Beneficial Effects of High-Intensity Interval Training and Dietary Changes Intervention on Hepatic Fat Accumulation in HFD-Induced Obese Rats

Lifestyle intervention encompassing nutrition and physical activity are effective strategies to prevent progressive lipid deposition in the liver. This study aimed to explore the effect of dietary change, and/or high-intensity interval training (HIIT) on hepatic lipid accumulation in high fat diet (HFD)-induced obese rats. We divided lean rats into lean control (LC) or HIIT groups (LH), and obese rats into obese normal chow diet (ND) control (ONC) or HIIT groups (ONH) and obese HFD control (OHC) or HIIT groups (OHH). We found that dietary or HIIT intervention significantly decreased body weight and the risk of dyslipidemia, prevented hepatic lipid accumulation. HIIT significantly improved mitochondrial fatty acid oxidation through upregulating mitochondrial enzyme activities, mitochondrial function and AMPK/PPARalpha/CPT1alpha pathway, as well as inhibiting hepatic de novo lipogenesis in obese HFD rats. These findings indicate that dietary alone or HIIT intervention powerfully improve intrahepatic storage of fat in diet induced obese rats. Keywords: Obesity, Exercise, Diet, Mitochondrial function, Lipid deposition.

The impact of low-mode symmetry on inertial fusion energy output in the burning plasma state

Indirect Drive Inertial Confinement Fusion Experiments on the National Ignition Facility (NIF) have achieved a burning plasma state with neutron yields exceeding 170 kJ, roughly 3 times the prior record and a necessary stage for igniting plasmas. The results are achieved despite multiple sources of degradations that lead to high variability in performance. Results shown here, for the first time, include an empirical correction factor for mode-2 asymmetry in the burning plasma regime in addition to previously determined corrections for radiative mix and mode-1. Analysis shows that including these three corrections alone accounts for the measured fusion performance variability in the two highest performing experimental campaigns on the NIF to within error. Here we quantify the performance sensitivity to mode-2 symmetry in the burning plasma regime and apply the results, in the form of an empirical correction to a 1D performance model. Furthermore, we find the sensitivity to mode-2 determined through a series of integrated 2D radiation hydrodynamic simulations to be consistent with the experimentally determined sensitivity only when including alpha-heating.

Achievement of Target Gain Larger than Unity in an Inertial Fusion Experiment

On December 5, 2022, an indirect drive fusion implosion on the National Ignition Facility (NIF) achieved a target gain G_{target} of 1.5. This is the first laboratory demonstration of exceeding "scientific breakeven" (or G_{target}>1) where 2.05 MJ of 351 nm laser light produced 3.1 MJ of total fusion yield, a result which significantly exceeds the Lawson criterion for fusion ignition as reported in a previous NIF implosion [H. Abu-Shawareb et al. (Indirect Drive ICF Collaboration), Phys. Rev. Lett. 129, 075001 (2022)PRLTAO0031-900710.1103/PhysRevLett.129.075001]. This achievement is the culmination of more than five decades of research and gives proof that laboratory fusion, based on fundamental physics principles, is possible. This Letter reports on the target, laser, design, and experimental advancements that led to this result.

Time-resolved X-ray diffraction diagnostic development for the National Ignition Facility

We present the development of an experimental platform that can collect four frames of x-ray diffraction data along a single line of sight during laser-driven, dynamic-compression experiments at the National Ignition Facility. The platform is comprised of a diagnostic imager built around ultrafast sensors with a 2-ns integration time, a custom target assembly that serves also to shield the imager, and a 10-ns duration, quasi-monochromatic x-ray source produced by laser-generated plasma. We demonstrate the performance with diffraction data for Pb ramp compressed to 150 GPa and illuminated by a Ge x-ray source that produces ∼7 × 1011, 10.25-keV photons/ns at the 400 μm diameter sample.

Dissecting cellular states of infiltrating microenvironment cells in melanoma by integrating single-cell and bulk transcriptome analysis

BACKGROUND

Cellular states of different immune cells can affect the activity of the whole immune microenvironment.

METHODS

Here, leveraging reference profiles of microenvironment cell states that were constructed based on single-cell RNA-seq data of melanoma, we dissected the composition of microenvironment cell states across 463 skin cutaneous melanoma (SKCM) bulk samples through CIBERSORT-based deconvolution of gene expression profiles and revealed high heterogeneity of their distribution. Correspondence analysis on the estimated cellular fractions of melanoma bulk samples was performed to identify immune phenotypes. Based on the publicly available clinical survival and therapy data, we analyzed the relationship between immune phenotypes and clinical outcomes of melanoma.

RESULTS

By analysis of the relationships among those cell states, we further identified three distinct tumor microenvironment immune phenotypes: "immune hot/active", "immune cold-suppressive" and "immune cold-exhausted". They were characterized by markedly different patterns of cell states: most notably the CD8 T Cytotoxic state, CD8 T Mixed state, B non-regulatory state and cancer-associated fibroblasts (CAFs), depicting distinct types of antitumor immune response (or immune activity). These phenotypes had prognostic significance for progression-free survival and implications in response to immune therapy in an independent cohort of anti-PD1 treated melanoma patients.

CONCLUSIONS

The proposed strategy of leveraging single-cell data to dissect the composition of microenvironment cell states in individual bulk tumors can also extend to other cancer types, and our results highlight the importance of microenvironment cell states for the understanding of tumor immunity.

Identifying the driver miRNAs with somatic copy number alterations driving dysregulated ceRNA networks in cancers

BACKGROUND

MicroRNAs (miRNAs) play critical roles in cancer initiation and progression, which were critical components to maintain the dynamic balance of competing endogenous RNA (ceRNA) networks. Somatic copy number alterations (SCNAs) in the cancer genome could disturb the transcriptome level of miRNA to deregulate this balance. However, the driving effects of SCNAs of miRNAs were insufficiently understood.

METHODS

In this study, we proposed a method to dissect the functional roles of miRNAs under different copy number states and identify driver miRNAs by integrating miRNA SCNAs profile, miRNA-target relationships and expression profiles of miRNA, mRNA and lncRNA.

RESULTS

Applying our method to 813 TCGA breast cancer (BRCA) samples, we identified 29 driver miRNAs whose SCNAs significantly and concordantly regulated their own expression levels and further inversely dysregulated expression levels of their targets or disturbed the miRNA-target networks they directly involved. Based on miRNA-target networks, we further constructed dynamic ceRNA networks driven by driver SCNAs of miRNAs and identified three different patterns of SCNA interference in the miRNA-mediated dynamic ceRNA networks. Survival analysis of driver miRNAs showed that high-level amplifications of four driver miRNAs (including has-miR-30d-3p, has-mir-30b-5p, has-miR-30d-5p and has-miR-151a-3p) in 8q24 characterized a new BRCA subtype with poor prognosis and contributed to the dysfunction of cancer-associated hallmarks in a complementary way. The SCNAs of driver miRNAs across different cancer types contributed to the cancer development by dysregulating different components of the same cancer hallmarks, suggesting the cancer specificity of driver miRNA.

CONCLUSIONS

These results demonstrate the efficacy of our method in identifying driver miRNAs and elucidating their functional roles driven by endogenous SCNAs, which is useful for interpreting cancer genomes and pathogenic mechanisms.

