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We investigate the dynamical mean-field theory (DMFT) from a quantum chemical perspective. Dynamical mean-field theory offers a formalism to extend quantum chemical methods for finite systems to infinite periodic problems within a local correlation approximation. In addition, quantum chemical techniques can be used to construct new ab initio Hamiltonians and impurity solvers for DMFT. Here, we explore some ways in which these things may be achieved. First, we present an informal overview of dynamical mean-field theory to connect to quantum chemical language. Next, we describe an implementation of dynamical mean-field theory where we start from an ab initio Hartree-Fock Hamiltonian that avoids double counting issues present in many applications of DMFT. We then explore the use of the configuration interaction hierarchy in DMFT as an approximate solver for the impurity problem. We also investigate some numerical issues of convergence within DMFT. Our studies are carried out in the context of the cubic hydrogen model, a simple but challenging test for correlation methods. Finally, we finish with some conclusions for future directions., (© 2011 American Institute of Physics.)

The mitotic checkpoint functions to ensure accurate chromosome segregation by regulating the progression from metaphase to anaphase. Once the checkpoint has been satisfied, it is inactivated in order to allow the cell to proceed into anaphase and complete the cell cycle. The minus end-directed microtubule motor dynein/dynactin has been implicated in the silencing of the mitotic checkpoint by "stripping" checkpoint proteins off kinetochores. A recent study suggested that Nordihydroguaiaretic acid (NDGA) stimulates dynein/dynactin-mediated transport of its cargo including ZW10 (Zeste White 10). We analyzed the effects of NDGA on dynein/dynactin dependent transport of the RZZ (Zeste White 10, Roughdeal, Zwilch) complex as well as other kinetochore components from kinetochores to spindle poles. Through this approach we have catalogued several kinetochore and centromere components as dynein/dynactin cargo. These include hZW10, hZwilch, hROD, hSpindly, hMad1, hMad2, hCENP-E, hCdc27, cyclin-B and hMps1. Furthermore, we found that treatment with NDGA induced a robust accumulation and complete stabilization of hZW10 at spindle poles. This finding suggests that NDGA may not induce dynein/dynactin transport but rather interfere with cargo release. Lastly, we determined that NDGA induced accumulation of checkpoint proteins at the poles requires dynein/dynactin-mediated transport, hZW10 kinetochore localization and kinetochore-microtubule attachments but not tension or Aurora B kinase activity.

Efficient electronic structure methods can be built around efficient tensor representations of the wavefunction. Here we first describe a general view of tensor factorization for the compact representation of electronic wavefunctions. Next, we use this language to construct a low-complexity representation of the doubles amplitudes in local second-order Møller-Plesset perturbation theory. We introduce two approximations--the direct orbital-specific virtual approximation and the full orbital-specific virtual approximation. In these approximations, each occupied orbital is associated with a small set of correlating virtual orbitals. Conceptually, the representation lies between the projected atomic orbital representation in Pulay-Saebø local correlation theories and pair natural orbital correlation theories. We have tested the orbital-specific virtual approximations on a variety of systems and properties including total energies, reaction energies, and potential energy curves. Compared to the Pulay-Saebø ansatz, we find that these approximations exhibit favorable accuracy and computational times while yielding smooth potential energy curves.

We report a novel on-chip Rayleigh imaging technique using wide-field laser illumination to measure optical scattering from individual single-walled carbon nanotubes (SWNTs) on a solid substrate with high spatial and spectral resolution. This method in conjunction with calibrated AFM measurements accurately measures the resonance energies and diameters for a large number of SWNTs in parallel. We apply this technique for fast mapping of key SWNT parameters, including the electronic-types and chiral indices for individual SWNTs, position and frequency of chirality-changing events, and intertube interactions in both bundled and distant SWNTs.

The density matrix renormalization group is a method that is useful for describing molecules that have strongly correlated electrons. Here we provide a pedagogical overview of the basic challenges of strong correlation, how the density matrix renormalization group works, a survey of its existing applications to molecular problems, and some thoughts on the future of the method.

Although metallic nanostructures are useful for nanoscale optics, all of their key optical properties are determined by their geometry. This makes it difficult to adjust these properties independently, and can restrict applications. Here we use the absolute intensity of Rayleigh scattering to show that single-walled carbon nanotubes can form ideal optical wires. The spatial distribution of the radiation scattered by the nanotubes is determined by their shape, but the intensity and spectrum of the scattered radiation are determined by exciton dynamics, quantum-dot-like optical resonances and other intrinsic properties. Moreover, the nanotubes display a uniform peak optical conductivity of approximately 8 e(2)/h, which we derive using an exciton model, suggesting universal behaviour similar to that observed in nanotube conductance. We further demonstrate a radiative coupling between two distant nanotubes, with potential applications in metamaterials and optical antennas.

Introduction: Nurses are involved in conducting research and incorporating evidence into their practice. However, barriers exist at the individual, unit, and organizational level related to understanding, conducting, and evaluating the evidence. The Emergency Nurses Association (ENA) conducted a study to understand levels of education in research, the extent of experience, and needs and barriers to research at the individual and organizational levels in emergency nursing., Methods: A cross-sectional survey design was used to poll members of the ENA. A 62-item survey instrument was designed to assess five areas: 1) nurses' research values, skills, experience, and awareness; 2) organizational settings' opportunities, barriers, and limitations to research; 3) nurses' understanding and comprehension of research and evidence; 4) presentation and accessibility of research; and 5) continuing educational topics to improve knowledge of the research process., Results: Respondents (n = 948) identified barriers at the individual level that included lack of knowledge about critiquing research studies and familiarity with the research process. Barriers at the unit level included obtaining help from administrators and other staff in starting a project or having the authority to change practice. Barriers at the institution level included lack of support systems such as protected time to conduct research or implement changes in practice., Discussion: Emergency nurses are highly motivated and interested in learning more about conducting and utilizing research to improve practice. Perceived personal, unit-based, and organizational barriers were identified through this research in an effort to highlight areas for improvement at the local and national levels., (Copyright © 2011 Emergency Nurses Association. Published by Mosby, Inc. All rights reserved.)

