Structural evolution of liquid silicates under conditions in Super-Earth interiors.

Molten silicates at depth are crucial for planetary evolution, yet their local structure and physical properties under extreme conditions remain elusive due to experimental challenges. In this study, we utilize in situ X-ray diffraction (XRD) at the Matter in Extreme Conditions (MEC) end-station of the Linear Coherent Linac Source (LCLS) at SLAC National Accelerator Laboratory to investigate liquid silicates. Using an ultrabright X-ray source and a high-power optical laser, we probed the local atomic arrangement of shock-compressed liquid (Mg,Fe)SiO3 with varying Fe content, at pressures from 81(9) to 385(40) GPa. We compared these findings to ab initio molecular dynamics simulations under similar conditions. Results indicate continuous densification of the O-O and Mg-Si networks beyond Earth's interior pressure range, potentially altering melt properties at extreme conditions. This could have significant implications for early planetary evolution, leading to notable differences in differentiation processes between smaller rocky planets, such as Earth and Venus, and super-Earths, which are exoplanets with masses nearly three times that of Earth.

Release dynamics of nanodiamonds created by laser-driven shock-compression of polyethylene terephthalate.

Laser-driven dynamic compression experiments of plastic materials have found surprisingly fast formation of nanodiamonds (ND) via X-ray probing. This mechanism is relevant for planetary models, but could also open efficient synthesis routes for tailored NDs. We investigate the release mechanics of compressed NDs by molecular dynamics simulation of the isotropic expansion of finite size diamond from different P-T states. Analysing the structural integrity along different release paths via molecular dynamic simulations, we found substantial disintegration rates upon shock release, increasing with the on-Hugnoiot shock temperature. We also find that recrystallization can occur after the expansion and hence during the release, depending on subsequent cooling mechanisms. Our study suggests higher ND recovery rates from off-Hugoniot states, e.g., via double-shocks, due to faster cooling. Laser-driven shock compression experiments of polyethylene terephthalate (PET) samples with in situ X-ray probing at the simulated conditions found diamond signal that persists up to 11 ns after breakout. In the diffraction pattern, we observed peak shifts, which we attribute to thermal expansion of the NDs and thus a total release of pressure, which indicates the stability of the released NDs.

Direct observation of strong momentum-dependent electron-phonon coupling in a metal.

Phonon scattering in metals is one of the most fundamental processes in materials science. However, understanding such processes has remained challenging and requires detailed information on interactions between phonons and electrons. We use an ultrafast electron diffuse scattering technique to resolve the nonequilibrium phonon dynamics in femtosecond-laser-excited tungsten in both time and momentum. We determine transient populations of phonon modes which show strong momentum dependence initiated by electron-phonon coupling. For phonons near Brillouin zone border, we observe a transient rise in their population on a timescale of approximately 1 picosecond driven by the strong electron-phonon coupling, followed by a slow decay on a timescale of approximately 8 picosecond governed by the weaker phonon-phonon relaxation process. We find that the exceptional harmonicity of tungsten is needed for isolating the two processes, resulting in long-lived nonequilibrium phonons in a pure metal. Our finding highlights that electron-phonon scattering can be the determinant factor in the phonon thermal transport of metals.

A hidden Markov model for continuous longitudinal data with missing responses and dropout.

We propose a hidden Markov model for multivariate continuous longitudinal responses with covariates that accounts for three different types of missing pattern: (I) partially missing outcomes at a given time occasion, (II) completely missing outcomes at a given time occasion (intermittent pattern), and (III) dropout before the end of the period of observation (monotone pattern). The missing-at-random (MAR) assumption is formulated to deal with the first two types of missingness, while to account for the informative dropout, we rely on an extra absorbing state. Estimation of the model parameters is based on the maximum likelihood method that is implemented by an expectation-maximization (EM) algorithm relying on suitable recursions. The proposal is illustrated by a Monte Carlo simulation study and an application based on historical data on primary biliary cholangitis.

Novel fabrication tools for dynamic compression targets with engineered voids using photolithography methods.

Mesoscale imperfections, such as pores and voids, can strongly modify the properties and the mechanical response of materials under extreme conditions. Tracking the material response and microstructure evolution during void collapse is crucial for understanding its performance. In particular, imperfections in the ablator materials, such as voids, can limit the efficiency of the fusion reaction and ultimately hinder ignition. To characterize how voids influence the response of materials during dynamic loading and seed hydrodynamic instabilities, we have developed a tailored fabrication procedure for designer targets with voids at specific locations. Our procedure uses SU-8 as a proxy for the ablator materials and hollow silica microspheres as a proxy for voids and pores. By using photolithography to design the targets' geometry, we demonstrate precise and highly reproducible placement of a single void within the sample, which is key for a detailed understanding of its behavior under shock compression. This fabrication technique will benefit high-repetition rate experiments at x-ray and laser facilities. Insight from shock compression experiments will provide benchmarks for the next generation of microphysics modeling.

