s survival rate. The current methods of diagnosis cannot do early stage or asymptomatic detection. So, detecting cancer-specific biomarkers can aid in the prognosis. Serum protein-based biomarkers carbohydrate antigen CA242, CA19-9, and carcinoembryonic antigen CEA are specific to pancreatic cancer. Thus, in this preliminary study, we aim to develop a nanoengineered electrochemical biosensor combined with machine learning to detect pancreatic cancer-specific biomarkers CA242, CA19-9, and CEA. Methodology: Nanoengineering the biosensor: The gold working electrode of the gold- biosensor (DRP-250AT) was coated with graphene oxide nano colloidal solution and kept in UV overnight for the graphene oxide nanosheet to crosslink with the working electrode. Detection of biomarkers using an electrochemical biosensor: First, a Crosslinker (DSP) was added to ethanol cleaned biosensor to bind the analytes. Following that antibody specific to each biomarker were added to the biosensors. The addition of TBS superblock prevented non-specific binding. Then different concentrations of biomarkers were added, and the corresponding sensor was subjected to various electrochemical analyses such as electrochemical impedance spectroscopy and voltammetry. SEM-EDAX analysis: The antigen-antibody binding on the biosensor's surface was confirmed. Automation and machine learning: Python code was developed to automate the analysis process and machine learning models (support vector machine and neural network) were used to classify the concentrations into various risk levels. The sensitivity of the developed tool was high when compared with conventional methods like ELISA and confocal microscopy. Results: From the electrochemical studies we found that with increasing concentration of biomarkers, there was a trend in output parameters: capacitance, resistance, impedance and area under the curve. By analyzing this trend, the concentrations of biomarkers can be detected. Using this data as input the machine learning model (accuracy greater than 80%) classified the concentrations into risk levels (normal, low risk, and high risk). Significance: Nanoengineering with graphene oxide nanosheets enhances the sensitivity of electrochemical biosensors. Automation and machine learning models help in the analysis of large datasets produced by this sensor. Overall, this device aids in the prognosis of pancreatic cancer. Our preliminary results are encouraging but more thorough research is required to make this diagnostic tool a working application. Citation Format: Meenal Karunanidhi, Hemalatha Kanniyappan, Edith Zhan, Ruth Mathew, Yani Sun, Junyi Wu, Yan Yan, Gnanasekar Munirathinum, Mathew T. Mathew. PancreaAlert: Intelligent nanoengineered biosensor for pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7289.

Abstract 7563: Efficacy of JPI-547, novel dual PARP inhibitor, in endometrial cancer cell line

Abstract Objectives: PARP inhibitor is effective in treating DNA repair deficiency endometrial cancer. Endometrial cancer (EC) is one of the most common gynecological cancers in developed countries and its incidence is increasing, and the prognosis of patients with early stage and low-risk EC is very good, but the prognosis of progressive and recurrent EC is poor. Novel PARP inhibitor JPI-547 is a PARP and tankyrase dual inhibitor, and in cancer cells, tankyrase inhibitor plays an important role in DNA repair, telomere maintenance, and cell survival. This experiment was conducted to determine whether the reactivity of the PTEN mutant EEC was increased by using the Novel PARP inhibitor. Method: Human endometrioid endometrial cancer cell lines, Hec-1A, Hec-1B and Ishikawa were obtained. Cell viability assay for the drugs Olaparib and JPI-547 were assessed. Colonies consisting of at least 50 cells were counted. The number of dead cells was counted in five different areas of the hemocytometer, and the experiment was performed three times. The percentage of dead cells was analyzed compared to the untreated group. We confirmed the efficacy by siRNA transfection and immunofluorescence. Result: When treated with Olaparib, there was no change in cell viability in the rest of the cells except for Ishikawa cells, which are PTEN mutations. It decreased by 35.4% in Ishikawa cells, whereas when treated with JPI-547, all cell lines Hec-1A, Hec-1B, and Ishikawa cell viability decreased by 28%, 34.3%, and 48.7%, respectively. PTEN knock-down reduced cell visibility by 28% when treated with olaparib, whereas when treated with JPI-547, Hec-1A (siCont) and Hec-1A (siPTEN) decreased by 26% and 42%, respectively, in all cells regardless of whether PTEN knock-down is present. When treated with Olaparib, dead cells were identified only in PTEN knock-down cells, increasing by 22%. When treated with JPI-547, dead cells increased by 25.5% and 33% in all cells of Hec-1A (siCont) and Hec-1A (siPTEN), respectively. It was confirmed that JPI-547 can reduce cell viability regardless of the formation of Rad51 according to PTEN. Conclusion: JPI-547, a novel PARP inhibitor, showed good efficacy in PTEN mutation and PTEN-wild-type EEC cell lines than in conventional PARP inhibitor. The effect of reducing survival of ECC cell line with JPI-547 was confirmed with or without PTEN mutation. Further evaluation and in vivo experiments are needed to prove the efficacy of JPI-547 in EC. Citation Format: Shin-Wha Lee, So-Hyun Nam, Su-Bin Park. Efficacy of JPI-547, novel dual PARP inhibitor, in endometrial cancer cell line [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7563.

