The strength of the radial-breathing mode in single-walled carbon nanotubes

We show by ab initio calculations that the electron-phonon coupling matrix element M of the radial breathing mode in single-walled carbon nanotubes depends strongly on tube chirality. For nanotubes of the same diameter the coupling strength |M|^2 is up to one order of magnitude stronger for zig-zag than for armchair tubes. For (n,m) tubes M depends on the value of (n-m) mod 3, which allows to discriminate semiconducting nano tubes with similar diameter by their Raman scattering intensity. We show measured resonance Raman profiles of the radial breathing mode which support our theoretical predictions

Biases in Inverse Ising Estimates of Near-Critical Behaviour

Inverse Ising inference allows pairwise interactions of complex binary systems to be reconstructed from empirical correlations. Typical estimators used for this inference, such as Pseudo-likelihood maximization (PLM), are biased. Using the Sherrington-Kirkpatrick (SK) model as a benchmark, we show that these biases are large in critical regimes close to phase boundaries, and may alter the qualitative interpretation of the inferred model. In particular, we show that the small-sample bias causes models inferred through PLM to appear closer-to-criticality than one would expect from the data. Data-driven methods to correct this bias are explored and applied to a functional magnetic resonance imaging (fMRI) dataset from neuroscience. Our results indicate that additional care should be taken when attributing criticality to real-world datasets

High-pressure x-ray scattering and computer simulation studies of density-induced polyamorphism in silicon

A low- to high-density pressure-driven phase transition in amorphous silicon is investigated by synchrotron x-ray diffraction in the diamond anvil cell. Complementary atomistic molecular dynamics computer simulations provide insight into the underlying structural transformations and allow us to interpret the structure factors obtained from experiment. During compression the form of the scattering function S (Q) changes abruptly at 13.5 GPa, indicating significant structural rearrangement in the amorphous solid. In particular, the first peak in S (Q) shifts to larger Q values. The changes are correlated with the occurrence of a low- to high-density (LDA-HDA) polyamorphic transition observed previously using Raman scattering and electrical conductivity measurements. The data are analyzed to provide real space (pair distribution function) information. The experimental data are compared with results from molecular dynamics (MD) simulations using a modified Stillinger-Weber many-body potential energy function in order to extract structural information on the densified amorphous material. We deduce that the polyamorphic transition involves an abrupt increase in the proportion of 5- and 6-coordinate Si atoms. The overall structure of the HDA polyamorph can be related to that of the LDA form by creation of highly-coordinated "defects" within the tetrahedrally-bonded LDA network. However classical and quantum MD simulations indicate that an even higher density amorphous state might exist, based on structures that resemble the densely-packed metallic polymorphs of crystalline Si. © 2007 The American Physical Society

Probing high pressure properties of single wall carbon nanotubes through fullerene encapsulation

The high pressure behavior of bundled 1.35±0.1nm diameter single wall carbon nanotubes (SWNT) filled with C70 fullerenes (usually called peapods) has been investigated by Raman spectroscopy and compared with the corresponding behavior of the nonfilled SWNT. We show experimentally that two reversible pressure-induced transitions take place in the compressed bundle SWNT. The first transition, in the 2–2.5GPa range, is in good correspondence with predictions of the thermodynamic instability of the nanotube circular cross section for the studied tube diameter. An interaction between the fullerenes and the tube walls is then observed at about 3.5GPa, which evidences a progressive deformation of the tube cross section. The second transition takes place at pressures between 10 and 30GPa, and is evidenced by two effects by a strong frequency downshift of the Raman transverse modes and the concomitant disappearance of the fullerenes Raman modes in peapods. The pressure at which the second transition takes place is strongly dependent on the nature of the pressure transmitting medium. We also report irreversible effects at high pressure as the shortening of the tubes, the formation of nanostructures and the disappearance of the C70 Raman signal in some cases. Transmission electron microscopy studies are also reported supporting these transformations

In Vitro Differentiation of Mouse Embryonic Stem Cells into Neurons of the Dorsal Forebrain

Pluripotent embryonic stem cells (ESCs) are able to differentiate into all cell types in the organism including cortical neurons. To follow the dynamic generation of progenitors of the dorsal forebrain in vitro, we generated ESCs from D6-GFP mice in which GFP marks neocortical progenitors and neurons after embryonic day (E) 10.5. We used several cell culture protocols for differentiation of ESCs into progenitors and neurons of the dorsal forebrain. In cell culture, GFP-positive cells were induced under differentiation conditions in quickly formed embryoid bodies (qEBs) after 10–12 day incubation. Activation of Wnt signaling during ESC differentiation further stimulated generation of D6-GFP-positive cortical cells. In contrast, differentiation protocols using normal embryoid bodies (nEBs) yielded only a few D6-GFP-positive cells. Gene expression analysis revealed that multiple components of the canonical Wnt signaling pathway were expressed during the development of embryoid bodies. As shown by immunohistochemistry and quantitative qRT-PCR, D6-GFP-positive cells from qEBs expressed genes that are characteristic for the dorsal forebrain such as Pax6, Dach1, Tbr1, Tbr2, or Sox5. qEBs culture allowed the formation of a D6-GFP positive pseudo-polarized neuroepithelium with the characteristic presence of N-cadherin at the apical pole resembling the structure of the developing neocortex

Autocrine Adenosine Regulates Tumor Polyfunctional CD73⁺CD4⁺ Effector T Cells Devoid of Immune Checkpoints.