Extended X-ray absorption fine structure of dynamically-compressed copper up to 1 terapascal

Large laser facilities have recently enabled material characterization at the pressures of Earth and Super-Earth cores. However, the temperature of the compressed materials has been largely unknown, or solely relied on models and simulations, due to lack of diagnostics under these challenging conditions. Here, we report on temperature, density, pressure, and local structure of copper determined from extended x-ray absorption fine structure and velocimetry up to 1 Terapascal. These results nearly double the highest pressure at which extended x-ray absorption fine structure has been reported in any material. In this work, the copper temperature is unexpectedly found to be much higher than predicted when adjacent to diamond layer(s), demonstrating the important influence of the sample environment on the thermal state of materials; this effect may introduce additional temperature uncertainties in some previous experiments using diamond and provides new guidance for future experimental design.

Identifying the personalized driver gene sets maximally contributing to abnormality of transcriptome phenotype in glioblastoma multiforme individuals

High heterogeneity in genome and phenotype of cancer populations made it difficult to apply population-based common driver genes to the diagnosis and treatment of cancer individuals. Characterizing and identifying the personalized driver mechanism for glioblastoma multiforme (GBM) individuals were pivotal for the realization of precision medicine. We proposed an integrative method to identify the personalized driver gene sets by integrating the profiles of gene expression and genetic alterations in cancer individuals. This method coupled genetic algorithm and random walk to identify the optimal gene sets that could explain abnormality of transcriptome phenotype to the maximum extent. The personalized driver gene sets were identified for 99 GBM individuals using our method. We found that genomic alterations in between one and seven driver genes could maximally and cumulatively explain the dysfunction of cancer hallmarks across GBM individuals. The driver gene sets were distinct even in GBM individuals with significantly similar transcriptomic phenotypes. Our method identified MCM4 with rare genetic alterations as previously unknown oncogenic genes, the high expression of which were significantly associated with poor GBM prognosis. The functional experiments confirmed that knockdown of MCM4 could significantly inhibit proliferation, invasion, migration, and clone formation of the GBM cell lines U251 and U118MG, and overexpression of MCM4 significantly promoted the proliferation, invasion, migration, and clone formation of the GBM cell line U87MG. Our method could dissect the personalized driver genetic alteration sets that are pivotal for developing targeted therapy strategies and precision medicine. Our method could be extended to identify key drivers from other levels and could be applied to more cancer types.

Structures of strong shocks in low-density helium and neon gases

Strong shocks are essential components in many high-energy-density environments such as inertial confinement fusion implosions. However, the experimental measurements of the spatial structures of such shocks are sparse. In this paper, the soft x-ray emission of a shock front in a helium gas mixture (90% helium, 10% neon) and a pure neon gas was spatially resolved using an imaging spectrometer. We observe that the shock width in the helium mixture gas is about twice as large as in the pure neon gas. Moreover, they exhibit different precursor layers, where electron temperature greatly exceeds ion temperature, extending for more than ∼350µm with the helium gas mixture but less than 30µm in the pure neon. At the shock front, calculations show that the electrons are strongly collisional with mean-free path two orders of magnitude shorter than the characteristic length of the shock. However, the helium ions can reach a kinetic regime as a consequence of their mean-free path being comparable to the scale of the shock. A radiation-hydrodynamic simulation demonstrates the impact of thermal conduction on the formation of the precursors with charge state, Z, playing a major role in heat flow and the precursor formation in both the helium mixture and the pure neon gases. Particle-in-cell simulations are also performed to study the ion kinetic effects on the formation of the observed precursors. A group of fast-streaming ions is observed leading the shock only in the helium gas mixture. Both effects explain the longer precursor layer in the helium shock.

The Heterogeneous Cellular States of Glioblastoma Stem Cells Revealed by Single Cell Analysis

Glioblastoma stem cells (GSCs) contributed to the progression, treatment resistance, and relapse of glioblastoma (GBM). However, current researches on GSCs were performed usually outside the human tumor microenvironment, ignoring the importance of the cellular states of primary GSCs. In this study, we leveraged single-cell transcriptome sequencing data of 6 independent GBM cohorts from public databases, and combined lineage and stemness features to identify primary GSCs. We dissected the cell states of GSCs and correlated them with the clinical outcomes of patients. As a result, we constructed a cellular hierarchy where GSCs resided at the center. In addition, we identified and characterized 2 different and recurrent GSCs subpopulations: proliferative GSCs (pGSCs) and quiescent GSCs (qGSCs). The pGSCs showed high cell cycle activity, indicating rapid cell division, while qGSCs showed a quiescent state. Then we traced the processes of tumor development by pseudo-time analysis and tumor phylogeny, and found that GSCs accumulated throughout the whole tumor development period. During the process, pGSCs mainly contributed to the early stage and qGSCs were enriched in the later stage. Finally, we constructed an 8-gene prognostic signature reflecting pGSCs activity and found that patients whose tumors were enriched for the pGSC signature had poor clinical outcomes. Our study highlights the primary GSCs heterogeneity and its correlation to tumor development and clinical outcomes, providing the potential targets for GBM treatment.

Ultrafast time-resolved 2D imaging of laser-driven fast electron transport in solid density matter using an x-ray free electron laser

High-power, short-pulse laser-driven fast electrons can rapidly heat and ionize a high-density target before it hydrodynamically expands. The transport of such electrons within a solid target has been studied using two-dimensional (2D) imaging of electron-induced Kα radiation. However, it is currently limited to no or picosecond scale temporal resolutions. Here, we demonstrate femtosecond time-resolved 2D imaging of fast electron transport in a solid copper foil using the SACLA x-ray free electron laser (XFEL). An unfocused collimated x-ray beam produced transmission images with sub-micron and ∼10 fs resolutions. The XFEL beam, tuned to its photon energy slightly above the Cu K-edge, enabled 2D imaging of transmission changes induced by electron isochoric heating. Time-resolved measurements obtained by varying the time delay between the x-ray probe and the optical laser show that the signature of the electron-heated region expands at ∼25% of the speed of light in a picosecond duration. Time-integrated Cu Kα images support the electron energy and propagation distance observed with the transmission imaging. The x-ray near-edge transmission imaging with a tunable XFEL beam could be broadly applicable for imaging isochorically heated targets by laser-driven relativistic electrons, energetic protons, or an intense x-ray beam.

High-resolution x-ray spectrometer for x-ray absorption fine structure spectroscopy

Two extended x-ray absorption fine structure flat crystal x-ray spectrometers (EFX's) were designed and built for high-resolution x-ray spectroscopy over a large energy range with flexible, on-shot energy dispersion calibration capabilities. The EFX uses a flat silicon [111] crystal in the reflection geometry as the energy dispersive optic covering the energy range of 6.3-11.4 keV and achieving a spectral resolution of 4.5 eV with a source size of 50 μm at 7.2 keV. A shot-to-shot configurable calibration filter pack and Bayesian inference routine were used to constrain the energy dispersion relation to within ±3 eV. The EFX was primarily designed for x-ray absorption fine structure (XAFS) spectroscopy and provides significant improvement to the Laboratory for Laser Energetics' OMEGA-60 XAFS experimental platform. The EFX is capable of performing extended XAFS measurements of multiple absorption edges simultaneously on metal alloys and x-ray absorption near-edge spectroscopy to measure the electron structure of compressed 3d transition metals.

