Modeling Pair Distribution Functions of Rare-Earth Phosphate Glasses Using Principal Component Analysis

The use of principal component analysis (PCA) to statistically infer features of local structure from experimental pair distribution function (PDF) data is assessed on a case study of rare-earth phosphate glasses (REPGs). Such glasses, codoped with two rare-earth ions (R and R') of different sizes and optical properties, are of interest to the laser industry. The determination of structure-property relationships in these materials is an important aspect of their technological development. Yet, realizing the local structure of codoped REPGs presents significant challenges relative to their singly doped counterparts; specifically, R and R' are difficult to distinguish in terms of establishing relative material compositions, identifying atomic pairwise correlation profiles in a PDF that are associated with each ion, and resolving peak overlap of such profiles in PDFs. This study demonstrates that PCA can be employed to help overcome these structural complications, by statistically inferring trends in PDFs that exist for a restricted set of experimental data on REPGs, and using these as training data to predict material compositions and PDF profiles in unknown codoped REPGs. The application of these PCA methods to resolve individual atomic pairwise correlations in t(r) signatures is also presented. The training methods developed for these structural predictions are prevalidated by testing their ability to reproduce known physical phenomena, such as the lanthanide contraction, on PDF signatures of the structurally simpler singly doped REPGs. The intrinsic limitations of applying PCA to analyze PDFs relative to the quality control of source data, data processing, and sample definition, are also considered. While this case study is limited to lanthanide-doped REPGs, this type of statistical inference may easily be extended to other inorganic solid-state materials and be exploited in large-scale data-mining efforts that probe many t(r) functions.

ChemDataExtractor: A Toolkit for Automated Extraction of Chemical Information from the Scientific Literature

The emergence of "big data" initiatives has led to the need for tools that can automatically extract valuable chemical information from large volumes of unstructured data, such as the scientific literature. Since chemical information can be present in figures, tables, and textual paragraphs, successful information extraction often depends on the ability to interpret all of these domains simultaneously. We present a complete toolkit for the automated extraction of chemical entities and their associated properties, measurements, and relationships from scientific documents that can be used to populate structured chemical databases. Our system provides an extensible, chemistry-aware, natural language processing pipeline for tokenization, part-of-speech tagging, named entity recognition, and phrase parsing. Within this scope, we report improved performance for chemical named entity recognition through the use of unsupervised word clustering based on a massive corpus of chemistry articles. For phrase parsing and information extraction, we present the novel use of multiple rule-based grammars that are tailored for interpreting specific document domains such as textual paragraphs, captions, and tables. We also describe document-level processing to resolve data interdependencies and show that this is particularly necessary for the autogeneration of chemical databases since captions and tables commonly contain chemical identifiers and references that are defined elsewhere in the text. The performance of the toolkit to correctly extract various types of data was evaluated, affording an F-score of 93.4%, 86.8%, and 91.5% for extracting chemical identifiers, spectroscopic attributes, and chemical property attributes, respectively; set against the CHEMDNER chemical name extraction challenge, ChemDataExtractor yields a competitive F-score of 87.8%. All tools have been released under the MIT license and are available to download from http://www.chemdataextractor.org .

Can nitro groups really anchor onto TiO2? Case study of dye-to-TiO2adsorption using azo dyes with NO2substituents

Molecular rationalization of the photovoltaic performance of dye-sensitized solar cells that employ azo dyes bearing a NO₂anchoring group.

Discovery of Black Dye Crystal Structure Polymorphs: Implications for Dye Conformational Variation in Dye-Sensitized Solar Cells

