The role of word form in gender processing during lexical access: A theoretical review and novel proposal in language comprehension.

In contrast to language production, there are few comprehension models of the representation and use of grammatical gender in long-term memory. To bridge this gap, we conducted a systematic review of empirical studies on the role of gender-form regularities in the recognition of nouns in isolation and within sentences. The results of a final sample of 40 studies suggest that there are two routes for the retrieval of gender during real-time comprehension: a form-based route and a lexical-based route. Our review indicates that the use of these routes depends on the degree of gender transparency of the language and the degree of overtness of the experimental paradigm. To accommodate these findings, we incorporate a dual-route mechanism within a general model of lexical access in comprehension, the AUSTRAL (Activation Using Structurally Tiered Representations and Lemmas) model, and identify directions for future research.

CRAMER: a lightweight, highly customizable web-based genome browser supporting multiple visualization instances.

SUMMARY: In recent years, the ability to generate genomic data has increased dramatically along with the demand for easily personalized and customizable genome browsers for effective visualization of diverse types of data. Despite the large number of web-based genome browsers available nowadays, none of the existing tools provides means for creating multiple visualization instances without manual set up on the deployment server side. The Cranfield Genome Browser (CRAMER) is an open-source, lightweight and highly customizable web application for interactive visualization of genomic data. Once deployed, CRAMER supports seamless creation of multiple visualization instances in parallel while allowing users to control and customize multiple tracks. The application is deployed on a Node.js server and is supported by a MongoDB database which stored all customizations made by the users allowing quick navigation between instances. Currently, the browser supports visualizing a large number of file formats for genome annotation, variant calling, reads coverage and gene expression. Additionally, the browser supports direct Javascript coding for personalized tracks, providing a whole new level of customization both functionally and visually. Tracks can be added via direct file upload or processed in real-time via links to files stored remotely on an FTP repository. Furthermore, additional tracks can be added by users via simple drag and drop to an existing visualization instance. AVAILABILITY AND IMPLEMENTATION: CRAMER is implemented in JavaScript and is publicly available on GitHub on https://github.com/FadyMohareb/cramer. The application is released under an MIT licence and can be deployed on any server running Linux or Mac OS. CONTACT: f.mohareb@cranfield.ac.uk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Marital status and stage of cancer at diagnosis: A systematic review.

Early cancer detection is fundamental to the promotion of better health in the community, but disparities remain in the likelihood of cancer being detected at an early stage, some of which relate to socio-demographic factors such as marital status. The aim of this study was to conduct a systematic review of research on the association between marital status and stage at diagnosis of different types of cancer. A comprehensive systematic literature search was run in the Medline and Scopus databases (from January 1990 to June 2014), identifying 245 and 208 articles on PubMed and Scopus respectively. Of these 453 studies, 18 were judged eligible for this systematic review. A quality assessment was performed on the studies using the 22 items in the STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) checklist. This review confirmed the important influence of being married on the earlier detection of cancer. None of the studies considered identified more cases of cancer in a later stage among married patients, and the majority of them reported a statically significant association between marital status and stage at diagnosis, with a positive effect of marriage on the likelihood of cancer being diagnosed at an early stage, for various types of malignancy. In particular, our meta-analysis showed that the unmarried have higher odds of having a later stage of breast cancer (OR = 1.287 95% CI: 1.025-1.617) or melanoma (OR = 1.350 95% CI: 1.161-1.570) at diagnosis. Specific interventions should be developed for the unmarried population to improve their chances of any neoplasms being diagnosed at an early stage, thereby reducing health disparities in the population at large.

SELECT-2: a phase II, double-blind, randomized, placebo-controlled study to assess the efficacy of selumetinib plus docetaxel as a second-line treatment of patients with advanced or metastatic non-small-cell lung cancer.

BACKGROUND: Combination of selumetinib plus docetaxel provided clinical benefit in a previous phase II trial for patients with KRAS-mutant advanced non-small-cell lung cancer (NSCLC). The phase II SELECT-2 trial investigated safety and efficacy of selumetinib plus docetaxel for patients with advanced or metastatic NSCLC. PATIENTS AND METHODS: Patients who had disease progression after first-line anti-cancer therapy were randomized (2 : 2 : 1) to selumetinib 75 mg b.i.d. plus docetaxel 60 or 75 mg/m2 (SEL + DOC 60; SEL + DOC 75), or placebo plus docetaxel 75 mg/m2 (PBO + DOC 75). Patients were initially enrolled independently of KRAS mutation status, but the protocol was amended to include only patients with centrally confirmed KRAS wild-type NSCLC. Primary end point was progression-free survival (PFS; RECIST 1.1); statistical analyses compared each selumetinib group with PBO + DOC 75 for KRAS wild-type and overall (KRAS mutant or wild-type) populations. RESULTS: A total of 212 patients were randomized; 69% were KRAS wild-type. There were no statistically significant improvements in PFS or overall survival for overall or KRAS wild-type populations in either selumetinib group compared with PBO + DOC 75. Overall population median PFS for SEL + DOC 60, SEL + DOC 75 compared with PBO + DOC 75 was 3.0, 4.2, and 4.3 months, HRs: 1.12 (90% CI: 0.8, 1.61) and 0.92 (90% CI: 0.65, 1.31), respectively. In the overall population, a higher objective response rate (ORR; investigator assessed) was observed for SEL + DOC 75 (33%) compared with PBO + DOC 75 (14%); odds ratio: 3.26 (90% CI: 1.47, 7.95). Overall the tolerability profile of SEL + DOC was consistent with historical data, without new or unexpected safety concerns identified. CONCLUSION: The primary end point (PFS) was not met. The higher ORR with SEL + DOC 75 did not translate into prolonged PFS for the overall or KRAS wild-type patient populations. No clinical benefit was observed with SEL + DOC in KRAS wild-type patients compared with docetaxel alone. No unexpected safety concerns were reported. TRIAL IDENTIFIER: Clinicaltrials.gov NCT01750281.

