Value Of Amplification Research Articles

Quantification of rupture directivity effects on strong ground motion during the 8 January 2022 MS6.9 Menyuan earthquake in Qinghai, China

On 8 January 2022, an MS6.9 earthquake occurred in the Menyuan county, Qinghai province at the northeastern margin of the Tibetan Plateau. A dense observatory network consisting of accelerographs and intensity meters has obtained many acceleration recordings in this region, which previously had only a few strong motion recordings. Using acceleration data recorded by 141 accelerographs and micro-electro mechanical system (MEMS)-based intensity meters within 100 km of the causative fault, we investigated the spatial distribution and attenuation characteristics of the near-source ground motion during this event. The observed response spectra were compared with the prediction obtained using the NGA-West2 models. It was found that, in the long-period section of >1.0 s, the acceleration response spectra in the rupture forward direction (southeast of the epicenter) were greater than the prediction, while observations on the northwest side were lower than the prediction. Through the spatial distribution of the ground motion and quantitative analysis of the residuals, we found that the rupture directivity effects on the ground motions were controlled by the spatial azimuth relative to the fault and the along-strike projected length of the rupture, which mainly affected the long-period portion of the >1.0 s. In the rupture forward direction, the spectral accelerations (SAs) with periods of 1.0–10.0 s were enhanced to 1.18–1.56 times the average. In the backward direction (northwest of the epicenter), the SAs with periods of 1.0–10.0 s were only 0.63–0.86 times the average. The rupture directivity effects during the MS6.9 (MW6.6) earthquake exhibited an obvious period-dependence and narrowband characteristics, and the amplification effects were the strongest at 5.0 s. The amplification factors in the straight forward directions were underestimated by the empirical model. Two typical velocity pulse records were observed in the rupture forward direction, and their response spectra were significantly amplified at long periods of greater than 1.0 s, with peak amplification values of 4.0–6.0 near the characteristic period of the pulses. This amplification was related to the resonance excited by a specific periodic pulse. Our study provides a reference of quantifying near-source effects for both moderate and major shallow crustal earthquakes by using MEMS recordings in this region.

Seismic site classification of Nakhon Nayok City, central Thailand, using the MASW technique

Shear-wave velocity (Vs) of soils in Nakhon Nayok City, Central Thailand were determined using the Multi-Channel Analysis of Surface Wave technique. The Vs. of 35 tested sites were weighted average to 30 m depth based on the National Earthquake Hazards Reduction Program (NEHRP) criteria, which revealed NEHRP site classes C, D, and E within the study area. Soil class C was found in the north of the city. Moreover, most of the residential area of Nakhon Nayok City is positioned on soil classes D and E. The soil in the area of study has an amplification value ranging from 1.4 to 3.9. The central and southwestern parts of the city, which mainly consist of soft sediments, have a higher amplification value than that in the northern part, which mainly consists of coarse grain soils of colluvial deposits. Based on the NEHRP and amplification value, the Nakhon Nayok City area will experience some effect from ground shaking from nearby and far away earthquake seismic sources.

Comparison of earthquake acceleration amplification values based on the CPTu and geomorphology approach in the area around the Lembang Fault, Indonesia

The Lembang Fault is one of the sources of earthquakes in the Bandung Basin area, Indonesia. Located at coordinates -6.795075°, 107.463449° to -6.865538°, 107.737159° and has a segment length of approximately 29 km, this fault has a potential earthquake hazard that needs to be taken into account. Earthquake hazards originating from its source, namely bedrock, must be analyzed up to the surface. For this reason, a study of the amplification value needs to be carried out. To date, an easy method for analyzing amplification is using the Vs30 approach based on CPTu and geomorphology. This paper aims to obtain amplification values based on the CPTu (electric sondir) and geomorphological methods. This study obtained a 43% agreement, which was indicated by the similarity of the amplification value, which was close to 1. The geomorphology method showed a larger value (more than 1.6). This finding indicates that the equation is used as if it were in an area with a PGA value below 0.1g. Meanwhile, the average value of the two methods is considered relevant, close to 1 or the same as at the earthquake's epicenter. In the future, a more comprehensive method is needed to evaluate the geomorphology equation and the CPTu correlation to the Vs.