Studies in vertebrate neuromuscular synapses have revealed previously that ATP, via P2Y receptors, plays a critical role in regulating postsynaptic gene expressions. An equivalent regulatory role of ATP and its P2Y receptors would not necessarily be expected for the very different situation of the brain synapses, but we provide evidence here for a brain version of that role. In cultured cortical neurons, the expression of P2Y(1) receptors increased sharply during neuronal differentiation. Those receptors were found mainly colocalized with the postsynaptic scaffold postsynaptic density protein 95 (PSD-95). This arises through a direct interaction of a PDZ domain of PSD-95 with the C-terminal PDZ-binding motif, D-T-S-L of the P2Y(1) receptor, confirmed by the full suppression of the colocalization upon mutation of two amino acids therein. This interaction is effective in recruiting PSD-95 to the membrane. Specific activation of P2Y(1) (G-protein-coupled) receptors induced the elevation of intracellular Ca(2+) and activation of a mitogen-activated protein kinase/Raf-1 signaling cascade. This led to distinct up-regulation of the genes encoding acetylcholinesterase (AChE(T) variant), choline acetyltransferase, and the N-methyl-d-aspartate receptor subunit NR2A. This was confirmed, in the example of AChE, to arise from P2Y(1)-dependent stimulation of a human ACHE gene promoter. That involved activation of the transcription factor Elk-1; mutagenesis of the ACHE promoter revealed that Elk-1 binding at its specific responsive elements in that promoter was induced by P2Y(1) receptor activation. The combined findings reveal that ATP, via its P2Y(1) receptor, can act trophically in brain neurons to regulate the gene expression of direct effectors of synaptic transmission.

Ethnopharmacological Evidence: Danggui buxue tang (DBT), a Chinese medicinal decoction that is being commonly used as hematopoietic medicine to treating woman menopausal irregularity, contains two herbs: radix Astragali and radix Angelicae Sinensis. Pharmacological results indicate that DBT can stimulate the production of erythropoietin (EPO), a specific hematopoietic growth factor, in cultured cells., Aim of the Study: In order to reveal the mechanism of DBT's hematopoietic function, this study investigated the activity of the DBT-induced EPO expression and the upstream regulatory cascade of EPO via hypoxia-induced signaling in cultured kidney fibroblasts (HEK293T)., Materials and Methods: DBT-induced mRNA expressions were revealed by real-time PCR, while the change of protein expressions were analyzed by Western blotting. For the analysis of hypoxia-dependent signaling, a luciferase reporter was used to report the transcriptional activity of hypoxia response element (HRE)., Results: The plasmid containing HRE, being transfected into HEK293T, was highly responsive to the challenge of DBT application. To account for the transcriptional activation of HRE, DBT treatment was shown to increase the mRNA and protein expressions of hypoxia-inducible factor-1α (HIF-1α). In addition, the activation of Raf/MEK/ERK signaling pathway by DBT could also enhance the translation of HIF-1α, suggesting the dual actions of DBT in stimulating the EPO expression in kidney cells., Conclusion: Our study indicates that HIF pathway plays an essential role in directing DBT-induced EPO expression in kidney. These results provide one of the molecular mechanisms of this ancient herbal decoction for its hematopoietic function., (Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.)

Acetylcholinesterase (AChE), a highly polymorphic enzyme with various splicing variants and molecular isoforms, plays an essential role in the cholinergic neurotransmission by hydrolyzing acetylcholine into choline and acetate. The AChE(T) variant is expressed in the brain and muscle: this subunit forms non-amphiphilic tetramers with a collagen tail (ColQ) as asymmetric AChE (A(12) AChE) in muscle, and amphiphilic tetramers with a proline-rich membrane anchor (PRiMA) as globular AChE (G(4) AChE) in the brain and muscle. During the brain development, the expression of amphiphilic G(4) AChE is up regulated and becomes the predominant form of AChE there. This up-regulation of G(4) AChE can be attributed to the increased expressions of both AChE(T) and PRiMA. A significant portion of this membrane-bound G(4) AChE is localized at the membrane rafts of the cell membranes derived from the brain. This raft association could be directed by PRiMA via its CRAC (cholesterol recognition/interaction amino acid consensus) motif and C-terminus. In cultured cortical neurons and muscles, the PRiMA-linked AChE was clustered and partially co-localized with synaptic proteins. The restricted localizations suggest that the raft association of PRiMA-linked AChE could account for its synaptic localization and function., (Copyright (c) 2010 Elsevier Ireland Ltd. All rights reserved.)

The ability to make electrical contact to single molecules creates opportunities to examine fundamental processes governing electron flow on the smallest possible length scales. We report experiments in which we controllably stretched individual cobalt complexes having spin S = 1, while simultaneously measuring current flow through the molecule. The molecule's spin states and magnetic anisotropy were manipulated in the absence of a magnetic field by modification of the molecular symmetry. This control enabled quantitative studies of the underscreened Kondo effect, in which conduction electrons only partially compensate the molecular spin. Our findings demonstrate a mechanism of spin control in single-molecule devices and establish that they can serve as model systems for making precision tests of correlated-electron theories.