Multi-frame, ultrafast, x-ray microscope for imaging shockwave dynamics.

Inertial confinement fusion (ICF) holds increasing promise as a potential source of abundant, clean energy, but has been impeded by defects such as micro-voids in the ablator layer of the fuel capsules. It is critical to understand how these micro-voids interact with the laser-driven shock waves that compress the fuel pellet. At the Matter in Extreme Conditions (MEC) instrument at the Linac Coherent Light Source (LCLS), we utilized an x-ray pulse train with ns separation, an x-ray microscope, and an ultrafast x-ray imaging (UXI) detector to image shock wave interactions with micro-voids. To minimize the high- and low-frequency variations of the captured images, we incorporated principal component analysis (PCA) and image alignment for flat-field correction. After applying these techniques we generated phase and attenuation maps from a 2D hydrodynamic radiation code (xRAGE), which were used to simulate XPCI images that we qualitatively compare with experimental images, providing a one-to-one comparison for benchmarking material performance. Moreover, we implement a transport-of-intensity (TIE) based method to obtain the average projected mass density (areal density) of our experimental images, yielding insight into how defect-bearing ablator materials alter microstructural feature evolution, material compression, and shock wave propagation on ICF-relevant time scales.

Atomistic deformation mechanism of silicon under laser-driven shock compression.

Silicon (Si) is one of the most abundant elements on Earth, and it is the most widely used semiconductor. Despite extensive study, some properties of Si, such as its behaviour under dynamic compression, remain elusive. A detailed understanding of Si deformation is crucial for various fields, ranging from planetary science to materials design. Simulations suggest that in Si the shear stress generated during shock compression is released via a high-pressure phase transition, challenging the classical picture of relaxation via defect-mediated plasticity. However, direct evidence supporting either deformation mechanism remains elusive. Here, we use sub-picosecond, highly-monochromatic x-ray diffraction to study (100)-oriented single-crystal Si under laser-driven shock compression. We provide the first unambiguous, time-resolved picture of Si deformation at ultra-high strain rates, demonstrating the predicted shear release via phase transition. Our results resolve the longstanding controversy on silicon deformation and provide direct proof of strain rate-dependent deformation mechanisms in a non-metallic system.

Diamond formation kinetics in shock-compressed C─H─O samples recorded by small-angle x-ray scattering and x-ray diffraction.

Extreme conditions inside ice giants such as Uranus and Neptune can result in peculiar chemistry and structural transitions, e.g., the precipitation of diamonds or superionic water, as so far experimentally observed only for pure C─H and H2O systems, respectively. Here, we investigate a stoichiometric mixture of C and H2O by shock-compressing polyethylene terephthalate (PET) plastics and performing in situ x-ray probing. We observe diamond formation at pressures between 72 ± 7 and 125 ± 13 GPa at temperatures ranging from ~3500 to ~6000 K. Combining x-ray diffraction and small-angle x-ray scattering, we access the kinetics of this exotic reaction. The observed demixing of C and H2O suggests that diamond precipitation inside the ice giants is enhanced by oxygen, which can lead to isolated water and thus the formation of superionic structures relevant to the planets' magnetic fields. Moreover, our measurements indicate a way of producing nanodiamonds by simple laser-driven shock compression of cheap PET plastics.

The Hedgehog-GLI Pathway Regulates MEK5-ERK5 Expression and Activation in Melanoma Cells.