Developing a platform for Fresnel diffractive radiography with 1 μm spatial resolution at the National Ignition Facility

An x-ray Fresnel diffractive radiography platform was designed for use at the National Ignition Facility. It will enable measurements of micron-scale changes in the density gradients across an interface between isochorically heated warm dense matter materials, the evolution of which is driven primarily through thermal conductivity and mutual diffusion. We use 4.75 keV Ti K-shell x-ray emission to heat a 1000 μm diameter plastic cylinder, with a central 30 μm diameter channel filled with liquid D₂, up to 8 eV. This leads to a cylindrical implosion of the liquid D₂ column, compressing it to ∼2.3 g/cm³. After pressure equilibration, the location of the D₂/plastic interface remains steady for several nanoseconds, which enables us to track density gradient changes across the material interface with high precision. For radiography, we use Cu He-α x rays at 8.3 keV. Using a slit aperture of only 1 μm width increases the spatial coherence of the source, giving rise to significant diffraction features in the radiography signal, in addition to the refraction enhancement, which further increases its sensitivity to density scale length changes at the D₂/plastic interface.

Revealing the functions of clonal driver gene mutations in patients based on evolutionary dependencies

The clonal mutations in driver genes enable cells to gradually acquire growth advantage in tumor development. Therefore, revealing the functions of clonal driver gene mutations is important. Here, we proposed the method FCMP that considered evolutionary dependencies to analyze the functions of clonal driver gene mutations in a single patient. Applying our method to five cancer types from The Cancer Genome Atlas, we identified specific functions and common functions of clonal driver gene mutations. We found that the clonal driver gene mutations in the same patient played multiple functions. We also found that clonal mutations in the same driver gene performed different functions in different patients. These findings suggested that the clonal driver gene mutations showed strong tumor heterogeneity. In the pan-cancer analysis, the immune-related functions for clonal driver gene mutations were shared by multiple cancer types. In addition, clonal mutations in some driver genes predicted the survival of patients in cancers.

A new class of variable-radii diffraction optics for high-resolution x-ray spectroscopy at the National Ignition Facility (invited)

A new class of crystal shapes has been developed for x-ray spectroscopy of point-like or small (a few mm) emission sources. These optics allow for dramatic improvement in both achievable energy resolution and total throughput of the spectrometer as compared with traditional designs. This class of crystal shapes, collectively referred to as the Variable-Radii Spiral (VR-Spiral), utilize crystal shapes in which both the major and minor radii are variable. A crystal using this novel VR-Spiral shape has now been fabricated for high-resolution Extended X-ray Absorption Fine Structure (EXAFS) experiments targeting the Pb-L₃ (13.0 keV) absorption edge at the National Ignition Facility. The performance of this crystal has been characterized in the laboratory using a microfocus x-ray source, showing that high-resolution high-throughput EXAFS spectra can be acquired using this geometry. Importantly, these successful tests show that the complex three-dimensional crystal shape is manufacturable with the required precision needed to realize the expected performance of better than 5 eV energy resolution while using a 30 mm high crystal. An improved generalized mathematical form for VR-Spiral shapes is also presented allowing improved optimization as compared to the first sinusoidal-spiral based design. This new formulation allows VR-Spiral spectrometers to be designed at any magnification with optimized energy resolution at all energies within the spectrometer bandwidth.

Diffraction enhanced imaging utilizing a laser produced x-ray source

Image formation by Fresnel diffraction utilizes both absorption and phase-contrast to measure electron density profiles. The low spatial and spectral coherence requirements allow the technique to be performed with a laser-produced x-ray source coupled with a narrow slit. This makes it an excellent candidate for probing interfaces between materials at extreme conditions, which can only be generated at large-scale laser or pulsed power facilities. Here, we present the results from a proof-of-principle experiment demonstrating an effective ∼2 μm laser-generated source at the OMEGA Laser Facility. This was achieved using slits of 1 × 30 μm² and 2 × 40 μm² geometry, which were milled into 30 μm thick Ta plates. Combining these slits with a vanadium He-like 5.2 keV source created a 1D imaging system capable of micrometer-scale resolution. The principal obstacles to achieving an effective 1 μm source are the slit tilt and taper-where the use of a tapered slit is necessary to increase the alignment tolerance. We demonstrate an effective source size by imaging a 2 ± 0.2 μm radius tungsten wire.

Lawson Criterion for Ignition Exceeded in an Inertial Fusion Experiment

For more than half a century, researchers around the world have been engaged in attempts to achieve fusion ignition as a proof of principle of various fusion concepts. Following the Lawson criterion, an ignited plasma is one where the fusion heating power is high enough to overcome all the physical processes that cool the fusion plasma, creating a positive thermodynamic feedback loop with rapidly increasing temperature. In inertially confined fusion, ignition is a state where the fusion plasma can begin "burn propagation" into surrounding cold fuel, enabling the possibility of high energy gain. While "scientific breakeven" (i.e., unity target gain) has not yet been achieved (here target gain is 0.72, 1.37 MJ of fusion for 1.92 MJ of laser energy), this Letter reports the first controlled fusion experiment, using laser indirect drive, on the National Ignition Facility to produce capsule gain (here 5.8) and reach ignition by nine different formulations of the Lawson criterion.

Systematic investigation of the prognostic impact of clonal status of somatic mutations across multiple cancer types

Tumors are genetically heterogeneous and many mutations are actually present in subclonal populations. The clonal status of mutations is valuable for accurate prognosis, clinical management. The aim of this study was to identify the clonal status of somatic mutations and systematically evaluate their prognostic values across various cancer types. We totally identified 227 clonal and 432 subclonal mutations contributed to prognosis and demonstrated the importance of clonal status in improving mutation-related clinical guidance. We further developed a customized multi-step approach to identify gene-specific prognostic patterns of clonal status at pan-cancer level and found some cancer-specific prognostic patterns. The 'subclonal-dependent risk' subpattern was one of the most common subpatterns, it usually accompanied by high genomic in-stability and high extent of intra-tumor heterogeneity and could be used to improve the accuracy of prognostic analysis. Our results revealed the importance of clonal status, especially subclonal mutation in clinical survival.

Transport of an intense proton beam from a cone-structured target through plastic foam with unique proton source modeling

Laser-accelerated proton beams are applicable to several research areas within high-energy density science, including warm dense matter generation, proton radiography, and inertial confinement fusion, which all involve transport of the beam through matter. We report on experimental measurements of intense proton beam transport through plastic foam blocks. The intense proton beam was accelerated by the 10ps, 700J OMEGA EP laser irradiating a curved foil target, and focused by an attached hollow cone. The protons then entered the foam block of density 0.38g/cm^{3} and thickness 0.55 or 1.00mm. At the rear of the foam block, a Cu layer revealed the cross section of the intense beam via proton- and hot electron-induced Cu-K_{α} emission. Images of x-ray emission show a bright spot on the rear Cu film indicative of a forward-directed beam without major breakup. 2D fluid-PIC simulations of the transport were conducted using a unique multi-injection source model incorporating energy-dependent beam divergence. Along with postprocessed calculations of the Cu-K_{α} emission profile, simulations showed that protons retain their ballistic transport through the foam and are able to heat the foam up to several keV in temperature. The total experimental emission profile for the 1.0mm foam agrees qualitatively with the simulated profile, suggesting that the protons indeed retain their beamlike qualities.

