Level Of Amplification Research Articles

The prognostic value of HER2 gene dosage and heterogeneity at a single-cell resolution in gastroesophageal adenocarcinoma.

473 Background: HER2 gene dosage (i.e. level of amplification) and heterogeneity are key prognostic variables for HER2+ gastroesophageal adenocarcinoma (GEA), yet no standardized approach to test these in routine clinical use exists. Here we modify the analytical pipeline for HER2 FISH to quantitatively estimate these prognostic variables and correlate them with clinical outcomes. Methods: Patients with metastatic HER2+ GEA who received trastuzumab-based therapy between 2011-2024 at Dana-Farber Cancer Institute and had available pre-treatment tissue for FISH analysis were included. HER2 FISH was conducted in a CLIA approved clinical pathology laboratory. Standard HER2/CEP17 ratio (an average of 50 cells) and individual cell HER2/CEP17 ratio were calculated. Kaplan-Meier method was used to estimate progression free (PFS) on trastuzumab-based therapy and overall survival (OS). Survival outcomes were adjusted for age, gender, tumor site, grade, prior resection, number of metastatic sites, and HER2 IHC using cox proportional hazard regression models. Results: A total of 77 patients were included. Median age was 60 years, 88% were male, and 92% had HER2 3+ tumors. Individual cells with HER2/CEP17 ratio ≥ 2.0 were defined as amplified (same cutoff as current bulk standard) and those with HER2/CEP17 ratio ≥ 4.95 (population median) were labeled highly HER2 amplified providing objective metrics to assess heterogeneity and gene dosage. Using these metrics we defined three subgroups: 1. Heterogenous (Het, n = 15): <75% cells HER2+; 2. Homogenous, low gene dosage (HL, n = 30): >75% cells HER2+, <50% cells with high HER2 amplification; 3. Homogenous, high gene dosage (HH, n = 32): >75% cells HER2+, >50% cells with high HER2 amplification. Cutoffs for both metrics were determined using data distribution patterns. The subgroups were prognostically relevant and PFS and OS were significantly lower for heterogenous tumors and numerically lower for homogenous tumors with low gene dosage after multivariable adjustment (Table). Conclusions: HER2 gene dosage and heterogeneity significantly impact outcomes in HER2+ GEA. More importantly by deconvoluting clinical HER2 FISH data at single cell level, we demonstrate an objective metric with prognostic value that could be adopted for routine clinical use and for patient stratification. Further insights into differing biology of these molecular subtypes are needed. Outcomes of patients by HER2 heterogeneity and gene dosage. Hazards ratio (HR) and p values are adjusted using multivariable cox proportional hazard regression model. PFS OS Patients, No. Median, mo HR (95%CI) P Value Median, mo HR (95%CI) P Value HH 32 16.2 1 16.4 1 HL 30 12.1 1.70 (0.79-3.66) 0.173 15.7 1.71 (0.93-3.14) 0.085 Het 15 6.7 3.12 (1.35-7.2) 0.008 12.4 2.72 (1.28-5.75) 0.009

MX/MWCNTs composite material aids new strategy for HBV-DNA electrochemical biosensor: achieving multi-level signal amplification and unlabeled detection

Hepatitis B virus DNA (HBV-DNA) serves as a crucial biomarker for the detection of the hepatitis B virus, with variations in its concentration in blood samples providing vital insights into patient infection and recovery status. We have developed an electrochemical biosensor tailored for HBV-DNA detection, exhibiting high sensitivity, specificity, and a broad detection range. The biosensor utilizes a composite material composed of MXene and multiwalled carbon nanotubes (MX/MWCNTs), prepared through a hand-shaking self-assembly technique, to modify the glassy carbon electrode (GCE) and serve as signal receivers. A meticulously designed padlock probe DNA specifically recognizes HBV-DNA and forms a double-stranded DNA structure, which is subsequently degraded by exonuclease III. The resulting sequence then hybridizes with a PolyT-primer to create template, triggering rolling circle amplification and releasing a substantial amount of pyrophosphate for the initial level of signal amplification. Subsequently, the pyrophosphate induces the release of methylene blue (MB) from MB@ZIF-90 composite, achieving a second level of signal amplification. The released MB is then adsorbed by the MX/MWNCNTs-modified GCE, which possesses cationic dye adsorption capabilities and a large specific surface area, generating a detection signal and completing the third level of amplification. This biosensor offers a detection range spanning from 1.0 pM to 1.0 × 106 pM, with a remarkable detection limit as low as 0.5 pM (3σ/S), and is capable of distinguishing base mismatches. Furthermore, it has demonstrated excellent specificity and recovery performance in serum testing. The performance of this biosensor demonstrates significant potential for clinical application, with the ultimate goal of improving the diagnosis and management of hepatitis B.Graphical

Prediction of response to anti-HER2 therapy using a multigene assay.

