Constraining cosmological parameters with needlet internal linear combination maps. II. Likelihood-free inference on needlet internal linear combination power spectra
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Broadly neutralizing antibodies (bNAbs) are currently being assessed in clinical trials for their ability to prevent HIV infection. Single chain variable fragments (scFv) of bNAbs have advantages over full antibodies as their smaller size permits improved diffusion into mucosal tissues and facilitates vector-driven gene expression. We have previously shown that scFv of bNAbs individually retain significant breadth and potency. Here we tested combinations of five scFv derived from bNAbs CAP256-VRC26.25 (V2-apex), PGT121 (N332-supersite), 3BNC117 (CD4bs), 8ANC195 (gp120-gp41 interface) and 10E8v4 (MPER). Either two or three scFv were combined in equimolar amounts and tested in the TZM-bl neutralization assay against a multiclade panel of 17 viruses. Experimental IC 50 and IC 80 data were compared to predicted neutralization titers based on single scFv titers using the Loewe additive and the Bliss-Hill model. Like full-sized antibodies, combinations of scFv showed significantly improved potency and breadth compared to single scFv. Combinations of two or three scFv generally followed an independent action model for breadth and potency with no significant synergy or antagonism observed overall although some exceptions were noted. The Loewe model underestimated potency for some dual and triple combinations while the Bliss-Hill model was better at predicting IC 80 titers of triple combinations. Given this, we used the Bliss-Hill model to predict the coverage of scFv against a 45-virus panel at concentrations that correlated with protection in the AMP trials. Using IC 80 titers and concentrations of 1μg/mL, there was 93% coverage for one dual scFv combination (3BNC117+10E8v4), and 96% coverage for two of the triple combinations (CAP256.25+3BNC117+10E8v4 and PGT121+3BNC117+10E8v4). Combinations of scFv, therefore, show significantly improved breadth and potency over individual scFv and given their size advantage, have potential for use in passive immunization.
Cancer is a leading cause of death in the US, second only to heart disease. It is primarily a result of a combination of an estimated two-nine genetic mutations (multi-hit combinations). Although a body of research has identified hundreds of cancer-causing genetic mutations, we don’t know the specific combination of mutations responsible for specific instances of cancer for most cancer types. An approximate algorithm for solving the weighted set cover problem was previously adapted to identify combinations of genes with mutations that may be responsible for individual instances of cancer. However, the algorithm’s computational requirement scales exponentially with the number of genes, making it impractical for identifying more than three-hit combinations, even after the algorithm was parallelized and scaled up to a V100 GPU. Since most cancers have been estimated to require more than three hits, we scaled out the algorithm to identify combinations of four or more hits using 1000 nodes (6000 V100 GPUs with ≈48×106 processing cores) on the Summit supercomputer at Oak Ridge National Laboratory. Efficiently scaling out the algorithm required a series of algorithmic innovations and optimizations for balancing an exponentially divergent workload across processors and for minimizing memory latency and inter-node communication. We achieved an average strong scaling efficiency of 90.14% (80.96%–97.96% for 200 to 1000 nodes), compared to a 100 node run, with 84.18% scaling efficiency for 1000 nodes. With experimental validation, the multi-hit combinations identified here could provide further insight into the etiology of different cancer subtypes and provide a rational basis for targeted combination therapy.
Here, alkyl combination reactions, along with their reverse alkane unimolecular decomposition reactions, are widely present in pyrolysis and combustion systems. These reactions occur mainly at temperatures at which their rate coefficients depend on pressure, and only a few studies have explored this dependence for large size alkyls. The accurate calculation of these kinetic data is limited by the size of the alkyl fragments involved, since the theoretical methods used are computationally expensive. Therefore, little reliable data is available for the modeling of real fuels alkane decomposition kinetics. In this paper, we propose an alternative approach that allows an accurate estimation of pressure-dependent kinetic rates for the combination of long-chain alkyl radicals, based on tabulated reaction models. The rates of combination of linear alkyls radicals forming ethane to pentane were calculated using the CASPT2-F12/cc-pVDZ-F12 level within VRC-TST theory combined with master-equation simulations. The computed high-pressure limit rate coefficients showed that n-propyl could be a minimum-size representative structure for larger n-alkyl chain, but this approach fails to capture the pressure dependence of the reaction that remains size-dependent for larger alkyls. The Geometric Mean Rule (GMR), a simple rule that links the self and cross-reactions of three alkyl radicals, is used to address this issue. Our theoretical calculations show for the first time that the GMR applies not only at the high-pressure limit, but also for every pressure explored. The GMR is shown to be accurate, with a maximum 22 % deviation in the falloff region for the estimation of rates for small alkyl combinations. Using this method, we propose a tabulated reaction rate rule for the combination of alkyl radicals up to C5+C5. The use of computed rate coefficients with the GMR approximation opens ways to develop pressure-dependent reaction rate rules for large n-alkyl combinations, based on accurate and computationally expensive theoretical calculations on smaller alkyl fragments.