Seismic vulnerability of the Campus II Universitas Syiah Kuala

Universitas Syiah Kuala (USK) is planning to develop a new campus (Campus II). The location of the study area is relatively close to the Seulimum fault which historically has generated a devastating earthquake. Therefore, a seismic vulnerability study is important to conduct in use for reference before the development. This study aims to determine the seismic vulnerability index in the Campus II development area of USK in Mesjid Raya District, Aceh Besar Regency using a Horizontal to Vertical Spectral Ratio (HVSR) method. Potential earthquake damage can be studied by analyzing the dominant frequency (f0), amplification (A0), seismic vulnerability (Kg), and Vs 30. The microtremor acquisition was carried out by using a Broadband seismometer with 100 sps at 37 measurement points with a distance of 500 meters for each station. We use the Geopsy software to analyze seismic data by applying Fourier transform and STA/LTA concept to Rayleigh waves and obtain the dominant frequency value. The 1D velocity inversion was derived by Dinver using the Neighborhood Algorithm (NA). The results of the analysis show that the dominant frequency value is higher around the STA17 point, while the amplification value and seismic vulnerability are highest in the north (at STA2 and STA3) and in the south (at STA28, STA29, and STA30). The higher amplification region is associated soft soil identified as alluvium (Qh). On the other hand, the 1D inversion results at a depth of 30 shows Vs values of 661.142 - 1106.31 m/s (at STA3 and STA17) which indicates the presence of bedrock, making it suitable for future development although more detail investigation is required.

OPTIMIZATION OF THE SHAPE AND DIMENSIONS OF THE CONTINUOUS SECTION OF THE DISCRETE-CONTINUOUS INTER-RESONANCE VIBRATING TABLE

Energy-efficient technologies are an important aspect of the development of mechanical engineering. Therefore, the creation of highly efficient vibration technological equipment is an urgent task. There are discrete-continuous inter-resonance vibration machines that have high values of dynamic amplification of oscillations. Rectangular plates or rods are used as the reactive mass of such vibrating machines. However, the rectangular shape of the plate may not be the optimal shape for achieving maximum energy efficiency. To conduct experimental studies of alternative plates with a variable cross-section to determine the optimal shape of the reactive mass of the vibration machine. Methodology. The selection of alternative options of plates with a variable cross-section, which would satisfy the necessary conditions of fastening and the value of the natural frequency of oscillations, was carried out. Experimental studies were carried out on a sample of an inter-resonance vibrating table. The value of the power supply voltage at which loads of different masses were separated from the working body of the vibrating table for each of the plate samples was compared. Findings (results) and originality (novelty). For the first time, experimental studies of the energy efficiency of inter-resonance vibration machines with plates with a variable cross-section installed as a reactive mass were conducted. It was found that the rhomboid shape of the plate is optimal when using it as a continuous section in a vibration machine with an electromagnetic drive. It was determined that the use of diamond-shaped plates as the reactive mass of the vibrating machine can improve the energy efficiency of the inter-resonance vibrating equipment. For further analysis of plates with a variable cross-section as a reactive mass of an inter-resonance vibration machine, it is necessary to calculate and compare their lumped inertia-stiffness parameters.