We present the discovery of a new crystal structure polymorph (1) and pseudopolymorph (2) of the Black Dye, one of the world's leading dyes for dye-sensitized solar cells, DSSCs (10.4% device performance efficiency). This reveals that Black Dye molecules can adopt multiple low-energy conformers. This is significant since it challenges existing models of the Black Dye···TiO2 adsorption process that renders a DSSC working electrode; these have assumed a single molecular conformation that refers to the previously reported Black Dye crystal structure (3). The marked structural differences observed between 1, 2, and 3 make the need for modeling multiple conformations more acute. Additionally, the ordered form of the Black Dye (1) provides a more appropriate depiction of its anionic structure, especially regarding its anchoring group and NCS bonding descriptions. The tendency toward NCS ligand isomerism, evidenced via the disordered form 2, has consequences for electron injection and electron recombination in Black Dye embedded DSSC devices. Dyes 2 and 3 differ primarily by the absence or presence of a solvent of crystallization, respectively; solvent environment effects on the dye are thereby elucidated. This discovery of multiple Black Dye conformers from diffraction, with atomic-level definition, complements recently reported nanoscopic evidence for multiple dye conformations existing at a dye···TiO2 interface, for a chemically similar DSSC dye; those results emanated from imaging and spectroscopy, but were unresolved at the submolecular level. Taken together, these findings lead to the general notion that multiple dye conformations should be explicitly considered when modeling dye···TiO2 interfaces in DSSCs, at least for ruthenium-based dye complexes.

Laser-wakefield accelerators as hard x-ray sources for 3D medical imaging of human bone

A bright μm-sized source of hard synchrotron x-rays (critical energy Ecrit > 30 keV) based on the betatron oscillations of laser wakefield accelerated electrons has been developed. The potential of this source for medical imaging was demonstrated by performing micro-computed tomography of a human femoral trabecular bone sample, allowing full 3D reconstruction to a resolution below 50 μm. The use of a 1 cm long wakefield accelerator means that the length of the beamline (excluding the laser) is dominated by the x-ray imaging distances rather than the electron acceleration distances. The source possesses high peak brightness, which allows each image to be recorded with a single exposure and reduces the time required for a full tomographic scan. These properties make this an interesting laboratory source for many tomographic imaging applications.

Preferred Molecular Orientation of Coumarin 343 on TiO2 Surfaces: Application to Dye-Sensitized Solar Cells

The dye···TiO2 interfacial structure in working electrodes of dye-sensitized solar cells (DSCs) is known to influence its photovoltaic device performance. Despite this, direct and quantitative reports of such structure remain sparse. This case study presents the application of X-ray reflectometry to determine the preferred structural orientation and molecular packing of the organic dye, Coumarin 343, adsorbed onto amorphous TiO2. Results show that the dye molecules are, on average, tilted by 61.1° relative to the TiO2 surface, and are separated from each other by 8.2 Å. These findings emulate the molecular packing arrangement of a monolayer of Coumarin 343 within its crystal structure. This suggests that the dye adsorbs onto TiO2 in one of its lowest energy configurations; that is, dye···TiO2 self-assembly is driven more by thermodynamic rather than kinetic means. Complementary DSC device tests illustrate that this interfacial structure compromises photovoltaic performance, unless a suitably sized coadsorbant is interdispersed between the Coumarin 343 chromophores on the TiO2 surface.

Direct Observation of the Injection Dynamics of a Laser Wakefield Accelerator Using Few-Femtosecond Shadowgraphy

We present few-femtosecond shadowgraphic snapshots taken during the nonlinear evolution of the plasma wave in a laser wakefield accelerator with transverse synchronized few-cycle probe pulses. These snapshots can be directly associated with the electron density distribution within the plasma wave and give quantitative information about its size and shape. Our results show that self-injection of electrons into the first plasma-wave period is induced by a lengthening of the first plasma period. Three-dimensional particle-in-cell simulations support our observations.

The aggregation of early-onset melanoma in young Western Australian families

BACKGROUND

Few studies have examined the familial aggregation of melanoma or its co-aggregation with other cancers using whole-population based designs. This study aimed to investigate aggregation patterns in young Western Australian families, using population-based linked health data to identify individuals born in Western Australia between 1974 and 2007, their known relatives, and all incident cancer diagnoses within the resulting 1,506,961 individuals.

METHODS

Cox proportional hazards regression models were used to compare the risk of melanoma for first-degree relatives of melanoma cases to that for first-degree relatives of controls, with bootstrapping used to account for correlations within families. The risk of (i) developing melanoma based on the number of first-degree relatives with other cancers, and (ii) developing non-melanoma cancers based on the number of first-degree relatives diagnosed with melanoma was also investigated.