Intelligent Algorithms Enable Photocatalyst Design and Performance Prediction

Photocatalysts have made great contributions to the degradation of pollutants to achieve environmental purification. The traditional method of developing new photocatalysts is to design and perform a large number of experiments to continuously try to obtain efficient photocatalysts that can degrade pollutants, which is time-consuming, costly, and does not necessarily achieve the best performance of the photocatalyst. The rapid development of photocatalysis has been accelerated by the rapid development of artificial intelligence. Intelligent algorithms can be utilized to design photocatalysts and predict photocatalytic performance, resulting in a reduction in development time and the cost of new catalysts. In this paper, the intelligent algorithms for photocatalyst design and photocatalytic performance prediction are reviewed, especially the artificial neural network model and the model optimized by an intelligent algorithm. A detailed discussion is given on the advantages and disadvantages of the neural network model, as well as its application in photocatalysis optimized by intelligent algorithms. The use of intelligent algorithms in photocatalysis is challenging and long term due to the lack of suitable neural network models for predicting the photocatalytic performance of photocatalysts. The prediction of photocatalytic performance of photocatalysts can be aided by the combination of various intelligent optimization algorithms and neural network models, but it is only useful in the early stages. Intelligent algorithms can be used to design photocatalysts and predict their photocatalytic performance, which is a promising technology.

Cancer screening with multicancer detection tests: A translational science review.

Multicancer detection (MCD) tests use a single, easily obtainable biospecimen, such as blood, to screen for more than one cancer concurrently. MCD tests can potentially be used to improve early cancer detection, including cancers that currently lack effective screening methods. However, these tests have unknown and unquantified benefits and harms. MCD tests differ from conventional cancer screening tests in that the organ responsible for a positive test is unknown, and a broad diagnostic workup may be necessary to confirm the location and type of underlying cancer. Among two prospective studies involving greater than 16,000 individuals, MCD tests identified those who had some cancers without currently recommended screening tests, including pancreas, ovary, liver, uterus, small intestine, oropharyngeal, bone, thyroid, and hematologic malignancies, at early stages. Reported MCD test sensitivities range from 27% to 95% but differ by organ and are lower for early stage cancers, for which treatment toxicity would be lowest and the potential for cure might be highest. False reassurance from a negative MCD result may reduce screening adherence, risking a loss in proven public health benefits from standard-of-care screening. Prospective clinical trials are needed to address uncertainties about MCD accuracy to detect different cancers in asymptomatic individuals, whether these tests can detect cancer sufficiently early for effective treatment and mortality reduction, the degree to which these tests may contribute to cancer overdiagnosis and overtreatment, whether MCD tests work equally well across all populations, and the appropriate diagnostic evaluation and follow-up for patients with a positive test.

Design and Testing of Friction-Type Nail-Tooth-Chain-Plate Residual-Film-Picking System