The 10-Metre Timed Walk (10MTW) is well established for use in assessment of patients with stroke. However, space limitations and the exhaustive nature of the test for many patients have resulted in many physiotherapists using a walk test of shorter distance. The aim of this study was to investigate the validity and reliability of a 6-Metre Timed Walk (6MTW) in patients with stroke. Forty-five patients with stroke (27 men and 18 women) participated in the study. Subjects performed two 6MTWs by using their usual walking aids. On the following day, subjects repeated the walk administered by a different tester. On a different day, subjects similarly performed two 10MTWs. Gait speed and cadence were calculated from the timed data. Isometric knee extensor strength of the paretic side was tested. Significant correlations were found between 6MTW and cadence, walking aids used, 10MTW, and isometric knee extensor strength (rho = 0.924, -0.868, 0.992, and 0.553 respectively, p < 0.0125). The ICC coefficients of test-retest and intertester reliability were 0.993 (p = 0.000) and 0.986 (p = 0.000), respectively. The 6MTW was shown to be valid and reliable for the assessment of the walking ability of patients with stroke and can be recommended especially in clinics with limited space.

The receptor tyrosine kinase c-Met is an attractive target for therapeutic blockade in cancer. Here, we describe MK-2461, a novel ATP-competitive multitargeted inhibitor of activated c-Met. MK-2461 inhibited in vitro phosphorylation of a peptide substrate recognized by wild-type or oncogenic c-Met kinases (N1100Y, Y1230C, Y1230H, Y1235D, and M1250T) with IC(50) values of 0.4 to 2.5 nmol/L. In contrast, MK-2461 was several hundredfold less potent as an inhibitor of c-Met autophosphorylation at the kinase activation loop. In tumor cells, MK-2461 effectively suppressed constitutive or ligand-induced phosphorylation of the juxtamembrane domain and COOH-terminal docking site of c-Met, and its downstream signaling to the phosphoinositide 3-kinase-AKT and Ras-extracellular signal-regulated kinase pathways, without inhibiting autophosphorylation of the c-Met activation loop. BIAcore studies indicated 6-fold tighter binding to c-Met when it was phosphorylated, suggesting that MK-2461 binds preferentially to activated c-Met. MK-2461 displayed significant inhibitory activities against fibroblast growth factor receptor (FGFR), platelet-derived growth factor receptor, and other receptor tyrosine kinases. In cell culture, MK-2461 inhibited hepatocyte growth factor/c-Met-dependent mitogenesis, migration, cell scatter, and tubulogenesis. Seven of 10 MK-2461-sensitive tumor cell lines identified from a large panel harbored genomic amplification of MET or FGFR2. In a murine xenograft model of c-Met-dependent gastric cancer, a well-tolerated oral regimen of MK-2461 administered at 100 mg/kg twice daily effectively suppressed c-Met signaling and tumor growth. Similarly, MK-2461 inhibited the growth of tumors formed by s.c. injection of mouse NIH-3T3 cells expressing oncogenic c-Met mutants. Taken together, our findings support further preclinical development of MK-2461 for cancer therapy.

We describe the joint application of the density matrix renormalization group and canonical transformation theory to multireference quantum chemistry. The density matrix renormalization group provides the ability to describe static correlation in large active spaces, while the canonical transformation theory provides a high-order description of the dynamic correlation effects. We demonstrate the joint theory in two benchmark systems designed to test the dynamic and static correlation capabilities of the methods, namely, (i) total correlation energies in long polyenes and (ii) the isomerization curve of the [Cu(2)O(2)](2+) core. The largest complete active spaces and atomic orbital basis sets treated by the joint DMRG-CT theory in these systems correspond to a (24e,24o) active space and 268 atomic orbitals in the polyenes and a (28e,32o) active space and 278 atomic orbitals in [Cu(2)O(2)](2+).

Canonical transformation (CT) theory describes dynamic correlation in multireference systems with large active spaces. Here we discuss CT theory's intruder state problem and why our previous approach of overlap matrix truncation becomes infeasible for sufficiently large active spaces. We propose the use of strongly and weakly contracted excitation operators as alternatives for dealing with intruder states in CT theory. The performance of these operators is evaluated for the H(2)O, N(2), and NiO molecules, with comparisons made to complete active space second order perturbation theory and Davidson-corrected multireference configuration interaction theory. Finally, using a combination of strongly contracted CT theory and orbital-optimized density matrix renormalization group theory, we evaluate the singlet-triplet gap of free base porphin using an active space containing all 24 out-of-plane 2p orbitals. Modeling dynamic correlation with an active space of this size is currently only possible using CT theory.

Trimethylation of lysine 9 on histone H3 (H3K9me3) is known both to be necessary for proper chromosome segregation and to increase in late G2. We investigated the role of late G2 methylation, specifically in mitotic progression, by inhibiting methylation for 2 hours prior to mitosis using the general methylation inhibitor adenosine dialdehyde (AdOx). AdOx inhibits all methylation events within the cell but, by shortening the treatment length to 2 hours and studying mitotic cells, the only methylation events that are affected are those that occur in late G2. We discovered that methylation events in this time period are crucial for proper mitosis. Mis-segregation of chromosomes is observed with AdOx treatment. Through studies of histone modifications, we have found that inhibiting late G2 methylation affects trimethylation of H3K9 and H4K20. The mitotic checkpoint is active and many kinetochore proteins localize properly, however, pericentric chromatin in these cells is found to be less compact (dense). The reduced integrity of pericentric heterochromatin might be responsible for a noted loss of tension at the centromere in AdOx-treated cells and activation of the spindle assembly checkpoint. We postulate that late G2 methylation is necessary for proper pericentric heterochromatin formation. The results suggest that a reduction in heterochromatin integrity might interfere both with microtubule attachment to chromosomes and with the proper sensing of tension from correct microtubule-kinetochore connections, either of which will result in activation of the mitotic checkpoint.