RESULTS

First-degree relatives of melanoma cases had a significantly greater incidence of melanoma than first-degree relatives of individuals not affected with melanoma (Hazard Ratio (HR)=3.58, 95% bootstrap confidence interval (CI): 2.43-5.43). Sensitivity analyses produced a higher hazard ratio estimate when restricted to melanoma cases diagnosed before 40 years of age (HR=3.77, bootstrap 95% CI: 2.49-6.39) and a lower estimate when only later-onset cases (>40 years) were considered (HR=2.45, bootstrap 95% CI: 1.23-4.82). No significant evidence was found for co-aggregation between melanoma and any other cancers.

CONCLUSIONS

Results indicated a strong familial basis of melanoma, with the higher than expected hazard ratio observed likely to reflect early-age at onset cases in this young cohort, supported by the results of the sensitivity analyses. Exploratory analyses suggested that the determinants of melanoma causing the observed aggregation within families may be independent of other malignancies, although these analyses were limited by the young age of the sample. Determining familial aggregation patterns will provide valuable knowledge regarding improved clinical risk prediction and the underlying biological mechanisms of melanoma and other cancers.

Concerted mitigation of O···H and C(π)···H interactions prospects sixfold gain in optical nonlinearity of ionic stilbazolium derivatives

DAST (4-dimethylamino-N-methyl-4-stilbazolium tosylate) is the most commercially successful organic nonlinear optical (NLO) material for frequency-doubling, integrated optics, and THz wave applications. Its success is predicated on its high optical nonlinearity with concurrent sufficient thermal stability. Many chemical derivatives of DAST have therefore been developed to optimize their properties; yet, to date, none have surpassed the overall superiority of DAST for NLO photonic applications. This is perhaps because DAST is an ionic salt wherein its NLO-active cation is influenced by multiple types of subtle intermolecular forces that are hard to quantify, thus, making difficult the molecular engineering of better functioning DAST derivatives. Here, we establish a model parameter, ηinter, that isolates the influence of intermolecular interactions on second-order optical nonlinearity in DAST and its derivatives, using second-harmonic generation (SHG) as a qualifier; by systematically mapping intercorrelations of all possible pairs of intermolecular interactions to ηinter, we uncover a relationship between concerted intermolecular interactions and SHG output. This correlation reveals that a sixfold gain in the intrinsic second-order NLO performance of DAST is possible, by eliminating the identified interactions. This prediction offers the first opportunity to systematically design next-generation DAST-based photonic device nanotechnology to realize such a prospect.

Anchoring groups for dye-sensitized solar cells

The dyes in dye-sensitized solar cells (DSSCs) require one or more chemical substituents that can act as an anchor, enabling their adsorption onto a metal oxide substrate. This adsorption provides a means for electron injection, which is the process that initiates the electrical circuit in a DSSC. Understanding the structure of various DSSC anchors and the search for new anchors are critical factors for the development of improved DSSCs. Traditionally, carboxylic acid and cyanoacrylic acid groups are employed as dye anchors in DSSCs. In recent years, novel anchor groups have emerged, which make a larger pool of materials available for DSSC dyes, and their associated physical and chemical characteristics offer interesting effects at the interface between dye and metal oxide. This review focuses especially on the structural aspects of these novel dye anchors for TiO2-based DSSCs, including pyridine, phosphonic acid, tetracyanate, perylene dicarboxylic acid anhydride, 2-hydroxylbenzonitrile, 8-hydroxylquinoline, pyridine-N-oxide, hydroxylpyridium, catechol, hydroxamate, sulfonic acid, acetylacetanate, boronic acid, nitro, tetrazole, rhodanine, and salicylic acid substituents. We anticipate that further exploration and understanding of these new types of anchoring groups for TiO2 substrates will not only contribute to the development of advanced DSSCs, but also of quantum dot-sensitized solar cells, water splitting systems, and other self-assembled monolayer-based technologies.

Coumarin 545: an emission reference dye with a record-low temperature coefficient for ratiometric fluorescence based temperature measurements

The emission intensities of coumarin 545 solution exhibit a low temperature dependence, with a record-low temperature coefficient of only ∼0.025% per °C.