HER2-positive breast cancer (BC), which constitutes 13-15% of cases, shows variable response to anti-HER2 therapies. HER2-positivity, defined as protein overexpression (immunohistochemistry (IHC) score 3+) or equivocal expression (IHC 2+) with evidence of HER2 gene amplification, determines the eligibility to anti-HER2 therapy. MammaTyper® assay (Cerca Biotech GmbH) is a RT-qPCR BC subtyping platform based on the mRNA expression of ERBB2, ESR1, PGR, and MKI67. This study aims to evaluate the accuracy of the MammaTyper® assay in predicting the response of HER2-positive patients to therapy. A well-characterized HER2-positive BC cohort of 287 cases diagnosed at Nottingham University hospitals between 2006 and 2018 was included. The cohort was divided into 2 groups: a trastuzumab-treated group (n=159) and a chemotherapy-only treated group (n=128). Tumor clinicopathologic characteristics were matched between the two groups. Cases with discordant HER2 status were validated through staining of surgical excision specimens. ERBB2 mRNA identified 251/287 (87.5%) cases as HER2-positive, 10.8% (31/287) as HER2 low and 1.7% (5/287) as HER2-negative. According to MammaTyper® assay, ERBB2-positive patients treated with anti-HER2 therapy had significantly prolonged 5-year disease (DFS) and distant metastasis (DMFS) free survival (HR=0.56, p=0.003 and HR=0.62, p=0.023, respectively). MammaTyper®-defined HER2-Enriched subtype showed better response to anti-HER2 therapy compared to IHC-defined subtypes, with significant differences in both 5-year DFS and BCSS (p=0.01 and <0.001, respectively). ERBB2-negative patients did not show survival difference between the group of patients who were treated with trastuzumab and those who were treated with chemotherapy only (p>0.05). Validation analysis revealed that 11/36 ERBB2-negative cases were IHC 2+/ISH positive with very low level of gene amplification and 25 cases were false classified as HER2 positive using current protocols. Combining MammaTyper® assay with IHC to assess HER2 status improves the identification of HER2-positive BC patients who would benefit from anti-HER2 therapy.

Trastuzumab Plus Pertuzumab Versus Cetuximab Plus Irinotecan in Patients With RAS/BRAF Wild-Type, HER2-Positive, Metastatic Colorectal Cancer (S1613): A Randomized Phase II Trial.

ERBB2 overexpression/amplification in RAS/BRAF wild-type (WT) metastatic colorectal cancer (mCRC; human epidermal growth factor receptor 2 [HER2]-positive mCRC) appears to be associated with limited benefit from anti-EGFR antibodies and promising responses to dual-HER2 inhibition; however, comparative efficacy has not been investigated. We conducted a randomized phase II trial to evaluate efficacy and safety of dual-HER2 inhibition against standard-of-care anti-EGFR antibody-based therapy as second/third-line treatment in HER2-positive mCRC. Patients with RAS/BRAF-WT mCRC after central confirmation of HER2 positivity (immunohistochemistry 3+ or 2+ and in situ hybridization amplified [HER2/CEP17 ratio >2.0]) were assigned (1:1) to either trastuzumab plus pertuzumab (TP; trastuzumab 6 mg/kg and pertuzumab 420 mg once every 3 weeks) or cetuximab plus irinotecan (CETIRI; cetuximab 500 mg/m2 and irinotecan 180 mg/m2 once every 2 weeks) until progression or unacceptable toxicity. Crossover to TP was allowed after progression on CETIRI. The primary end point was progression-free survival (PFS). Secondary end points included objective response rate (ORR), overall survival, safety, and HER2 gene copy number (GCN ≥20/<20) as a predictive factor. Between October 2017 and March 2022, 54 participants were assigned to TP (n = 26) and CETIRI (n = 28). Median PFS did not vary significantly by treatment: 4.7 (95% CI, 1.9 to 7.6) and 3.7 (95% CI, 1.6 to 6.7) months in the TP and CETIRI groups, respectively. Efficacy of TP versus CETIRI differed significantly by HER2 GCN (median PFS, GCN ≥20 [9.9 v 2.9 months] and GCN <20 [3.0 v 4.2 months], respectively; P interaction = .003). On TP, ORR was 34.6% (57.1% with GCN ≥20 v 9.1% with GCN <20) with median GCN of 29.7 versus 13.2 for responders and nonresponders, respectively (P = .004). Grade ≥3 adverse events occurred in 23.1% and 46.1% of participants with TP and CETIRI, respectively. TP appears to be a safe and effective cytotoxic chemotherapy-free option for patients with RAS/BRAF-WT, HER2-positive mCRC. Higher levels of HER2 amplification were associated with greater degree of clinical benefit from TP vis-à-vis CETIRI.