Prognostic significance of CDK6 amplification in esophageal squamous cell carcinoma

Dysregulation of CDK6 plays crucial roles in the carcinogenesis of many kinds of human malignancies. However, the role of CDK6 in esophageal squamous cell carcinoma (ESCC) is not well known. We investigated the frequency and prognostic value of CDK6 amplification to improve the risk stratification in patients with ESCC. Pan-cancer analysis of CDK6 was conducted on The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx) and Gene Expression Omnibus (GEO) databases. CDK6 amplification was detected in 502 ESCC samples by Fluorescence in situ hybridization (FISH) through tissue microarrays (TMA). Pan-cancer analysis revealed that CDK6 mRNA level was much higher in multiple kinds of cancers and higher CDK6 mRNA level indicated a better prognosis in ESCC. In this study, CDK6 amplification was detected in 27.5% (138/502) of patients with ESCC. CDK6 amplification was significantly correlated with tumor size (p = 0.044). Patients with CDK6 amplification tended to have a longer disease-free survival (DFS) (p = 0.228) and overall survival (OS) (p = 0.200) compared with patients without CDK6 amplification but of no significance. When further divided into I–II and III–IV stage, CDK6 amplification was significantly associated with longer DFS and OS in III-IV stage group (DFS, p = 0.036; OS, p = 0.022) rather than in I-II stage group (DFS, p = 0.776; OS, p = 0.611). On univariate and multivariate analysis of Cox hazard model, differentiation, vessel invasion, nerve invasion, invasive depth, lymph node metastasis and clinical stage were significantly associated with DFS and OS. Moreover, invasion depth was an independent factor for ESCC prognosis. Taken together, for ESCC patients in III-IV stage, CDK6 amplification indicated a better prognosis.

Identification of soil characteristics in the Central Java Region using the HVSR (Horizontal to Vertical Spectral Ratio) inversion method

This research aims as one of the efforts to mitigate earthquake disasters by using the HVSR method based on microtremor data at 28 BMKG seismic stations in the central Java Island region to estimate the dominant frequency (f0) and amplification (A0) that describe the dynamic characteristics of the soil and analyse the shear wave velocity at a depth of 30 meters (Vs30). The dominant frequency values in the study area range from 0.648 to 18.257 Hz. The amplification values scattered in the study area ranged from 0.788 - 7.496. This research also produces dominant period parameters (T0) and seismic vulnerability (Kg). The highest seismic vulnerability values are at BUJI in Buayan, Kebumen; GBJI in Gringsing, Batang; and SBJM in Sanden, Bantul. In addition, the Vs30 value is helpful to determine how strong the building foundation resists earthquakes. Based on the Vs value in the ground profile with ellipticity curve modelling, the Vs30 value ranges from 204.756 - 903.046 m/s. The distribution of Vs30 values shows that the research points in central Java are spread by a variety of hard and very dense soil types to soft rock (SC).

Analysis Of Liquifaction Potential Using The Method Microzonation in Coastal Zone at North Aceh District

Liquefaction is a natural phenomenon that occurs when previously sandy soil turns into mush as a result of an earthquake and has the potential to become a natural disaster if not anticipated early. the coastal zone of Dewantara District is included in the earthquake-prone area (referring to the results of previous studies, the value of the seismic vulnerability index is between 0.41 to 18.3 Kg, with the potential for damage caused to be medium and high risk) because most of the area is an area that has alluvial plains a wide beach and located on a tectonic route so that it is estimated that there is a potential follow-up threat after an earthquake occurs, in the form of liquefaction. Determination of the distribution of liquefaction potential due to earthquakes is determined based on data obtained from microtremor measurements. The specific objective of this study is to provide information regarding the potential and vulnerability of liquefaction to Policy Makers/Local Governments in evaluating plotting areas and/or preparing regional spatial plans based on disaster risk reduction/mitigation aspects. Based on the results of the processed data analysis, several important conclusions can be identified in this study. The character of soil vulnerability is related to the value of dominant frequency (f0), soil amplification (A0), and seismic vulnerability index (seismic vulnerability index). This relationship can be used to formulate whether an area has the potential to experience lateral ground motion (liquefaction) which potentially can affect the coastal area of ​​Dewantara District. Based on microseismic data analysis (standard deviation), several disaster-prone zone points were obtained in the north and east of the measurement point. In detail, this is shown by the map of the distribution of SVI values ​​in the Coastal Area which is in the range of 20-100, especially in the north it is at a value above 75, which allows for a higher chance of liquefaction on the condition that there are major earthquakes accompanied by with rock pores filled with fluid.