Ultrahigh Brilliance Multi-MeV γ-Ray Beams from Nonlinear Relativistic Thomson Scattering

We report on the generation of a narrow divergence (θ_{γ}<2.5  mrad), multi-MeV (E_{max}≈18  MeV) and ultrahigh peak brilliance (>1.8×10^{20}  photons s^{-1} mm^{-2}  mrad^{-2} 0.1% BW) γ-ray beam from the scattering of an ultrarelativistic laser-wakefield accelerated electron beam in the field of a relativistically intense laser (dimensionless amplitude a_{0}≈2). The spectrum of the generated γ-ray beam is measured, with MeV resolution, seamlessly from 6 to 18 MeV, giving clear evidence of the onset of nonlinear relativistic Thomson scattering. To the best of our knowledge, this photon source has the highest peak brilliance in the multi-MeV regime ever reported in the literature.

Abstract A66: Recommendations to address common barriers to diversity in oncology clinical trials: An industry perspective

Introduction: Racial and ethnic minority enrollment in clinical trials is still a challenge and current recruitment planning has failed to improve diverse representation in clinical trials. The following literature review identified common barriers to diverse trial enrollment resulting in suggested tactics to address these barriers for breast cancer clinical trials.

Methods: A literature review was conducted to identify barriers to oncology clinical trial enrollment for African American, Hispanic, Asian American, and Native American populations. A targeted review of barriers for patients in the lower socioeconomic status (SES) bracket was also performed. An advisory board of study coordinators was consulted to assess site–level awareness, barriers, and resources needed from the pharmaceutical industry. Additionally, ongoing initiatives were assessed including use of a Latino toolkit, patient navigators, and community outreach strategies.

Results: The number of evidence based recruitment strategies targeting ethnic minorities was found to be lacking. There are four key aspects that influence diverse patients' decisions to participate in trials: family/friends, finances, faith, and physicians/staff. Barriers identified affected a majority of the analyzed patient populations. These included: protocol inclusion/exclusion criteria; logistical concerns; few incentives for participating; and cultural factors. The informed consent form and process were cumbersome and not patient-centric; costs related to travel and co-pays, and mistrust of medical research and the pharmaceutical industry were also identified as common barriers. The primary barriers were lack of invitations and lack of awareness at multiple levels within medical institutions, health care professionals, communities, and the pharmaceutical industry. Suggestions to address enrollment barriers include education to increase awareness, a patient-centric approach to consent and trial discussions, and tailoring site selection strategies. Other suggestions are immersion into communities, patient reimbursement, cultural competency training, pro-active translations, early recruitment planning, and identifying processes for approaching non-English speaking patients. Epidemiology data should also be incorporated in planning to establish baseline and enrollment goals.

Conclusion: Although each of the analyzed populations is unique, common themes emerged. A patient-centric approach to increasing diversity in clinical trials should include considering a patient's key influences, addressing common concerns, conducting a properly informed consent process, and empowering a patient's decision making process. Gaps in current recruitment practices do still exist and further research on evidence based diverse recruitment strategies is also needed.

Citation Format: Kelly R. Kirsch, Gebra C. Carter, Jacqueline M. Cole, Allicia C. Girvan, Coleman K. Obasaju. Recommendations to address common barriers to diversity in oncology clinical trials: An industry perspective. [abstract]. In: Proceedings of the Sixth AACR Conference: The Science of Cancer Health Disparities; Dec 6–9, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2014;23(11 Suppl):Abstract nr A66. doi:10.1158/1538-7755.DISP13-A66

Adsorption properties of p-methyl red monomeric-to-pentameric dye aggregates on anatase (101) titania surfaces: first-principles calculations of dye/TiO₂ photoanode interfaces for dye-sensitized solar cells