Compared with the conventional horizontal conveyor-chain-type plastic-film-picking device, the longitudinal nail-tooth-chain-plate-type plastic-film-picking device developed by our team in the early stage has little tearing effect on the mulching film, and the separation effect of the plastic film and the impurity is better. With a view to further enhancing the performance of the plastic-film-picking device, this study optimized it and designed a friction-type nail-tooth-chain-plate plastic-film-picking chain that does not overload or slip and also facilitates the installation of functional components. The kinematic analysis of the picking nail teeth on the film-picking chain was carried out, and the motion equation and trajectory of the nail teeth during the operation were determined, as well as the requirements for the nail teeth to complete the mulching-film pickup. The key parameters of the plastic-film-picking system were determined by analyzing the no-leakage condition of the plastic film and the force. Moreover, the structural design and key parameters of the shovel-type film-lifting device were determined. According to the design results, a prototype was developed, and a multi-factor test of the operating parameters was carried out. The operating speed, spacing of the pickup nail teeth, depth of the film shovel into the soil, and distance between the tip of the film shovel and center of the picking drum were used as the experimental factors. The plastic-film pickup rate, impurity rate of the recovered mulching film, and traction resistance were used as the test indicators. A four-factor, five-level quadratic regression orthogonal combination experiment was conducted using the Central Composite Design (CCD). The effect of each test factor on the test index of the plastic-film-picking system was studied, the regression models were established, and the optimal parameter combination was acquired by using the multi-objective optimization method. When the working speed was 6 km/h, the pickup-nail-tooth spacing was 228.6 mm, the depth of the film-lifting shovel into the soil was 37 mm, and the distance between the tip of the film shovel and the center of the pickup drum was 130 mm, the field experiment shows that the plastic-film pickup rate was 90.12%, the impurity rate of the recovered mulching film was 8.96%, and the traction resistance was 19.905 kN. The relative errors between the test results and the predicted values of the regression models were less than 5%, indicating that the parameter optimization regression models were reliable, and the designed friction-type nail-tooth-chain-plate plastic-film-picking system met the technical requirements of agricultural-plastic-film recycling. The research results can provide a technical reference for the development of mulching-film collection machines.

Abstract 6768: Matched XPDX™derivative models as a platform for continuity across preclinical drug development

Abstract Drug discovery is a reductive process in which druglike entities are carried through increasingly complex assay formats to tease out the compounds best suited for human studies. In vivo efficacy remains the benchmark for successful preclinical drug development. Cell-based models are a mainstay in early stages but translatability of different models across platforms remains a challenge. In oncology, patient-derived xenografts (PDX) are the gold standard for animal studies because they recapitulate key features of human tumors including the cellular heterogeneity, growth patterns, and drug response of the original patient tumor. Ex vivo, PDX derivatives have the potential to harness these same traits thereby extending the utility of PDX models to earlier stages of preclinical drug development. The KIYA-Predict™ platform is a clinically validated tool for the assessment of ex vivo drug responses across a broad range of drug classes that when applied to XPDX models shows good correlation to in vivo drug responses and excellent intra-sample reproducibility over time. Working with the well-characterized XenoSTART™ XPDX model repository, Kiyatec has derived 2D cell lines and organotypic 3D-expansion cultures to complement the ex vivo predictive value of our KIYA-PREDICT™ XPDX drug response profiling (DRP) platform. The development of syngeneic models applicable to simpler, high-throughput library screening (2D formats) and lower-throughput more complex mechanistic studies (3D organotypic models) could alleviate the burden and pitfalls of extrapolating data across unrelated models. Matched sets of 2D cell lines (2D-XPDX™) and 3D organotypic (XPDXO™) cultures were established from single cell suspensions of digested, mouse-cell depleted XPDX™ tissue samples. Drug response profiling of the XPDX™ in their various ex vivo culture formats showed relative similarities across platforms. Genomic profiling of the derivates confirmed shared tissue origin and retention of genomic and phenotypic signatures to varying degrees across models. Mechanistic evaluation of 3D organotypic culture demonstrated that disease-relevant biomarkers and processes are maintained. Together these results demonstrate the feasibility of this novel drug discovery platform that avoids ambiguity imparted by discordant models. Citation Format: Melissa Millard, Aaron Carlson, Danielle Y. Nadeau, Kimberly J. Burgess, Alyssa Simonson, Armando Diaz, Michael Wick, Teresa DesRochers. Matched XPDX™derivative models as a platform for continuity across preclinical drug development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6768.

