Bip-Yorkie interaction determines oncogenic and tumor-suppressive roles of Ire1/Xbp1s activation.

Unfolded protein response (UPR) is the mechanism by which cells control endoplasmic reticulum (ER) protein homeostasis. ER proteostasis is essential to adapt to cell proliferation and regeneration in development and tumorigenesis, but mechanisms linking UPR, growth control, and cancer progression remain unclear. Here, we report that the Ire1/Xbp1s pathway has surprisingly oncogenic and tumor-suppressive roles in a context-dependent manner. Activation of Ire1/Xbp1s up-regulates their downstream target Bip, which sequesters Yorkie (Yki), a Hippo pathway transducer, in the cytoplasm to restrict Yki transcriptional output. This regulation provides an endogenous defensive mechanism in organ size control, intestinal homeostasis, and regeneration. Unexpectedly, Xbp1 ablation promotes tumor overgrowth but suppresses invasiveness in a Drosophila cancer model. Mechanistically, hyperactivated Ire1/Xbp1s signaling in turn induces JNK-dependent developmental and oncogenic cell migration and epithelial-mesenchymal transition (EMT) via repression of Yki. In humans, a negative correlation between XBP1 and YAP (Yki ortholog) target gene expression specifically exists in triple-negative breast cancers (TNBCs), and those with high XBP1 or HSPA5 (Bip ortholog) expression have better clinical outcomes. In human TNBC cell lines and xenograft models, ectopic XBP1s or HSPA5 expression alleviates tumor growth but aggravates cell migration and invasion. These findings uncover a conserved crosstalk between the Ire1/Xbp1s and Hippo signaling pathways under physiological settings, as well as a crucial role of Bip-Yki interaction in tumorigenesis that is shared from Drosophila to humans.

Simple Molecules under High-Pressure and High-Temperature Conditions: Synthesis and Characterization of α- and ß-C(NH)2 with Fully sp3 -Hybridized Carbon.

The elements hydrogen, carbon, and nitrogen are among the most abundant in the solar system. Still, little is known about the ternary compounds these elements can form under the high-pressure and high-temperature conditions found in the outer planets' interiors. These materials are also of significant research interest since they are predicted to feature many desirable properties such as high thermal conductivity and hardness due to strong covalent bonding networks. In this study, the high-pressure high-temperature reaction behavior of malononitrile H2 C(CN)2 , dicyandiamide (H2 N)2 C=NCN, and melamine (C3 N3 )(NH2 )3 was investigated in laser-heated diamond anvil cells. Two previously unknown compounds, namely α-C(NH)2 and ß-C(NH)2 , have been synthesized and found to have fully sp3 -hybridized carbon atoms. α-C(NH)2 crystallizes in a distorted ß-cristobalite structure, while ß-C(NH)2 is built from previously unknown imide-bridged 2,4,6,8,9,10-hexaazaadamantane units, which form two independent interpenetrating diamond-like networks. Their stability domains and compressibility were studied, for which supporting density functional theory calculations were performed.

Lactobacillus acidophilus ameliorates obesity in mice through modulation of gut microbiota dysbiosis and intestinal permeability.

Obesity associated with low-grade chronic inflammation and intestinal dysbiosis is considered as a worldwide public health crisis. In the meanwhile, different probiotics have demonstrated beneficial effects on this condition, thus increasing the interest in the development of probiotic treatments. In this context, the aim of this study is to investigate the anti-obesity effects of potential probiotic Lactobacillus acidophilus isolated from the porcine gut. Then, it is found that L. acidophilus reduces body weight, fat mass, inflammation and insulin resistance in mice fed with a high-fat diet (HFD), accompanied by activation in brown adipose tissue (BAT) as well as improvements of energy, glucose and lipid metabolism. Besides, our data indicate that L. acidophilus not only reverses HFD-induced gut dysbiosis, as indicated by the decreased Firmicutes-to-Bacteroidetes ratios and endotoxin bearing Gram-negative bacteria levels, but also maintains intestinal barrier integrity, reduces metabolic endotoxemia, and inhibits the TLR4 / NF- κB signaling pathway. In addition, the results of microbiome phenotype prediction by BugBase and bacterial functional potential prediction using PICRUSt show that L. acidophilus treatment improves the gut microbiota functions involving metabolism, immune response, and pathopoiesia. Furthermore, the anti-obesity effect is transmissible via horizontal faeces transfer from L. acidophilus-treated mice to HFD-fed mice. According to our data, it is seen that L. acidophilus could be a good candidate for probiotic of ameliorating obesity and associated diseases such as hyperlipidemia, nonalcoholic fatty liver diseases, and insulin resistance through its anti-inflammatory properties and alleviation of endothelial dysfunction and gut dysbiosis.