Toward an integrated platform for characterizing laser-driven, isochorically heated plasmas with 1 µm spatial resolution

Warm dense matter is a region of phase space that is of high interest to multiple scientific communities ranging from astrophysics to inertial confinement fusion. Further understanding of the conditions and properties of this complex state of matter necessitates experimental benchmarking of the current theoretical models. We discuss the development of an x-ray radiography platform designed to measure warm dense matter transport properties at large laser facilities such as the OMEGA Laser Facility. Our platform, Fresnel diffractive radiography, allows for high spatial resolution imaging of isochorically heated targets, resulting in notable diffractive effects at sharp density gradients that are influenced by transport properties such as thermal conductivity. We discuss initial results, highlighting the capabilities of the platform in measuring diffractive features with micrometer-level spatial resolution.

Revealing the contribution of somatic gene mutations to shaping tumor immune microenvironment

Interaction between tumor cells and immune cells determined highly heterogeneous microenvironments across patients, leading to substantial variation in clinical benefits from immunotherapy. Somatic gene mutations were found not only to elicit adaptive immunity but also to influence the composition of tumor immune microenvironment and various processes of antitumor immunity. However, due to an incomplete view of associations between gene mutations and immunophenotypes, how tumor cells shape the immune microenvironment and further determine the clinical benefit of immunotherapy is still unclear. To address this, we proposed a computational approach, inference of mutation effect on immunophenotype by integrated gene set enrichment analysis (MEIGSEA), for tracing back the genomic factor responsible for differences in immunophenotypes. MEIGSEA was demonstrated to accurately identify the previous confirmed immune-associated gene mutations, and systematic evaluation in simulation data further supported its performance. We used MEIGSEA to investigate the influence of driver gene mutations on the infiltration of 22 immune cell types across 19 cancers from The Cancer Genome Atlas. The top associated gene mutations with infiltration of CD8 T cells, such as CASP8, KRAS and EGFR, also showed extensive impact on other immune components; meanwhile, immune effector cells shared critical gene mutations that collaboratively contribute to shaping distinct tumor immune microenvironment. Furthermore, we highlighted the predictive capacity of gene mutations that are positively associated with CD8 T cells for the clinical benefit of immunotherapy. Taken together, we present a computational framework to help illustrate the potential of somatic gene mutations in shaping the tumor immune microenvironment.

Dynamic regulatory networks of T cell trajectory dissect transcriptional control of T cell state transition

T cells exhibit heterogeneous functional states, which correlate with responsiveness to immune checkpoint blockade and prognosis of tumor patients. However, the molecular regulatory mechanisms underlying the dynamic process of T cell state transition remain largely unknown. Based on single-cell transcriptome data of T cells in non-small cell lung cancer, we combined cell states and pseudo-times to propose a pipeline to construct dynamic regulatory networks for dissecting the process of T cell dysfunction. Candidate regulators at different stages were revealed in the process of tumor-infiltrating T cell dysfunction. Through comparing dynamic networks across the T cell state transition, we revealed frequent regulatory interaction rewiring and further refined critical regulators mediating each state transition. Several known regulators were identified, including TCF7, EOMES, ID2, and TOX. Notably, one of the critical regulators, TSC22D3, was frequently identified in the state transitions from the intermediate state to the pre-dysfunction and dysfunction state, exerting diverse roles in each state transition by regulatory interaction rewiring. Moreover, higher expression of TSC22D3 was associated with the clinical outcome of tumor patients. Our study embedded transcription factors (TFs) within the temporal dynamic networks, providing a comprehensive view of dynamic regulatory mechanisms controlling the process of T cell state transition.

Single-Cell Transcriptomic Analysis Reveals a Tumor-Reactive T Cell Signature Associated With Clinical Outcome and Immunotherapy Response In Melanoma

The infiltration of tumor-reactive T cells in the tumor site is associated with better survival and immunotherapy response. However, tumor-reactive T cells were often represented by the infiltration of total CD8+ T cells, which was confounded by the presence of bystander T cells. To identify tumor-reactive T cells at the cancer lesion, we performed integration analyses of three scRNA-seq data sets of T cells in melanoma. Extensive heterogeneous functional states of T cells were revealed in the tumor microenvironment. Among these states, we identified a subset of tumor-reactive T cells which specifically expressed tumor-reactive markers and T cell activation signature, and were strongly enriched for larger T cell receptor (TCR) clones. We further identified and validated a tumor-reactive T cell signature (TRS) to evaluate the tumor reactivity of T cells in tumor patients. Patients with high TRS scores have strong immune activity and high mutation burden in the TCGA-SKCM cohort. We also demonstrated a significant association of the TRS with the clinical outcomes of melanoma patients, with higher TRS scores representing better survival, which was validated in four external independent cohorts. Furthermore, the TRS scores exhibited greater performance on prognosis prediction than infiltration levels of CD8+ T cells and previously published prognosis-related signatures. Finally, we observed the capability of TRS to predict immunotherapy response in melanoma. Together, based on integrated analysis of single-cell RNA-sequencing, we developed and validated a tumor-reactive-related signature that demonstrated significant association with clinical outcomes and response to immunotherapy.

Experimental Observations of Laser-Driven Tin Ejecta Microjet Interactions

The study of high-velocity particle-laden flow interactions is of importance for the understanding of a wide range of natural phenomena, ranging from planetary formation to cloud interactions. Experimental observations of particle dynamics are sparse given the difficulty of generating high-velocity flows of many particles. Ejecta microjets are micron-scale jets formed by strong shocks interacting with imprinted surfaces to generate particle plumes traveling at several kilometers per second. As such, the interaction of two ejecta microjets provides a novel experimental methodology to study interacting particle streams. In this Letter, we report the first time sequences of x-ray radiography images of two interacting tin ejecta microjets taken on a platform designed for the OMEGA Extended Performance (OMEGA EP) laser. We observe that the microjets pass through each other unattenuated for the case of 11.7±3.2  GPa shock pressures and jet velocities of 2.2±0.5  km/s but show strong interaction dynamics for 116.0±6.1  GPa shock pressures and jet velocities of 6.5±0.5  km/s. We find that radiation-hydrodynamic simulations of the experiments are able to capture many aspects of the collisional behavior, such as the attenuation of jet velocity in the direction of propagation, but are unable to match the full spread of the strongly interacting cloud.

Prognostic impact of a lymphocyte activation-associated gene signature in GBM based on transcriptome analysis

Background

Glioblastoma multiforme (GBM) is a highly, malignant tumor of the primary central nervous system. Patients diagnosed with this type of tumor have a poor prognosis. Lymphocyte activation plays important roles in the development of cancers and its therapeutic treatments.

Objective

We sought to identify an efficient lymphocyte activation-associated gene signature that could predict the progression and prognosis of GBM.