We investigate the possibility of reducing the complexity of multireference perturbation theory through cumulant based approximations to the high-order density matrices that appear in such theories. Our test cases show that while the cumulant approximated forms are degraded in accuracy relative to the parent theory and exhibit intruder state problems that must be carefully handled, they may provide a route to a simple estimation of dynamic correlation when the parent perturbation theory is infeasible. Nonetheless, further work is clearly needed on better approximations to the denominators in the perturbation theory.

We propose an analytic response theory for the density matrix renormalization group, whereby response properties correspond to analytic derivatives of density matrix renormalization group observables with respect to the applied perturbations. Both static and frequency-dependent response theories are formulated and implemented. We evaluate our pilot implementation by calculating static and frequency-dependent polarizabilities of short oligodiacetylenes. The analytic response theory is competitive with dynamical density matrix renormalization group methods and yields significantly improved accuracies when using a small number of density matrix renormalization group states. Strengths and weaknesses of the analytic approach are discussed.

We describe the results of a theoretical study of transport through gated metallic graphene nanoribbons using a nonequilibrium Green function method. Although analogies with quantum field theory predict perfect transmission of chiral fermions through gated regions in one dimension, we find perfect reflection of chiral fermions in armchair ribbons for specific configurations of the gate. This effect should be measurable in narrow graphene constrictions gated by a charged carbon nanotube.

Canonical transformation (CT) theory provides a rigorously size-extensive description of dynamic correlation in multireference systems, with an accuracy superior to and cost scaling lower than complete active space second order perturbation theory. Here we expand our previous theory by investigating (i) a commutator approximation that is applied at quadratic, as opposed to linear, order in the effective Hamiltonian, and (ii) incorporation of the three-body reduced density matrix in the operator and density matrix decompositions. The quadratic commutator approximation improves CT's accuracy when used with a single-determinant reference, repairing the previous formal disadvantage of the single-reference linear CT theory relative to singles and doubles coupled cluster theory. Calculations on the BH and HF binding curves confirm this improvement. In multireference systems, the three-body reduced density matrix increases the overall accuracy of the CT theory. Tests on the H(2)O and N(2) binding curves yield results highly competitive with expensive state-of-the-art multireference methods, such as the multireference Davidson-corrected configuration interaction (MRCI+Q), averaged coupled pair functional, and averaged quadratic coupled cluster theories.

Cytoplasmic dynein functions at several sites during mitosis; however, the basis of targeting to each site remains unclear. Tandem mass spectrometry analysis of mitotic dynein revealed a phosphorylation site in the dynein intermediate chains (ICs) that mediates binding to kinetochores. IC phosphorylation directs binding to zw10 rather than dynactin, and this interaction is needed for kinetochore dynein localization. Phosphodynein associates with kinetochores from nuclear envelope breakdown to metaphase, but bioriented microtubule (MT) attachment and chromosome alignment induce IC dephosphorylation. IC dephosphorylation stimulates binding to dynactin and poleward streaming. MT depolymerization, release of kinetochore tension, and a PP1-gamma mutant each inhibited IC dephosphorylation, leading to the retention of phosphodynein at kinetochores and reduced poleward streaming. The depletion of kinetochore dynactin by moderate levels of p50(dynamitin) expression disrupted the ability of dynein to remove checkpoint proteins by streaming at metaphase but not other aspects of kinetochore dynein activity. Together, these results suggest a new model for localization of kinetochore dynein and the contribution of kinetochore dynactin.

Historically, only relatively low-throughput or expensive methods have been available to measure cell migration. Hepatocyte growth factor (HGF) is a ligand for the tyrosine kinase receptor Met that, in addition to mediating proliferation and survival, increases cell motility and metastasis. The authors have developed a high-throughput imaging assay for measuring inhibition of HGF-induced scattering in human HPAF-II pancreatic adenocarcinoma cells. Following treatment with test compounds and HGF for 24 h, cells are labeled with a nuclear stain and imaged at 10x magnification. The proximity of neighboring nuclei is measured, and the distribution of internuclear distances across each field of view is used to calculate the fraction of scattered cells. This method of analysis can be extended to other cell types and signaling pathways and, compared with other membrane-based migration assays currently available, the assay is significantly lower in cost, is less labor intensive, and provides higher throughput.

The intracellular level of glutathione (GSH) was significantly decreased after the addition of andrographolide (1) to cell cultures of HepG2. When the molecular interaction between andrographolide and GSH was investigated under a condition mimicking the in vivo environment, we observed that the level of GSH dropped in the presence of andrographolide. Stoichiometric analysis indicates that the reaction between these two reactants was 1 to 1 at pH 7 and followed second order kinetics. The activation energy of the overall reaction was 41.9+/-10 kJ x mol(-1) according to the Arrhenius equation. Using a micro-liquid-liquid extraction method followed by micellar electrokinetic chromatographic separation, two major products were isolated and identified, and their chemical structures were determined as 14-deoxy-12-(glutathione-amino)-andrographolide (2) and 14-deoxy-12-(glutathione-S-yl)-andrographolide (3). Based on these structural findings, a hypothetical mechanism of reaction between glutathione and andrographolide was proposed. It is concluded that the alpha,beta-unsaturated lactone moiety of andrographolide reacts with GSH through a Michael addition followed by dehydration of the adduct.