Pressure induced phase transitions of bulk CsGeCl3 and ultrafast laser pulse induced excited-state properties of CsGeCl3 quantum dots.

First-principles calculations are carried out to investigate the structural, electronic, and optical properties of CsGeCl3. The results indicate that CsGeCl3 undergoes three structural phase transitions from Cm or R3m to Pm3̄m at 8.5 GPa, from Pm3̄m to ppPv-Pnma at 9.4 GPa, and from ppPv-Pnma to I4mm at 64 GPa, respectively. Meanwhile, the relation between the band gap and pressure implies that the band gap value of ppPv-Pnma is 1.56 eV at 40 GPa, making it a potential photovoltaic material. Based on pressure-induced stable structures, the CsGeCl3 quantum dots (QDs) have been fabricated to investigate the excited-state properties by tuning ultrafast laser pulses based on time-dependent density functional theory (TDDFT). The excited-state properties show that CsGeCl3 QDs have a wider absorption range compared with their bulk materials and their optical responses can be regulated by changing the laser intensity and wavelength. Our results further reveal that the R3m-QDs exhibit excellent optical performance and have potential applications in optoelectronic devices.

Pressure-induced reconstructive phase transitions, polarization with metallicity, and enhanced hardness in antiperovskite MgCNi3.

In general, hydrostatic pressure can suppress electrical polarization, instead of creating and/or enhancing polarization like strain engineering. Here, a combination of first-principles calculations and CALYPSO crystal structures prediction is used to point out that hydrostatic pressure applied on antiperovskite MgCNi3 can stabilize polarization with metallicity, and thus a polar metal can exist under high pressure. Strikingly, the metallic polar phase of MgCNi3 exhibits an original linear-cubic coupling between polar and nonpolar modes, resulting in an asymmetrical double-well when the polarization is switched. Moreover, another novel phase of MgCNi3 under high pressure possesses an enhanced hardness stemming from a robust s-s electrons interaction of an unexpected C-C bond, rather than typical sp3 orbital hybridization. These discoveries open new routes to design superhard materials and polar metals.

Dissociation of dinitrogen on iron clusters: a detailed study of the Fe16 + N2 case.

The coalescence of two Fe8N as well as the structure of the Fe16N2 cluster were studied using density functional theory with the generalized gradient approximation and a basis set of triple-zeta quality. It was found that the coalescence may proceed without an energy barrier and that the geometrical structures of the resulting clusters depend strongly on the mutual orientations of the initial moieties. The dissociation of N2 is energetically favorable on Fe16, and the nitrogen atoms share the same Fe atom in the lowest energy state of the Fe16N2 species. The attachment of two nitrogen atoms leads to a decrease in the total spin magnetic moment of the ground-state Fe16 host by 6 µB due to the peculiarities of chemical bonding in the magnetic clusters. In order to gain insight into the dependence of properties on charge and to estimate the bonding energies of both N atoms, we performed optimizations of Fe16N and the singly charged ions of both Fe16N2 and Fe16N. It was found that the electronic properties of the Fe16N2 cluster, such as electron affinity and ionization energy, do not appreciably depend on the attachment of nitrogen atoms but that the average binding energy per atom changes significantly. The lowering in total energy due to the attachment of two N atoms was found to be nearly independent of charge. The IR and Raman spectra were simulated for Fe16N2 and its ions, and it was found that the positions of the most intense peaks in the IR spectra strongly depend on charge and therefore present fingerprints of the charged states. The chemical bonding in the ground-state Fe16N20,±1 species was described in terms of the localized molecular orbitals.