Methods

We used univariate Cox proportional hazards regression and stepwise regression algorithm to develop a lymphocyte activation-associated gene signature in the training dataset (TCGA, n = 525). Then, the signature was validated in two datasets, including GSE16011 (n = 150) and GSE13041 (n = 191) using the Kaplan Meier method. Univariate and multivariate Cox proportional hazards regression models were used to adjust for clinicopathological factors.

Results

We identified a lymphocyte activation-associated gene signature (TCF3, IGFBP2, TYRO3 and NOD2) in the training dataset and classified the patients into high-risk and low-risk groups with significant differences in overall survival (median survival 15.33 months vs 12.57 months, HR = 1.55, 95% CI [1.28-1.87], log-rank test P < 0.001). This signature showed similar prognostic values in the other two datasets. Further, univariate and multivariate Cox proportional hazards regression models analysis indicated that the signature was an independent prognostic factor for GBM patients. Moreover, we determined that there were differences in lymphocyte activity between the high- and low-risk groups of GBM patients among all datasets. Furthermore, the lymphocyte activation-associated gene signature could significantly predict the survival of patients with certain features, including IDH-wildtype patients and patients undergoing radiotherapy. In addition, the signature may also improve the prognostic power of age.

Conclusions

In summary, our results suggested that the lymphocyte activation-associated gene signature is a promising factor for the survival of patients, which is helpful for the prognosis of GBM patients.

Design and expected performance of a variable-radii sinusoidal spiral x-ray spectrometer for the National Ignition Facility

A novel high-resolution x-ray spectrometer for point-like emission sources has been developed using a crystal shape having both a variable major and a variable minor radius of curvature. This variable-radii sinusoidal spiral spectrometer (VR-Spiral) allows three common spectrometer design goals to be achieved simultaneously: 1. reduction of aberrations and improved spectral (energy) resolution, 2. reduction of source size broadening, and 3. use of large crystals to improve total throughput. The VR-Spiral concept and its application to practical spectrometer design are described in detail. This concept is then used to design a spectrometer for an extreme extended x-ray absorption fine structure experiment at the National Ignition Facility looking at the Pb L₃ absorption edge at 13.0352 keV. The expected performance of this VR-Spiral spectrometer, both in terms of energy resolution and spatial resolution, is evaluated through the use of a newly developed raytracing tool, xicsrt. Finally, the expected performance of the VR-Spiral concept is compared to that of spectrometers based on conventional toroidal and variable-radii toroidal crystal geometries showing a greatly improved energy resolution.

Identifying Key Somatic Copy Number Alterations Driving Dysregulation of Cancer Hallmarks in Lower-Grade Glioma

Somatic copy-number alterations (SCNAs) are major contributors to cancer development that are pervasive and highly heterogeneous in human cancers. However, the driver roles of SCNAs in cancer are insufficiently characterized. We combined network propagation and linear regression models to design an integrative strategy to identify driver SCNAs and dissect the functional roles of SCNAs by integrating profiles of copy number and gene expression in lower-grade glioma (LGG). We applied our strategy to 511 LGG patients and identified 98 driver genes that dysregulated 29 cancer hallmark signatures, forming 143 active gene-hallmark pairs. We found that these active gene-hallmark pairs could stratify LGG patients into four subtypes with significantly different survival times. The two new subtypes with similar poorest prognoses were driven by two different gene sets (one including EGFR, CDKN2A, CDKN2B, INFA8, and INFA5, and the other including CDK4, AVIL, and DTX3), respectively. The SCNAs of the two gene sets could disorder the same cancer hallmark signature in a mutually exclusive manner (including E2F_TARGETS and G2M_CHECKPOINT). Compared with previous methods, our strategy could not only capture the known cancer genes and directly dissect the functional roles of their SCNAs in LGG, but also discover the functions of new driver genes in LGG, such as IFNA5, IFNA8, and DTX3. Additionally, our method can be applied to a variety of cancer types to explore the pathogenesis of driver SCNAs and improve the treatment and diagnosis of cancer.

Transcriptomic heterogeneity of driver gene mutations reveals novel mutual exclusivity and improves exploration of functional associations

Background

Lung adenocarcinoma (LUAD), as the most common subtype of lung cancer, is the leading cause of cancer deaths in the world. The accumulation of driver gene mutations enables cancer cells to gradually acquire growth advantage. Therefore, it is important to understand the functions and interactions of driver gene mutations in cancer progression.

Methods

We obtained gene mutation data and gene expression profile of 506 LUAD tumors from The Cancer Genome Atlas (TCGA). The subtypes of tumors with driver gene mutations were identified by consensus cluster analysis.

Results

We found 21 significantly mutually exclusive pairs consisting of 20 genes among 506 LUAD patients. Because of the increased transcriptomic heterogeneity of mutations, we identified subtypes among tumors with non‐silent mutations in driver genes. There were 494 mutually exclusive pairs found among driver gene mutations within different subtypes. Furthermore, we identified functions of mutually exclusive pairs based on the hypothesis of functional redundancy of mutual exclusivity. These mutually exclusive pairs were significantly enriched in nuclear division and humoral immune response, which played crucial roles in cancer initiation and progression. We also found 79 mutually exclusive triples among subtypes of tumors with driver gene mutations, which were key roles in cell motility and cellular chemical homeostasis. In addition, two mutually exclusive triples and one mutually exclusive triple were associated with the overall survival and disease‐specific survival of LUAD patients, respectively.

Conclusions

We revealed novel mutual exclusivity and generated a comprehensive functional landscape of driver gene mutations, which could offer a new perspective to understand the mechanisms of cancer development and identify potential biomarkers for LUAD therapy.

Exploring expectations and perceptions of different manual therapy techniques in chronic low back pain: a qualitative study

BACKGROUND

Chronic low back pain (CLBP) prevalence has steadily increased over the last two decades. Manual therapy (MT) is recommended within a multimodal management approach to improve pain and disability although evidence investigating the patients' experience of MT is scarce.

OBJECTIVE

To explore expectations and perceptions of MT techniques in people with CLBP.

METHODS

A qualitative study embedded sequential to an experimental trial using semi-structured interviews (SSI) explored participants' experiences of thrust, non-thrust and sham technique. Purposive sampling enabled variance in age and CLBP duration. An evidence informed topic guide was used. Data were analysed using thematic analysis (TA). Respondent validation and peer debriefing enhanced trustworthiness. The Consolidating Criteria for Reporting Qualitative Studies (COREQ) reported methodological rigour.

FINDINGS

Ten participants (50% male) with a mean age of 29.1 years (Standard Deviation (SD): 7.9, range: 19-43), a mean pain intensity of 4.5 on a Numeric Rating Scale (NRS) 0-10 (SD: 1.5, range: 2-7), a mean Oswestry Disability Score (ODI) of 9 (SD: 4.6, range: 2-17) and a mean Tampa Scale of Kinesiophobia (TSK) score of 38.6 (SD: 4.8, range: 30-45) participated. Four themes were identified: understanding of pain; forming expectations; perception of care; re-evaluation of body awareness and management. Understanding of CLBP is formed by an individuals' pain perception and exchange with social environment. This, combined with communication with physiotherapist influenced expectations regarding the MT technique.