Georgia Tech (Prime Recipient), the University of Texas at El Paso (UTEP) and the National Energy Technology Laboratory (NETL) investigated a hybrid fuel cell/ gas turbine system concept as a combined heat and hybrid power (CHHP) system for both robust and high power-to-process heat ratio cogeneration. The novelty of the proposed system entailed the distinct, elevated electrical efficiencies it maintains while simultaneously supporting a broad span of heating needs (e.g., supply temperatures) demanded across variable heat loads. The scope included: 1) leveraging a pioneering national lab facility configured for dynamic system operability development of hybrid fuel cell/gas turbine cycles; 2) enabling technology development to adjust and modulate the quality and quantity of thermal supply to bottoming heat loads via novel extreme temperature gas bypass valves. Hybrid fuel cell/gas turbine systems have primarily been reduced-to-practice in a constrained (e.g., initial proof-of-concept) manner and have still demonstrated considerable electrical efficiencies. However, these pre-pilot systems have focused upon electrical efficiencies and electrical power generation as the exclusive energy demand. Such hybrid systems had not been extensively researched or developed for flexible and variable operation consisting of both power and heat demands; however, these variable combined power and heat demands are characteristic of many types of manufacturers such as animal/poultry processing, bakeries and milk/flour/pastry manufacturing, textile mills, and electrochemical processing. Commercially, developing the system into a working combined heat and power system benefits these types of manufacturers by allowing them to meet their power and heat demands at a lower cost, higher efficiency, and/or through onsite generation. Therefore, the technical scope of this project was largely to study and facilitate these hybrid systems as combined heat and hybrid power (CHHP) systems that include dynamic operability for variable heat and power loads and/or grid dynamics for various types of manufacturers. Simulation results were used to predict the performance of the CHHP system and conceptually develop it to achieve desired dynamic operability. Experimentally, the primary goal was to design, manufacture, and experiment upon a high-temperature bypass valve. Experimental data included air mass flow rates through the valve orifice when the valve was changed to variable extent between fully closed and fully open. The experimental data was then used to create a semi-empirical computational model of the bypass valve. Concluded simulation goals for the research included developing computational heat exchanger models for the hybrid system inclusive of the bottoming heat exchanger and the recuperative heat exchanger, and then combining the computational recuperator model with the computational valve model. Afterwards, the computational models were then integrated to predict the dynamic operation of hybrid fuel cell/gas turbine cycles throughout a design space and reporting such. The scope stated in the preceding paragraph was packaged into five specific goals: 1) enabling the simulation of dynamic combined heat and power through the creation of computational, modular heat exchanger models; 2) simulation and exploration of the CHHP system’s performance by integrating the heat exchanger models with the national lab’s pre-existing hybrid system (computational) simulation, but without the recuperator bypass valve concept in order to initially determine how the (baseline) system behaves and can be controlled in order to meet variable heat and power demands; 3) development and initial deployment of the high-temperature recuperator bypass valve technology in order to confirm and characterize the approach; 4) usage of the experimental data for the valve to create a semi-empirical computational model for the bypass valve which could then be combined with the heat exchanger computational models; 5) repeat of the second task of simulating and exploring the system’s performance, but this time including the bypass valve to resolve its efficacy. Tasks were successfully completed, and the general notion of flexibly operating, high electrical efficiency CHHP was further corroborated. Supportive details are provided in the report.