Abstract 4794: Impact of prior upper endoscopy on gastric cancer stage and survival

Abstract Background: While gastric cancer (GC) incidence in the US has decreased, 5-year survival remains at 34.5%. Early diagnosis offers curative or treatable options, yet many cases are detected at an advanced stage with poor prognosis. In high-incidence East Asian countries with established screening programs, endoscopic screening demonstrates stage shift towards early GC diagnosis and reduced GC-related mortality. Analyses of these programs have reported benefit of endoscopic screening up to 36 months prior to diagnosis. This study explores the impact of esophagogastroduodenoscopy (EGD) in this timeframe on GC stage at diagnosis and survival in an older US population. Methods: The SEER-Medicare database was queried from 2000 to 2017 for patients 68 years of age or older with histologically confirmed GC with continuous Medicare enrollment for at least 36 months prior to GC diagnosis. We excluded patients with prior cancer history and those diagnosed by autopsy or death certificate. Medicare claims files were searched for EGD claims 6-36 months prior to GC diagnosis. We excluded claims in the 6 months prior to diagnosis to avoid capturing potential diagnostic EGD. We defined the exposed group as patients with an EGD claim 6-36 months prior to GC diagnosis (Prior EGD) and the unexposed group as patients with no EGD claim in this period (No Prior EGD). Propensity score analysis balanced baseline differences for patients with and without Prior EGD using covariates sex, age and year of diagnosis, race and ethnicity, rural/urban, comorbidity, SES, and marital status. The primary outcome was in situ/local-stage GC (early) at diagnosis compared to regional/distant-stage (advanced). Secondary outcomes were 5-year overall and GC-specific survival. The adjusted odds of having in situ/local-stage GC diagnosis compared to regional/distant-stage was estimated using logistic regression, and survival analysis was done using the Kaplan-Meier method. Results: In 10,572 patients with GC (57.5% male, mean age 78.8 years), 16.4% had Prior EGD (n=1,736). Patients with Prior EGD had a significantly higher proportion of GC diagnosed in local stage compared to patients with No Prior EGD (45.7% vs. 30.2%, p < 0.001). After controlling for confounders, Prior EGD group had two-fold increased odds of GC diagnosis at early-stage compared with No Prior EGD (OR=1.99, 95% CI: 1.88-2.10). Compared with No Prior EGD, Prior EGD was associated with higher overall survival (5-year survival 32.1% vs. 22.7%, p<0.001) and GC-specific survival (5-year survival 46.0% vs. 31.1%, p<0.001), both driven by early-stage disease. Conclusions: Our analysis demonstrates that EGD up to 36 months prior to the diagnosis of GC is associated with earlier stage at diagnosis and improved overall and GC-specific survival. This study of an older population suggests that endoscopic screening may be beneficial even in a low-incidence country such as the US and warrants further study. Citation Format: Sophie Wagner, Jennifer S. Ferris, Josephine Soddano, Ji Yoon Yoon, Sheila D. Rustgi, Haley Zylberberg, Jeong Yun Yang, Yongmei Huang, Ling Chen, Chin Hur. Impact of prior upper endoscopy on gastric cancer stage and survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4794.

Abstract 6113: Racial disparity in HER2-positive breast cancer: A single cancer center registry review