Evaluation and comparison of the sensitivity of three commercial RT-qPCR kits used for the detection of SARS-CoV-2 in Santiago, Chile.

The COVID-19 pandemic is still in force, causing global public health challenges and threats. Although vaccination and herd immunity have proven to be the most efficient way to control the pandemic, massive and early testing of patients using the RT-qPCR technique is crucial for constant genomic surveillance. The appearance of variants of SARS-CoV-2 with new mutations can reduce the efficiency of diagnostic detection. In this sense, several commercial RT-qPCR kits have been the target of extensive analysis because low assay performance could lead to false-negative diagnoses. In this study, we evaluated the performance of three commercial RT-qPCR kits; Thermo Fisher (TaqMan 2019-nCoV Assay Kit v1), BGI and Roche (LightCycler® Multiplex RNA Virus Master) used for the diagnosis of COVID-19 throughout the pandemic in Santiago de Chile. Under our best assay conditions, we found significant differences in Cq amplification values for control and viral probes, against the same nasopharyngeal swab samples (NPSs). In addition, in some cases, the sensitivity of the RT-qPCR kits decreased against viral variants. Our study suggests evaluating the RT-qPCR kits used to detect SARS-CoV-2 because variants such as Omicron, which has several mutations, can compromise their detection and underestimate viral circulation.

Screening of strictocidine synthase and lysine decarboxylase gene involved in alkaloid biosynthesis in plants of Catharanthus rosea, Adathoda vasica and Wedelia trilobata

Alkaloids are naturally occurring nitrogenous organic compounds of plant and display vast range of pharmacological properties such as anticancer, antiviral, anti-diabetic, antioxidant and antimicrobial activities. Medicinal plants are the main source of secondary metabolites and the enzymatic pathway involved in its production may be enhanced to increase synthesis of metabolites. The strictocidine synthase (STR) and lysine decarboxylase (LDC) gene are involved in biosynthesis of monoterpenoid indole alkaloid and quinolizidine alkaloid respectively. In the present study, STR and LDC gene were analyzed in Catharanthus roseus, Adathoda vasica and Wedelia trilobata using real time PCR. The PCR results showed S shaped curve with Ct value for amplification of target gene which was found in Catharanthus roseus for STR gene and in Catharanthus roseus and Adathoda vasica for LDC gene. For further confirmation of target, gene samples were separated on agarose gel for size determination and the size of STR gene was found to be 1.1 kb and LDC gene was 1.3 kb respectively. Thus this study should be beneficial for academic as well as industrial point of view from production of alkaloids in plants by enhancing STR and LDC gene synthesis and alkaloids should also be used for isolation and characterization for pharmaceutical applications.

Study of pig dna analysis methods in cosmetics: a review

Collagen is one of the components used for cosmetics. Functionally, collagen is derived from pig fat, which functions as a skin conditioning agent (Emollient), emulsion stabilizer (Emulsifier), and as ingredient to increase the viscosity of cosmetic preparations. The method that can detect pig content is the PCR method, which can confirm the presence of DNA content in pigs. In this study, an analysis of cosmetic products containing porcine DNA was carried out using the PCR method. This research was divided into two stages: the initial stage was DNA extraction, and the second stage was PCR analysis. This research is a study through literature study using the narrative review technique. This study aimed to collect information and examine the analysis method of identifying pig DNA contained in cosmetics to obtain the right and accurate way through a literature approach. From the literature study results, it can be concluded that the best extraction method for the isolation of porcine DNA in cosmetic preparations is the extraction method with the Boom Method, while the DNA analysis used to identify porcine DNA in cosmetics is RT-PCR (Real-time Polymerase Chain Reaction). Conventional PCR is because both methods have their respective advantages. The RT-PCR (Real-time Polymerase Chain Reaction) method can amplify and quantify the number of target DNA molecules. The Conventional PCR Method can form DNA bands based on the amplification value.