High-throughput and computational tools provide a new opportunity to calculate combined bioactivity of exposure to diverse chemicals acting through a common mechanism. We used high throughput in vitro bioactivity data and exposure predictions from the U.S. EPA’s Toxicity and Exposure Forecaster (ToxCast and ExpoCast) to estimate combined estrogen receptor (ER) agonist activity of non-pharmaceutical chemical exposures for the general U.S. population. High-throughput toxicokinetic (HTTK) data provide conversion factors that relate bioactive concentrations measured in vitro (µM), to predicted population geometric mean exposure rates (mg/kg/day). These data were available for 22 chemicals with ER agonist activity and were estimated for other ER bioactive chemicals based on the geometric mean of HTTK values across chemicals. For each chemical, ER bioactivity across ToxCast assays was compared to predicted population geometric mean exposure at different levels of in vitro potency and model certainty. Dose additivity was assumed in calculating a Combined Exposure-Bioactivity Index (CEBI), the sum of exposure/bioactivity ratios. Combined estrogen bioactivity was also calculated in terms of the percent maximum bioactivity of chemical mixtures in human plasma using a concentration-addition model. Estimated CEBIs vary greatly depending on assumptions used for exposure and bioactivity. In general, CEBI values were <1 when using median of the estimated general population chemical intake rates, while CEBI were ≥1 when using the upper 95th confidence bound for those same intake rates for all chemicals. Concentration-addition model predictions of mixture bioactivity yield comparable results. Based on current in vitro bioactivity data, HTTK methods, and exposure models, combined exposure scenarios sufficient to influence estrogen bioactivity in the general population cannot be ruled out. Future improvements in screening methods and computational models could reduce uncertainty and better inform the potential combined effects of estrogenic chemicals.
Here, a key challenge for current and upcoming cosmic microwave background lensing measurements is their sensitivity to biases from extragalactic foregrounds, such as Sunyaev-Zel'dovich signals or cosmic infrared background emission. Several methods have been developed to mitigate these lensing foreground biases, dividing broadly into multifrequency cleaning approaches and modifications to the estimator geometry, but how to optimally combine these methods has not yet been explored in detail. In this paper, we examine which combination of lensing foreground mitigation strategies is best able to reduce the impact of foreground contamination for a Simons Observatory-like experiment while preserving maximal signal-to-noise. Although the optimal combination obtained depends on whether bias reduction or variance reduction is prioritized and on whether polarization data is used, generally, we find that combinations involving both geometric (profile hardening, source hardening, or shear) and multifrequency (symmetric cleaning) methods perform best. For lensing power spectrum measurements from temperature (polarization and temperature), our combined estimator methods are able to reduce the bias below σ/4 or 0.3% (0.1%), a factor of 16 (30) lower than the standard quadratic estimator bias, at a modest signal-to-noise cost of only 18% (12%). In contrast, single-method foreground-mitigation approaches struggle to reduce the bias to a negligible level below σ/2 without incurring a large noise penalty. For upcoming and current experiments, our combined methods therefore represent a promising approach for making lensing measurements with negligible foreground bias.
Abstract Background In the patients with pulmonary embolism (PE), PE itself can cause haemoptysis and other reasons can also cause haemoptysis. Therefore, the clinical characteristics and the causes of haemoptysis are lacking. Methods A retrospective analysis was performed that involved screening 583 PE patients and determining that haemoptysis occurred in 141 cases. Of these, eight cases were omitted due to anticoagulation‐related haemoptysis or unavailable data, leaving 133 cases that were enrolled in final analysis (127 acute and 6 chronic case of PE). We classified the acute PE patients who combined with diseases which can cause haemoptysis to non‐simple group (n = 61) and those without these diseases to simple group (n = 66). Results The incidence of haemoptysis in PE patients was 23.75%. In the simple group, the amount of haemoptysis ≤ 5 mL was 80.30% (53/66) and ≤ 20 mL was 90.91% (60/66). In the non‐simple group who combined with lung cancer, the amount of haemoptysis ≤ 5 mL was 68.4% (26/38) and ≤ 20 mL was 86.8% (33/38). Further analyses revealed that the amount of haemoptysis in the non‐simple group was larger than that in the simple group (median 5 [5‐125] vs. 5 [5‐5], p < 0.001; volume ≥ 100 mL: 29.5% vs. 6.1%, p < 0.001). Among all the PE patients, chronic thromboembolic pulmonary hypertension (CTEPH), PE combined with tuberculosis (TB) and PE combined with bronchiectasis were independent risk factors for the amount of haemoptysis ≥ 100 mL (OR = 15.00, (95% CI: 2.235‐100.652); 12.00, (3.101‐46.437); 60.00, (6.552‐549.441), respectively). Conclusions The haemoptysis caused by acute PE or PE combined with lung cancer was mild and was characterised by blood in sputum. PE combined with TB, bronchiectasis and CTEPH are associated with moderate to massive haemoptysis, with a greater risk of haemoptysis ≥ 100 mL.