The production of CD73-derived adenosine (Ado) by Tregs has been proposed as a resistance mechanism to anti-PD-1 therapy in murine tumor models. We reported that human Tregs express the ectonucleotidase CD39, which generates AMP from ATP, but do not express the AMPase CD73. In contrast, CD73 defined a subset of effector CD4 <sup>+</sup> T cells (Teffs) enriched in polyfunctional Th1.17 cells characterized by expression of CXCR3, CCR6, and MDR1, and production of IL17A/IFNγ/IL22/GM-CSF. CD39 <sup>+</sup> Tregs selectively targeted CD73 <sup>+</sup> Teffs through cooperative degradation of ATP into Ado inhibiting and restricting the ability of CD73 <sup>+</sup> Teffs to secrete IL17A. CD73 <sup>+</sup> Teffs infiltrating breast and ovarian tumors were functionally blunted by Tregs expressing upregulated levels of CD39 and ATPase activity. Moreover, tumor-infiltrating CD73 <sup>+</sup> Teffs failed to express inhibitory immune checkpoints, suggesting that CD73 might be selected under pressure from immune checkpoint blockade therapy and thus may represent a nonredundant target for restoring antitumor immunity.Significance: Polyfunctional CD73 <sup>+</sup> T-cell effectors lacking other immune checkpoints are selectively targeted by CD39 overexpressing Tregs that dominate the breast tumor environment. Cancer Res; 78(13); 3604-18. ©2018 AACR

Alteration of ribosome function upon 5-fluorouracil treatment favors cancer cell drug-tolerance.

Mechanisms of drug-tolerance remain poorly understood and have been linked to genomic but also to non-genomic processes. 5-fluorouracil (5-FU), the most widely used chemotherapy in oncology is associated with resistance. While prescribed as an inhibitor of DNA replication, 5-FU alters all RNA pathways. Here, we show that 5-FU treatment leads to the production of fluorinated ribosomes exhibiting altered translational activities. 5-FU is incorporated into ribosomal RNAs of mature ribosomes in cancer cell lines, colorectal xenografts, and human tumors. Fluorinated ribosomes appear to be functional, yet, they display a selective translational activity towards mRNAs depending on the nature of their 5'-untranslated region. As a result, we find that sustained translation of IGF-1R mRNA, which encodes one of the most potent cell survival effectors, promotes the survival of 5-FU-treated colorectal cancer cells. Altogether, our results demonstrate that "man-made" fluorinated ribosomes favor the drug-tolerant cellular phenotype by promoting translation of survival genes

Lysyl oxidase drives tumour progression by trapping EGF receptors at the cell surface

Lysyl oxidase (LOX) remodels the tumour microenvironment by cross-linking the extracellular matrix. LOX overexpression is associated with poor cancer outcomes. Here, we find that LOX regulates the epidermal growth factor receptor (EGFR) to drive tumour progression. We show that LOX regulates EGFR by suppressing TGFβ1 signalling through the secreted protease HTRA1. This increases the expression of Matrilin2 (MATN2), an EGF-like domain-containing protein that traps EGFR at the cell surface to facilitate its activation by EGF. We describe a pharmacological inhibitor of LOX, CCT365623, which disrupts EGFR cell surface retention and delays the growth of primary and metastatic tumour cells in vivo. Thus, we show that LOX regulates EGFR cell surface retention to drive tumour progression, and we validate the therapeutic potential of inhibiting this pathway with the small molecule inhibitor CCT365623

Feasibility of an in situ measurement device for bubble size and distribution

The feasibility of in situ measurement device for bubble size and distribution was explored. A novel in situ probe measurement system, the EnviroCam™, was developed. Where possible, this probe incorporated strengths, and minimized weaknesses of historical and currently available real-time measurement methods for bubbles. The system was based on a digital, high-speed, high resolution, modular camera system, attached to a stainless steel shroud, compatible with standard Ingold ports on fermenters. Still frames and/or video were produced, capturing bubbles passing through the notch of the shroud. An LED light source was integral with the shroud. Bubbles were analyzed using customized commercially available image analysis software and standard statistical methods. Using this system, bubble sizes were measured as a function of various operating parameters (e.g., agitation rate, aeration rate) and as a function of media properties (e.g., viscosity, antifoam, cottonseed flour, and microbial/animal cell broths) to demonstrate system performance and its limitations. For selected conditions, mean bubble size changes qualitatively compared favorably with published relationships. Current instrument measurement capabilities were limited primarily to clear solutions that did not contain large numbers of overlapping bubbles