Insights into the Structures and Bonding of Medium-Sized Cerium-Doped Boron Clusters.

Since the discovery of metal-doped boron clusters attracted great significance to create a new class of materials, research interests have been directed to chemical bonding and structural evolution of lanthanide boride clusters. Here, we perform an extensive ground-state structure search for the CeBn and CeBn- clusters in the size range from 9 to 18 using the Crystal structure AnaLYsis by Particle Swarm Optimization method and density functional theory optimization. It is found that the ground-state structures in both neutral and anionic series possess half-sandwich geometry. The host boron moiety in neutral series has a tendency to form borophene-like geometry. The pentagonal and hexagonal holes are more common in the larger anionic CeBn- series. The theoretical photoelectron spectroscopy has been simulated by applying time-dependent density functional theory calculations. The neutral CeB14 cluster is identified as a magic cluster on the basis of its robust relative stability with respect to its neighbors. Electronic structure and chemical bonding analyses reveal that the CeB14 cluster possesses a large HOMO-LUMO gap and enhanced stability with strong delocalized π and δ bonding via interactions between the Ce 5d- and B 2p-AOs.

Investigation of the Structure and Luminescence Mechanism of Tm3+-Doped LiYF4: New Theoretical Perspectives.

The absorption and emission transitions of Tm3+-doped LiYF4 have been extensively investigated due to the excellent properties and enormous applications of these materials as laser materials. However, the challenging issues regarding the local structure and luminescence mechanism have not been conclusively established to date. To address these challenges, the CALYPSO structure search method is employed, and the results first reveal the ground-state structure of Tm3+-doped LiYF4, which crystallizes in the space group P4̅ (No. 81) of the tetragonal system. The Y3+ ions are replaced by Tm3+ ions, forming a local configuration of [TmF8]5-. Furthermore, the complete Stark energy levels of Tm3+-doped LiYF4 are predicted by using our newly developed WEPMD method, which provides preliminary preparation for further spectral exploration. Judd-Ofelt analysis is performed to evaluate the electric dipole transition intensities. Two prominent transitions, 3H5 → 3H6 (1223 nm) and 3H4 → 3H6 (801 nm), are predicted to be good candidates for near-infrared lasers. This study not only is useful for determining the luminescence properties of Tm3+-doped LiYF4 but also offers an effective way to search for other rare-earth-doped lasing crystals for the future design of lasing materials.

Unraveling the local structure and luminescence evolution in Nd3+-doped LiYF4: a new theoretical approach.

Neodymium ion (Nd3+)-doped yttrium lithium fluoride (LiYF4, YLF) laser crystals have shown significant prospects as excellent laser materials in many kinds of solid-state laser systems. However, the origins of the detailed information of their local structure and luminescence evolution are still poorly understood. Herein, we use an unbiased CALYPSO structure searching technique and density functional theory to study the local structure of Nd3+-doped YLF. Our results reveal a new stable phase with the P4[combining macron] (No. 81) space group for Nd3+-doped YLF, indicating that the host Y3+ ion site was naturally occupied by the Nd3+ ion impurity. On the basis of our newly developed WEPMD method, we adopt a specific type of orthogonal correlation crystal field to obtain a new set of crystal-field parameters as well as 182 complete Stark energy levels. Many absorption and emission lines for Nd3+-doped YLF are calculated and discussed based on Judd-Ofelt theory, and our results indicate that some of the observed absorption and emission lines are perfectly reproduced by our theoretical calculations. Additionally, we predict several promising transition lines in the visible and near-infrared spectral regions, including the electronic dipole emission lines 4F5/2 → 4I9/2 at 808 nm and 2H9/2 → 4I9/2 at 799 nm, as well as the magnetic dipole emission lines 4F3/2(27) → 4I11/2(6) at 1047 nm and 4F3/2(27) → 4I11/2(8) at 1052 nm. These transition channels indicate that Nd3+-doped YLF laser crystals have greatly promising laser actions for serving as a solid-state laser material.

Mechanical properties of tantalum carbide from high-pressure/high-temperature synthesis and first-principles calculations.