Abstract Background: Racial disparity outcomes in HER2-positive breast cancer have been previously described but the literature is limited. We examined data from our cancer center registry to investigate racial disparity in HER2-positive breast cancer. Method: We retrospectively queried patients diagnosed with HER2-positive breast cancer from Houston Methodist Cancer Center registry from 2016 to 2022. Patients’ demographics, cancer staging, treatment and outcomes including recurrence and survival were recorded and analyzed. We used the distressed communities index (DCI), a composite metric of multiple socioeconomic factors based on the patient’s zip code at diagnosis, as a surrogate of socioeconomic status. Multivariable logistic regression and Cox proportional hazards analysis were used. A p value <0.05 is considered statistically significant. Results: From 2016 to 2022, 992 patients were retrieved. 58.4% (579/992) patients were White, 17.3% (172/992) black, 16.2% (161/992) Hispanic and 8.1% (80/992) Asian. Although Black and Hispanic patients lived in more distressed communities, Black and Asian patients were diagnosed with more advanced disease. There were no statistically significant differences in neoadjuvant treatment received and pathologic complete response (pCR) rate among racial groups (table 1). Patients with higher stages are more likely to receive neoadjuvant treatment (OR: 5.49 [CI: 3.61-8.49] and 5.59 [CI: 3.15-10.2] for Stage 2 and 3 respectively). ER-HER2+ subtype was the only predictor of achieving pCR (OR: 0.47, CI: 0.29-0.79). Younger age, receiving neoadjuvant treatment and earlier stages were associated with improved all-cause mortality. There were no differences in receiving neoadjuvant treatment between racial groups, DCI; race and DCI are not associated with pCR or all-cause mortality. Conclusion: Our retrospective study from a single institution revealed no significant racial disparities in the treatment and outcome of HER2-positive breast cancers. Table 1. Characteristics of HER2-positive breast cancer in different racial groups Variables Asian, N = 80 Black, N = 172 Spanish, N = 161 White, N = 579 p-value Age (at diagnosis), mean (SD) 54 (13) 54 (12) 53 (13) 57 (13) <0.001 Distressed communities index, mean (SD) 28 (28) 49 (31) 49 (31) 35 (29) <0.001 HER2 subtype 0.7 ER-HER2+ 33/80 (41%) 64/169 (38%) 55/161 (34%) 204/576 (35%) ER+HER2+ 47/80 (59%) 105/169 (62%) 106/161 (66%) 372/576 (65%) Cancer stage 0.010 0 4/80 (5.0%) 4/172 (2.3%) 8/161 (5.0%) 31/579 (5.4%) 1 34/80 (43%) 51/172 (30%) 52/161 (32%) 227/579 (39%) 2 14/80 (18%) 44/172 (26%) 49/161 (30%) 172/579 (30%) 3 12/80 (15%) 30/172 (17%) 23/161 (14%) 52/579 (9.0%) 4 13/80 (16%) 30/172 (17%) 16/161 (9.9%) 63/579 (11%) Unknown 3/80 (3.8%) 13/172 (7.6%) 13/161 (8.1%) 34/579 (5.9%) Received neoadjuvant 0.074 No 31/66 (47%) 68/136 (50%) 54/134 (40%) 263/497 (53%) Yes 35/66 (53%) 68/136 (50%) 80/134 (60%) 234/497 (47%) Complete pathological response 0.9 No 17/35 (49%) 34/70 (49%) 40/75 (53%) 111/230 (48%) Yes 18/35 (51%) 36/70 (51%) 35/75 (47%) 119/230 (52%) Mortality (all cause) 0.052 Alive 76/80 (95%) 150/172 (87%) 147/161 (91%) 540/579 (93%) Dead 4/80 (5.0%) 22/172 (13%) 14/161 (8.7%) 39/579 (6.7%) Citation Format: Alan Hodges, Cornelius Rosenbaum, Claudia Santana, Polly A. Niravath, Hanh Mai, Dharamvir Jain, Jenny C. Chang, Jiaqiong Xu, Kai Sun. Racial disparity in HER2-positive breast cancer: A single cancer center registry review [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6113.

Effective Cataract Identification System using Deep Convolution Neural Network

INTRODUCTION: The paper introduces a novel approach for the early detection of cataracts using images captured using smartphones. Cataracts are a significant global eye disease that can lead to vision impairment in individuals aged 40 and above. In this article, we proposed a deep convolution neural network (CataractsNET) trained using an open dataset available in Github which includes images collected through google searches and images generated using standard augmentation mechanism.
 OBJECTIVES: The main objective of this paper is to design and implement a lightweight network model for cataract identification that outperforms other state-of-the-art network models in terms of accuracy, precision, recall, and F1 Score.
 METHODS: The proposed neural network model comprises nine layers, guaranteeing the extraction of significant details from the input images and achieving precise classification. The dataset primarily comprises cataract images sourced from a standardized dataset that is publicly available on GitHub, with 8000 training images and 1600 testing images.
 RESULTS: The proposed CataractsNET model achieved an accuracy of 96.20%, precision of 96.1%, recall of 97.6%, and F1 score of 96.1%. These results demonstrate that the proposed method outperforms other deep learning models like ResNet50 and VGG19.
 CONCLUSION: The paper concludes that identifying cataracts in the earlier stages is crucial for effective treatment and reducing the likelihood of experiencing blindness. The widespread use of smartphones makes this approach accessible to a broad audience, allowing individuals to check for cataracts and seek timely consultation with ophthalmologists for further diagnosis.