The optical and electronic properties of dye aggregates of p-methyl red on a TiO2 anatase (101) surface were modeled as a function of aggregation order (monomer to pentameric dye) via first-principles calculations. A progressive red-shifting and intensity increase toward the visible region in UV-vis absorption spectra is observed from monomeric-to-tetrameric dyes, with each molecule in a given aggregate binding to one of the four possible TiO2 (101) adsorption sites. The pentamer exhibits a blue-shifted peak wavelength in the UV-vis absorption spectra and less absorption intensity in the visible region in comparison; a corresponding manifestation of H-aggregation occurs since one of these five molecules cannot occupy an adsorption site. This finding is consistent with experiment. Calculated density of states (DOS) and partial DOS spectra reveal similar dye···TiO2 nanocomposite conduction band characteristics but different valence band features. Associated molecular orbital distributions reveal dye-to-TiO2 interfacial charge transfer in all five differing aggregate orders; meanwhile, the level of intramolecular charge transfer in the dye becomes progressively localized around its azo- and electron-donating groups, up to the tetrameric dye/TiO2 species. Dye adsorption energies and dye coverage levels are calculated and compared with experiment. Overall, the findings of this case study serve to aid the molecular design of azo dyes toward better performing DSSC devices wherein they are incorporated. In addition, they provide a helpful example reference for understanding the effects of dye aggregation on the adsorbate···TiO2 interfacial optical and electronic properties.

Modeling electron density distributions from X-ray diffraction to derive optical properties: constrained wavefunction versus multipole refinement

The rational design of next-generation optical materials requires an understanding of the connection between molecular structure and the solid-state optical properties of a material. A fundamental challenge is to utilize the accurate structural information provided by X-ray diffraction to explain the properties of a crystal. For years, the multipole refinement has been the workhorse technique for transforming high-resolution X-ray diffraction datasets into the detailed electron density distribution of crystalline material. However, the electron density alone is not sufficient for a reliable calculation of the nonlinear optical properties of a material. Recently, the X-ray constrained wavefunction refinement has emerged as a viable alternative to the multipole refinement, offering several potential advantages, including the calculation of a wide range of physical properties and seeding the refinement process with a physically reasonable starting point. In this study, we apply both the multipole refinement and the X-ray constrained wavefunction technique to four molecules with promising nonlinear optical properties and diverse structural motifs. In general, both techniques obtain comparable figures of merit and generate largely similar electron densities, demonstrating the wide applicability of the X-ray constrained wavefunction method. However, there are some systematic differences between the electron densities generated by each technique. Importantly, we find that the electron density generated using the X-ray constrained wavefunction method is dependent on the exact location of the nuclei. The X-ray constrained wavefunction refinement makes smaller changes to the wavefunction when coordinates from the Hartree-Fock-based Hirshfeld atom refinement are employed rather than coordinates from the multipole refinement, suggesting that coordinates from the Hirshfeld atom refinement allow the X-ray constrained wavefunction method to produce more accurate wavefunctions. We then use the experimentally derived wavefunctions to calculate the molecular dipole moment, polarizability, hyperpolarizability, and refractive index and show that these are in good agreement with the values calculated using ab initio methods. Thus, this study shows that experimental wavefunctions can be reliably generated from X-ray diffraction datasets, and that optical properties can be reliably calculated from these wavefunctions. Such a concerted interplay of experiment and computation via the X-ray constrained wavefunction refinement stands to enable the molecular engineering of tailor-made next-generation optical materials.

Variation in optoelectronic properties of azo dye-sensitized TiO2 semiconductor interfaces with different adsorption anchors: carboxylate, sulfonate, hydroxyl and pyridyl groups

The optoelectronic properties of four azo dye-sensitized TiO2 interfaces are systematically studied as a function of a changing dye anchoring group: carboxylate, sulfonate, hydroxyl, and pyridyl. The variation in optoelectronic properties of the free dyes and those in dye/TiO2 nanocomposites are studied both experimentally and computationally, in the context of prospective dye-sensitized solar cell (DSSC) applications. Experimental UV/vis absorption spectroscopy, cyclic voltammetry, and DSSC device performance testing reveal a strong dependence on the nature of the anchor of the optoelectronic properties of these dyes, both in solution and as dye/TiO2 nanocomposites. First-principles calculations on both an isolated dye/TiO2 cluster model (using localized basis sets) and each dye modeled onto the surface of a 2D periodic TiO2 nanostructure (using plane wave basis sets) are presented. Detailed examination of these experimental and computational results, in terms of light harvesting, electron conversion and photovoltaic device performance characteristics, indicates that carboxylate is the best anchoring group, and hydroxyl is the worst, whereas sulfonate and pyridyl groups exhibit competing potential. Different sensitization solvents are found to affect critically the extent of dye adsorption achieved in the dye-sensitization of the TiO2 semiconductor, especially where the anchor is a pyridyl group.