Malignant melanoma is the deadliest skin cancer, with a poor prognosis in advanced stages. We recently showed that the extracellular signal-regulated kinase 5 (ERK5), encoded by the MAPK7 gene, plays a pivotal role in melanoma by regulating cell functions necessary for tumour development, such as proliferation. Hedgehog-GLI signalling is constitutively active in melanoma and is required for proliferation. However, no data are available in literature about a possible interplay between Hedgehog-GLI and ERK5 pathways. Here, we show that hyperactivation of the Hedgehog-GLI pathway by genetic inhibition of the negative regulator Patched 1 increases the amount of ERK5 mRNA and protein. Chromatin immunoprecipitation showed that GLI1, the major downstream effector of Hedgehog-GLI signalling, binds to a functional non-canonical GLI consensus sequence at the MAPK7 promoter. Furthermore, we found that ERK5 is required for Hedgehog-GLI-dependent melanoma cell proliferation, and that the combination of GLI and ERK5 inhibitors is more effective than single treatments in reducing cell viability and colony formation ability in melanoma cells. Together, these findings led to the identification of a novel Hedgehog-GLI-ERK5 axis that regulates melanoma cell growth, and shed light on new functions of ERK5, paving the way for new therapeutic options in melanoma and other neoplasms with active Hedgehog-GLI and ERK5 pathways.

Loss-of-Function Mutations in TRAF7 and KLF4 Cooperatively Activate RAS-Like GTPase Signaling and Promote Meningioma Development.

Meningiomas are the most common benign brain tumors. Mutations of the E3 ubiquitin ligase TRAF7 occur in 25% of meningiomas and commonly cooccur with mutations in KLF4, yet the functional link between TRAF7 and KLF4 mutations remains unclear. By generating an in vitro meningioma model derived from primary meningeal cells, we elucidated the cooperative interactions that promote meningioma development. By integrating TRAF7-driven ubiquitinome and proteome alterations in meningeal cells and the TRAF7 interactome, we identified TRAF7 as a proteostatic regulator of RAS-related small GTPases. Meningioma-associated TRAF7 mutations disrupted either its catalytic activity or its interaction with RAS GTPases. TRAF7 loss in meningeal cells altered actin dynamics and promoted anchorage-independent growth by inducing CDC42 and RAS signaling. TRAF deficiency-driven activation of the RAS/MAPK pathway promoted KLF4-dependent transcription that led to upregulation of the tumor-suppressive Semaphorin pathway, a negative regulator of small GTPases. KLF4 loss of function disrupted this negative feedback loop and enhanced mutant TRAF7-mediated cell transformation. Overall, this study provides new mechanistic insights into meningioma development, which could lead to novel treatment strategies. SIGNIFICANCE: The intricate molecular cross-talk between the ubiquitin ligase TRAF7 and the transcription factor KLF4 provides a first step toward the identification of new therapies for patients with meningioma.

The Noonan Syndrome Gene Lztr1 Controls Cardiovascular Function by Regulating Vesicular Trafficking.

RATIONALE: Noonan syndrome (NS) is one of the most frequent genetic disorders. Bleeding problems are among the most common, yet poorly defined complications associated with NS. A lack of consensus on the management of bleeding complications in patients with NS indicates an urgent need for new therapeutic approaches. OBJECTIVE: Bleeding disorders have recently been described in patients with NS harboring mutations of LZTR1 (leucine zipper-like transcription regulator 1), an adaptor for CUL3 (CULLIN3) ubiquitin ligase complex. Here, we assessed the pathobiology of LZTR1-mediated bleeding disorders. METHODS AND RESULTS: Whole-body and vascular specific knockout of Lztr1 results in perinatal lethality due to cardiovascular dysfunction. Lztr1 deletion in blood vessels of adult mice leads to abnormal vascular leakage. We found that defective adherent and tight junctions in Lztr1-depleted endothelial cells are caused by dysregulation of vesicular trafficking. LZTR1 affects the dynamics of fusion and fission of recycling endosomes by controlling ubiquitination of the ESCRT-III (endosomal sorting complex required for transport III) component CHMP1B (charged multivesicular protein 1B), whereas NS-associated LZTR1 mutations diminish CHMP1B ubiquitination. LZTR1-mediated dysregulation of CHMP1B ubiquitination triggers endosomal accumulation and subsequent activation of VEGFR2 (vascular endothelial growth factor receptor 2) and decreases blood levels of soluble VEGFR2 in Lztr1 haploinsufficient mice. Inhibition of VEGFR2 activity by cediranib rescues vascular abnormalities observed in Lztr1 knockout mice Conclusions: Lztr1 deletion phenotypically overlaps with bleeding diathesis observed in patients with NS. ELISA screening of soluble VEGFR2 in the blood of LZTR1-mutated patients with NS may predict both the severity of NS phenotypes and potential responders to anti-VEGF therapy. VEGFR inhibitors could be beneficial for the treatment of bleeding disorders in patients with NS.

Nature of Hexagonal Silicon Forming via High-Pressure Synthesis: Nanostructured Hexagonal 4H Polytype.