Transcriptomic analysis of EGFR co-expression and activation in glioblastoma reveals associations with its ligands

Abstract Background Approximately half of the IDH-wildtype glioblastomas (GBM) exhibit EGFR amplification. Additionally, genomic changes that occur in the extracellular domain of EGFR can lead to ligand-hypersensitivity (R108K/A289V/G598V) or ligand-independence (EGFRvIII). Unlike in lung adenocarcinoma (LUAD), clinical trials with EGFR inhibitors showed no survival benefit for GBM and it remains unclear why. We aimed to elucidate differences in molecular mechanisms of EGFR activation and regulation between GBM and LUAD. Methods We used RNA-sequencing data to find EGFR co-regulated genes and pathways in GBM and compare EGFR signaling patterns between GBM and LUAD. Cellular origins of expression signals were determined by analyzing single-cell RNA sequencing data. Results We identified two ligands (BTC/EREG) among the significant EGFR predictor genes (TCGA-GBM: n=169, Intellance-2: n=166). Their expression was inversely correlated with EGFR amplification and incidence of ligand-sensitive mutations. Ligands were expressed by non-malignant cells and differed in their primary source of expression (BTC: neurons, EREG: myeloid). High expression of MDM2 and CDK4 was less common in EGFR-amplified GBMs with ligand-sensitive mutations compared to those without these mutations. Our analyses revealed distinct transcriptional profiles between GBM and LUAD when comparing tumors carrying activating mutations. Conclusions BTC and EREG are negatively associated with EGFR expression in GBM. These findings emphasize the role of ligands in regulating EGFR, where EGFR activation seems to be modulated by the highly varying levels of EGFR amplification, sensitivity of the receptor towards ligands and ligand expression levels. Ligand expression levels and EGFR mutations could refine patient stratification for EGFR-targeted therapies in GBM.

Adenocarcinoma of the rete testis: clinicopathological study of 18 cases with emphasis on MET amplification and a review of the literature.

Knowledge regarding adenocarcinoma of the rete testis (ACRT) is extremely limited due to its scarcity. This study enrolled 18 patients with ACRT from multiple institutions. Clinicopathological and immunohistochemical features were investigated, together with a comprehensive review of 95 previously reported cases. One case was assessed using next-generation sequencing (NGS). The median age of the patient cohort was 54 years (range = 20-69 years), with the majority presenting with a testicular mass (13 of 18); predominantly right-sided (11 of 18). Six patients died within the second year following diagnosis. The morphology of ACRT spans a wide spectrum, including newly identified mucinous carcinoid-like features, with mucous cells floating in mucus and signet-ring cells. Notably, transition from a benign to a malignant rete epithelium was noted in 38.9% of cases (seven of 18). Immunohistochemically, tumour cells most frequently showed strong positivity for CK7 (12 of 16) and CK20 (10 of 17), with occasionally positivity for calretinin (three of 16), WT-1 (two of 17) and PAX-8 (two of 15). According to NGS in a single case, MET was amplified, leading to the patient benefiting from mesenchymal-epidermal transition factor (MET) inhibitors. Furthermore, MET amplification was assessed in 13 cases using fluorescence in-situ hybridisation and detected in two cases (15.4%). No significant correlation between MET amplification and mesenchymal-epidermal transition factor (MET) levels was observed in the cases studied. Primary ACRT is a rare malignant tumour which poses a diagnostic challenge, and is associated with poor prognosis. Cases of ACRT with MET amplification might represent promising candidates for the treatment with MET inhibitors.

