Minnesota Supercomputing Institute

. We further tested MN15 for 10 transition-metal coordination energies, the entire S66x8 database of noncovalent interactions, 21 transition-metal reaction barrier heights, 69 electronic excitation energies of organic molecules, 31 semiconductor band gaps, seven transition-metal dimer bond lengths, and 193 bond lengths of 47 organic molecules. The MN15 functional not only performs very well for our training set, which has 481 pieces of data, but also performs very well for our test set, which has 823 data that are not in our training set. The test set includes both ground-state properties and molecular excitation energies. For the latter MN15 achieves simultaneous accuracy for both valence and Rydberg electronic excitations when used with linear-response time-dependent density functional theory, with an MUE of less than 0.3 eV for both types of excitations.

Persistent androgen receptor (AR) transcriptional activity underlies resistance to AR-targeted therapy and progression to lethal castration-resistant prostate cancer (CRPC). Recent success in retargeting persistent AR activity with next generation androgen/AR axis inhibitors such as enzalutamide (MDV3100) has validated AR as a master regulator during all stages of disease progression. However, resistance to next generation AR inhibitors limits therapeutic efficacy for many patients. One emerging mechanism of CRPC progression is AR gene rearrangement, promoting synthesis of constitutively active truncated AR splice variants (AR-V) that lack the AR ligand-binding domain. In this study, we show that cells with AR gene rearrangements expressing both full-length and AR-Vs are androgen independent and enzalutamide resistant. However, selective knock-down of AR-V expression inhibited androgen-independent growth and restored responsiveness to androgens and antiandrogens. In heterogeneous cell populations, AR gene rearrangements marked individual AR-V-dependent cells that were resistant to enzalutamide. Gene expression profiling following knock-down of full-length AR or AR-Vs showed that AR-Vs drive resistance to AR-targeted therapy by functioning as constitutive and independent effectors of the androgen/AR transcriptional program. Further, mitotic genes deemed previously to be unique AR-V targets were found to be biphasic targets associated with a proliferative level of signaling output from either AR-Vs or androgen-stimulated AR. Overall, these studies highlight AR-Vs as key mediators of persistent AR signaling and resistance to the current arsenal of conventional and next generation AR-directed therapies, advancing the concept of AR-Vs as therapeutic targets in advanced disease.

This article reviews the fundamentals of variational transition state theory (VTST), its recent theoretical development, and some modern applications. The theoretical methods reviewed here include multidimensional quantum mechanical tunneling, multistructural VTST (MS-VTST), multi-path VTST (MP-VTST), both reaction-path VTST (RP-VTST) and variable reaction coordinate VTST (VRC-VTST), system-specific quantum Rice-Ramsperger-Kassel theory (SS-QRRK) for predicting pressure-dependent rate constants, and VTST in the solid phase, liquid phase, and enzymes. We also provide some perspectives regarding the general applicability of VTST.

We have expanded the livestock gene editing toolbox to include transcription activator-like (TAL) effector nuclease (TALEN)- and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-stimulated homology-directed repair (HDR) using plasmid, rAAV, and oligonucleotide templates. Toward the genetic dehorning of dairy cattle, we introgressed a bovine POLLED allele into horned bull fibroblasts. Single nucleotide alterations or small indels were introduced into 14 additional genes in pig, goat, and cattle fibroblasts using TALEN mRNA and oligonucleotide transfection with efficiencies of 10-50% in populations. Several of the chosen edits mimic naturally occurring performance-enhancing or disease- resistance alleles, including alteration of single base pairs. Up to 70% of the fibroblast colonies propagated without selection harbored the intended edits, of which more than one-half were homozygous. Edited fibroblasts were used to generate pigs with knockout alleles in the DAZL and APC genes to model infertility and colon cancer. Our methods enable unprecedented meiosis-free intraspecific and interspecific introgression of select alleles in livestock for agricultural and biomedical applications.

We introduce a new implementation of time-dependent density-functional theory which allows the entire spectrum of a molecule or extended system to be computed with a numerical effort comparable to that of a single standard ground-state calculation. This method is particularly well suited for large systems and/or large basis sets, such as plane waves or real-space grids. By using a superoperator formulation of linearized time-dependent density-functional theory, we first represent the dynamical polarizability of an interacting-electron system as an off-diagonal matrix element of the resolvent of the Liouvillian superoperator. One-electron operators and density matrices are treated using a representation borrowed from time-independent density-functional perturbation theory, which permits us to avoid the calculation of unoccupied Kohn-Sham orbitals. The resolvent of the Liouvillian is evaluated through a newly developed algorithm based on the nonsymmetric Lanczos method. Each step of the Lanczos recursion essentially requires twice as many operations as a single step of the iterative diagonalization of the unperturbed Kohn-Sham Hamiltonian. Suitable extrapolation of the Lanczos coefficients allows for a dramatic reduction of the number of Lanczos steps necessary to obtain well converged spectra, bringing such number down to hundreds (or a few thousands, at worst) in typical plane-wave pseudopotential applications. The resulting numerical workload is only a few times larger than that needed by a ground-state Kohn-Sham calculation for a same system. Our method is demonstrated with the calculation of the spectra of benzene, C(60) fullerene, and of chlorophyll a.