GENETIC DIVERSITY OF NEPENTHES GRACILIS IN HEATH FOREST IN SOUTH AND CENTRAL PARTS OF KALIMANTAN

Nepenthes gracilis is found in the lowlands in the form of peat swamp forest, heath forests and is widely distributed in Thailand, Sumatra, Peninsular Malaysia, Singapore, Kalimantan, and Sulawesi. The unique characteristics of the plant, potential benefits and threats of declining population of N. gracilis impacted this plant as a conservation priority in the heath forest. Characterization of N. gracilis applied before implementing conservation actions. The conservation approach proceeded by analyzing the genetic diversity of N. gracilis from various types of heath forest. The research object used as genetic material was the leaf part of N. gracilis. The sampling locations of N. gracilis were in the heath forest of Guntung Ujung village, Gambut sub-district, Banjar regency, South Kalimantan (Location 1), heath forest in Tabalong Regency, South Kalimantan (Location 2), heath forest in East Kotawaringin Regency, Central Kalimantan (Location 3), heath forest of the Nyaru Menteng Arboretum, Palangkaraya, Central Kalimantan (Location 4). The tools and materials used for genetic analysis with PCR-RAPD markers are divided into several stages of work: DNA extraction, DNA quality and quantity testing, DNA visualization, and data analysis. The results show that OPP-09 and OPBH-20 were the primers with the highest amplification success for N. gracilis plants from the heath forest and the amplification values are 52.5% and 51.25%. The percentages of polymorphism bands were 97.62% and 95.24%, respectively. Disturbed heath forest with open canopy cover showed an indication of low genetic diversity shown by N. gracilis originating from location 1 and location 4 of heath forests and the highest genetic diversity value, and the highest percentage of locus polymorphism value (79%) was shown by N. gracilis location 3 with relatively undisturbed forest cover and classified as old growth. It is crucial to preserve the heath forest cover from damage to maintain high genetic diversity of N. gracilis. Genetic relationships between populations can be a barometer in conservation programs for N. gracilis.

YTHDF1 amplification is correlated with worse outcome and lower immune cell infiltrations in breast cancer.

N6-methyladenosine (m6A) is a common RNA modification on eukaryotic mRNA and some of the m6A regulatory proteins play a crucial role in breast cancer. However, the copy number variations for m6A regulatory proteins and their role in clinicopathological characteristics and survival in breast cancer remain unclear. In this study, we screened the m6A related genes alterations in breast cancer by analyzing the Molecular Taxonomy of Breast Cancer International Consortium and The Cancer Genome Atlas database, and further analyzed the clinical prognostic value of YTHDF1 amplification. The YTH domain family (YTHDF3 and YTHDF1) amplification exhibited higher alteration rates among 10 m6A regulatory genes. YTHDF1 and YTHDF3 amplification resulted in higher mRNA expression (P< 0.0001). Protein expression of YTHDF1 and YTHDF3 were higher in breast cancer (P< 0.0001). YTHDF1 amplification presented a high correlation with worse clinicopathological characteristics and overall survival in patients with breast cancer. Cox regression analysis showed that YTHDF1 amplification was an independent risk factor for 10-year overall survival in breast cancer (Hazard ratio: 1.663; 95% confidence interval: 1.298-2.131; P< 0.001). Gene set enrichment analysis revealed that the downstream target of YTHDF1 may be related to MYC signaling regulation and T cell differentiation. Moreover, YTHDF1 amplification and high expression resulted in lower immune cell infiltration. YTHDF1 knockdown retrained proliferation, migration and invasion in breast cancer cells in vitro. We found significant worse clinical characteristics and lower immune infiltrates in patients with YTHDF1 amplification. The findings indicate that YTHDF1 amplification may be a potential target for the treatment of breast cancer.