Hexagonal Si allotropes are expected to enhance light absorption in the visible range as compared to common cubic Si with diamond structure. Therefore, synthesis of these materials is crucial for the development of Si-based optoelectronics. In this work, we combine in situ high-pressure high-temperature synthesis and vacuum heating to obtain hexagonal Si. High pressure is one of the most promising routes to stabilize these allotropes. It allows one to obtain large-volume nanostructured ingots by a sequence of direct solid-solid transformations, ensuring high-purity samples for detailed characterization. Thanks to our synthesis approach, we provide the first evidence of a polycrystalline bulk sample of hexagonal Si. Exhaustive structural analysis, combining fine-powder X-ray and electron diffraction, afforded resolution of the crystal structure. We demonstrate that hexagonal Si obtained by high-pressure synthesis correspond to Si-4H polytype (ABCB stacking) in contrast with Si-2H (AB stacking) proposed previously. This result agrees with prior calculations that predicted a higher stability of the 4H form over 2H form. Further physical characterization, combining experimental data and ab initio calculations, have shown a good agreement with the established structure. Strong photoluminescence emission was observed in the visible region for which we foresee optimistic perspectives for the use of this material in Si-based photovoltaics.

ERK5 is activated by oncogenic BRAF and promotes melanoma growth.

Malignant melanoma is among the most aggressive cancers and its incidence is increasing worldwide. Targeted therapies and immunotherapy have improved the survival of patients with metastatic melanoma in the last few years; however, available treatments are still unsatisfactory. While the role of the BRAF-MEK1/2-ERK1/2 pathway in melanoma is well established, the involvement of mitogen-activated protein kinases MEK5-ERK5 remains poorly explored. Here we investigated the function of ERK5 signaling in melanoma. We show that ERK5 is consistently expressed in human melanoma tissues and is active in melanoma cells. Genetic silencing and pharmacological inhibition of ERK5 pathway drastically reduce the growth of melanoma cells and xenografts harboring wild-type (wt) or mutated BRAF (V600E). We also found that oncogenic BRAF positively regulates expression, phosphorylation, and nuclear localization of ERK5. Importantly, ERK5 kinase and transcriptional transactivator activities are enhanced by BRAF. Nevertheless, combined pharmacological inhibition of BRAFV600E and MEK5 is required to decrease nuclear ERK5, that is critical for the regulation of cell proliferation. Accordingly, combination of MEK5 or ERK5 inhibitors with BRAFV600E inhibitor vemurafenib is more effective than single treatments in reducing colony formation and growth of BRAFV600E melanoma cells and xenografts. Overall, these data support a key role of the ERK5 pathway for melanoma growth in vitro and in vivo and suggest that targeting ERK5, alone or in combination with BRAF-MEK1/2 inhibitors, might represent a novel approach for melanoma treatment.

Transition from silicene monolayer to thin Si films on Ag(111): comparison between experimental data and Monte Carlo simulation.

Scanning tunneling microscopy (STM), Auger electron spectroscopy (AES) and low energy electron diffraction have been used to follow the growth of Si films on Ag(111) at various temperatures. Using a simple growth model, we have simulated the distribution of film thickness as a function of coverage during evaporation, for the different temperatures. In the temperature regime where multilayer silicene has been claimed to form (470-500 K), a good agreement is found with AES intensity variations and STM measurements within a Ag surfactant mediated growth, whereas a model with multilayer silicene growth fails to reproduce the AES measurements.

A joint model for longitudinal and survival data based on an AR(1) latent process.

A critical problem in repeated measurement studies is the occurrence of nonignorable missing observations. A common approach to deal with this problem is joint modeling the longitudinal and survival processes for each individual on the basis of a random effect that is usually assumed to be time constant. We relax this hypothesis by introducing time-varying subject-specific random effects that follow a first-order autoregressive process, AR(1). We also adopt a generalized linear model formulation to accommodate for different types of longitudinal response (i.e. continuous, binary, count) and we consider some extended cases, such as counts with excess of zeros and multivariate outcomes at each time occasion. Estimation of the parameters of the resulting joint model is based on the maximization of the likelihood computed by a recursion developed in the hidden Markov literature. This maximization is performed on the basis of a quasi-Newton algorithm that also provides the information matrix and then standard errors for the parameter estimates. The proposed approach is illustrated through a Monte Carlo simulation study and the analysis of certain medical datasets.

Luciferase Reporter Assays to Study Transcriptional Activity of Hedgehog Signaling in Normal and Cancer Cells.