Influence of the displacement out of the center of mass and nonaxiality of the dipole on the thermodynamics of liquids composed of linear dipole molecules.

We present results for organic liquids modeled as linear rods with an embedded point dipole shifted from the geometrical center. Previously, we have obtained results for the vapor-liquid equilibrium (VLE) of similar systems with centered point dipoles. Our results included both models and applications to real systems. Results presented here are based on a previous work ( Phys. Rev. E 2003, 68, 021201) on the structural properties of these systems where relevant results about the appearance of dimers were found. Now, we have also performed systematic simulations on these systems to calculate the VLE of models with different aspect ratios, dipole shifts, and dipole strengths using the Gibbs ensemble Monte Carlo (GEMC) to calculate equilibrium densities and vapor pressure at each temperature. The applications considered here include some important substances such as 1-amines, acetonitrile, and 1-alcohols whose intermolecular parameters were fitted from our model simulations. Furthermore, we have used quantum chemistry calculations to obtain a reliable charge distribution, and we have applied our model to predict the vapor pressure of alpha,omega-diols where experimental results are rather scarce. Our results show a general improvement of the agreement between experiment and models compared to centered dipole models previously used. Results for amines are particularly remarkable.

A coarse-graining approach for the proton complex in protonated aluminosilicates.

We have developed a computational framework for the adsorption of linear alkanes in protonated aluminosilicates. These zeolites contain trace amounts of water that form hydrated proton complexes. The presence of hydrated protons makes the simulations at the fully atomistic level difficult. Instead of constructing an elaborate and complex model, we show that an approach based on a coarse-graining of the proton-complex accurately describes the available experimental isotherms, Henry coefficients, heats of adsorption, and oxygen-proton distances. Our approach is supported by MP2 quantum mechanical simulations. The model gives remarkably good agreement with experimental data beyond the initial calibration set.

A novel orientation-dependent potential model for prolate mesogens.

An intermolecular potential is introduced for the study of molecular mesogenic fluids. The model combines distinct features of the well-known Gay-Berne and Kihara potentials by incorporating dispersive interactions dependent on the relative pair orientation to a spherocylinder molecular core. Results of a Monte Carlo simulation study focused on the liquid crystal phases exhibited by the model fluid are presented. For the chosen potential parameters, molecular aspect ratio L*=5 and temperatures T*=2, 3, and 5, isotropic, nematic, smectic-A, and hexatic phases are found. The location of the phase boundaries as well as the equation of state of the fluid and further thermodynamical and structural parameters are discussed and contrasted to the Kihara fluid. In comparison to this latter fluid, the model induces the formation of ordered liquid crystalline phases at lower packing fractions and it favors, in particular, the appearance of layered hexatic ordering as a consequence of the greater attractive interaction assigned to the parallel side-to-side molecular pair configurations. The results contribute to the evaluation of the role of specific interaction energies in the mesogenic behavior of prolate molecular liquids in dense environments.

Parsons-Lee and Monte Carlo study of soft repulsive nematogens.

A general approach based on the Parsons-Lee theory for soft repulsive molecular fluids is employed to investigate the nematogenic behavior of prolate thermotropic liquid crystals over a broad temperature range. The theory is solved for the particular case of the Kihara soft repulsive spherocylinder model, which is mapped into an effective hard core interaction with a temperature-dependent molecular diameter, expected to resemble the average size and shape of the soft molecules at a given temperature. The reduction of the effective molecular diameter with temperature in the Kihara soft repulsive fluid implies implicitly an increase of the elongation of the molecule and induces the stabilization of the nematic phase at smaller effective packing fractions, contrary to what is found for other fluid models. The rationalization of this effect in terms of excluded volume steric arguments is corroborated by the good general agreement between the Parsons-Lee approach and Monte Carlo simulations for the equation of state of the fluid in the vicinity of the isotropic-nematic transition.

Structure and stability of small TiO2 nanoparticles.