PPM1D/Wip1 is amplified, overexpressed, and mutated in human non-Hodgkin's lymphomas.

Wip1, is a p53-dependent Ser/Thr phosphatase involved in the timely termination of DDR. The PPM1D gene encoding Wip1 is deregulated and thus gained an oncogene character in common human solid tumors and cell lines. This study assessed the oncogenic potential of the PPM1D gene in human non- Hodgkin's lymphomas (NHL), the most common hematological malignancy worldwide. FFPE human lymphoid hyperplasia (LH) (n = 17) and NHL tumor lymph node samples (n = 65) and human NHL cell lines were used to assess the oncogenic potential of the PPM1D gene in the present study. Copy number gain and mRNA expression analysis of the PPM1D/Wip1 gene were assessed by qRT-PCR analysis. Mutational analysis of Exon 6 of the PPM1D gene was performed by PCR amplification and Sanger sequencing. Expressions of Wip1 and p53 proteins were assessed by immunohistochemistry and Western blot analysis. We found that PPM1D gained gene copy number in NHL tumors by 0.7-8 times compared to the control (p < 0.01). Increased PPM1D/Wip1 gene copy number was associated with higher mRNA and protein expression in human NHL samples (p < 0.01). Overexpression of Wip1 in NHL tumors and NHL cell lines was associated with amplification level and was unaffected by p53 status. Furthermore, a heterozygous type insertion mutation was detected in exon 6 (c.1553_1554insA) of the PPM1D gene particularly in DLBCL samples. Wip1 may have oncogenic potential, perhaps playing a role in the onset and progression of human NHL. The possible significance of Wip1 overexpression to chemotherapy response in NHL remains an intriguing question that requires more exploration.

Signal growth in a pure time-modulated transmission line and the loss effect.

We present the first comprehensive study for signal growth in transmission lines (TL) with purely time-modulated characteristic impedance (infinite superluminality). This study pioneers the investigation into the effects of varying the cell's electrical length and the impact of loss on momentum bandgaps and amplification levels. It also thoroughly examines how time-modulated transmission line truncation by a static load influences the sensitivity of amplification gain to the relative phase between the incoming signal and modulation, comparing these findings with the case of parametric amplification. Varying is accomplished by loading TLs with a sinusoidally time-modulated capacitor (TMC). The study starts with a simple lumped model cell to facilitate understanding of the phenomena. Following this, transmission lines are introduced, and the effects of incorporating loss are examined. To accomplish this, three models are investigated: a lossless L-C TL lumped model loaded with a shunt lossless TMC and a TL loaded with a shunt lossless and lossy TMC. Dispersion diagrams are plotted and momentum bandgaps are identified at a modulation frequency double the signal frequency. Within the momentum bandgap, only imaginary frequencies are found and correlated to momentum bandgap width and signal growth level. Signal growth is confirmed using harmonic balance and transient simulations, and the results are consistent with the dispersion diagram outcomes.

ICT Integration and Students’ 21st-Century Learning Skills in ELT

Information and Communication Technology (ICT) has become essential in developing nations in recent years, greatly influencing a number of industries, including ELT and education. However, although incorporating technology into instruction is emphasized in today's educational environment, research on how these affects students’ abilities for 21st-century learning has yielded mixed results that leads to the inconsistent information, including in Indonesia. Therefore, to address this issue, ICT integration in ELT and its impact on students' learning capabilities at SMA N 3 Yogyakarta are examined in this qualitative case study. Data from 10 grade X participants spread across five classrooms were collected through document analysis, classroom observation, and in-depth interviews. The results showed that ICT integration is common, mostly at the passive and amplification levels. Citizenship, collaboration, creativity, and communication all showed positive effects; however, critical thinking and character still need further evaluation. To get the most out of ICT and help instructors develop 21st-century abilities, effective teaching methods and frameworks are advised. It is also suggested that standardized rules and guidelines should be established for the incorporation of ICT in education.

