Flat histogram simulation of lattice polymer systems

We demonstrate the use of a new algorithm called the Flat Histogram sampling algorithm for the simulation of lattice polymer systems. Thermodynamics properties, such as average energy or entropy and other physical quantities such as end-to-end distance or radius of gyration can be easily calculated using this method. Ground-state energy can also be determined. We also explore the accuracy and limitations of this method. Key words: Monte Carlo algorithms, flat histogram sampling, HP model, lattice polymer systemsComment: 7 RevTeX two-column page

Identification of a Blood-Based Protein Biomarker Panel for Lung Cancer Detection

Lung cancer is the deadliest cancer worldwide, mainly due to its advanced stage at the time of diagnosis. A non-invasive method for its early detection remains mandatory to improve patients’ survival. Plasma levels of 351 proteins were quantified by Liquid Chromatography-Parallel Reaction Monitoring (LC-PRM)-based mass spectrometry in 128 lung cancer patients and 93 healthy donors. Bootstrap sampling and least absolute shrinkage and selection operator (LASSO) penalization were used to find the best protein combination for outcome prediction. The PanelomiX platform was used to select the optimal biomarker thresholds. The panel was validated in 48 patients and 49 healthy volunteers. A 6-protein panel clearly distinguished lung cancer from healthy individuals. The panel displayed excellent performance: area under the receiver operating characteristic curve (AUC) = 0.999, positive predictive value (PPV) = 0.992, negative predictive value (NPV) = 0.989, specificity = 0.989 and sensitivity = 0.992. The panel detected lung cancer independently of the disease stage. The 6-protein panel and other sub-combinations displayed excellent results in the validation dataset. In conclusion, we identified a blood-based 6-protein panel as a diagnostic tool in lung cancer. Used as a routine test for high- and average-risk individuals, it may complement currently adopted techniques in lung cancer screening.publishedVersio

1D-2D-3D Transformation Synthesis of Hierarchical Metal-Organic Framework Adsorbent for Multicomponent Alkane Separation

A new hierarchical MOF consisting of Cu(II) centers connected by benzene-tricarboxylates (BTC) is prepared by thermoinduced solid transformation of a dense CuBTC precursor phase. The mechanism of the material formation has been thoroughly elucidated and revealed a transformation of a ribbon-like 1D building unit into 2D layers and finally a 3D network. The new phase contains excess copper, charge compensated by systematic hydroxyl groups, which leads to an open microporous framework with tunable permanent mesoporosity. The new phase is particularly attractive for molecular separation. Energy consumption of adsorptive separation processes can be lowered by using adsorbents that discriminate molecules based on adsorption entropy rather than enthalpy differences. In separation of a 11-component mixture of C1-C6 alkanes, the hierarchical phase outperforms the structurally related microporous HKUST-1 as well as silicate-based hierarchical materials. Grand canonical Monte Carlo (GCMC) simulation provides microscopic insight into the structural host-guest interaction, confirming low adsorption enthalpies and significant entropic contributions to the molecular separation. The unique three-dimensional hierarchical structure as well as the systematic presence of Cu(II) unsaturated coordination sites cause this exceptional behavior.status: publishe

Monitoring of Circulating Tumor DNA Improves Early Relapse Detection After Axicabtagene Ciloleucel Infusion in Large B-Cell Lymphoma: Results of a Prospective Multi-Institutional Trial