The effect of the nanostructure on the photochemistry of TiO2 is an active field of research owing to its applications in photocatalysis and photovoltaics. Despite this interest, little is known of the structure of small particles of this oxide with sizes at the nanometer length scale. Here we present a computational study that locates the global minima in the potential energy surface of Ti(n)O2n clusters with n = 1-15. The search procedure does not refer to any of the known TiO2 polymorphs, and is based on a novel combination of simulated annealing and Monte Carlo basin hopping simulations, together with genetic algorithm techniques, with the energy calculated by means of an interatomic potential. The application of several different methods increases our confidence of having located the global minimum. The stable structures are then refined by means of density functional theory calculations. The results from the two techniques are similar, although the methods based on interatomic potentials are unable to describe some subtle effects. The agreement is especially good for the larger particles, with n = 9-15. For these sizes the structures are compact, with a preference for a central octahedron and a surrounding layer of 4- and 5-fold coordinated Ti atoms, although there seems to be some energy penalty for particles containing the 5-fold coordinated metal atoms with square base pyramid geometry and dangling Ti=O bonds. The novel structures reported provide the basis for further computational studies of the effect of nanostructure on adsorption, photochemistry, and nucleation of this material.

Crowding effects in binary mixtures of rod-like and spherical particles.

Crowding effects relevant to the phase stability of binary mixtures of rod-like and spherical particles are investigated by means of Monte Carlo simulations in the isobaric NPT ensemble. The two types of particles are represented, respectively, by freely rotating hard spherocylinders of a moderate aspect ratio (L/sigma = 5) and hard spheres of the same diameter sigma. Molar fractions of spheres ranging xHS = 0.00-0.37 are considered with the aim of characterizing the crowding effects on the liquid crystal phases of the hard spherocylinder fluid induced by the spherical component as depleting agent. We find that the addition of the spherical crowder is beneficial for the stabilization of the layers of the rod-like particles characteristic of the smectic phase. On the contrary, the addition of spheres has a negative impact upon the stability of the nematic phase, where the rod-like particles tend to align collectively parallel to each other. Interestingly, the spheres tend to arrange forming rod-like clusters in the nematic phase and lamellar structures in the smectic phase, which is compensated by the entropy gained by the spherocylinder particles in each phase. The main results are in qualitative agreement with recent experimental and theoretical studies and serve to test the prediction of current equations of state for these types of binary mixtures.

Evidence for liquid phase reactions during single bubble acoustic cavitation.

We extended the recent experiment by Lepoint et al. [Sonochemistry and Sonoluminescence, NATO ASI Series, Series C 524, Kluwer Academic Publishers, Dordrecht/Boston/London, 1999, p. 285], involving a so-called single bubble sonochemistry process, to a three-phase system. We have found experimental evidence that a single cavitating bubble can activate the oxidation of I- ions after the injection of a CCl4 liquid drop in the bubble trapping apparatus. The solvent drop (CCl4 is almost water insoluble) is pushed towards the bubble position and forms a thin film on the bubble surface. When the acoustic pressure drive is increased above 100 kPa, the three-phase system gives rise to a dark filament, indicating the complexation reaction between starch (added to the water phase) and I2. I2 species is the product of surface reactions involving bubble-induced decomposition of CCl4. Further increase of the acoustic drive causes the thin CCl4 film to separate from the bubble and stops I2 production. The study of the chemical activity of this three-phase system could give new advances on dynamics of the bubble collapse.

Liquid crystal behavior of the Kihara fluid.

The liquid crystal phases of the Kihara fluid have been studied in computer simulations. The work focuses on the isotropic-nematic-smectic-A triple point region, especially relevant for the understanding of the properties and the design of real mesogens with specific phase diagrams. The Kihara interaction resembles more appropriately than other related models, the shape of elongated polymers and biomolecules, and a closer assertion is provided for the role of the configurational entropy and the dispersive interactions in the behavior of such molecules in dense phases or under macromolecular crowding conditions.

Solution of the Percus-Yevick equation for square well spherocylinders.

The Percus-Yevick equation for square-well spherocylinders has been numerically solved for some selected orientations following a methodology proposed previously for different fluids of elongated molecules. The equation is solved for particles of aspect ratios ranging from L/sigma=0.3 up to L/sigma=5.0, attractive range lambda/sigma=1.5, and packing fractions within eta=0.1-0.3. The resulting pair correlation functions are checked against isothermal-isobaric Monte Carlo simulations and good agreement is found for the short-range structure, at intermolecular distances within one molecular diameter sigma to contact for each of the selected orientations. At larger distances, the integral equation tends to overestimate the pair correlations. The results confirm the prediction of reference-system average Mayer-function perturbation theory for short aspect ratios, reaching the Onsager limit for the greater aspect ratios. Some instabilities of the solution for the longest models and higher densities are tentatively discussed in terms of their possible relation to frustration phenomena found in some polymer and complex systems.

Aids e câncer / Aids and cancer

Os autores apresentam uma revisão a respeito dos tumores mais frequentes em pacientes aidéticos. É dada ênfase ao Sarcoma de Kaposi, Linfomas não-Hodgkin e tumores anogenitais. Aborda-se aspectos epidemiológicos etiológicos, clínicos, prognósticos e terapêuticos