Multiple Instance Learning for WSI: A comparative analysis of attention-based approaches

Whole slide images (WSI), obtained by high-resolution digital scanning of microscope slides at multiple scales, are the cornerstone of modern Digital Pathology. However, they represent a particular challenge to artificial intelligence (AI)-based/AI-mediated analysis because pathology labeling is typically done at slide-level, instead of tile-level. It is not just that medical diagnostics is recorded at the specimen level, the detection of oncogene mutation is also experimentally obtained, and recorded by initiatives like The Cancer Genome Atlas (TCGA), at the slide level. This configures a dual challenge: (a) accurately predicting the overall cancer phenotype and (b) finding out what cellular morphologies are associated with it at the tile level. To better understand and address these challenges, two existing weakly supervised Multiple Instance Learning (MIL) approaches were explored and compared: Attention MIL (AMIL) and Additive MIL (AdMIL). These architectures were analyzed on tumor detection (a task where these models obtained good results previously) and TP53 mutation detection (a much less explored task). For tumor detection, we built a dataset from Lung Squamous Cell Carcinoma (TCGA-LUSC) slides, with 349 positive and 349 negative slides. The patches were extracted from 5× magnification. For TP53 mutation detection, we explored a dataset built from Invasive Breast Carcinoma (TCGA-BRCA) slides, with 347 positive and 347 negative slides. In this case, we explored three different magnification levels: 5×, 10×, and 20×. Our results show that a modified additive implementation of MIL matched the performance of reference implementation (AUC 0.96), and was only slightly outperformed by AMIL (AUC 0.97) on the tumor detection task. TP53 mutation was most sensitive to features at the higher applications where cellular morphology is resolved. More interestingly from the perspective of the molecular pathologist, we highlight the possible ability of these MIL architectures to identify distinct sensitivities to morphological features (through the detection of regions of interest, ROIs) at different amplification levels. This ability for models to obtain tile-level ROIs is very appealing to pathologists as it provides the possibility for these algorithms to be integrated in a digital staining application for analysis, facilitating the navigation through these high-dimensional images and the diagnostic process.

Influence of quasi-electrostatic support on amplification of space charge waves in amplification section of a superheterodyne free electron laser

Abstract In this work, a theoretical study of the influence of a quasi-electrostatic support on the amplification level of the slow space charge wave (SCW) in the amplification section of a superheterodyne free electron laser (FEL) was carried out. One of the ways to significantly increase the saturation level of the slow SCW is maintaining the conditions of a three-wave parametric resonance between the slow, fast SCWs and the resulting pump electric field. This can be done by introducing the quasi-electrostatic support in the superheterodyne FEL amplification section. Also, it was found that the generated pump electric field significantly influences the maintenance of parametric resonance conditions. As a result, this increases the saturation level of the slow SCW by 70%. Finally, the quasi-electrostatic support significantly reduces the maximum value of the electrostatic undulator pump field strength, which is necessary to achieve the maximum saturation level of the slow SCW.

Enhanced scattering from an almost-periodic optical temporal slab

We showcase the impact of almost-periodicity on the parametric amplification associated with the first-order momentum gap in photonic time-crystals with time-varying permittivity. Utilizing a vectorial coupled-wave theory approach, we rigorously analyze the scattering by a temporal slab of the considered medium. We pinpoint a critical regime wherein flaws in material tuning paradoxically enhance amplification due to the coupling of fewer, broader modes, resulting in a higher and broader pulselike amplification envelope. Additionally, we demonstrate that the intensity reflectances of time-reversed waves corresponding to secondary “Bragg” resonances achieve remarkably high levels of subharmonic parametric amplification, with the epsilon-near-zero regime serving as a preferred candidate for experimental implementation. Our counterintuitive findings highlight the potential of intentionally leveraging modulation desynchronization and impurities in the temporal unit cell of photonic time-crystals to enhance both the level and the bandwidth of amplification. Published by the American Physical Society 2024

Automated manufacturing and characterization of clinical grade autologous CD20 CAR T cells for the treatment of patients with stage III/IV melanoma.