As a member of the refractory metal carbide family of materials, TaC is a promising candidate for ultra-high temperature ceramics (UHTC) with desirable mechanical strength. TaC sample quality and therefore mechanical properties are strongly dependent on synthesis method, and atomistic origins of mechanical failure are difficult to assign. Here, we have successfully synthesized high quality densified TaC samples at 5.5 GPa and 1400 °C using the high pressure and high temperature (HPHT) sintering method, with Vickers hardness determined to be 20.9 GPa. First-principles calculations based on the recently developed strain-stress method show that the ideal indentation strength of TaC is about 23.3 GPa in the (11[combining macron]0)[001] direction, in excellent agreement with experimental results. The detailed indentation shear deformation analysis and structural snapshots from the calculations indicate that the slip dislocations of TaC layers are the main structural deformation mode during the Vickers indentation process, and that the strong directional Ta-C bonds are responsible for the high mechanical strength of TaC. HPHT synthesis is shown to produce TaC samples with superior strength, and together with accurate first-principles calculations offers crucial insights for rational design and synthesis of novel and advanced UHTC materials.

Tuning of Structure Evolution and Electronic Properties through Palladium-Doped Boron Clusters: PdB16 as a Motif for Boron-Based Nanotubes.

Transition metal-doped electronic deficiency boron clusters have led to a vast variety of electronic bonding properties in chemistry and materials science. We have determined the ground state structures of PdBn0/- (n = 10-20) clusters by performing CALYPSO search and density functional theory (DFT) optimization. The identified lowest energy structures for both neutral and anionic Pd-doped boron clusters follow the structure evolution from two dimensional (2D) planar configurations to 3D distorted Pd-centered drum-like or tubular structures. Photoelectron spectra are simulated by time-dependent DFT theoretical calculations, which is a powerful method to validate our obtained ground-state structures. More interestingly, two "magic" number clusters, PdB12 and PdB16, are found with enhanced stability in the middle size regime studied. Subsequently, molecular orbital and adaptive natural density partitioning analyses reveal that the high stability of the PdB16 cluster originates from doubly σ π aromatic and bonding interactions of d-type atomic orbitals of the Pd atom with tubular B16 units. The tubular C8v PdB16 cluster, with robust relative stability, is an ideal embryo for forming finite and infinite nanotube nanomaterials.

Insights into the Microstructure and Transition Mechanism for Nd3+-Doped Bi4Si3O12: A Promising Near-Infrared Laser Material.

Due to its unusual optical properties, neodymium ion (Nd3+)-doped bismuth silicate (Bi4Si3O12, BSO) is widely used for its excellent medium laser amplification in physics, chemistry, biomedicine, and other research fields. Although the spectral transitions and luminescent mechanisms of Nd3+-doped BSO have been investigated experimentally, theoretical research is severely limited due to the lack of detailed information about the microstructure and the doping site of Nd3+-doped BSO, as well as the electric and magnetic dipole transition mechanisms. Herein, we systematically study the microstructure and doping site of Nd3+-doped BSO using an unbiased CALYPSO structure search method in conjunction with first-principles calculations. The result indicates that the Nd3+ ion impurity occupies the host Bi3+ ion site with trigonal symmetry, forming a unique semiconducting phase. Based on our newly developed WEPMD method, the electric dipole and magnetic dipole transition lines, including a large number of absorption and emission lines, in the region of visible and near-infrared spectra of Nd3+-doped BSO are calculated. It is found that the 4G5/2 → 4I9/2, 2H9/2 → 4I9/2, and 4F3/2 → 4I11/2 channels are promising laser actions of Nd3+-doped BSO. These findings indicate that Nd3+-doped BSO crystals can serve as a promising multifunctional material for optical laser devices.

Probing the structural and electronic properties of zirconium doped boron clusters: Zr distorted B12 ligand framework.