Abstract 3762: 11,000-plex aptamer based proteomics of bladder cancer urine for the discovery of novel disease biomarkers

Abstract In search of more accurate, non-invasive biomarkers of bladder cancer (BC), a comprehensive aptamer-based screen of urine proteins was conducted using urine samples from a BC cohort, followed by systems biology analyses. Following an initial 1317-plex screen, an extended 11,000 plex aptamer-based proteomic screen is in progress. Based on the initial screen, 30 urine proteins were next ELISA validated in an independent cohort of 68 subjects, and the results are shown in Table 1. Of 21 urine proteins that discriminated BC from urology clinic controls (UC), urine D-dimer displayed the highest ROC AUC value (0.96) and sensitivity (95%) (Table 1). Furthermore, 9 urine proteins significantly discriminated more advanced BC (T1-T4) from earlier stages (Ta-Tis), with IL-8 and MMP-12 being the best performers. Urine MMP12 exhibited the highest specificity of 80% at fixed sensitivity for identifying advanced BC. Systems biology analysis implicated molecular functions related to extracellular matrix, collagen, integrin, heparin and transmembrane tyrosine kinase signaling in BC susceptibility, with HNF4A and NFKB1 emerging as key molecular regulators. STEM analysis of the dysregulated pathways implicated a functional role for the immune system, complement and interleukins in BC disease progression. Urine C2, D-dimer, and Elastase were additionally ELISA validated in a second BC cohort of Chinese ethnicity. Thus, comprehensive proteomics and independent ELISA validation have uncovered novel urine biomarkers for initial BC diagnosis and subsequent disease progression, that warrant further head to head comparison with current diagnostic tests. Citation Format: Chandra Mohan, Kamala Vanarsa, Jessica Castillo, Long Wang, Yair Lotan. 11,000-plex aptamer based proteomics of bladder cancer urine for the discovery of novel disease biomarkers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3762.

First Report of Leaf Spot of Pineapple (Ananas comosus (L.) Merr Caused by Neoscytalidium dimidiatum in Malaysia.

In June 2017, severe leaf spots symptoms were observed by growers on pineapple leaves of Josapine variety in in Alor Pongsu (5°01'60.00" N, 100°34' 59.99" E), Perak,northwest of Peninsular Malaysia. The early infection stage shows that several brown spots could be observed, which then would merge to form large brown to creamy white lesions that cover all the leaf surface. This infection finally caused the plant to die after a while. Disease observations conducted from 2018 - 2023 showed that 10-15% incidences of the disease were observed in several pineapple farms located in Johor, Kedah, and Sarawak. The aim of this study to confirm the causal pathogen of the disease by performing isolation, pathogenicity testing, and identification of the primary causal pathogen from 20 samples of infected leaves collected from Alor Pongsu. The leaf tissues between infected and healthy were cut into small pieces (0.5 cm 0.5 cm), and surface sterilized with 1% sodium hypochlorite for 30 seconds, followed by 70% ethanol for 30 seconds, and rinsed thrice with sterilized water before placing on Potato Dextrose Agar (PDA). The PDA plates were incubated at room temperature (28 ± 2℃) in natural light. After five days of incubation, the potential causal pathogen was purified using a single conidial isolation technique for morphological and molecular characterizations. All 32 isolates displayed similar phenotypes. Based on morphological observation on PDA, the colonies were initially white of aerial mycelia but gradually darkened as the culture aged. Microscopic features of the 14-day-old fungal culture showed that the mycelia were branched with 0- 1 septa, pigmented, and brown. Arthroconidia were ellipsoid to ovoid or round shaped, hyaline, with rounded apex, truncate base, and occurring singly or in chains averaging 9 ± 3 × 5 ± 2 μm (n = 20). Based on the morphological characteristics, the fungal isolates were tentatively identified as Neoscytalidium species. A representative isolate of Neoscytalidium coded as UiTMPMD2 was further identified through PCR implication of the internal transcribed spacer (ITS) region using ITS1 and ITS4 primers and BLAST homology search as Neoscytalidium dimidiatum (Penz.) Crous & Slippers based on 100% similarity (575 bp out of 575 bp) to a reference sequence (accession no. KU204558.1). The sequence was deposited in Gen Bank (accession no. OR366479) with reference sequence code of INBio:30A. Pathogenicity tests were performed on 10 whole plants of Josapine pineapple (4 months old) using a leaf inoculating method (Wu et al. 2022) in a glasshouse (25-32°C) and repeated twice. Four mature leaves per each plant were wounded at two points and inoculated with mycelium PDA plugs from 7-days-old cultures of N. dimidiatum. Control plants were wounded in the same manner but inoculated with sterilized PDA plugs. Seven days post inoculation, leaf spot symptoms were observed on treated plants with the pathogen, while the control plants remained symptomless. Pathogen was successfully reisolated from brown leaf spot symptoms in which the cultural and morphological characteristics were identical to those of the originals. Neoscytalidium dimidiatum has a wide range of hosts and it has been reported in Malaysia to cause stem canker on pitahaya (Mohd et al. 2003; Khoo et al. 2023 ) and fruit rot of guava (Ismail et al. 2021). To the best of our knowledge this is the first report of N. dimidiatum causing leaf spots on pineapples in Malaysia. This report establishes a foundation for further study ofN. dimidiatum that can effectively address the disease in pineapple.