Abstract Genome data from cancer patients represents relationships between the presence of a gene mutation and cancer occurrence in a patient. Different types of cancer in human are thought to be caused by combinations of two to nine gene mutations. Identifying these combinations through traditional exhaustive search requires the amount of computation that scales exponentially with the combination size and in most cases is intractable even for cutting-edge supercomputers. We propose a parameter-free heuristic approach that leverages the intrinsic topology of gene-patient mutations to identify carcinogenic combinations. The biological relevance of the identified combinations is measured by using them to predict the presence of tumor in previously unseen samples. The resulting classifiers for 16 cancer types perform on par with exhaustive search results, and score the average of 80.1% sensitivity and 91.6% specificity for the best choice of hit range per cancer type. Our approach is able to find higher-hit carcinogenic combinations targeting which would take years of computations using exhaustive search.
We have generated 81 independently controllable beams using a spatial light modulator and combined them on a diffractive combiner, to characterize the combiner and develop a fast phase error detection scheme. A key parameter of the diffractive combiner is measured in a new way, enabling an efficient combination when programming calibrated phases of each beam. This testbed provides a platform for development of advanced feedback phase control of high channel-count beam combination.
A combined cooling, heating, and power system, including a working fluid cycling between a compressor and a turbine in combination with a power generator. A humidifying regenerator is disposed between the compressor and the turbine, and in combination with the working fluid upstream and again downstream of the turbine to humidify and then dehumidify the working fluid. A working fluid heat exchanger is in combination with the working fluid between the turbine and the humidifying regenerator for further heat the working fluid. The heat exchanger is in combination with a heat source that heats both the working fluid and provides a separate heating medium. A cooling device is in combination with the working fluid between the humidifying regenerator and the compressor, wherein the cooling device cools the working fluid before entering the compressor and provides a separate cooling medium.
Novel therapies combined with radiation continue to be of significant interest in the developmental treatment paradigm of gynecologic cancers. Clinical implementation of immunotherapy in oncology has rapidly changed the treatment landscape, options, paradigm, and outcomes through clinical trials. Immunotherapy has emerged as a therapeutic pillar in the treatment of solid tumors with demonstrable synergistic activity when combined with radiation therapy and chemoradiotherapy by an alteration or enhancement of the immune system. In solid tumors, radiation therapy induces migration of dendritic cells, T cell activation, and proliferation, and increases in tumor-infiltrating lymphocytes. These immunomodulatory effects in conjunction with immune checkpoint blockade are currently under active investigation in the adjuvant, definitive, and metastatic settings. Results from early phase trials demonstrate promising efficacy and overall tolerable toxicity profiles of combined modality treatment. There is significant interest in optimizing the treatment for patients with locally advanced cervical cancer beyond the standard of care—chemoradiation—which has been in place for the last 30 years. The majority of cervical cancer emerges after persistent infection with a high-risk subtype of the human papillomavirus, where viral oncoproteins lead to cellular changes and immortalization. As a result, immune tolerance can develop, resulting in cancer. Knowledge of the mechanism of human papillomavirus–related oncogenesis suggests that immune therapy or checkpoint blockade can reinvigorate an antitumor immune response. Current clinical trials are exploring the therapeutic potential of these approaches. Uterine cancers have been grouped into 4 molecular subclasses by their driver mutations, mutational burden, and copy-number alterations. Of these subgroups, the polymerase epsilon–mutated and microsatellite-unstable may represent up to 40% of endometrial cancers, and they have been shown to be immunogenic. Because of the inherent immunogenicity of these MSI-high tumors, combined immune modulation strategies, including chemotherapy, radiation, and immunotherapy and immune checkpoint inhibitor therapy, are being explored to improve treatment outcomes. In this review, we explore current immunomodulatory and multimodality therapeutic approaches in the treatment of cervical and uterine cancer through ongoing clinical trials investigating the combination of immunotherapy and radiation therapy.