Structure design and experimental study on ultrasonic vibration–assisted induction brazing cubic boron nitride abrasive tools

Brazed superabrasive tool has been widely used in machining of difficult-to-cut materials to improve the machining efficiency and quality. However, the severe wear and associated short service life have to be faced for conventional induction brazed (CIB) abrasive tools during machining processes, owing to its weak bonding strength between abrasive grains and metal-bonded phases. In this case, the method of ultrasonic vibration–assisted induction brazing (UVAIB) was proposed to fabricate tools, through introducing ultrasonic vibration into brazing process to improve the abrasive bonding strength. Here, a novel UVAIB device was developed, and the geometric designation parameters were optimized using a finite element simulating method. In addition, the performance of UVAIB device was tested in terms of the impedance and amplitude. Subsequently, the comparative experiment trials were performed with the brazed abrasive tools under the CIB and UVAIB method. Results show that the ultrasonic energy loss of UVAIB device can be reduced, and then, the amplification value and vibration uniformity reach 8 and 92%, respectively. In addition, a large number of pores and macro-cracks inside tool’s metallic matrix for CIB can be observed, whereas the number of pores is reduced by 75%, and only fewer and smaller micro-cracks are found for UVAIB. Furthermore, compared with the grains’ intergranular fracture for CIB, UVAIB exhibits the transgranular fracture mode due to its higher bonding strength after adopting the ultrasonic vibrating method.

Estrogen Receptor Alpha Gene Amplification Is an Independent Predictor of Long-Term Outcome in Postmenopausal Patients with Endocrine-Responsive Early Breast Cancer.

Estrogen receptor (ER) expression is a prognostic parameter in breast cancer, and a prerequisite for the use of endocrine therapy. In ER+ early breast cancer, however, no receptor-associated biomarker exists that identifies patients with a particularly favorable outcome. We have investigated the value of ESR1 amplification in predicting the long-term clinical outcome in tamoxifen-treated postmenopausal women with endocrine-responsive breast cancer. 394 patients who had been randomized into the tamoxifen-only arm of the prospective randomized ABCSG-06 trial of adjuvant endocrine therapy with available formalin-fixed, paraffin-embedded tumor tissue were included in this analysis. IHC ERα expression was evaluated both locally and in a central lab using the Allred score, while ESR1 gene amplification was evaluated by FISH analysis using the ESR1/CEP6 ratio indicating focal copy number alterations. Focal ESR1 copy-number elevations (amplifications) were detected in 187 of 394 (47%) tumor specimens, and were associated with a favorable outcome: After a median follow-up of 10 years, women with intratumoral focal ESR1 amplification had a significantly longer distant recurrence-free survival [adjusted HR, 0.48; 95% confidence interval (CI), 0.26-0.91; P = 0.02] and breast cancer-specific survival (adjusted HR 0.47; 95% CI, 0.27-0.80; P = 0.01) as compared with women without ESR1 amplification. IHC ERα protein expression, evaluated by Allred score, correlated significantly with focal ESR1 amplification (P < 0.0001; χ2 test), but was not prognostic by itself. Focal ESR1 amplification is an independent and powerful predictor for long-term distant recurrence-free and breast cancer-specific survival in postmenopausal women with endocrine-responsive early-stage breast cancer who received tamoxifen for 5 years.

Prognostic value of molecular cytology by one-step nucleic acid amplification (OSNA) assay of peritoneal washings in advanced gastric cancer patients

Peritoneal dissemination is a common form of gastric cancer (GC) recurrence, despite surgery with curative intent. This study aimed to evaluate the prognostic value of intraperitoneal lavage One-Step Nucleic Acid Amplification (OSNA) assay in advanced GC patients. OSNA assay targeting CK-19 mRNA was applied to detect free cancer cells (FCC) in intraperitoneal lavage samples obtained during gastrectomy. A total of 82 GC patients were enrolled to investigate the correlation between OSNA assay and patient’s prognosis. Of the 82 patients, OSNA assay was positive in 25 (30.5%) patients. The median OS in OSNA positive patients was significantly lower than in OSNA negative patients (19 vs 45 months). Positive OSNA assay result was a significant unfavourable prognostic factor in both, univariable (HR 3.45, 95% CI 0.95–12.48; p = 0.0030) and multivariable analysis (HR 3.10, 95% CI 1.22–8.54; p = 0.0298). Positive OSNA assay in intraperitoneal lavage is a valuable indicator of poor survival in advanced GC patients after multimodal treatment. After further confirmation on larger sample size, OSNA assay of peritoneal washings could be considered an adjunct tool to conventional cytology, the current gold standard, to provide precise intraoperative staging and additional prognostic information.