The eukaryote centromere was initially defined cytologically as the primary constriction on vertebrate chromosomes and functionally as a chromosomal feature with a relatively low recombination frequency. Structurally, the centromere is the foundation for sister chromatid cohesion and kinetochore formation. Together these provide the basis for interaction between chromosomes and the mitotic spindle, allowing the efficient segregation of sister chromatids during cell division. Although centromeric (CEN) DNA is highly variable between species, in all cases the functional centromere forms in a chromatin domain defined by the substitution of histone H3 with the centromere specific H3 variant centromere protein A (CENP-A), also known as CENH3. Kinetochore formation and function are dependent on a variety of regional epigenetic modifications that appear to result in a loop chromatin conformation providing exterior CENH3 domains for kinetochore construction, and interior heterochromatin domains essential for sister chromatid cohesion. In addition pericentric heterochromatin provides a structural element required for spindle assembly checkpoint function. Advances in our understanding of CENH3 biology have resulted in a model where kinetochore location is specified by the epigenetic mark left after dilution of CENH3 to daughter DNA strands during S phase. This results in a self-renewing and self-reinforcing epigenetic state favorable to reliably mark centromere location, as well as to provide the optimal chromatin configuration for kinetochore formation and function.

We introduce a Lagrangian formulation of the density matrix renormalisation group (DMRG). We present Lagrangians which, when minimised, yield the optimal DMRG wavefunction in a variational sense, both within the general matrix product ansatz and within the canonical form of the matrix product that is constructed within the DMRG sweep algorithm. Some of the results obtained are similar to elementary expressions in Hartree-Fock theory, and we draw attention to such analogies. The Lagrangians introduced here will be useful in developing theories of analytic response and derivatives in the DMRG.

Accurate chromosomal segregation is monitored by the mitotic checkpoint, and an increased rate of chromosomal missegregation leads to chromosomal instability (CIN). Here, we demonstrate that the HBV X protein (HBx) binds BubR1, a component of the mitotic checkpoint complex and co-localizes with BubR1 at the kinetochores. HBx binding to BubR1 attenuates the association between BubR1 and CDC20, an activator of the anaphase-promoting complex/cyclosome (APC/C) and induces slippage of mitotic arrest in the presence of microtubule poisons. In addition, HBx binding to BubR1 results in the accumulation of lagging chromosomes and chromosome bridges. In contrast, a C-terminally truncated HBx mutant (HBx(1-100)) fails to bind BubR1 and does not cause aberrant chromosomal segregation. This provides a novel mechanism for dysregulation of the mitotic checkpoint by a viral pathogen linking it to the accumulation of chromosomal instability in HBV-associated hepatocarcinogenesis.

In previous work we have shown that the density matrix renormalization group (DMRG) enables near-exact calculations in active spaces much larger than are possible with traditional complete active space algorithms. Here, we implement orbital optimization with the DMRG to further allow the self-consistent improvement of the active orbitals, as is done in the complete active space self-consistent field (CASSCF) method. We use our resulting DMRG-CASSCF method to study the low-lying excited states of the all-trans polyenes up to C24H26 as well as beta-carotene, correlating with near-exact accuracy the optimized complete pi-valence space with up to 24 active electrons and orbitals, and analyze our results in the light of the recent discovery from resonance Raman experiments of new optically dark states in the spectrum.

Objective: The relationship of apolipoprotein E (APOE) genotype to lifetime cognitive decline was examined over 22 years in a large community-based population study., Method: The sample for the present study was derived from follow-up of a probability sample of the adult household residents of East Baltimore. From the Baltimore cohort of the Epidemiologic Catchment Area Study, genotype data were collected on 818 participants at the study's fourth wave between 2003 and 2004. Participants were administered the Mini-mental State Examination (MMSE) at all four study waves. Three tests of verbal learning - immediate recall, delayed recall, and word recognition - were completed at waves 3 and 4. The 659 participants for whom genetic data were available had also completed cognitive testing at all time points. Test scores and changes in these scores were examined by APOE genotype group (x/x or 4/x) in younger and older subcohorts defined by age at wave 4 (< or > or = age 65)., Results: Cross-sectional wave 4 scores on all four cognitive tasks were lower in APOEepsilon4 carriers when compared to non-carriers. In longitudinal univariate models epsilon4 carriers in the younger cohort demonstrated a greater annual rate of decline on a delayed recall task and MMSE. After adjusting for covariates only the decline in the delayed recall task was significant., Conclusion: We report an association between APOE genotype and decline in delayed recall and possibly MMSE over this extended time period limited to younger individuals. The lack of an association between APOE and decline in older individuals is likely to be the result of survival bias. Although a clear association exists between APOE genotype and cognitive decline or dementia in late life, these findings suggest that over the lifespan the relationship between APOE and cognitive decline is more complicated.

The mitotic checkpoint ensures proper chromosome segregation by monitoring two critical events during mitosis. One is kinetochore attachment to the mitotic spindle, and the second is the alignment of chromosomes at the metaphase plate, resulting in tension across sister kinetochores (reviewed in [1, 2]). Mitotic-checkpoint proteins are known to accumulate at unaligned chromosomes that have not achieved proper kinetochore-microtubule attachments or established an adequate level of tension across sister kinetochores. Here, we report that hZW10 and hROD, two components of the evolutionarily conserved RZZ complex, accumulate at kinetochores in response to the loss of tension. By using live-cell imaging and FRAP, we showed that the accumulation of hZW10 at tensionless kinetochores stems from a 4-fold reduction of kinetochore turnover rate. We also found that cells lacking hZW10 escape loss-of-tension-induced mitotic-checkpoint arrest more rapidly than those arrested in response to the lack of kinetochore-microtubule attachments. Furthermore, we show that pharmacological inhibition of Aurora B kinase activity with ZM447439 in the absence of tension, but not in the absence of kinetochore-microtubule attachments, results in the loss of hZW10, hROD, and hBub1 from kinetochores. We therefore conclude that Aurora B kinase activity is required for the accumulation of tension-sensitive mitotic-checkpoint components, such as hZW10 and hROD, in order to maintain mitotic-checkpoint arrest.

