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  • 1
    In: The Lancet, Elsevier BV, Vol. 401, No. 10388 ( 2023-05), p. 1584-1594
    Type of Medium: Online Resource
    ISSN: 0140-6736
    RVK:
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2023
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    SSG: 5,21
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  • 2
    Online Resource
    Online Resource
    American Chemical Society (ACS) ; 2023
    In:  ACS Applied Optical Materials Vol. 1, No. 1 ( 2023-01-27), p. 314-320
    In: ACS Applied Optical Materials, American Chemical Society (ACS), Vol. 1, No. 1 ( 2023-01-27), p. 314-320
    Type of Medium: Online Resource
    ISSN: 2771-9855 , 2771-9855
    Language: English
    Publisher: American Chemical Society (ACS)
    Publication Date: 2023
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  • 3
    In: ACS Omega, American Chemical Society (ACS), Vol. 8, No. 3 ( 2023-01-24), p. 3478-3483
    Type of Medium: Online Resource
    ISSN: 2470-1343 , 2470-1343
    Language: English
    Publisher: American Chemical Society (ACS)
    Publication Date: 2023
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  • 4
    Online Resource
    Online Resource
    American Chemical Society (ACS) ; 2023
    In:  ACS Applied Optical Materials Vol. 1, No. 7 ( 2023-07-28), p. 1326-1331
    In: ACS Applied Optical Materials, American Chemical Society (ACS), Vol. 1, No. 7 ( 2023-07-28), p. 1326-1331
    Type of Medium: Online Resource
    ISSN: 2771-9855 , 2771-9855
    Language: English
    Publisher: American Chemical Society (ACS)
    Publication Date: 2023
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  • 5
    In: The Oncologist, Oxford University Press (OUP), Vol. 28, No. 8 ( 2023-08-03), p. 691-698
    Abstract: Pancreatic cancer (PC) represents an aggressive disease with median overall survival (OS) of less than 1 year in the front-line setting. FOLFIRINOX and gemcitabine and paclitaxel (GP) are standard of care options for these patients; however, optimal selection of therapy is challenging. Methods Comprehensive genomic profiling was performed on 8358 PC patients. Outcomes were available for 1149 metastatic PC patients treated with 1L FOLFIRINOX or GP. A scar-based measure of HRD was called using a machine learning-based algorithm incorporating copy number and indel features. Results A scar-based HRD signature (HRDsig) was identified in 9% of patients. HRDsig significantly co-occurred with biallelic alterations in BRCA1/2, PALB2, BARD1, and RAD51C/D, but encompassed a larger population than that defined by BRCA1/BRCA2/PALB2 (9% vs. 6%). HRDsig was predictive of 1L FOLFIRNOX chemotherapy benefit with doubled OS relative to gemcitabine and paclitaxel (GP) (rwOS aHR 0.37 [0.22-0.62]), including 25% of the population with long-term (2 year+) survival in a real-world cohort of patients. Less benefit from FOLFIRINOX was observed in the HRDsig(−) population. Predictive value was seen in both the BRCA1/2/PALB2 mutant and wildtype populations, suggesting additional value to mutational profiling. Conclusion A scar-based HRD biomarker was identified in a significant fraction of PC patients and is predictive of FOLFIRINOX benefit. Incorporating a biomarker like HRDsig could identify the right patients for platinum chemotherapy and potentially reduce FOLFIRINOX use by over 40%, minimizing toxicities with similar survival outcomes. Confirmatory studies should be performed.
    Type of Medium: Online Resource
    ISSN: 1083-7159 , 1549-490X
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
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  • 6
    Online Resource
    Online Resource
    MDPI AG ; 2022
    In:  Journal of Marine Science and Engineering Vol. 10, No. 9 ( 2022-08-26), p. 1198-
    In: Journal of Marine Science and Engineering, MDPI AG, Vol. 10, No. 9 ( 2022-08-26), p. 1198-
    Abstract: Transient characteristics of wave generation in the wave channel can provide unique and important information in contrast to the steady and periodic motion of propagation waves. In this paper, a new analytical solution is proposed for a transient wavemaker problem in the wave channel. The mathematical model of the wavemaker problem is established based on the linear potential wave theory, and a new analytical solution for the corresponding initial and boundary-value problem is presented. The present solution methodology is motivated and developed from old methods shown in literature. The present solution can be mathematically reformulated and shown to be identical to the previous solution using different solution methodology. The present analytical solution is further compared with numerical results and experiments to validate the mathematical model. The present solution is used to calculate the steady state generated wave forms that compare very well with the steady wave theory both in wave length and wave period. The present solution is also used to study unsteady characteristics of wave heights and wave lengths of the leading waves. The present analytical solution methodology can provide an easier approach to obtain the analytical solution for transient wave generation problem in the wave channel.