The Diagnostic Value of the Thermostatic Amplification of Ribonucleic Acid in Bronchoalveolar Lavage Fluid in Smear-Negative Pulmonary Tuberculosis.

ObjectiveThis study aimed to determine the value of the simultaneous amplification and testing for Mycobacterium tuberculosis in bronchoalveolar lavage fluid (BALF) in the diagnosis of smear-negative pulmonary tuberculosis (PTB).MethodsA total of 316 patients were selected, of which 197 had smear-negative PTB (observation group), and 119 did not have TB (control group). Bronchoscopy was performed in both groups, and BALF samples were collected for acid-fast bacilli smears, simultaneous amplification/testing for TB (SAT-TB), and BACTEC MGIT 960 cultures. The sensitivity, specificity, positive predictive, and negative predictive values of SAT-TB in BALF for the diagnosis of negative TB were calculated.ResultsThe sensitivity of SAT-TB detection was 45.18%, which was significantly higher than smears and slightly lower than cultures. The specificity of SAT-TB was 99.16%, which differed slightly from the other two methods. The positive predictive value was 98.89%, which was not significantly different from the other two methods. The negative predictive value of SAT-TB was 58.91%, which was higher than smears and slightly lower than cultures.ConclusionThe very high specificity and negative prediction of SAT-TB in BALF means that the method has great application value for the rapid diagnosis of smear-negative PTB.

Abstract 511: Prognostic relevance of 3q amplification in squamous cell carcinoma of the lung

Abstract Introduction: Amplification of 3q is the most common genetic alteration identified in squamous cell carcinoma of the lung (LUSC) with the most frequent amplified region being 3q26-3q28. It has been described in preinvasive and invasive LUSC and represents one of the most striking molecular differences between LUSC and adenocarcinoma. Many studies evaluated the prognostic value of 3q amplification; however, they either studied the entire region (~40 genes) or 1-2 genes of biological relevance (e.g SOX-2, p63). In this analysis, we aim to describe the prognostic relevance of 3q by focusing on a minimal common region (MCR) of amplification within 3q constituted of 25 genes. Additionally, we examined the association between MCR amplification and other genetic alterations commonly found in LUSC, such as CDKN2A deletion. Results: We conducted an analysis of 499 cases of LUSC from The Cancer Genome Atlas (TCGA). The majority identified as white (90.2%) and 9.8% as African American (AA) or Asians; 73.7% were males, 7 patients had stage IV disease. We found amplification of MCR (chr3:181,711,924-183,428,101) ~1.7MB within a large amplified region between (chr3:170,169,718-187,736,569) ~17.5MB on chr 3q. All 25 genes within MCR were found to be frequently amplified. Molecular data was available for 476 patients in CBioPortal, amplification of MCR was found in 221 (44.3%) cases whereas 255 (51%) cases had no amplification. Median disease specific survival of MCR-amplified cases was significantly longer than non-amplified cases (NR versus 9.25 years; 95% LowerCI: 5.24; log-rank p&amp;lt;0.05). Median progression-free interval for amplified cases was 8 years (95% LowerCI: 5.1) versus 4.9 years (95% LowerCI: 3.5) for non-amplified cases (Log-rank p&amp;lt;0.05). In multivariable analysis, MCR amplification was associated with significantly improved progression-free survival (HR for progression 0.67, CI 0.47-0.95, p=0.024) and disease specific survival (HR for death 0.59, CI 0.38-0.94, p=0.025). CDKN2A homozygous deletion, a common genetic alteration in lung cancer, was detected in 126 patients, 70 with MCR amplification and 56 with no amplification. CDKN2A deletion was associated with MCR amplification (Fisher’s exact test p=0.02121; OR: 1.64, 95% CI: 1.07-2.54). Conclusion: Amplification of the 25-gene MCR within 3q was present in 44% of this cohort mainly composed of Caucasian patients with early stage LUSC. It was also associated with lower risk of progression and better disease specific survival. This analysis is a strong indicator for the prognostic relevance of the 25-gene MCR within 3q. We are further evaluating its prognostic relevance in a racially diverse patient population with advanced LUSC. Citation Format: Fawzi Abu Rous, Rebecca Chacko, Shannon Carskadon, Shanker Kalyana-Sundaram, Pin Li, Sunny Singh, Laila Poisson, Shirish Gadgeel, Nallasivam Palanisamy. Prognostic relevance of 3q amplification in squamous cell carcinoma of the lung [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 511.