CONCLUSION

Expectations for MT were formed by an individual's social environment and previous experience. A treatment technique is perceived as positive if its characteristics are aligned with the individual's understanding of pain and if care is delivered in an informative and reassuring manner.

The multi-optics high-resolution absorption x-ray spectrometer (HiRAXS) for studies of materials under extreme conditions

We report the development of a high-resolution spectrometer for extended x-ray absorption fine structure (EXAFS) studies of materials under extreme conditions. A curved crystal and detector in the spectrometer are replaceable such that a single body is employed to perform EXAFS measurements at different x-ray energy intervals of interest. Two configurations have been implemented using toroidal crystals with Ge 311 reflection set to provide EXAFS at the Cu K-edge (energy range 8.9-9.8 keV) and Ge 400 reflection set to provide EXAFS at the Ta L3-edge (9.8-10.7 keV). Key performance characteristics of the spectrometer were found to be consistent with design parameters. The data generated at the National Ignition Facility have shown an ≃3 eV spectral resolution for the Cu K-edge configuration and ≃6 eV for the Ta L3-edge configuration.

A new class of focusing crystal shapes for Bragg spectroscopy of small, point-like, x-ray sources in laser produced plasmas

This paper describes a new class of focusing crystal forms for the x-ray Bragg crystal spectroscopy of small, point-like, x-ray sources. These new crystal forms are designed with the aid of sinusoidal spirals, a family of curves, whose shapes are defined by only one parameter, which can assume any real value. The potential of the sinusoidal spirals for the design x-ray crystal spectrometers is demonstrated with the design of a toroidally bent crystal of varying major and minor radii for measurements of the extended x-ray absorption fine structure near the Ta-L3 absorption edge at the National Ignition Facility.

Dissecting the Invasion-Associated Long Non-coding RNAs Using Single-Cell RNA-Seq Data of Glioblastoma

Glioblastoma (GBM) is characterized by rapid and lethal infiltration of brain tissue, which is the primary cause of treatment failure and deaths for GBM. Therefore, understanding the molecular mechanisms of tumor cell invasion is crucial for the treatment of GBM. In this study, we dissected the single-cell RNA-seq data of 3345 cells from four patients and identified dysregulated genes including long non-coding RNAs (lncRNAs), which were involved in the development and progression of GBM. Based on co-expression network analysis, we identified a module (M1) that significantly overlapped with the largest number of dysregulated genes and was confirmed to be associated with GBM invasion by integrating EMT signature, experiment-validated invasive marker and pseudotime trajectory analysis. Further, we denoted invasion-associated lncRNAs which showed significant correlations with M1 and revealed their gradually increased expression levels along the tumor cell invasion trajectory, such as VIM-AS1, WWTR1-AS1, and NEAT1. We also observed the contribution of higher expression of these lncRNAs to poorer survival of GBM patients. These results were mostly recaptured in another validation data of 7930 single cells from 28 GBM patients. Our findings identified lncRNAs that played critical roles in regulating or controlling cell invasion and migration of GBM and provided new insights into the molecular mechanisms underlying GBM invasion as well as potential targets for the treatment of GBM.

2D monochromatic x-ray imaging for beam monitoring of an x-ray free electron laser and a high-power femtosecond laser

In pump-probe experiments with an X-ray Free Electron Laser (XFEL) and a high-power optical laser, spatial overlap of the two beams must be ensured to probe a pumped area with the x-ray beam. A beam monitoring diagnostic is particularly important in short-pulse laser experiments where a tightly focused beam is required to achieve a relativistic laser intensity for generation of energetic particles. Here, we report the demonstration of on-shot beam pointing measurements of an XFEL and a terawatt class femtosecond laser using 2D monochromatic Kα imaging at the Matter in Extreme Conditions end-station of the Linac Coherent Light Source. A thin solid titanium foil was irradiated by a 25-TW laser for fast electron isochoric heating, while a 7.0 keV XFEL beam was used to probe the laser-heated region. Using a spherical crystal imager (SCI), the beam overlap was examined by measuring 4.51 keV Kα x rays produced by laser-accelerated fast electrons and the x-ray beam. Measurements were made for XFEL-only at various focus lens positions, laser-only, and two-beam shots. Successful beam overlapping was observed on ∼58% of all two-beam shots for 10 μm thick samples. It is found that large spatial offsets of laser-induced Kα spots are attributed to imprecise target positioning rather than shot-to-shot laser pointing variations. By applying the Kα measurements to x-ray Thomson scattering measurements, we found an optimum x-ray beam spot size that maximizes scattering signals. Monochromatic x-ray imaging with the SCI could be used as an on-shot beam pointing monitor for XFEL-laser or multiple short-pulse laser experiments.

Constraining physical models at gigabar pressures

High-energy-density (HED) experiments in convergent geometry are able to test physical models at pressures beyond hundreds of millions of atmospheres. The measurements from these experiments are generally highly integrated and require unique analysis techniques to procure quantitative information. This work describes a methodology to constrain the physics in convergent HED experiments by adapting the methods common to many other fields of physics. As an example, a mechanical model of an imploding shell is constrained by data from a thin-shelled direct-drive exploding-pusher experiment on the OMEGA laser system using Bayesian inference, resulting in the reconstruction of the shell dynamics and energy transfer during the implosion. The model is tested by analyzing synthetic data from a one-dimensional hydrodynamics code and is sampled using a Markov chain Monte Carlo to generate the posterior distributions of the model parameters. The goal of this work is to demonstrate a general methodology that can be used to draw conclusions from a wide variety of HED experiments.

Revealing the subtyping of non-small cell lung cancer based on genomic evolutionary patterns by multi-region sequencing

Accurately classifying patients with non-small cell lung cancer (NSCLC) from the perspective of tumor evolution has not been systematically studied to date. Here, we reconstructed phylogenetic relationships of somatic mutations in 100 early NSCLC patients (327 lesions) through reanalyzing the TRACERx data. Based on the genomic evolutionary patterns presented on the phylogenetic trees, we grouped NSCLC patients into three evolutionary subtypes. The phylogenetic trees among three subtypes exhibited distinct branching structures, with one subtype representing branched evolution and another reflecting the early accumulation of genomic variation. However, in the evolutionary pattern of the third subtype, some mutations experienced selective sweeps and were gradually replaced by multiple newly formed subclonal populations. The subtype patients with poor prognosis had higher intra-tumor heterogeneity and subclonal diversity. We combined genomic heterogeneity with clinical phenotypes analysis and found that subclonal expansion results in the progression and deterioration of the tumor. The molecular mechanisms of subtype-specific Early Driver Feature (EDF) genes differed across the evolutionary subtypes, reflecting the characteristics of the subtype itself. In summary, our study provided new insights on the stratification of NSCLC patients based on genomic evolution that can be valuable for us to understand the development of pulmonary tumor profoundly.