    Type of Medium: Online Resource
    ISSN: 2077-1312
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
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  • 7
    Online Resource
    Online Resource
    American Society of Clinical Oncology (ASCO) ; 2023
    In:  Journal of Clinical Oncology Vol. 41, No. 16_suppl ( 2023-06-01), p. 539-539
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 41, No. 16_suppl ( 2023-06-01), p. 539-539
    Abstract: 539 Background: Pathologic mutations in BRCA1, BRCA2 and PALB2 lead to impaired homologous recombination repair (HRR). Cells with defects in HRR are dependent on non-homologous DNA end joining for DNA repair through the poly(ADP-ribose) polymerase (PARP) catalytic activity. PARP inhibitors (olaparib, talazoparib) are FDA-approved therapies that are toxic to tumors with HRR deficiency (HRD) and are recommended as adjuvant therapy in high-risk germline BRCA (g BRCA) positive BC. Despite the clinical implications of HRD, the prevalence of HRR alterations and HRD signature in early-stage primary BC and its association with hormone receptor (HR) status has not been well characterized. Methods: This study used the nationwide (US-based, ~280 US cancer clinics) de-identified Flatiron Health-Foundation Medicine BC clinico-genomic database and included patients (pts) who underwent tissue comprehensive genomic profiling (FoundationOne/FoundationOneCDx) between 2014 and 2022. The analysis included all pts with BC who presented with “early” stage I-III disease), had a primary tissue specimen collected within 3 months of diagnosis, and had a reportable novel scar-based HRD signature (HRDsig). Results: A total of 896 primary BC pts with stage I-III met our inclusion criteria. Of these early BC pts 21% (188/896) were HRDsig+ (stage I: 17% (32/188); stage II: 22% (84/376); and stage III: 22% (72/332)). For early BC pts, high rates of HRDsig+ were seen in g BRCA (87% [34/39] ), somatic BRCA (s BRCA, 78% [14/18]), and g PALB2 (71% [5/7] ) mutated tumors, with a lower rate seen with other HRR genes [16% (10/63); ATM, BARD1, BRIP1, CDK12, CHEK1, CHEK2, FANCL, sPALB2, RAD51B, RAD51C, RAD51D and RAD54L]. HRDsig+ was also detected in 16% (135/832) of BC without g/s BRCA or g PALB2 mutations. BC pts who presented with stage I-III disease has similar prevalence of HRDsig+ when compared to those with stage IV disease (21% [188/896] vs 23% [177/767], p = 0.31), with similar trends in HR+ disease (HR+/HER2+: 7% [4/57] vs 9% [4/45], p = 0.73; and HR+/HER2-: 17% [78/466] vs 18% [82/463], p = 0.73). Conversely, in HR- cohorts, decreased prevalence of HRDsig+ was observed in the stage I-III vs stage IV cohort (HR-/HER2+: 3% [1/38] vs 18% [6/33], p = 0.04; HR-/HER2-: 31% [99/321] vs 38% [83/216], p = 0.08). Conclusions: In this study, HR+/HER2- group was the most common early BC subtype, followed by HR-/HER2-, HR+/HER2+, and HR-/HER2+. This distribution is similar to the SEER study, and closely reflects that of the general population. We observed the expected high rates of HRDsig+ in early-stage BC pts with g/s BRCA or g PALB2 mutations where clinical trial data already support the use of PARP inhibitors for early and advanced disease. Importantly, HRDsig positivity was also seen in 16% of early BC without g/s BRCA or g PALB2, and clinical trials will be needed to determine if these pts could also benefit from HRD directed therapies.
    Type of Medium: Online Resource
    ISSN: 0732-183X , 1527-7755
    RVK:
    RVK:
    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2023
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  • 8
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2022
    In:  Cancer Research Vol. 82, No. 12_Supplement ( 2022-06-15), p. 1243-1243
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 82, No. 12_Supplement ( 2022-06-15), p. 1243-1243
    Abstract: Background: NCCN guidelines for first-line treatment of patients with metastatic pancreatic cancer includes either FOLFIRINOX or gemcitabine plus paclitaxel; however, these two treatment regimens have not been compared in a randomized clinical trial. In this study, we investigated genomic predictors of treatment response to guide this treatment decision. Methods: We selected 1,250 patients with metastatic pancreatic cancer who were treated with first-line FOLFIRINOX (FOLF, n = 588) or gemcitabine plus paclitaxel (G+P, n = 662) within the nationwide de-identified Flatiron Health-Foundation Medicine clinico-genomic database (CGDB). The de-identified data originated from approximately 280 US cancer clinics (~800 sites of care). Comprehensive genomic profiling was performed by Foundation Medicine on tumor samples from each patient as part of the standard of care. Gain/loss status as well as loss of heterozygosity (LOH) status of each chromosome arm was assessed using a custom research-use only algorithm that utilizes copy number model calls for each segment and SNP MAF information from sequencing data. Univariable Cox proportional hazards regression was used to identify chromosome arm-level aneuploidies associated with survival in patients treated with first-line FOLF or G+P. In each treatment cohort, a multivariable Cox model was built using the bidirectional stepwise regression procedure to select aneuploidy features associated with survival. A binary risk score was calculated based on the linear predictor of the multivariable Cox model and