Orbital Optimization in the Density Matrix Renormalization Group, with applications to polyenes and \beta-carotene

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 optimisation with the Density Matrix Renormalization Group 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 DMRGCASSCF 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 optimised complete \pi-valence space with up to 24 active electrons and orbitals, and analyse our results in the light of the recent discovery from Resonance Raman experiments of new optically dark states in the spectrum.Comment: 16 pages, 8 figure

AREsite: a database for the comprehensive investigation of AU-rich elements

AREsite is an online resource for the detailed investigation of AU-rich elements (ARE) in vertebrate mRNA 3′-untranslated regions (UTRs). AREs are one of the most prominent cis-acting regulatory elements found in 3′-UTRs of mRNAs. Various ARE-binding proteins that possess RNA stabilizing or destabilizing functions are recruited by sequence-specific motifs. Recent findings suggest an essential role of the structural mRNA context in which these sequence motifs are embedded. AREsite is the first database that allows to quantify the structuredness of ARE motif sites in terms of opening energies and accessibility probabilities. Moreover, we also provide a detailed phylogenetic analysis of ARE motifs and incorporate information about experimentally validated targets of the ARE-binding proteins TTP, HuR and Auf1. The database is publicly available at: http://rna.tbi.univie.ac.at/AREsite

Prediction of infrared light emission from pi-conjugated polymers: a diagrammatic exciton basis valence bond theory

There is currently a great need for solid state lasers that emit in the infrared, as this is the operating wavelength regime for applications in telecommunications. Existing $\pi$--conjugated polymers all emit in the visible or ultraviolet, and whether or not $\pi$--conjugated polymers that emit in the infrared can be designed is an interesting challenge. On the one hand, the excited state ordering in trans-polyacetylene, the $\pi$--conjugated polymer with relatively small optical gap, is not conducive to light emission because of electron-electron interaction effects. On the other hand, excited state ordering opposite to that in trans-polyacetylene is usually obtained by chemical modification that increases the effective bond-alternation, which in turn increases the optical gap. We develop a theory of electron correlation effects in a model $\pi$-conjugated polymer that is obtained by replacing the hydrogen atoms of trans-polyacetylene with transverse conjugated groups, and show that the effective on-site correlation in this system is smaller than the bare correlation in the unsubstituted system. An optical gap in the infrared as well as excited state ordering conducive to light emission is thereby predicted upon similar structural modifications.Comment: 15 pages, 15 figures, 1 tabl

Infrared spectra and optical constants of astronomical ices: III. Propane, propylene, and propyne

Infrared (IR) spectra of the hydrocarbon ices C3H8 (propane), C3H6 (propylene, propene), and C3H4 (propyne, methylacetylene) are relevant to the study of the low-temperature chemistry and spectroscopy of objects within and beyond the Solar System, but IR band strengths and absorption coefficients are lacking for these compounds. Here we present new IR spectra of crystalline and non-crystalline forms of C3H8, C3H6, and C3H4. Measurements of ice density and refractive index also are reported, two quantities needed to compute IR absorption coefficients, band strengths, optical constants, and, ultimately, abundances of propane, propylene, and propyne in extraterrestrial environments and in laboratory experiments. Suggestions and interpretations are offered regarding the multiple crystalline forms of propane and propylene observed. Applications and extensions are described

Resveratrol regulates the PTEN/AKT pathway through androgen receptor-dependent and -independent mechanisms in prostate cancer cell lines

The tumor suppressor gene PTEN (phosphatase and tensin homolog deleted on chromosome 10) and the androgen receptor (AR) play important roles in tumor development and progression in prostate carcinogenesis. Among many functions, PTEN negatively regulates the cytoplasmic phosphatidylinositol-3-kinase/AKT anti-apoptotic pathway; and nuclear PTEN affects the cell cycle by also negatively regulating the MAPK pathway via cyclin D. Decreased PTEN expression is correlated with prostate cancer progression. Over-expression of AR and upregulation of AR transcriptional activity are often observed in the later stages of prostate cancer. Recent studies indicate that PTEN regulates AR activity and stability. However, the mechanism of how AR regulates PTEN has never been studied. Furthermore, resveratrol, a phytoalexin enriched in red grapes, strawberries and peanuts, has been shown to inhibit AR transcriptional activity in prostate cancer cells. In this study, we use prostate cancer cell lines to test the hypothesis that resveratrol inhibits cellular proliferation in both AR-dependent and -independent mechanisms. We show that resveratrol inhibits AR transcriptional activity in both androgen-dependent and -independent prostate cancer cells. Additionally, resveratrol stimulates PTEN expression through AR inhibition. In contrast, resveratrol directly binds epidermal growth factor receptor (EGFR) rapidly inhibiting EGFR phosphorylation, resulting in decreased AKT phosphorylation, in an AR-independent manner. Thus, resveratrol may act as potential adjunctive treatment for late-stage hormone refractory prostate cancer. More importantly, for the first time, our study demonstrates the mechanism by which AR regulates PTEN expression at the transcription level, indicating the direct link between a nuclear receptor and the PI3K/AKT pathway