We present a detailed investigation of the acene series using high-level wave function theory. Our ab initio density matrix renormalization group algorithm has enabled us to carry out complete active space calculations on the acenes from napthalene to dodecacene correlating the full pi-valence space. While we find that the ground state is a singlet for all chain lengths, examination of several measures of radical character, including the natural orbitals, effective number of unpaired electrons, and various correlation functions, suggests that the longer acene ground states are polyradical in nature.

The canonical transformation theory of Yanai and Chan [J. Chem. Phys. 124, 194106 (2006)] provides a rigorously size-extensive description of dynamical correlation in multireference problems. Here we describe a new formulation of the theory based on the extended normal ordering procedure of Mukherjee and Kutzelnigg [J. Chem. Phys. 107, 432 (1997)]. On studies of the water, nitrogen, and iron oxide potential energy curves, the linearized canonical transformation singles and doubles theory is competitive in accuracy with some of the best multireference methods, such as the multireference averaged coupled pair functional, while computational timings (in the case of the iron oxide molecule) are two to three orders of magnitude faster and comparable to those of the complete active space second-order perturbation theory. The results presented here are greatly improved both in accuracy and in cost over our earlier study as the result of a new numerical algorithm for solving the amplitude equations.

To overcome the limitations of the traditional state-averaging approaches in excited state calculations, where one solves and represents all states between the ground state and excited state of interest, we have investigated a number of new excited state algorithms. Building on the work of van der Vorst and Sleijpen [SIAM J. Matrix Anal. Appl. 17, 401 (1996)], we have implemented harmonic Davidson and state-averaged harmonic Davidson algorithms within the context of the density matrix renormalization group (DMRG). We have assessed their accuracy and stability of convergence in complete-active-space DMRG calculations on the low-lying excited states in the acenes ranging from naphthalene to pentacene. We find that both algorithms offer increased accuracy over the traditional state-averaged Davidson approach, and, in particular, the state-averaged harmonic Davidson algorithm offers an optimal combination of accuracy and stability in convergence.

The cytotoxicity of andrographolide to HepG2 human hepatoma cells was investigated in the present study. Growth of HepG2 cells was affected in the presence of andrographolide with an IC(50) of 40.2 microM after 48 h treatment. Flow cytometric analysis and DNA fragmentation assay revealed that andrographolide induced cell cycle arrest at G2/M phase and a late apoptosis of the cells. The occurrence of cell cycle arrest was accompanied by the collapse of mitochondrial membrane potential (MMP) and an intracellular increase of hydrogen peroxide (H(2)O(2)) but a decrease of superoxide radicals (O(2)(-)) and reduced glutathione. In the treated cells, expression of Bax as well as the transcriptional controller of this pro-apoptotic gene, p53, was upregulated but not other apoptotic proteins such as Bad, Bcl-2 and Bcl-X(L). Although the activity of caspase-3, which has direct effect on apoptosis, was also enhanced by the presence of andrographolide, cell death of HepG2 could neither be prevented by a specific inhibitor of capsase-3 nor the pan-caspase inhibitor-zVAD (Val-Ala-Asp), indicating that it was a caspase-independent cell death. Since the overall percentage of apoptotic cells was relatively small throughout the experimental studies, we conclude that the cytotoxic effect of andrographolide on HepG2 cells is primary attributed to the induction of cell cycle arrest via the alteration of cellular redox status.

hSgo2 (previously annotated as Tripin) was recently reported to be a new inner centromere protein that is essential for centromere cohesion (Kitajima et al., 2006). In this study, we show that hSgo2 exhibits a dynamic distribution pattern, and that its localization depends on the BUB1 and Aurora B kinases. hSgo2 is concentrated at the inner centromere of unattached kinetochores, but extends toward the kinetochores that are under tension. This localization pattern is reminiscent of MCAK, which is a microtubule depolymerase that is believed to be a key component of the error correction mechanism at kinetochores. Indeed, we found that hSgo2 is essential for MCAK to localize to the centromere. Delocalization of MCAK accounts for why cells depleted of hSgo2 exhibit kinetochore attachment defects that go uncorrected, despite a transient delay in the onset of anaphase. Consequently, these cells exhibit a high frequency of lagging chromosomes when they enter anaphase. We confirmed that hSgo2 is associated with PP2A, and we propose that it contributes to the spatial regulation of MCAK activity within inner centromere and kinetochore.

Aims: To investigate the morphological and chemical changes in attached cells of Pseudomonas aeruginosa (ATCC 14886) at different stages of biofilm development on two different types of substrata., Methods and Results: The development of primary biofilm on aluminium plates representing metals and on CaF(2) discs representing dielectric materials was monitored by FTIR microscopy, ESEM, EDAX and protein analysis by SDS-PAGE. A unique cellular feature similar in morphology to pili was observed on the surface of P. aeruginosa adhering on aluminium but not on CaF(2). Results derived from FTIR analysis confirm on both substrata the successive importance of polysaccharides and proteins during the biofilm development. These results also revealed that the increase of the ratio of carboxylates to amide I was higher with the aluminium plates than with the CaF(2) discs. The number of cells adhered and the amount of oxygen incorporated in adhered cells on the latter materials were, respectively, less and almost nil in comparison with the former. Protein analysis of the lysates of cells by SDS-PAGE revealed that expression of one protein with a molecular weight of 45 kDa, was greatly enhanced in attached cells on both substrata. However, expression of another protein with molecular weight of 35 kDa was up-regulated only in cells adhering on CaF(2) but not in those on aluminium., Conclusion: Depending on the nature of the surface, new proteinaceous complexes and cellular features were formed in the attachment process of P. aeruginosa., Significance and Impact of the Study: The pattern of P. aeruginosa cells adhering onto CaF(2) discs and aluminium plates is different. Formation of biofilm is more difficult on CaF(2) than on aluminium.