categorized as high vs low using a median threshold. Results: Among the FOLF-treated cohort, we identified six aneuploidy features associated with survival (Bonferroni adjusted p & lt; 0.05). FOLF-treated patients with a low FOLF risk score had better survival compared to those with a high FOLF risk score (HR: 0.46, 95%CI: 0.34-0.61, p = & lt;0.001). This association was not observed among G+P-treated patients (HR: 0.86, 95%CI: 0.66-1.11, p = 0.25). Among the G+P treated cohort; eight aneuploidy features were associated with survival (Bonferroni adjusted p & lt; 0.05). G+P-treated patients with a low G+P risk score had better survival compared to patients with a high G+P risk score (HR: 0.43, 95%CI: 0.33-0.57, p = & lt;0.001). This association was not observed among FOLF-treated patients (HR: 0.86, 95%CI: 0.66-1.12, p = 0.25). These findings remained after adjusting for clinical features including surgery and ECOG performance status (HRG+P: 0.52, p = & lt;0.001; HRFOLF: 0.5, p = & lt;0.001). Conclusions: In metastatic pancreatic cancer, we found different chromosome arm-level aneuploidies were associated with survival for FOLF and G+P regimens which suggests an aneuploidy-based risk score may have utility in choosing first-line treatment. Citation Format: Kuei-Ting Chen, Radwa Sharaf, Garrett Frampton, Lee Albacker, Ericka Ebot. Identification of aneuploidy biomarkers associated with response to first-line treatment of metastatic pancreatic cancer [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 1243.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2022
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  • 9
    Online Resource
    Online Resource
    MDPI AG ; 2022
    In:  Journal of Marine Science and Engineering Vol. 10, No. 6 ( 2022-05-27), p. 738-
    In: Journal of Marine Science and Engineering, MDPI AG, Vol. 10, No. 6 ( 2022-05-27), p. 738-
    Abstract: In this study, the problem of surface waves induced by water flow in a flow channel was investigated. The mathematical model based on the potential wave theory was established, and a new analytic solution to the corresponding initial and boundary value problem was proposed. To confirm our analytic solution, the mathematical model was applied to simulate experiments conducted in a flow channel in the laboratory. Using our analytic solution, water surface elevations and flow velocities at certain locations in the channel were compared with experimental results. Comparisons between our analytic solution and experimental results confirmed our theory that amplitudes and propagating phases are in very close agreement. Our analytic solution can be used to calculate variations in pressure and velocity along the water depth, which are expensive to calibrate and obtain in experiments. Although our analytic solution was established based on linear theory, it is very practical for applications studying the basic properties of surface elevation, velocity, and pressure of the flow field induced by water current both in space and time.
    Type of Medium: Online Resource
    ISSN: 2077-1312
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
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  • 10
    In: JCO Precision Oncology, American Society of Clinical Oncology (ASCO), , No. 6 ( 2022-08)
    Abstract: Mesothelioma is an aggressive malignancy with heterogeneous outcomes that are partly driven by the differential efficacy of existing therapies across histologic types and sites of origin. Large-scale molecular analysis of mesothelioma and its subtypes has the potential to inform future therapeutic strategies. MATERIALS AND METHODS We analyzed 1,294 mesotheliomas {980 pleural (malignant pleural mesothelioma [MPM]) and 314 peritoneal (malignant peritoneal mesothelioma [MPeM] )} using next-generation sequencing, determined programmed death ligand-1 (PD-L1) expression and histology in a subset of cases, and assessed MTAP /CDKN2A copy-number status by fluorescence in situ hybridization and T-cell infiltration in an independent cohort. RESULTS The molecular landscape of MPM was characterized by inactivating alterations in CDKN2A (49%), BAP1 (44%), CDKN2B (42%), MTAP (34%), and NF2 (33%). Compared with epithelioid MPM, nonepithelioid (ie, biphasic and sarcomatoid) MPM had identical tumor mutational burden (median 1.25 mut/Mb, P = .63), more commonly expressed PD-L1 (74% v 51%, P = .02), and was more likely to harbor MTAP, CDKN2A, and CDKN2B copy loss ( P 〈 .05). Fluorescence in situ hybridization confirmed that homozygous MTAP loss was enriched in nonepithelioid MPM. Relative to MPM, MPeM had comparable tumor mutational burden and PD-L1 expression. The molecular profile of MPeM was similar to MPM, with the distinction that PBRM1 alterations occurred at higher frequency (16% v 7%, P 〈 .01). ALK rearrangements were only observed in MPeM. CONCLUSION Regardless of histology and location, the molecular landscape of mesothelioma primarily consists of inactivating alterations in tumor suppressor genes, with enrichment of certain alterations in distinct subsets (eg, MTAP loss in nonepithelioid tumors). Given the limited efficacy of current therapies for this disease, novel approaches targeting recurring alterations should be explored.
    Type of Medium: Online Resource
    ISSN: 2473-4284
    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2022
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