Point-of-care (POC) manufacturing of chimeric antigen receptor (CAR) modified T cell has expanded rapidly over the last decade. In addition to the use of CD19 CAR T cells for hematological diseases, there is a growing interest in targeting a variety of tumor-associated epitopes. Here, we report the manufacturing and characterization of autologous anti-CD20 CAR T cells from melanoma patients within phase I clinical trial (NCT03893019). Using a second-generation lentiviral vector for the production of the CD20 CAR T cells on the CliniMACS Prodigy®. We demonstrated consistency in cell composition and functionality of the products manufactured at two different production sites. The T cell purity was >98.5%, a CD4/CD8 ratio between 2.5 and 5.5 and transduction rate between 34% and 61% on day 12 (harvest). Median expansion rate was 53-fold (range, 42-65-fold) with 1.7-3.8×109 CAR T cells at harvest, a sufficient number for the planned dose escalation steps (1×105/kg, 1×106/kg, 1×107/kg BW). Complementary research of some of the products pointed out that the CAR+ cells expressed mainly central memory T-cell phenotype. All tested CAR T cell products were capable to translate into T cell activation upon engagement of CAR target cells, indicated by the increase in pro-inflammatory cytokine release and by the increase in CAR T cell amplification. Notably, there were some interindividual, cell-intrinsic differences at the level of cytokine release and amplification. CAR-mediated T cell activation depended on the level of CAR cognate antigen. In conclusion, the CliniMACS Prodigy® platform is well suited for decentralized POC manufacturing of anti-CD20 CAR T cells and may be likewise applicable for the rapid and automated manufacturing of CAR T cells directed against other targets. https://clinicaltrials.gov/study/NCT03893019?cond=Melanoma&term=NCT03893019&rank=1, identifier NCT03893019.

Achieving precise dual detection: One-tube reverse transcription-recombinase aided amplification (RT-RAA) combined with lateral flow strip (LFS) assay for RNA and DNA target genes from pepper mild mottle virus and Colletotrichum species in crude plant samples

Ensuring the detection sensitivity of both RNA-derived and DNA-derived target genes in a single reaction has posed a significant challenge for on-site detection of plant pathogens. This challenge was addressed by developing a one-tube dual RT-RAA assay combined with LFS for the rapid on-site detection of pepper mild mottle virus (PMMoV) and four Colletotrichum species causing anthracnose in Solanaceous crops. By testing four different combinations of primer groups, two combinations were precisely adjusted within the dual RT-RAA system to balance amplification efficiency and maintain consistent levels of amplification in crude plant samples. Utilizing commercially accessible small-scale equipment and following a streamlined optimization strategy, the assay achieved a limit of detection of 0.32 copies/μL of target genes in the reaction. Importantly, it demonstrated no cross-reactivity with other plant pathogens, thereby affirming the high sensitivity and specificity of the developed dual RT-RAA-LFS detection assay. Moreover, the entire process took only 25 min from sample collection to the visible presentation of results. The assay was validated with 60 field samples and 10 seed samples, producing results consistent with reverse transcription quantitative polymerase chain reaction (RT-qPCR). Notably, it successfully detected PMMoV in systemic leaves without visible symptoms three days post-inoculation, underscoring its effectiveness in early disease detection. This streamlined strategy offers a valuable approach for rapid, low-cost, and highly sensitive on-site simultaneous detection of RNA genome-contained PMMoV and DNA genome-contained Colletotrichum species.

A Combined Sensor Design Applied to Large-Scale Measurement Systems.

The photoelectric sensing unit in a large-space measurement system primarily determines the measurement accuracy of the system. Aiming to resolve the problem whereby existing sensing units have difficulty accurately measuring the hidden points and free-form surfaces in large components, in this study, we designed a multi-node fusion of a combined sensor. Firstly, a multi-node fusion hidden-point measurement model and a solution model are established, and the measurement results converge after the number of nodes is simulated to be nine. Secondly, an adaptive front-end photoelectric conditioning circuit, including signal amplification, filtering, and adjustable level is designed, and the accuracy of the circuit function is verified. Then, a nonlinear least-squares calibration method is proposed by combining the constraints of the multi-position vector cones, and the internal parameters of the probe, in relation to the various detection nodes, are calibrated. Finally, a distributed system and laser tracking system are introduced to establish a fusion experimental validation platform, and the results show that the standard deviation and accuracy of the three-axis measurement of the test point of the combined sensor in the measurement area of 7000 mm × 7000 mm × 3000 mm are better than 0.026 mm and 0.24 mm, respectively, and the accuracy of the length measurement is within 0.28 mm. Further, the measurement accuracy of the hidden point of the aircraft hood and the free-form surface is better than 0.26 mm, which can meet most of the industrial measurement needs and expand the application field of large-space measurement systems.