​Cross Genera Marker Transferability and Genetic Diversity Analysis in Elite Cultivars of Mungbean [Vigna radiata (L.) Wilczek

Backgrounds: To increase the accessibility of molecular markers for germplasm evaluation, genetic analysis and new cultivar development in mung bean, cross genera transferability of microsatellites (SSR) was studied. Methods: Forty simple sequence repeat markers developed for adzuki bean were used to amplify genomic DNA extracted from 70 diverse elite cultivars of greengram. Result: All SSR markers (100%) generated repeatable and clear products, signifying a high genomic homology between two species of Vigna. Among the 40 amplified markers, only 11 (28%) were highly polymorphic in 70 diverse elite cultivars of greengram. The polymorphism information content (PIC) ranged between 0.64 to 0.88 with an average of 0.81, while number of alleles ranged with 6 to 12 with an average of 9.27 alleles per locus. The multiple locus amplification and high PIC values indicated the effectiveness of the transferable SSRs in mungbean. Cluster analysis based on UPGMA grouped the studied genotypes into eleven clusters. The Jaccard’s similarity coefficient ranged from 0.17 to 0.46 indicating the extent of transitional amount of genetic variability within the tested genotypes.

The 16s ribosomal ribonucleic acid microorganisms’ detection in mesenteric lymph nodes by a polymerase chain reaction in view of colorectal cancer

Objective: This study proposes a method to detect 16s rRNA microorganisms in mesenteric lymph nodes (MLN) using a polymerase chain reaction (PCR) in patients with colorectal cancer (CRC). Material and methods: To quantify the presence of microorganisms in MLN, it is proposed to determine the dependence of the accumulated amplification products on the number of colony-forming units of bacteria (CFU/ml). The pure culture of Escherichia coli, GFP 6 serotype of biotype 1 (ATCC® 25922GFP™) with the CFU values from 102 to 108 (group 1) as well as the mixtures of E.coli with CFU/ml from 102 to 108 with the MLN tissues (group 2) were calibrated. The third group consisted of the MLN patients (60 people) with CRC without bowel obstruction. The 16s rRNA bacteria in MLN was detected by using real-time PCR by the BIO-RAD CFX96 amplifier. Results: To assess the dependence of the bacteria’s CFU/ml logarithm on the value of the threshold cycle amplification, a model was developed in the form of an equation. The amplification curves, threshold cycle values, and PCR efficiency differ from the first two groups. This can be due to the presence of DNA amplification-inhibiting compounds as well as the non-specific binding of MLN primers to DNA. Therefore, a mathematical model of the second group (suspension of E.Coli and MLN) was used to study the translocation of microorganisms in MLN. According to the developed mathematical model, depending on the values of the threshold amplification cycles, the positive PCR result in the study group (patients with CRC) was detected in 15 patients (25%). At the same time, the level of CFU/ml with bacterial translocation in MLN does not exceed 104. Conclusion: The developed method allows to determine the microbial DNA in MLN quantitatively in a wide range of its concentrations (102 to 108 CFU).