TiO2-assisted photoisomerization of azo dyes using self-assembled monolayers: case study on para-methyl red towards solar-cell applications

The optical and electronic properties of a TiO2 nanoparticle-assisted photo-isomerizable surface, prepared by an azo dye/TiO2 nanocomposite film, are examined experimentally and computationally. The azo dye, para-methyl red, undergoes photoisomerization at room temperature, catalyzed by the TiO2 nanoparticle supports, while it exhibits negligible photoisomerization in solvents under otherwise identical conditions. Density functional theory and time-dependent density functional theory are employed to explain the origin of this photoisomerization in these dye···TiO2 nanoparticle self-assembled monolayers (SAMs). The device performance of these SAMs when embedded into dye-sensitized solar cells is used to further elucidate the nature of this azo dye photoisomerization and relate it to the ensuing optoelectronic properties.

Quantum confinement-induced tunable exciton states in graphene oxide

Graphene oxide has recently been considered to be a potential replacement for cadmium-based quantum dots due to its expected high fluorescence. Although previously reported, the origin of the luminescence in graphene oxide is still controversial. Here, we report the presence of core/valence excitons in graphene-based materials, a basic ingredient for optical devices, induced by quantum confinement. Electron confinement in the unreacted graphitic regions of graphene oxide was probed by high resolution X-ray absorption near edge structure spectroscopy and first-principles calculations. Using experiments and simulations, we were able to tune the core/valence exciton energy by manipulating the size of graphitic regions through the degree of oxidation. The binding energy of an exciton in highly oxidized graphene oxide is similar to that in organic electroluminescent materials. These results open the possibility of graphene oxide-based optoelectronic device technology.

Data mining with molecular design rules identifies new class of dyes for dye-sensitised solar cells

Big data science informs energy research: large-scale screening of crystal structures identifies unforeseen class of dyes for dye-sensitised solar cells.

Abstract P5-07-08: Restoration of APC decreases tumorigenic potential in breast cancer cells

Mutations of the Adenomatous Polyposis Coli (APC) tumor suppressor gene have been reported in 5-70% of human breast cancers. APC is most well known for its role as a negative regulator of the Wnt/b-catenin pathway, where APC sequesters β-catenin and targets it for degradation via the proteasome. The breast cancer cell line, DU4475, has a single point mutation in the mutation cluster region of APC, coding for an early stop and subsequent truncated protein, lacking the β-catenin binding domain. Preliminary data using a TOPFlash reporter assay suggested that Wnt/β-catenin pathway was active, which was validated with immunofluorescence (IF) showing nuclear localization of β-catenin. Our overall hypothesis is that restoration of APC will decrease tumorigenic potential in DU4475 breast cancer cells. To test our hypothesis, we have generated DU4475 cells stably expressing GFP (control) (DU4475-GFP), a GFP-tagged internal fragment of APC that includes the β-catenin binding domain (DU4475-APCmid), and a GFP-tagged C-terminal fragment of APC that includes the microtubule binding domain of APC (DU4475-APCC-ter). After selection using G418, the GFP positive cells were sorted using a cell sorter. Results from TOPFlash reporter assay and IF demonstrated a modest decrease in Wnt/β-catenin activity in DU4475-APCmid cells. In addition, we observed decreased proliferation as measured in a growth assay in DU4475-APCmid cells compared to the control cells. We also observed a 17% increase in cleaved caspase-3 and only a minimal decrease in cell proliferation as measured by phospho-Histone H3 using IF in 3D cultures upon APCmid re-introduction. We also observed decreases in Cyclin D1, Cyclin B1, Early Growth Response 1, and HIF1α in DU4475-APCmid using real time PCR. These changes suggest that the re-introduction of the central domain of the APC tumor suppressor results in alterations in cell growth and gene expression changes indicative of an increased tumorigenic phenotype in vitro. Ongoing studies in the laboratory are dissecting the signaling pathways downstream of APC restoration to identify therapeutic targets that may be used to restore the functional alterations of mutant APC. These studies have generated a system to be utilized for in vivo tumor and metastasis formation under the control of APC mutation in a human cell culture model.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P5-07-08.