Feedbacks, Pattern Effects, and Efficacies in a Large Ensemble of HadGEM3‐GC3.1‐LL Historical Simulations

AbstractClimate feedbacks over the historical period (here defined as 1850–2014) have been investigated in large ensembles of historical and single forcing experiments (hist‐ghg, hist‐aer, and hist‐nat), with 47 members for each experiment. Across the historical ensemble with all forcings, a range in estimated Effective Climate Sensitivity (EffCS) between approximately 3–6 K is found, a considerable spread stemming solely from initial condition uncertainty. The spread in EffCS is associated with varying Sea Surface Temperature (SST) patterns seen across the ensemble due to their influence on different feedback processes. For example, the level of polar amplification is strongly correlated with the amount of sea ice melt per degree of global warming. This mechanism is related to the large spread in shortwave clear‐sky feedbacks and is the main contributor to the different forcing efficacies seen across the different forcing agents, although in HadGEM3‐GC3.1‐LL these differences in forcing efficacy are shown to be small. The spread in other feedbacks is also investigated, with the level of tropical SST warming strongly correlated with the longwave clear‐sky feedbacks, and the local surface‐air‐temperatures well correlated with the spread in cloud radiative effect feedbacks. The metrics used to understand the spread in feedbacks can also help to explain the disparity between feedbacks seen in the historical experiment simulations and modeled estimate of the feedbacks seen in the real world derived from an atmosphere‐only experiment prescribed with observed SSTs (termed amip‐piForcing).

Maternal Spargel/dPGC-1 is critical for embryonic development and influences chorion gene amplification via Cyclin E activity

The function of spargel/dPGC-1 in Drosophila oogenesis has been unequivocally established. Here, we sought to assess whether Spargel protein or RNA is essential for developmentally competent eggs. The trans-heterozygotic combination of two spargel mutant alleles allowed us to decrease Spargel expression to very low levels. Using this model, we now demonstrated the requirement for Spargel in eggshell patterning and embryonic development, which led us to establish that spargel is a maternal effect gene. Further examination of Spargel's potential mechanism of action in eggshell biogenesis revealed that low levels of Spargel in the adult ovary cause diminished Cyclin E activity, resulting in reduced chorion gene amplification levels, leading to eggshell biogenesis defects. Thus, another novel role for spargel/dPGC-1 is exposed whereby, through Cyclin E activity, this conserved transcriptional coactivator regulates the chorion gene amplification process.

An efficient DNAzyme-locked leakless enzyme-free amplification system for alpha-foetoprotein detection in liver cancer and breast cancer.

Alpha-foetoprotein (AFP) is taken as a diagnostic tumor marker for the screening and diagnosis of cancer. Nucleic acid-based isothermal amplification strategies are emerging as a potential technology in early screening and clinical diagnosis of AFP. The leakages between hairpins dramatically increase the background and reduce the sensitivity. Thus, it is necessary to develop some strategies to reduce the leakage for isothermal amplification strategies. A DNAzyme-locked leakless enzyme-free amplification system was developed for AFP detection in liver cancer and breast cancer. AFP could open the apt-hairpin and initiate the catalytic hairpin assembly (CHA) reaction to produce a Y-shaped duplex. Two tails of a Y-shaped duplex cleaved the two kinds of leakless hairpins. Then, the third tail of the Y-shaped duplex catalyzed the second CHA between the cleaved leakless hairpins to recover the fluorescent intensity. The limit of detection reached 5fg/mL by the two levels of signal amplifications. Importantly, the leakless hairpin design effectively reduced leakage between hairpins and weakened the background. In addition, it also showed a great promising potential for AFP detection in early screening and clinical diagnosis.

