Biodiversity Informatics
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Four-pion state in UPC
Full text linkThe production of four pion events in ultraperipheral heavy-ion collisions at RHIC and LHC energies is studied. Preliminary H1 data is used to enhance the understanding of the poorly known process. Predictions for photon-nucleus interactions are calculated for various excited states of mesons. Agreement between theoretical predictions and available STAR data at RHIC is presented. The comparison of the four-pion invariant mass spectrum and nuclear total cross section indicates that rho(1570) plays a crucial role in accurately describing existing experimental data. Nuclear predictions for LHC energy in the central region of rapidity are also provided.
Two-body densities as a framework for dynamical imaging and their connection to ultra-peripheral collisions
Full text linkWe present results on two-parton densities in coordinate space which capture a fuller dynamical picture of the proton’s internal structure, including information on the relative position between quarks and gluons in the transverse plane. The connection of such two-body densities to observables, proceeds in QCD, via the definition of double generalized parton distributions (DGPDs) that can be accessed in the production of two vector mesons, or two dimuon systems in ultraperipheral collisions (UPCs) through a double scattering process
Identification of tumor microenvironment-based gene prognostic signature with promising predictive value for chemo‐immunotherapy outcomes in lung adenocarcinoma patients
Full text linkObjectives: The tumor microenvironment (TME) plays a critical role in tumor progression and therapeutic response. We aimed to establish a TME-associated gene signature for lung adenocarcinoma (LUAD) patients.
Materials and Methods: We comprehensively analyzed the gene expression data of 513 LUAD patients deriving from The Cancer Genome Atlas (TCGA) database. To estimate the composition of TME, The Estimation of Stromal and Immune cells in malignant tumor tissue using the Expression data (ESTIMATE) algorithm was used. We then utilized protein-protein interaction (PPI) analysis, LASSO, and COX regression to explore the related candidate genes with survival. Eventually, a three-gene signature was constructed for risk stratification. Furthermore, we investigated its predictive value in advanced LUAD patients who received chemotherapy alone or combined with anti-PD-1 inhibitors.
Results: We identified three genes, namely CCR2, CD40LG, and CCL21, to construct a TME-associated risk stratification gene signature. This gene signature was independently linked to patients\u27 overall survival (OS) among the TCGA dataset (HR, 1.99; 95% CI 1.36-2.93, p < 0.001) and GEO dataset (HR, 1.62; 95%CI 1.19-2.20, p < 0.001). The addition of anti-PD-1 inhibitor Siltuximab to chemotherapy resulted in significantly longer progression-free survival (PFS) in low-risk patients (HR, 0.33; 95% CI: 0.20 - 0.56, p < 0.001) but not in those with high- risk (HR, 0.56; 95% CI:0.24 - 1.31, p = 0.173). Moreover, in patients who received Sintilimab combined with chemotherapy, PFS was significantly different between the high- and low-risk group (HR,1.958; 95%CI:1.079-3.555, p = 0.024), whereas no significant difference was found in chemotherapy alone treated patients (HR, 1.303; 95%CI: 0.610-2.784, p = 0.492).
Conclusions: This study generated a three-gene prognostic signature based on TME-associated core genes in patients with LUAD. This gene signature has good value for prognosis prediction. In addition, this signature correlated with treatment outcomes among patients treated with chemotherapy combined with anti-PD1 therapy
Aberrant Immunohistochemical stains among 573 cases of Diffuse Mesothelioma
Full text linkBackground: Diagnosis of malignant mesothelioma often requires differentiating it from other metastatic malignancies including breast cancer, lung cancer, ovarian cancer, colorectal cancer, etc. Immunohistochemical stains (IHC) are important means to assist in confirming mesothelioma and ruling out metastatic cancers. Although mesothelial specific markers have been used for diagnosis, aberrant immunostains were also observed in clinical practice which often confounded the diagnosis. In this study, we analyzed the positive rate of commonly used IHC markers in the diagnosis of mesothelioma among 573 patients.
Design: 427 cases of epithelioid mesothelioma, 87 cases of biphasic mesothelioma and 59 cases with sarcomatoid mesothelioma were retrieved from the pathology consultation files between 2020-2023. The positive rates of over 50 IHC markers including over 30 aberrant IHC markers were analyzed.
Results: The positive rates of mesothelial markers, such as calretinin, WT-1 and D2-40, and epithelial markers, such as cytokeratins, were highest in epithelioid type, intermediate in biphasic type and lowest in sarcomatoid type mesothelioma. The mesenchymal marker vimentin and additional marker GATA-3 were highly expressed in sarcomatoid mesothelioma. The highest loss rate of BAP-1 was in epithelioid type, while the highest loss rate of MTAP was in sarcomatoid type. The CDKN2A (p16) deletion was observed equally in both epithelioid and sarcomatoid/biphasic types. Over 30 aberrant markers were observed. For epithelioid type, commonly observed aberrant IHC markers included MOC-31, BerEP4, PAX-8, p63, CK20, NKX3.1 and ER. For biphasic type, significant aberrant IHC markers included MOC-31, Ber-EP4, PAX8, CK20 and p40. For sarcomatoid type, notable aberrant IHC markers included p63, SMA, ERG and CD31. Among these aberrant IHC markers, MOC-31, Ber-EP4 and p63 were more commonly observed in pleural epithelioid mesothelioma, whereas PAX-8 in peritoneal epithelioid mesothelioma.
Conclusions: Our data demonstrated that aberrant immunostains were common in all of the histological types of mesothelioma. Therefore, the diagnosis of mesothelioma should be based on correlation of clinical presentation, radiological findings, and selective panel of immunostains, and should not be distracted by aberrant immunostains
Disparities in Response to the All of Us Research Program COVID-19 Participant Experience (COPE) Survey
Full text linkThis study demonstrated the successful longitudinal recruitment of a large number of diverse participants to the COPE survey in a very short time, empowered by the All of Us Research Program, its infrastructure, and databases. Despite the disparity of response rates across demographic groups, the data collected in the COPE surveys will enable researchers to investigate how the pandemic differentially affects diverse populations and their health status across the United States. Additionally, the findings highlight the need for future research aimed at improving response rates among underrepresented groups, ensuring the All of Us Research Program achieves its goals of diversity and inclusivity in research
Let It Flow, Let It Go: Sexuality, Gender Construction, and Worldmaking through Microteatro
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