A 14-year longitudinal study of the impact of clean indoor air legislation on state smoking prevalence, USA, 1997-2010

While clean indoor air legislation at the state level is an evidence-based recommendation, only limited evidence exists regarding the impact of clean indoor air policies on state smoking prevalence. Using state smoking prevalence data from 1997 to 2010, a repeated measures observational analysis assessed the association between clean indoor air policies (i.e., workplace, restaurant, and bar) and state smoking prevalence while controlling for state cigarette taxes and year. The impacts from the number of previous years with any clean indoor air policy, the number of policies newly in effect during the current year, and the number of policies in effect the previous year were analyzed. Findings indicate a smoking prevalence predicted decrease of 0.13 percentage points (p = 0.03) for each additional year one or more clean indoor air policies were in effect, a predicted decrease of 0.12 percentage points (p = 0.09) for each policy newly in effect in the current year, and a predicted decrease of 0.22 percentage points (p = 0.01) for each policy in effect in the previous year on the subsequent year. Clean indoor air policies show measurable associations with reductions in smoking prevalence within a year of implementation above and beyond taxes and time trends. Further efforts are needed to diffuse clean indoor air policies across states and provinces that have not yet adopted such policies.ECU Open Access Fun

Biophysical characterisation of the Bcl-x pre-mRNA and binding specificity of the ellipticine derivative GQC-05 : implication for alternative splicing regulation

The BCL2L1 gene expresses two isoforms of Bcl-x protein via the use of either of two alternative 5′ splice sites (5′ss) in exon 2. These proteins have antagonistic actions, Bcl-XL being anti-apoptotic and Bcl-XS pro-apoptotic. In a number of cancers the Bcl-XL isoform is over-expressed, resulting in cancer cell survival and growth, so switching splicing to the Xs isoform could have therapeutic benefits. We have previously proposed that a putative G-quadruplex (G4) exists downstream of the XS 5′ss and shown that the ellipticine derivative GQC-05, a previously identified DNA G4-specific ligand, induces an increase in the XS/XL ratio both in vitro and in cells. Here, we demonstrate that this G4 forms in vitro and that the structure is stabilised in the presence of GQC-05. We also show that GQC-05 binds RNA non-specifically in buffer conditions, but selectively to the Bcl-x G4 in the presence of nuclear extract, highlighting the limitations of biophysical measurements taken outside of a functional environment. We also demonstrate that GQC-05 is able to shift the equilibrium between competing G4 and duplex structures towards the G4 conformation, leading to an increase in accessibility of the XS 5′ss, supporting our previous model on the mechanism of action of GQC-05

The effectiveness, acceptability and cost-effectiveness of psychosocial interventions for maltreated children and adolescents: an evidence synthesis.