Nationwide frequency-dependent seismic site amplification models for Iceland

Seismic wave amplification due to localized site conditions or site-effects, is an important aspect of regional seismic hazard assessment. In the absence of systematic studies of frequency-dependent site-effects during strong Icelandic earthquakes, various local site proxies of large-scale studies in other seismic regions have been used and/or proposed for application in Iceland. Recently, however, earthquake site-effects were rigorously quantified for 34 strong-motion stations in Southwest Iceland for the first time and correlated to distinct Icelandic geological units of hard rock, rock, lava rock, and sedimentary soil. These units are prevalent throughout Iceland and in this study therefore, we present 1) nationwide maps of proxies (e.g. slope, Vs30, geological units) that may contribute to a better estimation of site effects and associated, 2) frequency-dependent site-amplification maps of Iceland relative to the median ground-motion prediction of Rahpeyma et al. (2023) [55]. We particularly focus on the two transform zones of the country, on the basis of digital elevation models and detailed geological maps. Specifically, the frequency-dependent site factors for each geological unit are presented at 1, 2, 5, 7, 10–30 Hz, and PGA. Finally, for comparison, we generate site amplification maps based on recent large-scale models developed in other seismic regions and/or applied in other studies (e.g., ESRM20) as well as various site proxies they are based on (e.g., geology- and slope-based inferred VS30, geomorphological sedimentary thickness). We compare site-proxy maps and amplification maps from both Icelandic and large-scale, non-Icelandic, models. Specifically, neither spatial patterns nor amplification levels in either proxy or amplification maps from large-scale non-Icelandic studies resemble those observed from local quantitative strong-motion research as presented in this study. We attribute the discrepancy primarily to the young geology of Iceland and its formation history. Additionally, this study compares model performance across frequencies by assessing the bias of model predictions against empirical site amplifications in the South Iceland Seismic Zone, accounting for site-to-site variability of residuals indicating the superior performance of the local amplification model. The results presented in this study now allow a more informed estimation of earthquake ground motion amplitudes on various geological units that are expected to result in more reliable and information-based seismic hazard estimates in Iceland.

Abstract PO5-01-04: HER2 Amplification Level and Focal/Broad Region Size as Predictors of Treatment Response in Neoadjuvant Chemotherapy and Anti-HER2 Therapy for HER2-Positive Breast Cancer

Abstract Background: Neoadjuvant chemotherapy combined with anti-HER2 therapy has become the standard treatment approach for HER2-positive breast cancer. However, not all HER2-positive patients can achieve pathological complete response after neoadjuvant therapy. This raises the question of which subset of HER2+ patients derive the greatest benefit from pre-operative HER2-targeted treatment. Therefore, this study aims to determine whether the level and amplification region size of HER2 amplification are associated with the efficacy of neoadjuvant chemotherapy combined with anti-HER2 therapy. Methods: A total of 523 breast cancer samples were collected from 2017 to 2018, among which 202 cases were HER2-positive patients. Among these, 55 HER2-positive patients received neoadjuvant chemotherapy combined with anti-HER2 targeted therapy. The amplification status of HER2 was assessed using immunohistochemistry/fluorescence in situ hybridization (IHC/FISH) and next-generation sequencing (NGS). The HER2/CEP17 ratio, determined by FISH, was used to represent the amplification level of HER2. The size of the amplification region was calculated using NGS and neighboring genes located in chr17q. Amplification regions smaller than 1 Mb were classified as focal amplification, while those larger than 1 Mb were classified as broad amplification. Results: We compared the HER2/ERBB2 status of 523 breast cancer patients using different detection methods and found a high concordance between ERBB2 amplification detected by NGS and HER2-positivity detected by IHC and FISH, with a sensitivity of 96.0%, specificity of 97.8%, and overall concordance of 97.1%. Based on the HER2/CEP17 ratio determined by FISH, we observed that using a threshold of 6 for classification, the high amplification group had a significantly higher pCR rate compared to the low amplification group (86.7% vs. 41.7%; p=0.037, odds ratio [OR]=0.121, 95% confidence interval [CI]: 0.009-0.919). Moreover, the focal amplification group showed a higher pCR rate compared to the broad amplification group (65.9% vs. 30.8%, p=0.051, OR=0.237, 95% CI: 0.045-1.035). Additionally, within the low amplification group (HER2/CEP17 &amp;lt; 6), the pCR rate was 66.7% for focal amplification and 20% for broad amplification, suggesting that focal amplification of ERBB2 may further guide clinical benefit in the low HER2/CEP17 ratio group. Conclusion: This study demonstrates a high concordance between ERBB2 amplification determined by NGS and HER2-positivity determined by IHC/FISH. High HER2/CEP17 ratio and focal amplification of ERBB2 are associated with a higher pCR rate in neoadjuvant chemotherapy combined with anti-HER2 targeted therapy. Citation Format: Ning Liao, Guochun Zhang, Xinze Lv, Kai Li, Ting Hou, Zhou Zhang. HER2 Amplification Level and Focal/Broad Region Size as Predictors of Treatment Response in Neoadjuvant Chemotherapy and Anti-HER2 Therapy for HER2-Positive Breast Cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-01-04.