As an extension of boron based materials, transition-metal doped boron clusters deserve interest in controlling size-dependent structural and electronic properties. Herein, using the Crystal structure AnaLYsis by Particle Swarm Optimization (CALYPSO) method and density functional theory (DFT) calculations, we have performed a global search for the lowest-energy structures of ZrBQn (Q = 0, -1) clusters with n = 10-20. The results show that the ground-state structures of the obtained clusters feature a distinctive structural evolution pattern, from half-sandwich bowl to distorted drum-like and then to Zr-centered distorted tubular motifs. For the sake of validating the current ground-state structures, photoelectron spectra are predicted from time-dependent DFT calculations. More interestingly, the neutral and anionic ZrB12 clusters are found to possess enhanced stability in the size regime studied here. The stability of the closed shell half-sandwich ZrB12 cluster is analyzed by intrinsic bond orbital (IBO) and Adaptive Natural Density Partitioning (AdNDP) methods, which indicates that the stability mechanism is caused by the dopant Zr atom breaking the boron bowl's triangle B3 unit to form a quasi-linear B3 unit in B12 and strengthen both the interaction of the B-B σ-bonds and the Zr-B π-bonds.

Insights into the effects produced by doping of medium-sized boron clusters with ruthenium.

Modification of properties of boron nanoparticles by doping with transition metals presents a challenging problem because the number of isomers of both doped and un-doped nanoparticles rapidly increases with the nanoparticle size. Here, we perform a study of neutral and anionic Ru-doped boron clusters RuBn (n = 9-20) using the unbiased CALYPSO structural search method in combination with density functional theory calculations. Our results show that the neutral RuB9 cluster possesses a perfect planar wheel-like geometrical structure, whereas the RuBn clusters prefer structures of the half-sandwich type in the range of 10 ≤ n ≤ 14, drum-like type in the range of 15 ≤ n ≤ 18 and cage-like structures for larger n values. The geometrical structures of the lowest total energy states of the RuBn- anions are similar to those of the corresponding neutrals, except for RuB10-, RuB11-, RuB14-, RuB15- and RuB20-. The neutral RuB12 and RuB14 clusters are found to exhibit enhanced stability with respect to the rest of the RuBn clusters due to the delocalized bonding between the Ru atom and the boron host.

Novel structural phases and the electrical properties of Si3B under high pressure.

We report a detailed theoretical study of the electronic structure, phase stability, elastic and mechanical properties of Si3B in the pressure range of 0-160 GPa by employing the crystal structure analysis by particle swarm optimization (CALYPSO) method combined with first-principles calculations. Our theoretical predictions reveal that, as the pressure increases, Si3B moves through the following sequence of phases: P3121 → C2/m → P21/m, and the corresponding transition pressures are computed to be 30 and 64 GPa, respectively. The results of band structures, density of states and electronic localization functions indicate that all three phases act as metallic with strong covalent bonding. The Vickers hardness of C2/m and P21/m phases has been estimated by Gao's, Lyakhov-Oganov's and Simunek's models, implying that Si3B is a potential hard material with a hardness value of ∼20 GPa. The superconducting critical temperatures of polymeric Si3B are also uncovered to be 3.6 K for the C2/m phase at 50 GPa and 5.7 K for the P21/m phase at 100 GPa. Our results enrich the crystal structures of the Si-B system and provide a further understanding of structures and their properties.

Prediction of hypervalent molecules: investigation on MnC (M = Li, Na, K, Rb and Cs; n = 1-8) clusters.

New hypervalent molecules have emerged from a systematic exploration of the structure and bonding of MnC (M = Li, Na, K, Rb and Cs; n = 1-8) clusters via an unbiased CALYPSO structure investigation combined with density functional theory. The global minimum structures are obtained at the B3LYP/6-311+G* and CCSD(T)/6-311+G* levels of theory. The observed growth behavior clearly indicates that the ground state of MnC (M = Li, Na, K, Rb and Cs; n = 1-8) is transformed from a planar to a three-dimensional (3D) structure at n = 4. A maximum of six alkali atoms can be bound atomically to a carbon atom. The determination of the averaged binding energies Eb(n), fragmentation energies ΔE(n) and HOMO-LUMO energy gaps unambiguously supports the stability of M6C. This indicated conclusively that 6 is a magic Li-coordination number for C. The nature of bonding is further investigated by an insightful analysis of the highest occupied molecular orbital (HOMO) and the topology of chemical bonds for the most stable clusters. In the final step, electron localization functions (ELF) and density of states (DOS) are determined in order to consolidate the acquired information on the studied electronic structures.