Large databases (>10(6) sequences) used in metaproteomic and proteogenomic studies present challenges in matching peptide sequences to MS/MS data using database-search programs. Most notably, strict filtering to avoid false-positive matches leads to more false negatives, thus constraining the number of peptide matches. To address this challenge, we developed a two-step method wherein matches derived from a primary search against a large database were used to create a smaller subset database. The second search was performed against a target-decoy version of this subset database merged with a host database. High confidence peptide sequence matches were then used to infer protein identities. Applying our two-step method for both metaproteomic and proteogenomic analysis resulted in twice the number of high confidence peptide sequence matches in each case, as compared to the conventional one-step method. The two-step method captured almost all of the same peptides matched by the one-step method, with a majority of the additional matches being false negatives from the one-step method. Furthermore, the two-step method improved results regardless of the database search program used. Our results show that our two-step method maximizes the peptide matching sensitivity for applications requiring large databases, especially valuable for proteogenomics and metaproteomics studies.

Depending on mass and metallicity as well as evolutionary phase, stars occasionally experience convective-reactive nucleosynthesis episodes. We specifically investigate the situation when nucleosynthetically unprocessed, H-rich material is convectively mixed with a He-burning zone, for example in convectively unstable shell on top of electron-degenerate cores in AGB stars, young white dwarfs or X-ray bursting neutron stars. Such episodes are frequently encountered in stellar evolution models of stars of extremely low or zero metal content [...] We focus on the convective-reactive episode in the very-late thermal pulse star Sakurai's object (V4334 Sagittarii). Asplund etal. (1999) determined the abundances of 28 elements, many of which are highly non-solar, ranging from H, He and Li all the way to Ba and La, plus the C isotopic ratio. Our simulations show that the mixing evolution according to standard, one-dimensional stellar evolution models implies neutron densities in the He that are too low to obtain a significant neutron capture nucleosynthesis on the heavy elements. We have carried out 3D hydrodynamic He-shell flash convection [...] we assume that the ingestion process of H into the He-shell convection zone leads only after some delay time to a sufficient entropy barrier that splits the convection zone [...] we obtain significantly higher neutron densities (~few 10^15 1/cm^3) and reproduce the key observed abundance trends found in Sakurai's object. These include an overproduction of Rb, Sr and Y by about 2 orders of magnitude higher than the overproduction of Ba and La. Such a peculiar nucleosynthesis signature is impossible to obtain with the mixing predictions in our one-dimensional stellar evolution models. [...] We determine how our results depend on uncertainties of nuclear reaction rates, for example for the C13(\alpha, n)O16 reaction.

The thermoelastic properties of ferropericlase Mg(1-x)Fe(x)O (x = 0.1875) throughout the iron high-to-low spin cross-over have been investigated by first principles at Earth's lower mantle conditions. This cross-over has important consequences for elasticity such as an anomalous bulk modulus (K(S)) reduction. At room temperature the anomaly is somewhat sharp in pressure but broadens with increasing temperature. Along a typical geotherm it occurs across most of the lower mantle with a more significant K(S) reduction at approximately 1,400-1,600 km depth. This anomaly might also cause a reduction in the effective activation energy for diffusion creep and lead to a viscosity minimum in the mid-lower mantle, in apparent agreement with results from inversion of data related with mantle convection and postglacial rebound.

Parasexuality contributes to diversity and adaptive evolution of haploid (monokaryotic) fungi. However, non-sexual genetic exchange mechanisms are not defined in dikaryotic fungi (containing two distinct haploid nuclei). Newly emerged strains of the wheat stem rust pathogen, Puccinia graminis f. sp. tritici (Pgt), such as Ug99, are a major threat to global food security. Here, we provide genomics-based evidence supporting that Ug99 arose by somatic hybridisation and nuclear exchange between dikaryons. Fully haplotype-resolved genome assembly and DNA proximity analysis reveal that Ug99 shares one haploid nucleus genotype with a much older African lineage of Pgt, with no recombination or chromosome reassortment. These findings indicate that nuclear exchange between dikaryotes can generate genetic diversity and facilitate the emergence of new lineages in asexual fungal populations.