Quantitative analysis of the spatial distance between autophagy-related membrane structures and the endoplasmic reticulum in Saccharomyces cerevisiae

ABSTRACT Macroautophagy/autophagy is the process by which cells degrade their cytoplasmic proteins or organelles in vacuoles to maintain cellular homeostasis under severe environmental conditions. In the yeast Saccharomyces cerevisiae, autophagy-related (Atg) proteins essential for autophagosome formation accumulate near the vacuole to form the dot-shaped phagophore assembly site/pre-autophagosomal structure (PAS). The PAS then generates the phagophore/isolation membrane (PG), which expands to become a closed double-membrane autophagosome. Hereinafter, we refer to the PAS, PG, and autophagosome as autophagy-related structures (ARSs). During autophagosome formation, Atg2 is responsible for tethering the ARS to the endoplasmic reticulum (ER) via ER exit sites (ERESs), and for transferring phospholipids from the ER to ARSs. Therefore, ARS and the ER are spatially close in the presence of Atg2 but are separated in its absence. Because the contact of an ARS with the ER must be established at the earliest stage of autophagosome formation, it is important to know whether the ARS is tethered to the ER. In this study, we developed a rapid and objective method to estimate tethering of the ARS to the ER by measuring the distance between the ARS and ERES under fluorescence microscopy, and found that tethering of the ARS to the ER was lost without Atg1. This method might be useful to predict the tethering activity of Atg2. Abbreviation: ARS, autophagy-related structure; Dautas, automated measurement of the distance between autophagy-related structures and ER exit sites analysis system; ERES, endoplasmic reticulum exit site; PAS, phagophore assembly site/pre-autophagosomal structure; PCR, polymerase chain reaction; PG, phagophore/isolation membrane; prApe1, precursor of vacuolar aminopeptidase I; Qautas, quantitative autophagy-related structure analysis system; SD/CA; synthetic dextrose plus casamino acid medium; WT, wild-type

Abstract 3380: HER2 overexpression induces breast tumorigenesis in a non cell autonomous manner by inducing oxidative stress in the tissue microenvironment

Abstract Breast cancer is the most common cancer type in the world. Approximately 70% of pre-malignant breast tumours, known as ductal carcinoma in situ (DCIS), and 20% of invasive breast tumours overexpress HER2. Although molecular mechanisms of HER2 function in breast tumour cells have been extensively studied, our knowledge on how HER2 drives breast tumourigenesis at its pre-malignant stage is quite limited. Here, we investigate the HER2-overexpression driven cellular events at the earliest stages of breast tumourigenesis using in vitro, in vivo and ex vivo models. Using mouse models of HER2+ breast cancer and clinical samples of patients with DCIS, we showed that breast cancer stem cells (BCSCs) reside in HER2-negative population of tumour cells and arise from a HER2-negative cell-of-origin. Proteomics and metabolomics analyses of mammary ducts isolated from the MMTV-Neu mice at the pre-cancerous stage showed that HER2/Neu overexpression alters the energy metabolism in mammary epithelial cells in vivo. Furthermore, we have observed an accumulation of reactive oxygen species levels in pre-cancerous mammary ducts, which consequently causes oxidative stress induction and DNA damage in both HER2-positive and HER2-negative epithelial cells. Collectively, our findings indicate that HER2 overexpression in normal mammary epithelia may lead to a genotoxic tissue microenvironment that may consequently result in the accumulation of further somatic mutations in HER2-negative cell populations, which contain BCSCs and their cell-of-origin. Our findings therefore illustrate a novel mechanism explaining the HER2-driven breast tumour initiation and thus provide new avenues of research for developing novel preventive approaches against breast cancer. Citation Format: Sevim Beyza Gurler, Oliver Wagstaff, Lili Dimitrova, Fuhui Chen, Robert Pedley, William Weston, Ian Donaldson, Brian A. Telfer, David Novo, Kyriaki Pavlou, George Taylor, Yaqing Ou, Kaye Williams, Andrew Gilmore, Keith Brennan, Ahmet Ucar. HER2 overexpression induces breast tumorigenesis in a non cell autonomous manner by inducing oxidative stress in the tissue microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3380.