BACKGROUND: Child maltreatment is a substantial social problem that affects large numbers of children and young people in the UK, resulting in a range of significant short- and long-term psychosocial problems. OBJECTIVES: To synthesise evidence of the effectiveness, cost-effectiveness and acceptability of interventions addressing the adverse consequences of child maltreatment. STUDY DESIGN: For effectiveness, we included any controlled study. Other study designs were considered for economic decision modelling. For acceptability, we included any study that asked participants for their views. PARTICIPANTS: Children and young people up to 24 years 11 months, who had experienced maltreatment before the age of 17 years 11 months. INTERVENTIONS: Any psychosocial intervention provided in any setting aiming to address the consequences of maltreatment. MAIN OUTCOME MEASURES: Psychological distress [particularly post-traumatic stress disorder (PTSD), depression and anxiety, and self-harm], behaviour, social functioning, quality of life and acceptability. METHODS: Young Persons and Professional Advisory Groups guided the project, which was conducted in accordance with Cochrane Collaboration and NHS Centre for Reviews and Dissemination guidance. Departures from the published protocol were recorded and explained. Meta-analyses and cost-effectiveness analyses of available data were undertaken where possible. RESULTS: We identified 198 effectiveness studies (including 62 randomised trials); six economic evaluations (five using trial data and one decision-analytic model); and 73 studies investigating treatment acceptability. Pooled data on cognitive-behavioural therapy (CBT) for sexual abuse suggested post-treatment reductions in PTSD [standardised mean difference (SMD) -0.44 (95% CI -4.43 to -1.53)], depression [mean difference -2.83 (95% CI -4.53 to -1.13)] and anxiety [SMD -0.23 (95% CI -0.03 to -0.42)]. No differences were observed for post-treatment sexualised behaviour, externalising behaviour, behaviour management skills of parents, or parental support to the child. Findings from attachment-focused interventions suggested improvements in secure attachment [odds ratio 0.14 (95% CI 0.03 to 0.70)] and reductions in disorganised behaviour [SMD 0.23 (95% CI 0.13 to 0.42)], but no differences in avoidant attachment or externalising behaviour. Few studies addressed the role of caregivers, or the impact of the therapist-child relationship. Economic evaluations suffered methodological limitations and provided conflicting results. As a result, decision-analytic modelling was not possible, but cost-effectiveness analysis using effectiveness data from meta-analyses was undertaken for the most promising intervention: CBT for sexual abuse. Analyses of the cost-effectiveness of CBT were limited by the lack of cost data beyond the cost of CBT itself. CONCLUSIONS: It is not possible to draw firm conclusions about which interventions are effective for children with different maltreatment profiles, which are of no benefit or are harmful, and which factors encourage people to seek therapy, accept the offer of therapy and actively engage with therapy. Little is known about the cost-effectiveness of alternative interventions. LIMITATIONS: Studies were largely conducted outside the UK. The heterogeneity of outcomes and measures seriously impacted on the ability to conduct meta-analyses. FUTURE WORK: Studies are needed that assess the effectiveness of interventions within a UK context, which address the wider effects of maltreatment, as well as specific clinical outcomes. STUDY REGISTRATION: This study is registered as PROSPERO CRD42013003889. FUNDING: The National Institute for Health Research Health Technology Assessment programme

Spatiotemporal controlled delivery of nanoparticles to injured vasculature

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2010.Cataloged from PDF version of thesis. Vita.Includes bibliographical references.Complex multimodal nanoparticles (NP) that target and deliver therapeutic agents to a site of disease are a promising direction in modem medicine. As a starting point for innovation, we designed a hybrid NP system combining the benefits of liposomes and polymeric NPs. These particles have a polymeric surface which displays targeting ligands while avoiding macrophage uptake. A liposome-like layer provides in vivo biocompatibility and a hydrophobic core allows for high-capacity small molecule drug delivery. Targeting ligands that bind injured vasculature were discovered and optimized by screening an M13 bacteriophage library (109 independent clones) against collagen IV, the major component of the basement membrane. Relative binding affinities using ELISA identified the lead targeting candidate, which bound with 900-fold greater relative affinity to collagen IV when compared with the unselected library. The selected peptide sequence was synthesized and tested for its ability to actively target the hybrid NP system. Paclitaxel, an anti-proliferative drug, was chosen as the delivered pharmaceutical. Drug release was modified through a slow-eluting paclitaxel conjugate using controlled ester hydrolysis (drug release -10-12 days in vitro). To test these targeted NPs, injured vasculature was approximated using an aortic smooth muscle culture embedded on a collagen IV matrix. In this setting, the hybrid NPs showed clear evidence of increased potency using the selected ligands. In experimental animal models of surgery-induced vascular injury, targeted NPs showed a four-fold improved retention at angioplastied aortas over intact aortas ex vivo. Targeted NPs were tested as intraarterially delivered therapy to angioplastied carotid arteries in vivo and showed a two-fold better localization at injury sites versus scrambled-peptide and non-targeted NPs. Targeted NPs were also tested using a systemic, intravenous infusion administered postprocedure on Day I and 6 and resulted in lower neointima-to-media (N/M) scores at two weeks compared to FDA-approved Taxol@ and injury-only groups (N/Msham= -249 + 0.046, vs. N/MTaxol=0.837 ± 0.087, N/MNP=0.749 ± 0.136 and N/MPep-NP=0.662 ± 0.169, all P < 0.01 vs. injury-only, mean ± SEM, n=5). These findings indicate that complex, multilayered NPs can functionally target and treat injured vasculature, a clinical problem of primary importance.by Juliana Maria Chan.Ph.D