Electrical conductivity is engendered in a pyrene containing hexa-zirconium(<sc>iv</sc>) metal–organic framework by physically encapsulating fullerenes within MOF cavity.

A new versatile single-ion electrolyte with a Grotthuss-like Li conduction mechanism is proposed to address the issue of Li metal batteries.

Eleven experimentally characterized complexes containing heterobimetallic bonds between elements of the f-block and other elements were examined by quantum chemical methods: [(η(5)-C(5)H(5))(2)(THF)LuRu(η(5)-C(5)H(5))(CO)(2)], [(η(5)-C(5)Me(5))(2)(I)ThRu(η(5)-C(5)H(5))(CO)(2)], [(η(5)-C(5)H(5))(2)YRe(η(5)-C(5)H(5))(2)], [{N(CH(2)CH(2)NSiMe(3))(3)}URe(η(5)-C(5)H(5))(2)], [Y{Ga(NArCh)(2)}{C(PPh(2)NSiH(3))(2)}(CH(3)OCH(3))(2)], [{N(CH(2)CH(2)NSiMe(3))(3)}U{Ga(NArCH)(2)}(THF)], [(η(5)-C(5)H(5))(3)UGa(η(5)-C(5)Me(5))], [Yb(η(5)-C(5)H(5)){Si(SiMe(3))(3)(THF)(2)}], [(η(5)-C(5)H(5))(3)U(SnPh(3))], [(η(5)-C(5)H(5))(3)U(SiPh(3))], and (Ph[Me]N)(3)USi(SiMe(3))(3). Geometries in good agreement with experiment were obtained at the density functional level of theory. The multiconfigurational complete active space self-consistent field method (CASSCF) and subsequent corrections with second order perturbation theory (CASPT2) were applied to further understand the electronic structure of the lanthanide/actinide-metal (or metal-metalloid) bonds. Fragment calculations and energy-decomposition analyses were also performed and indicate that charge transfer occurs from one supported metal fragment to the other, while the bonding itself is always dominated by ionic character.

Fatty acid-binding proteins (FABP) are known central regulators of both metabolic and inflammatory pathways, but their role in tumor development remains largely unexplored. Here, we report that host expression of epidermal FABP (E-FABP) protects against mammary tumor growth. We find that E-FABP is highly expressed in macrophages, particularly in a specific subset, promoting their antitumor activity. In the tumor stroma, E-FABP-expressing tumor-associated macrophages (TAM) produce high levels of IFN-β through upregulation of lipid droplet formation in response to tumors. E-FABP-mediated IFN-β signaling can further enhance recruitment of tumoricidal effector cells, in particular natural killer cells, to the tumor stroma for antitumor activity. These findings identify E-FABP as a new protective factor to strengthen IFN-β responses against tumor growth.

ion, all functionals except M11-L correctly predict the ground spin state to be quintet. However, quantitatively, most of the functionals are not close to the experimentally determined spin-state splitting energies. For FeO all functionals predict quintet to be the ground spin state. For the 14 iron complexes, the hybrid functionals B3LYP, MPW1B95 and MN15 correctly predict the ground spin state of 13 out of 14 complexes and PW6B95 gets all the 14 complexes right. The local functionals, OPBE, OLYP and M06-L, predict the correct ground spin state for 12 out of 14 complexes. Two of the tested functionals are not recommended to be used for this type of study, in particular M08-SO and M11-L, because M08-SO systematically overstabilizes the high spin state, and M11-L systematically overstabilizes the low spin state.

The density matrix renormalization group (DMRG) is a powerful method to treat static correlation. Here we present an inexpensive way to calculate correlation energy starting from a DMRG wave function using pair-density functional theory (PDFT). We applied this new approach, called DMRG-PDFT, to study singlet-triplet gaps in polyacenes and polyacetylenes that require active spaces larger than the feasibility limit of the conventional complete active-space self-consistent field (CASSCF) method. The results match reasonably well with the most reliable literature values and have only a moderate dependence on the compression of the initial DMRG wave function. Furthermore, DMRG-PDFT is significantly less expensive than other commonly applied ways of adding additional correlation to DMRG, such as DMRG followed by multireference perturbation theory or multireference configuration interaction.

The physical basis for the “hydrophobic effect” is studied using a simple statistical mechanical model of water, the “MB” model, in which water molecules are represented as Lennard-Jones disks with hydrogen bonding arms. Using a four-state framework developed by Muller [Acc. Chem. Res. 23, 23 (1990)], and extended by Lee and Graziano [J. Am. Chem. Soc. 118, 5163 (1996)], we find the model reproduces the fingerprints of hydrophobicity, namely, the large positive heat capacity, and temperatures TH and TS at which the enthalpy and entropy of transfer, respectively, are zero. Further, the behavior can be interpreted readily in terms of hydrogen bonds that are either made or broken in the bulk or in the first solvation shell around a nonpolar solute. We find that inserting a nonpolar solute into cold water causes ordering and strengthening of the H bonds in the first shell, but that the reverse applies in hot water. This provides a physical interpretation for the crossover temperatures TH and TS.