Energy Flow in Thin Shell Implosions and Explosions

Energy flow and balance in convergent systems beyond petapascal energy densities controls the fate of late-stage stars and the potential for controlling thermonuclear inertial fusion ignition. Time-resolved x-ray self-emission imaging combined with a Bayesian inference analysis is used to describe the energy flow and the potential information stored in the rebounding spherical shock at 0.22 PPa (2.2 Gbar or billions of atmospheres pressure). This analysis, together with a simple mechanical model, describes the trajectory of the shell and the time history of the pressure at the fuel-shell interface, ablation pressure, and energy partitioning including kinetic energy of the shell and internal energy of the fuel. The techniques used here provide a fully self-consistent uncertainty analysis of integrated implosion data, a thermodynamic-path independent measurement of pressure in the petapascal range, and can be used to deduce the energy flow in a wide variety of implosion systems to petapascal energy densities.

Foil backlighter development at the OMEGA laser facility for extended x-ray absorption fine structure experiments

Extended x-ray absorption fine structure (EXAFS) measurements require a bright and continuous x-ray source and a detection system with high spectral resolution to capture the modulations of the absorption coefficient above the material absorption edge. When performing EXAFS measurements under laser-driven dynamic compression, it is hence critical to optimize the backlighter x-ray emission. A series of experiments has been conducted at the OMEGA laser facility to characterize titanium (Z = 22), iron (Z = 26), germanium (Z = 32), molybdenum (Z = 42), silver (Z = 47), and gold (Z = 79) foil backlighters irradiated with 3 kJ-12 kJ of laser energy. The spectra have been recorded using a dual crystal spectrometer (DCS), a two-channel transmission spectrometer covering 11 keV-45 keV and 19 keV-90 keV energy bands. The DCS has been calibrated so that the spectral intensities can be compared between different campaigns.

Dissecting the Functional Mechanisms of Somatic Copy-Number Alterations Based on Dysregulated ceRNA Networks across Cancers

Somatic copy-number alterations (SCNAs) drive tumor growth and evolution. However, the functional roles of SCNAs across the genome are still poorly understood. We provide an integrative strategy to characterize the functional roles of driver SCNAs in cancers based on dysregulated competing endogenous RNA (ceRNA) networks. We identified 44 driver SCNAs in lower-grade glioma (LGG). The dysregulated patterns losing all correlation relationships dominated dysregulated ceRNA networks. Homozygous deletion of six genes in 9p21.3 characterized an LGG subtype with poor prognosis and contributed to the dysfunction of cancer-associated pathways in a complementary way. The pan-cancer analysis showed that different cancer types harbored different driver SCNAs through dysregulating the crosstalk with common ceRNAs. The same SCNAs destroyed their ceRNA networks through different miRNA-mediated ceRNA regulations in different cancers. Additionally, some SCNAs performed different functional mechanisms in different cancers, which added another layer of complexity to cancer heterogeneity. Compared with previous methods, our strategy could directly dissect functional roles of SCNAs from the view of ceRNA networks, which not only complemented the functions of protein-coding genes but also provided a new avenue to characterize the functions of noncoding RNAs. Also, our strategy could be applied to more types of cancers to identify pathogenic mechanism driven by the SCNAs.

CellMarker: a manually curated resource of cell markers in human and mouse

One of the most fundamental questions in biology is what types of cells form different tissues and organs in a functionally coordinated fashion. Larger-scale single-cell sequencing and biology experiment studies are now rapidly opening up new ways to track this question by revealing substantial cell markers for distinguishing different cell types in tissues. Here, we developed the CellMarker database (http://biocc.hrbmu.edu.cn/CellMarker/ or http://bio-bigdata.hrbmu.edu.cn/CellMarker/), aiming to provide a comprehensive and accurate resource of cell markers for various cell types in tissues of human and mouse. By manually curating over 100 000 published papers, 4124 entries including the cell marker information, tissue type, cell type, cancer information and source, were recorded. At last, 13 605 cell markers of 467 cell types in 158 human tissues/sub-tissues and 9148 cell makers of 389 cell types in 81 mouse tissues/sub-tissues were collected and deposited in CellMarker. CellMarker provides a user-friendly interface for browsing, searching and downloading markers of diverse cell types of different tissues. Furthermore, a summarized marker prevalence in each cell type is graphically and intuitively presented through a vivid statistical graph. We believe that CellMarker is a comprehensive and valuable resource for cell researches in precisely identifying and characterizing cells, especially at the single-cell level.

Prioritizing Gene Cascading Paths to Model Colorectal Cancer Through Engineered Organoids

Engineered organoids by sequential introduction of key mutations could help modeling the dynamic cancer progression. However, it remains difficult to determine gene paths which were sufficient to capture cancer behaviors and to broadly explain cancer mechanisms. Here, as a case study of colorectal cancer (CRC), functional and dynamic characterizations of five types of engineered organoids with different mutation combinations of five driver genes (APC, SMAD4, KRAS, TP53, and PIK3CA) showed that sequential introductions of all five driver mutations could induce enhanced activation of more hallmark signatures, tending to cancer. Comparative analysis of engineered organoids and corresponding CRC tissues revealed sequential introduction of key mutations could continually shorten the biological distance from engineered organoids to CRC tissues. Nevertheless, there still existed substantial biological gaps between the engineered organoid even with five key mutations and CRC samples. Thus, we proposed an integrative strategy to prioritize gene cascading paths for shrinking biological gaps between engineered organoids and CRC tissues. Our results not only recapitulated the well-known adenoma–carcinoma sequence model (e.g., AKST-organoid with driver mutations in APC, KRAS, SMAD4, and TP53), but also provided potential paths for delineating alternative pathogenesis underlying CRC populations (e.g., A-organoid with APC mutation). Our strategy also can be applied to both organoids with more mutations and other cancers, which can improve and innovate mechanism across cancer patients for drug design and cancer therapy.

Measurements of pressure-induced Kβ line shifts in ramp compressed cobalt up to 8 Mbar

We report measurements of K-shell fluorescence lines induced by fast electrons in ramp-compressed Co targets. The fluorescence emission was stimulated by fast electrons generated through short-pulse laser-solid interaction with an Al target layer. Compression up to 2.1× solid density was achieved while maintaining temperatures well below the Fermi energy, effectively removing the thermal effects from consideration. We observed small but unambiguous redshifts in the Kβ fluorescence line relative to unshifted Cu Kα. Redshifts up to 2.6 eV were found to increase with compression and to be consistent with predictions from self-consistent models based on density-functional theory.

Discovering Rare Genes Contributing to Cancer Stemness and Invasive Potential by GBM Single-Cell Transcriptional Analysis

Single-cell RNA sequencing presents the sophisticated delineation of cell transcriptomes in many cancer types and highlights the tumor heterogeneity at higher resolution, which provides a new chance to explore the molecular mechanism in a minority of cells. In this study, we utilized publicly available single-cell RNA-seq data to discover and comprehensively dissect rare genes existing in few glioblastoma (GBM) cells. Moreover, we designed a framework to systematically identify 51 rare protein-coding genes (PCGs) and 47 rare long non-coding RNAs (lncRNAs) in GBM. Patients with high expression levels of rare genes like CYB5R2 and TPPP3 had worse overall survival and disease-free survival, implying their potential implication in GBM progression and prognosis. We found that these rare genes tended to be specifically expressed in GBM cancer stem cells, which emphasized their ability to characterize stem-like cancer cells and implied their contribution to GBM growth. Furthermore, rare genes were enriched in a 17-cell subset, which was located in an individual branch of the pseudotime trajectory of cancer progression and exhibited high cell cycle activity and invasive potential. Our study captures the rare genes highly expressed in few cells, deepens our understanding of special states during GBM tumorigenesis and progression such as cancer stemness and invasion, and proposes potential targets for cancer therapy.