The measurement of the transcriptional activity of the HH signaling pathway is widely used as an indication of pathway activation. Luciferase reporter assays are powerful tools to measure the specific ability of a transcription factor to bind to its consensus sequence and to activate transcription of target genes. Here, we describe a protocol to measure the transcriptional activity of the HH pathway in normal and cancer cells. This technique allows studying the activity of GLI transcription factors and their modulation by drugs and/or other factors.

Cooperative integration between HEDGEHOG-GLI signalling and other oncogenic pathways: implications for cancer therapy.

The HEDGEHOG-GLI (HH-GLI) signalling is a key pathway critical in embryonic development, stem cell biology and tissue homeostasis. In recent years, aberrant activation of HH-GLI signalling has been linked to several types of cancer, including those of the skin, brain, lungs, prostate, gastrointestinal tract and blood. HH-GLI signalling is initiated by binding of HH ligands to the transmembrane receptor PATCHED and is mediated by transcriptional effectors that belong to the GLI family, whose activity is finely tuned by a number of molecular interactions and post-translation modifications. Several reports suggest that the activity of the GLI proteins is regulated by several proliferative and oncogenic inputs, in addition or independent of upstream HH signalling. The identification of this complex crosstalk and the understanding of how the major oncogenic signalling pathways interact in cancer is a crucial step towards the establishment of efficient targeted combinatorial treatments. Here we review recent findings on the cooperative integration of HH-GLI signalling with the major oncogenic inputs and we discuss how these cues modulate the activity of the GLI proteins in cancer. We then summarise the latest advances on SMO and GLI inhibitors and alternative approaches to attenuate HH signalling through rational combinatorial therapies.

Surgical management of pancreatic neuroendocrine neoplasms.

Pancreatic neuroendocrine neoplasms are relatively rare entities, representing approximately 1% to 2% of all pancreatic tumors. Owing to their rarity as well as their relatively indolent natural history, treatment approaches are not yet standardized. A formal pancreatic resection is usually mandatory for large and localized sporadic pancreatic tumors or in the presence of symptoms. However, in small and asymptomatic lesions, a conservative approach consisting in a careful wait-and-see policy is going to appear as more appropriate, particularly when, to remove the lesion, an aggressive surgical procedure is required, such as pancreaticoduodenectomy or distal splenopancreatectomy, depending on the localization of the tumor. Surgery has also a significant role in locally advanced and metastatic forms. In the setting of MEN 1 syndrome or Von-Hippel Lindau disease, the tumor size and the possible symptoms should be considered in the evaluation of a proper treatment.

A new constant memory recursion for hidden Markov models.

We develop the recursion for hidden Markov (HM) models proposed by Bartolucci and Besag (2002), and we show how it may be used to implement an estimation algorithm for these models that requires an amount of memory not depending on the length of the observed series of data. This recursion allows us to obtain the conditional distribution of the latent state at every occasion, given the previous state and the observed data. With respect to the estimation algorithm based on the well-known Baum-Welch recursions, which requires an amount of memory that increases with the sample size, the proposed algorithm also has the advantage of not requiring dummy renormalizations to avoid numerical problems. Moreover, it directly allows us to perform global decoding of the latent sequence of states, without the need of a Viterbi method and with a consistent reduction of the memory requirement with respect to the latter. The proposed approach is compared, in terms of computing time and memory requirement, with the algorithm based on the Baum-Welch recursions and with the so-called linear memory algorithm of Churbanov and Winters-Hilt. The comparison is also based on a series of simulations involving an HM model for continuous time-series data.

Culture and isolation of melanoma-initiating cells.

Melanoma is the most aggressive skin cancer. This unit illustrates protocols for culture and isolation of human melanoma cancer stem cells/tumor-initiating cells (CSC/TIC). We describe two complementary methods to enrich for melanoma CSC/TIC. The first approach exploits the ability of CSC/TIC to grow as tumor spheres in low-adherent culture conditions, as previously shown for neural stem cells and human embryonic stem cells. As a second approach, melanoma CSC/TIC are enriched by fluorescence-activated cell sorting for the aldehyde dehydrogenase (ALDH) enzyme activity. We previously showed that melanoma cells with high ALDH activity (ALDH(high)) are endowed with higher self-renewal and tumorigenic abilities than the population with low activity (ALDH(low)), suggesting that ALDH might be a good marker to select for melanoma CSC/TIC. This unit will also describe how to functionally test melanoma CSC/TIC by determining self-renewal in vitro and tumor-forming abilities in vivo using orthotopic xenograft assay.