Although the majority of patients with relapsed or refractory large B-cell lymphoma respond to axicabtagene ciloleucel (axi-cel), only a minority of patients have durable remissions. This prospective multicenter study explored the prognostic value of circulating tumor DNA (ctDNA) before and after standard-of-care axi-cel for predicting patient outcomes. Lymphoma-specific variable, diversity, and joining gene segments (VDJ) clonotype ctDNA sequences were frequently monitored via next-generation sequencing from the time of starting lymphodepleting chemotherapy until progression or 1 year after axi-cel infusion. We assessed the prognostic value of ctDNA to predict outcomes and axi-cel-related toxicity. A tumor clonotype was successfully detected in 69 of 72 (96%) enrolled patients. Higher pretreatment ctDNA concentrations were associated with progression after axi-cel infusion and developing cytokine release syndrome and/or immune effector cell-associated neurotoxicity syndrome. Twenty-three of 33 (70%) durably responding patients versus 4 of 31 (13%) progressing patients demonstrated nondetectable ctDNA 1 week after axi-cel infusion ( < .0001). At day 28, patients with detectable ctDNA compared with those with undetectable ctDNA had a median progression-free survival and OS of 3 months versus not reached ( < .0001) and 19 months versus not reached ( = .0080), respectively. In patients with a radiographic partial response or stable disease on day 28, 1 of 10 patients with concurrently undetectable ctDNA relapsed; by contrast, 15 of 17 patients with concurrently detectable ctDNA relapsed ( = .0001). ctDNA was detected at or before radiographic relapse in 29 of 30 (94%) patients. All durably responding patients had undetectable ctDNA at or before 3 months after axi-cel infusion. Noninvasive ctDNA assessments can risk stratify and predict outcomes of patients undergoing axi-cel for the treatment of large B-cell lymphoma. These results provide a rationale for designing ctDNA-based risk-adaptive chimeric antigen receptor T-cell clinical trials

1D-2D-3D Transformation Synthesis of Hierarchical Metal–Organic Framework Adsorbent for Multicomponent Alkane Separation

A new hierarchical MOF consisting of Cu­(II) centers connected by benzene-tricarboxylates (BTC) is prepared by thermoinduced solid transformation of a dense CuBTC precursor phase. The mechanism of the material formation has been thoroughly elucidated and revealed a transformation of a ribbon-like 1D building unit into 2D layers and finally a 3D network. The new phase contains excess copper, charge compensated by systematic hydroxyl groups, which leads to an open microporous framework with tunable permanent mesoporosity. The new phase is particularly attractive for molecular separation. Energy consumption of adsorptive separation processes can be lowered by using adsorbents that discriminate molecules based on adsorption entropy rather than enthalpy differences. In separation of a 11-component mixture of C₁–C₆ alkanes, the hierarchical phase outperforms the structurally related microporous HKUST-1 as well as silicate-based hierarchical materials. Grand canonical Monte Carlo (GCMC) simulation provides microscopic insight into the structural host–guest interaction, confirming low adsorption enthalpies and significant entropic contributions to the molecular separation. The unique three-dimensional hierarchical structure as well as the systematic presence of Cu­(II) unsaturated coordination sites cause this exceptional behavior

Identification of a Blood-Based Protein Biomarker Panel for Lung Cancer Detection

Lung cancer is the deadliest cancer worldwide, mainly due to its advanced stage at the time of diagnosis. A non-invasive method for its early detection remains mandatory to improve patients’ survival. Plasma levels of 351 proteins were quantified by Liquid Chromatography-Parallel Reaction Monitoring (LC-PRM)-based mass spectrometry in 128 lung cancer patients and 93 healthy donors. Bootstrap sampling and least absolute shrinkage and selection operator (LASSO) penalization were used to find the best protein combination for outcome prediction. The PanelomiX platform was used to select the optimal biomarker thresholds. The panel was validated in 48 patients and 49 healthy volunteers. A 6-protein panel clearly distinguished lung cancer from healthy individuals. The panel displayed excellent performance: area under the receiver operating characteristic curve (AUC) = 0.999, positive predictive value (PPV) = 0.992, negative predictive value (NPV) = 0.989, specificity = 0.989 and sensitivity = 0.992. The panel detected lung cancer independently of the disease stage. The 6-protein panel and other sub-combinations displayed excellent results in the validation dataset. In conclusion, we identified a blood-based 6-protein panel as a diagnostic tool in lung cancer. Used as a routine test for high- and average-risk individuals, it may complement currently adopted techniques in lung cancer screening