Robust and reliable methods for the manipulation of neural cell lines, by passaging, plating, dye labeling, imaging, fixation, and immunocytochemistry, are required to enable consistent, reproducible screens to be performed. We describe herein procedures and processes we have established to maximize the level of consistency of cell plating, fixation, and dye or antibody labeling, to ensure that assays which we are running on a routine basis remain consistent across long periods of time. These procedures involve a variety of fully or semiautomated steps, using high-quality commercially available liquid handling and dispensing technology.

We have devised a local ab initio density matrix renormalization group algorithm to describe multireference correlations in large systems. For long molecules that are extended in one of their spatial dimensions, we can obtain an exact characterization of correlation, in the given basis, with a cost that scales only quadratically with the size of the system. The reduced scaling is achieved solely through integral screening and without the construction of correlation domains. We demonstrate the scaling, convergence, and robustness of the algorithm in polyenes and hydrogen chains. We converge to exact correlation energies (in the sense of full configuration interaction, with 1-10 microE(h) precision) in all cases and correlate up to 100 electrons in 100 active orbitals. We further use our algorithm to obtain exact energies for the metal-insulator transition in hydrogen chains and compare and contrast our results with those from conventional quantum chemical methods.

The repair of chromosomal double-strand breaks (DSBs) is essential to normal cell growth, and homologous recombination is a universal process for DSB repair. We explored DSB repair mechanisms in the yeast Saccharomyces cerevisiae using single-strand oligonucleotides with homology to both sides of a DSB. Oligonucleotide-directed repair occurred exclusively via Rad52- and Rad59-mediated single-strand annealing (SSA). Even the SSA domain of human Rad52 provided partial complementation for a null rad52 mutation. The repair did not involve Rad51-driven strand invasion, and moreover the suppression of strand invasion increased repair with oligonucleotides. A DSB was shown to activate targeting by oligonucleotides homologous to only one side of the break at large distances (at least 20 kb) from the break in a strand-biased manner, suggesting extensive 5' to 3' resection, followed by the restoration of resected DNA to the double-strand state. We conclude that long resected chromosomal DSB ends are repaired by a single-strand DNA oligonucleotide through two rounds of annealing. The repair by single-strand DNA can be conservative and may allow for accurate restoration of chromosomal DNAs with closely spaced DSBs.

Introduction: Little is known about how continued pain after discharge from the emergency department is managed by patients, and how it may interfere with the functional status of patients. The purpose of this pilot study was to evaluate pain management practices, patient satisfaction with pain medications, and how continued pain after ED discharge may influence the functional status of patients who presented with chief complaints of abdominal, chronic, abscess, or trauma-related pain., Methods: This prospective, descriptive study was conducted at 2 Level 1 trauma hospitals. Twenty-nine patients completed an emergency department discharge questionnaire and follow-up phone survey. Data were collected via telephone interviews an average of 72 hours after discharge., Results: On emergency department discharge, patients reported pain intensity that had not decreased significantly at the time of the home interview. Most patients (78%) used ED-prescribed medications and reported a high level of satisfaction with their pain relief (7.2 +/- 2.1). Continued pain after ED discharge primarily interfered with patient's ability to work (7.3 +/- 3.8), to go outside for social activities (6.5 +/- 4.1) and to ambulate (5.0 +/- 4.1)., Discussion: Patients in this study, on average, continued to experience pain for up to 96 hours after discharge from the emergency department. They reported a high level of pain relief from their ED-prescribed medications. However, interference with functions of daily living due to continued pain was substantial. Further studies are needed to examine the paradoxical reports of high satisfaction with pain relief yet substantial functional limitations experienced by patients after ED discharge.

The assembly of the centromere, a specialized region of DNA along with a constitutive protein complex which resides at the primary constriction and is the site of kinetochore formation, has been puzzling biologists for many years. Recent advances in the fields of chromatin, microscopy, and proteomics have shed a new light on this complex and essential process. Here we review recently discovered mechanisms and proteins involved in determining mammalian centromere location and assembly. The centromeric core protein CENP-A, a histone H3 variant, is hypothesized to designate centromere localization by incorporation into centromere-specific nucleosomes and is essential for the formation of a functional kinetochore. It has been found that centromere localization of centromere protein A (CENP-A), and therefore centromere determination, requires proteins involved in histone deacetylation, as well as base excision DNA repair pathways and proteolysis. In addition to the incorporation of CENP-A at the centromere, the formation of heterochromatin through histone methylation and RNA interference is also crucial for centromere formation. The assembly of the centromere and kinetochore is complex and interdependent, involving epigenetics and hierarchical protein-protein interactions.

The aim of this study was to explore factors influencing emergency department (ED) clinicians' use of opioids in treating selected patients. Patients who either received or did not receive opioids in the ED, as well as their nurses and physicians, were interviewed before patient discharge. We found that the decrease in patients' mean (SD) pain intensity from the time of admission to the ED (7.3 +/- 2.4 on a 0 to 10 numeric rating scale) to discharge (5.0 +/- 2.9) was statistically significant (t93 = 8.4, p < 0.001, 95 percent CI = 1.7, 2.8) for all groups except those with trauma-related pain. The factor that most frequently led physicians of patients with abdominal pain and nurses in general to administer no opioids was that the patient was "not in that much pain." However, the patients in question had self-reported pain scores that indicated moderate pain. Our findings lead us to conclude that clinicians inaccurately infer severity of patient pain. This in turn can influence the prescription of opioids and the patient's decrease in pain.