Abstract 2295: Circulating T cell receptor repertoire analysis improves cancer early detection

Abstract Background: Cancer screening by liquid biopsy promises to detect cancer early when it can be cured. However, current liquid biopsy approaches based on circulating tumor DNA (ctDNA) detect only a minority of early-stage cancers, because these tumors shed little ctDNA and plasma sample volume is limited. For liquid biopsy to realize its potential for the early detection of cancer, sensitivity for the earliest stage disease must be improved. Methods: We set out to improve sensitivity of liquid biopsy for cancer early detection by exploiting tumor recognition by T cells through sequencing of the circulating T cell receptor repertoire. Using gDNA extracted from blood buffy coats, we studied a cohort of 451 lung cancer patients (86% with stage I disease) and 525 subjects without cancer, enriched for older individuals with a history of smoking. We performed genomic DNA TCR beta chain sequencing to yield a median of 81,088 TCR clonotypes in cancer patients and 112,588 clonotypes in non-cancer controls. We built a TCR sequence similarity nearest neighbor graph to cluster >68M distinct TCR clonotypes into TCR repertoire functional units (RFUs). The TCR frequencies of RFUs were tested for association with cancer status and significantly associated RFUs were combined using a support vector machine model into a TCR RFU cancer score. This model was evaluated by 10-fold cross-validation (CV) and compared to a ctDNA panel of 237 mutation hotspots in 154 lung cancer driver genes (IDT™) and to a panel of 17 lung cancer related protein biomarkers (Olink®) in 87 subjects. Results: We identified 177 cancer-associated TCR RFUs at FDR≤0.10, including 83 RFUs that were enriched in cancer samples with a TCR count log2-fold change between 0.05 and 1.31, and 94 that were enriched in controls with a log2-fold change between 0.07 and 0.40. We observed 56 of the 83 cancer-enriched RFUs had decreasing TCR counts with increasing age across the cohort, coupled with higher counts in cancer patients relative to age-matched controls. The TCR RFU cancer score achieved a cross-validated ROC AUC of 0.69 for cancer status prediction, with the AUC for stage I cancers similar to that of stage II-IV (0.69 vs. 0.70). 44% of stage I cancers (test samples of each CV fold) were detected by the TCR model at a specificity of 80%. We saw a substantial gain in sensitivity for stage I cancer when TCR RFUs were added to ctDNA and proteins, with a ~15-20%-point increase seen at the 90% target specificity level typical for cancer screening tests. Likewise, sensitivity increased at the 99% specificity level used in multi-cancer early detection, with 35% of stage I lung cancers detected, which could not be achieved by any analyte alone. Conclusion: We demonstrate detection of a significant fraction of early lung cancer cases from blood by analyzing the circulating TCR repertoire and show that this signal is complementary to established analytes such as proteins and ctDNA. Citation Format: Yilong Li, Michelle Nahas, Dennis Stephens, Kate Froburg, Emma Hintz, Devin Champagne, Amaneet Lochab, Markus Brown, Jesse Abhyankar, Jasper Braun, Michelle Dinh, María Antonia Fortuño, María-del-Mar Ocon, Andrea Pasquier, Inés María Luque, Christopher W. Seder, Jeffrey A. Borgia, Luis Miguel Seijo, Luis M. Montuenga, Roman Yelensky. Circulating T cell receptor repertoire analysis improves cancer early detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2295.