As electronic structure methods are being used to obtain quantitatively accurate reaction energies and barrier heights for increasingly larger systems, the choice of an efficient basis set is becoming more critical. The optimum strategy for achieving basis set convergence can depend on the way that electron correlation is treated and can take advantage of flexibility in the order in which basis functions are added. Here we study several approaches for estimating accurate reaction energies and barrier heights from post-Hartree-Fock electronic structure calculations. First and second, we evaluate methods of estimating the basis set limit of second order Møller-Plesset perturbation theory and of coupled cluster theory with single and double excitations and a quasiperturbative treatment of connected triple excitations by using explicitly correlated basis functions (in the F12a implementation) along with valence, polarization, and diffuse one-electron basis functions. Third, we test the scheme of adding a higher-order correction to MP2 results (sometimes called MP2∕CBS + ΔCCSD(T)). Finally, we evaluate the basis set requirements of these methods in light of comparisons to Weizmann-3.2, Weizmann-4, and CCSDT(2)(Q)∕CBS+CV+R results.

The WG5 committee, at its meeting in Delft, May 2005, decided to include co-arrays in the next Fortran Standard. A special issue of Fortran Forum in August 1998 explained the feature, but since many of the details of the version adopted by WG5 differ from the 1998 version, it seems appropriate to describe it afresh in a self-contained article.A Fortran program containing co-arrays is interpreted as if it were replicated a fixed number of times and all copies were executed asynchronously. Each copy has its own set of data objects and is called an image. The array syntax of Fortran is extended with additional trailing subscripts in square brackets to give a clear and straightforward representation of access to data on other images.References without square brackets are to local data, so code that can run independently is uncluttered. Only where there are square brackets, or where there is a procedure call and the procedure contains square brackets, is communication between images involved.The additional syntax requires support in the compiler, but it has been designed to be easy to implement and to give the compiler scope both to apply its optimizations within each image and to optimize the communication between images.The extension includes intrinsic procedures to synchronize images, to return the number of images, to return the index of the current image, and to perform collective actions.

With a dataset of more than 600 million small RNAs deeply sequenced from mouse hippocampal and staged sets of mouse cells that underwent reprogramming to induced pluripotent stem cells, we annotated the stem-loop precursors of the known miRNAs to identify isomoRs (miRNA-offset RNAs), loops, non-preferred strands, and guide strands. Products from both strands were readily detectable for most miRNAs. Changes in the dominant isomiR occurred among the cell types, as did switches of the preferred strand. The terminal nucleotide of the dominant isomiR aligned well with the dominant off-set sequence suggesting that Drosha cleavage generates most miRNA reads without terminal modification. Among the terminal modifications detected, most were non-templated mono- or di-nucleotide additions to the 3'-end. Based on the relative enrichment or depletion of specific nucleotide additions in an Ago-IP fraction there may be differential effects of these modifications on RISC loading. Sequence variation of the two strands at their cleavage sites suggested higher fidelity of Drosha than Dicer. These studies demonstrated multiple patterns of miRNA processing and considerable versatility in miRNA target selection.

Metaproteomics characterizes proteins expressed by microorganism communities (microbiome) present in environmental samples or a host organism (e.g. human), revealing insights into the molecular functions conferred by these communities. Compared to conventional proteomics, metaproteomics presents unique data analysis challenges, including the use of large protein databases derived from hundreds or thousands of organisms, as well as numerous processing steps to ensure high data quality. These challenges limit the use of metaproteomics for many researchers. In response, we have developed an accessible and flexible metaproteomics workflow within the Galaxy bioinformatics framework. Via analysis of human oral tissue exudate samples, we have established a modular Galaxy-based workflow that automates a reduction method for searching large sequence databases, enabling comprehensive identification of host proteins (human) as well as "meta-proteins" from the nonhost organisms. Downstream, automated processing steps enable basic local alignment search tool analysis and evaluation/visualization of peptide sequence match quality, maximizing confidence in results. Outputted results are compatible with tools for taxonomic and functional characterization (e.g. Unipept, MEGAN5). Galaxy also allows for the sharing of complete workflows with others, promoting reproducibility and also providing a template for further modification and enhancement. Our results provide a blueprint for establishing Galaxy as a solution for metaproteomic data analysis. All MS data have been deposited in the ProteomeXchange with identifier PXD001655 (http://proteomecentral.proteomexchange.org/dataset/PXD001655).