Highlights: • Lenvatinib combined with radiation significantly inhibits thyroid cancer growth. • Combined therapy induced apoptosis and G2/M phase cell cycle arrest. • Irradiation increased cellular uptake of lenvatinib into cancer cells. • Combined therapy suggests a new therapeutic strategy for advanced thyroid cancer. Although surgical treatment cures >90% of differentiated thyroid cancer (DTC) patients, the remaining patients, including advanced DTC cases, have poor clinical outcomes. These patients with inoperable disease have only two choices of radioactive iodine therapy and tyrosine kinase inhibitors such as lenvatinib, which have a high incidence of treatment-related adverse events and can only prolong progression free survival by approximately 5–15 months. In this study, we investigated the antitumor effects of combination therapy with lenvatinib and radiation (CTLR) for DTC. CTLR synergistically inhibited cell replication and colony formation in vitro and tumor growth in nude mice without apparent toxicities and suppressed the expression of proliferation marker (Ki-67). CTLR also induced apoptosis and G2/M phase cell cycle arrest. Moreover, quantitative analysis of the intracellular uptake of lenvatinib using liquid chromatography and mass spectrometry demonstrated that intracellular uptake of lenvatinib was significantly increased 48 h following irradiation. These data suggest that increased membrane permeability caused by irradiation increases the intracellular concentration of levatinib, contributing to the synergistic effect. This mechanism-based potential of combination therapy suggests a powerful new therapeutic strategy for advanced thyroid cancer with fewer side effects and might be a milestone for developing a regimen in clinical practice.
The SiO 2 /Al 2 O 3 mole ratio, pore size, and acid sites are the key parameters of zeolite’s activity in lignin pyrolysis. In this study, the comparison of individual Y and M zeolites, the combined ‘Y + M’ sample after regeneration, and their effect on lignin pyrolysis were studied in five cycles (regeneration and reuse). The results were explained using Brunauer, Emmet, and Teller (BET), micropore surface area (MSA), and total acid sites (TAS) analyses. In comparison with the individual Y or M zeolite sample, the consistent higher catalytic activities of the combined ‘Y + M’ sample in repeated cycles were observed. Pyrolysis heavy oils were characterized by nuclear magnetic resonance (NMR) spectroscopy and gel permeation chromatography (GPC). The NMR analyses revealed that with increased zeolite regeneration cycles, p-hydroxy phenyl and methoxyl groups increased. Decreases in guaiacyl phenolic hydroxyl were less for the combined ‘Y + M’ sample than the individual Y and M zeolites. Lower weight average (M w ) of heavy oil for the combined ‘Y + M’ sample indicated the enhanced cleavage of lignin structures in pyrolysis. These results support the higher catalytic activity of regenerated zeolites for the combined ‘Y + M’ sample compared with individual Y and M zeolites due to the improved MSA and TAS.