Ground State Properties of the Polar Alkali-Metal-Ytterbium and Alkaline-Earth-Metal-Ytterbium Molecules: A Comparative Study.

The accurate knowledge of electronic properties is important for creating and manufacturing ultracold molecules. We report here the ab initio quantum chemistry calculations on the properties of alkali-metal-ytterbium AM-Yb (AM = Li, Na, K, Rb, Cs) and alkaline-earth-metal-ytterbium AEM-Yb (AEM = Be, Mg, Ca, Sr, Ba) molecules for their electronic ground state. The potential energy curves (PECs) and permanent dipole moments (PDMs) are calculated on the basis of the multireference configuration interaction (MRCI) level of theory, where the core-valence correlations and scalar relativistic effects are included. The related spectroscopic constants are also determined. The results demonstrate that the dissociation energies and PDMs of AEM-Yb are smaller than those of AM-Yb molecules, and an interesting trend of the dissociation energy has been observed. This work provides favorable information for the experimental study of forming ultracold molecules via photoassociation technique.

Probing the low-energy structures of aluminum-magnesium alloy clusters: a detailed study.

The effect of Mg doping on the growth behavior and the electronic properties of aluminum clusters has been investigated theoretically using the CALYPSO (Crystal structure AnaLYsis by Particle Swarm Optimization) method in combination with density functional theory calculations. Compared to pure aluminum clusters, the structure of Mg-doped clusters shows the charming transformation with increasing atomic number. The photoelectron spectra (PES) of the global minima of anionic Aln and AlnMg (n = 3-20) clusters have been calculated based on the time-dependent density functional theory (TD-DFT) method. The reliability of our theoretical methodology is easily corroborated by the good agreement between the experimental PES and the simulated spectra. Our findings bring forth an ionic bonding with enhanced stability for the Al6Mg cluster, paired with a surprisingly large HOMO-LUMO gap, as would be expected from the magic number of 20 valence electrons.

Large polarization and dielectric response in epitaxial SrZrO3 films.

First-principles calculations are performed to investigate the ferroelectric and dielectric properties of (001) epitaxial SrZrO3 thin films under misfit strain. A rich phase diagram is predicted. By condensing the polar instability, the ferroelectric Pmc21 and Ima2 phases can coexist under tensile strain (about 3.7%-5.2%/5.7%). Combining in-plane ferroelectric (FExy) and out-of-plane in-phase antiferrodistortive (IAFDz) modes, another new Pmc21 state (P > 56 µC cm(-2)) occurs with increase in the tensile strain. The paraelectric I4/mcm and ferroelectric P4mm phases emerge around -3.2%/-3.7% and -6.4%/-7.4% compressive strain, respectively. The former exhibits an intense out-of-plane dielectric response, while the latter possesses a rather large polarization (∼ 110 µC cm(-2)). The large polarization and dielectric response are discussed in relationship to strain-driven structural distortion.

Deciphering the Structural Evolution and Electronic Properties of Magnesium Clusters: An Aromatic Homonuclear Metal Mg17 Cluster.

The structures and electronic properties of low-energy neutral and anionic Mgn (n = 3-20) clusters have been studied by utilizing a widely adopted CALYPSO structure searching method coupled with density functional theory calculations. A large number of low-energy isomers are optimized at the B3PW91 functional with the 6-311+G(d) basis set. The optimized geometries clearly indicate that a structural transition from hollow three-dimensional configurations to filled-cage-like structures occurs at n = 16 for both neutral and anionic clusters. Based on the anionic ground state structures, photoelectron spectra are simulated using time-dependent density functional theory (TD-DFT) and compared with experimental results. The good agreement validates that the current ground state structures, obtained from the symmetry-unconstrained searches, are true global minima. A detailed chemical bonding analysis distinctly indicates that the Mg17 cluster is the first neutral locally π-aromatic homonuclear all-metal cluster, which perfectly satisfies Hückel's well-known 4N + 2 rule.