Self-Generated Magnetic and Electric Fields at a Mach-6 Shock Front in a Low Density Helium Gas by Dual-Angle Proton Radiography

Shocks are abundant both in astrophysical and laboratory systems. While the electric fields generated at shock fronts have recently attracted great attention, the associated self-generated magnetic field is rarely studied, despite its ability to significantly affect the shock profile in the nonideal geometry where density and temperature gradients are not parallel. We report here the observation of a magnetic field at the front of a Mach ∼6 shock propagating in a low-density helium gas system. Proton radiography from different projection angles not only confirms the magnetic field's existence, but also provides a quantitative measurement of the field strength in the range ∼5 to 7 T. X-ray spectrometry allowed inference of the density and temperature at the shock front, constraining the plasma conditions under which the magnetic and electric fields are generated. Simulations with the particle-in-cell code lsp attribute the self-generation of the magnetic field to the Biermann battery effect (∇n_{e}×∇T_{e}).

Identifying mutual exclusivity across cancer genomes: computational approaches to discover genetic interaction and reveal tumor vulnerability

Systematic sequencing of cancer genomes has revealed prevalent heterogeneity, with patients harboring various combinatorial patterns of genetic alteration. In particular, a phenomenon that a group of genes exhibits mutually exclusive patterns has been widespread across cancers, covering a broad spectrum of crucial cancer pathways. Recently, there is considerable evidence showing that, mutual exclusivity reflects alternative functions in tumor initiation and progression, or suggests adverse effects of their concurrence. Given its importance, numerous computational approaches have been proposed to study mutual exclusivity using genomic profiles alone, or by integrating networks and phenotypes. Some of them have been routinely used to explore genetic associations, which lead to a deeper understanding of carcinogenic mechanisms and reveals unexpected tumor vulnerabilities. Here, we present an overview of mutual exclusivity from the perspective of cancer genome. We describe the common hypothesis underlying mutual exclusivity, summarize the strategies for the identification of significant mutually exclusive patterns, compare the performance of representative algorithms from simulated data sets and discuss their common confounders.

Monochromatic 2D Kα Emission Images Revealing Short-Pulse Laser Isochoric Heating Mechanism

The rapid heating of a thin titanium foil by a high intensity, subpicosecond laser is studied by using a 2D narrow-band x-ray imaging and x-ray spectroscopy. A novel monochromatic imaging diagnostic tuned to 4.51 keV Ti Kα was used to successfully visualize a significantly ionized area (⟨Z⟩>17±1) of the solid density plasma to be within a ∼35  μm diameter spot in the transverse direction and 2  μm in depth. The measurements and a 2D collisional particle-in-cell simulation reveal that, in the fast isochoric heating of solid foil by an intense laser light, such a high ionization state in solid titanium is achieved by thermal diffusion from the hot preplasma in a few picoseconds after the pulse ends. The shift of Kα and formation of a missing Kα cannot be explained with the present atomic physics model. The measured Kα image is reproduced only when a phenomenological model for the Kα shift with a threshold ionization of ⟨Z⟩=17 is included. This work reveals how the ionization state and electron temperature of the isochorically heated nonequilibrium plasma are independently increased.

X-ray streaked refraction enhanced radiography for inferring inflight density gradients in ICF capsule implosions

In the quest for reaching ignition of deuterium-tritium (DT) fuel capsule implosions, experiments on the National Ignition Facility (NIF) have shown lower final fuel areal densities than simulated. Possible explanations for reduced compression are higher preheat that can increase the ablator-DT ice density jump and induce mix at that interface or reverberating shocks. We are hence developing x-ray Refraction Enhanced Radiography (RER) to infer the inflight density profiles in layered fuel capsule implosions. We use a 5 μm slit backlit by a Ni 7.8 keV He-α NIF laser driven x-ray source positioned at 20 mm from the capsule to cast refracted images of the inflight capsule onto a streak camera in a high magnification (M ∼ 60×) setup. Our first experiments have validated our setup that recorded a streaked x-ray fringe pattern from an undriven high density carbon (HDC) capsule consistent with ray tracing calculations at the required ∼6 μm and 25 ps resolution. Streaked RER was then applied to inflight layered HDC capsule implosions using a hydrogen-tritium fuel mix rather than DT to reduce neutron yields and associated backgrounds. The first RER of an imploding capsule revealed strong features associated with the ablation front and ice-ablator interface that are not visible in standard absorption radiographs.

Analysis of CSF1PO and D18S51 Loci Based on Ion Torrent PGM™ Platform

OBJECTIVES

To analyse and detect CSF1PO and D18S51 loci by next generation sequencing （NGS） technology for the study on their sequence polymorphism.

METHODS

The peripheral blood samples were collected from 165 unrelated individuals of Chinese Han population. DNA samples were obtained by QIAamp DNA Mini kit. The library was constructed by Ion Plus Fragment Library. DNA sequencing analysis was performed on Ion Torrent PGM™ Platform. The newfound alleles were verified by Sanger sequencing. Data were analysed by Torrent Suite™ v5.0.2 and Integrative Genomics Viewer for the genotype identification and frequency count. The data were analysed statistically by PowerState v12.

RESULTS

The length and sequence polymorphisms of CSF1PO and D18S51 loci were simultaneously obtained by NGS technology. A new genotype was found on CSF1PO locus, and two new genotypes on D18S51 locus. Sanger sequencing was used to verify the newfound alleles found by NGS technology, and the results of verification showed consistency.

CONCLUSIONS

The structure of core repeats on CSF1PO and D18S51 loci was detected by NGS in this study for the improvement of the identifying performance of locus.

A new toroidal x-ray crystal spectrometer for the diagnosis of high energy density plasmas at the National Ignition Facility

The here-described spectrometer was developed for the extended x-ray absorption fine structure spectroscopy of high-density plasmas at the National Ignition Facility. It employs as the Bragg reflecting element a new type of toroidally bent crystal with a constant and very large major radius R and a much smaller, locally varying, minor radius r. The focusing properties of this crystal and the experimental arrangement of the source and detector make it possible to (a) fulfill the conditions for a perfect imaging of an ideal point source for each wavelength, (b) obtain a high photon throughput, (c) obtain a high spectral resolution by eliminating the effects of source-size broadening, and (d) obtain a one-dimensional spatial resolution with a high magnification perpendicular to the main dispersion plane.

Developing a high-flux, high-energy continuum backlighter for extended x-ray absorption fine structure measurements at the National Ignition Facility

Extended X-ray absorption fine structure (EXAFS) spectroscopy is a powerful tool for in situ characterization of matter in the high energy density regime. An EXAFS platform is currently being developed on the National Ignition Facility. Development of a suitable X-ray backlighter involves minimizing the temporal duration and source size while maximizing spectral smoothness and brightness. One approach involves imploding a spherical shell, which generates a high-flux X-ray flash at stagnation. We present results from a series of experiments comparing the X-ray source properties produced by imploded empty and Ar-filled capsules.