The industries examined in this report primarily rely on moderate-temperature heat provided by gas- or coal-fired boilers and combined heat and power (CHP) plants, delivered through standard process steam systems. High-temperature energy demands are often industry-specific and typically exceed the capabilities of high-temperature gas-cooled reactors (HTGRs). While it is technically feasible to replace process steam from fossil-based heat sources with nuclear energy, certain industries, such as methanol production and pulp and paper, face technoeconomic challenges in integrating nuclear energy without major changes or a technological shift. This is mainly due to the limited external energy demand remaining after the use of internal byproducts, waste heat recovery, and simple efficiency improvements. Achieving full decarbonization of these processes with nuclear energy would require significant technological advancements, involving experimental technology and substantial investments, making widespread adoption in existing industrial plants unlikely in the near term. This study reviews TES options in the context of enabling a flexible CHP supply while maintaining a steady nuclear heat input. Heat storage systems that interface between the reactor primary fluid and the CHP system offer superior performance and flexibility. Specifically, steam extraction downstream of the reheater with a two-tank molten-salt TES appears as the best solution regarding thermodynamic system benefits and system drawbacks. Using selected system configurations, a conceptual design of an industrial energy park was developed for industries with varying energy demands, such as steel production plants utilizing electric arc furnaces (EAFs) and chemical plants, as well as for those with constant energy demands, like petroleum refineries. This design highlights the capabilities of TES and explores its potential business cases. The study also conceptually develops the potential for integrating additional energy sources with nuclear systems through the implementation of TES. The potential of the HTGR-TES-CHP system was also evaluated considering key uncertainties such as industrial demand profiles, external grid access availability, and eligible tax credit levels, using the Holistic Energy Resource Optimization Network. Sensitivity of net present value to these uncertainties was analyzed to determine the optimal number of nuclear reactors (and CHP systems) and the suitable TES capacity. The results were interpreted from a decision-maker’s perspective, focusing on three key areas: deployment strategy (oversized units vs. undersized units with TES support), industrial process characteristics (thermal-intensive single profiles vs. electricity-intensive combined profiles), and operational goals (maximizing profits vs. minimizing natural gas (NG) consumption or external grid dependence). The optimization results indicate that the HTGR-TES-CHP system significantly reduces reliance on NG boilers for individual industrial processes by 9-60% (in NG capacity factor), with an average reduction of 38%, compared to standalone NG boiler operation case (Business As Usual [BAU]). For combined industrial processes, the reduction ranges from 37-77%, with an average of 60%. Additionally, the system greatly reduces dependence on external grids. In meeting industrial electrical demands, a 33-100% self-sufficient internal electricity supply is achieved for single industrial process, with an average of 74%, compared to the BAU scenario, where 100% of electricity is imported. For combined processes, 35-100% of internal electricity demands are met by the reactor, with an average of 73%. At last, the relative NG price levels at which the proposed HTGR-TES-CHP system can cost-effectively enter the market currently dominated by existing NG boilers were estimated. For a moderate HTGR CAPEX level ($\$$2500/kWth, $\$$6329/kWe), the analysis suggests that NG prices must be 2.5 to 7 times higher than HTGR variable operating and maintenance costs for single industrial process, and 5.5 to 9.5 times higher for a combined process scenario. Tax credit modeling shows that the Investment Tax Credit significantly reduces the price threshold needed to break even, making the system competitive with NG boilers in certain cases.
A combination of measurements of the inclusive top-quark pair production cross-section performed by ATLAS and CMS in proton–proton collisions at centre-of-mass energies of 7 and 8 TeV at the LHC is presented. The cross-sections are obtained using top-quark pair decays with an opposite-charge electron–muon pair in the final state and with data corresponding to an integrated luminosity of about 5 fb$^{−1}$ at $ \sqrt{s} $ = 7 TeV and about 20 fb$^{−1}$ at $ \sqrt{s} $ = 8 TeV for each experiment. The combined cross-sections are determined to be 178.5 ± 4.7 pb at $ \sqrt{s} $ = 7 TeV and $ {243.3}_{-5.9}^{+6.0} $ pb at $ \sqrt{s} $ = 8 TeV with a correlation of 0.41, using a reference top-quark mass value of 172.5 GeV. The ratio of the combined cross-sections is determined to be R$_{8/7}$ = 1.363 ± 0.032. The combined measured cross-sections and their ratio agree well with theory calculations using several parton distribution function (PDF) sets. The values of the top-quark pole mass (with the strong coupling fixed at 0.118) and the strong coupling (with the top-quark pole mass fixed at 172.5 GeV) are extracted from the combined results by fitting a next-to-next-to-leading-order plus next-to-next-to-leading-log QCD prediction to the measurements. Using a version of the NNPDF3.1 PDF set containing no top-quark measurements, the results obtained are $ {m}_t^{\textrm{pole}}={173.4}_{-2.0}^{+1.8} $ GeV and $ {\alpha}_{\textrm{s}}\left({m}_Z\right)={0.1170}_{-0.0018}^{+0.0021} $.[graphic not available: see fulltext]