We propose a theory to describe dynamic correlations in bonding situations where there is also significant nondynamic character. We call this the canonical transformation (CT) theory. When combined with a suitable description of nondynamic correlation, such as given by a complete-active-space self-consistent Field (CASSCF) or density matrix renormalization group wave function, it provides a theory to describe bonding situations across the entire potential energy surface with quantitative accuracy for both dynamic and nondynamic correlation. The canonical transformation theory uses a unitary exponential ansatz, is size consistent, and has a computational cost of the same order as a single-reference coupled cluster theory with the same level of excitations. Calculations using the CASSCF based CT method with single and double operators for the potential energy curves for water and nitrogen molecules, the BeH(2) insertion reaction, and hydrogen fluoride and boron hydride bond breaking, consistently yield quantitative accuracies typical of equilibrium region coupled cluster theory, but across all geometries, and better than obtained with multireference perturbation theory.

The prospect of manipulating endogenous neural stem cells to replace damaged tissue and correct functional deficits represents a novel mechanism for treating a variety of central nervous system disorders. Using human neural precursor cultures and a variety of assays for studying stem cell behavior we have screened two libraries of commercially available compounds using an endpoint high content screening assay. We then performed detailed follow-up mechanistic studies on confirmed hits using endpoint and kinetics assays to characterize and differentiate the mechanisms of action of these compounds. The screening cascade employed successfully identified a number of active compounds with differing mechanisms of action. This approach shows how hits from a phenotypic screen can be prioritized and characterized by high content screening to identify potentially novel mechanisms and druggable targets to take forward into more conventional high-throughput screening approaches.

To assess the separation of dynamic and nondynamic correlations and orbital choice, we calculate the molecular structure and harmonic vibrational frequencies of ozone with the recently developed tailored coupled cluster singles and doubles method (TCCSD). We employ the Hartree-Fock and complete active space (CAS) self-consistent field (SCF) orbitals to perform TCCSD calculations. When using the Hartree-Fock orbitals, it is difficult to reproduce the experimental vibrational frequency of the asymmetric stretching mode. On the other hand, the TCCSD based on the CASSCF orbitals in a correlation consistent polarized valence triple zeta basis yields excellent results with the two symmetric vibrations differing from the experimental harmonic values by 2 cm(-1) and the asymmetric vibration differing by 9 cm(-1).

A great deal of information can be gained from kinetic fluorescence-based measurement of cellular responses; however, until recently the use of such approaches has been limited by the manual nature of the instrumentation available. Higher-throughput kinetic studies of signaling pathways are greatly facilitated by new confocal, liquid handling-enabled, high content screening (HCS) platforms. In the present work, we have implemented one such instrument, the BD(TM) Pathway HT bioimager (BD Biosciences, Rockville, MD), for studying regulation of neuronal signaling pathways. We have established a neuronal calcium oscillation model, whereby rate of oscillation, amplitude of oscillation, and level of synchronicity across the culture can be measured. We have implemented membrane potential measurement using fluorescence resonance energy transfer-based dyes, for single cell characterization on this platform, showing the benefits of a truly flexible excitation and recording system; this dye combination cannot be readily implemented on all HCS platforms because of constraints of excitation wavelengths. We have validated long-term intracellular calcium imaging experiments, using innovative dyes and BD Pathway HT's spinning disk-based confocal excitation. To maximize both throughput and reproducibility, walk-away automation integration of this bioimaging technology has been implemented, producing an affordable, compact platform for fully automated kinetic HCS.

The vertebrate kinetochore is a complex structure that specifies the attachments between the chromosomes and microtubules of the spindle and is thus essential for accurate chromosome segregation. Kinetochores are assembled on centromeric chromatin through complex pathways that are coordinated with the cell cycle. In the light of recent discoveries on how proteins assemble onto kinetochores and interact with each other, we review these findings in this article (which is part of the Chromosome Segregation and Aneuploidy series), and discuss their implications for the current mitotic checkpoint models - the template model and the two-step model. The template model proposes that Mad1-Mad2 at kinetochores acts as a template to change the conformation of another binding molecule of Mad2. This templated change in conformation is postulated as a mechanism for the amplification of the 'anaphase wait' signal. The two-step model proposes that the mitotic checkpoint complex (MCC) is the kinetochore-independent anaphase inhibitor, and the role of the unaligned kinetochore is to sensitize the anaphase-promoting complex/cyclosome (APC/C) to MCC-mediated inhibition.

We describe the theory and implementation of two extensions to the density-matrix renormalization-group (DMRG) algorithm in quantum chemistry: (i) to work with an underlying nonorthogonal one-particle basis (using a biorthogonal formulation) and (ii) to use non-Hermitian and complex operators and complex wave functions, which occur naturally in biorthogonal formulations. Using these developments, we carry out ground-state calculations on ethene, butadiene, and hexatriene, in a polarized atomic-orbital basis. The description of correlation in these systems using a localized nonorthogonal basis is improved over molecular-orbital DMRG calculations, and comparable to or better than coupled-cluster calculations, although we encountered numerical problems associated with non-Hermiticity. We believe that the non-Hermitian DMRG algorithm may further become useful in conjunction with other non-Hermitian Hamiltonians, for example, similarity-transformed coupled-cluster Hamiltonians.