Two-dimensional MoS2 2H, 1T, and 1T' crystalline phases with incorporated adatoms: theoretical investigation of electronic and optical properties.

Although there has been progress in studying the electronic and optical properties of monolayer and near-monolayer (two-dimensional, 2D) MoS2 upon adatom adsorption and intercalation, understanding the underlying atomic-level behavior is lacking, particularly as related to the optical response. Alkali atom intercalation in 2D transition metal dichalcogenides (TMDs) is relevant to chemical exfoliation methods that are expected to enable large scale production. In this work, focusing on prototypical 2D MoS2, the adsorption and intercalation of Li, Na, K, and Ca adatoms were investigated for the 2H, 1T, and 1T' phases of the TMD by the first principles density functional theory in comparison to experimental characterization of 2H and 1T 2D MoS2 films. Our electronic structure calculations demonstrate significant charge transfer, influencing work function reductions of 1-1.5 eV. Furthermore, electrical conductivity calculations confirm the semiconducting versus metallic behavior. Calculations of the optical spectra, including excitonic effects using a many-body theoretical approach, indicate enhancement of the optical transmission upon phase change. Encouragingly, this is corroborated, in part, by the experimental measurements for the 2H and 1T phases having semiconducting and metallic behavior, respectively, thus motivating further experimental exploration. Overall, our calculations emphasize the potential impact of synthesis-relevant adatom incorporation in 2D MoS2 on the electronic and optical responses that comprise important considerations toward the development of devices such as photodetectors or the miniaturization of electroabsorption modulator components.

EMAGE mouse embryo spatial gene expression database: 2014 update.

EMAGE (http://www.emouseatlas.org/emage/) is a freely available database of in situ gene expression patterns that allows users to perform online queries of mouse developmental gene expression. EMAGE is unique in providing both text-based descriptions of gene expression plus spatial maps of gene expression patterns. This mapping allows spatial queries to be accomplished alongside more traditional text-based queries. Here, we describe our recent progress in spatial mapping and data integration. EMAGE has developed a method of spatially mapping 3D embryo images captured using optical projection tomography, and through the use of an IIP3D viewer allows users to view arbitrary sections of raw and mapped 3D image data in the context of a web browser. EMAGE now includes enhancer data, and we have spatially mapped images from a comprehensive screen of transgenic reporter mice that detail the expression of mouse non-coding genomic DNA fragments with enhancer activity. We have integrated the eMouseAtlas anatomical atlas and the EMAGE database so that a user of the atlas can query the EMAGE database easily. In addition, we have extended the atlas framework to enable EMAGE to spatially cross-index EMBRYS whole mount in situ hybridization data. We additionally report on recent developments to the EMAGE web interface, including new query and analysis capabilities.

Optically Transparent Lead Halide Perovskite Polycrystalline Ceramics.

We utilize room-temperature uniaxial pressing at applied loads achievable with low-cost, laboratory-scale presses to fabricate freestanding CH3NH3PbX3 (X- = Br-, Cl-) polycrystalline ceramics with millimeter thicknesses and optical transparency up to ∼70% in the infrared. As-fabricated perovskite ceramics can be produced with desirable form factors (i.e., size, shape, and thickness) and high-quality surfaces without any postprocessing (e.g., cutting or polishing). This method should be broadly applicable to a large swath of metal halide perovskites, not just the compositions shown here. In addition to fabrication, we analyze microstructure-optical property relationships through detailed experiments (e.g., transmission measurements, electron microscopy, X-ray tomography, optical profilometry, etc.) as well as modeling based on Mie theory. The optical, electrical, and mechanical properties of perovskite polycrystalline ceramics are benchmarked against those of single-crystalline analogues through spectroscopic ellipsometry, Hall measurements, and nanoindentation. Finally, γ-ray scintillation from a transparent MAPbBr3 ceramic is demonstrated under irradiation from a 137Cs source. From a broader perspective, scalable methods to produce freestanding polycrystalline lead halide perovskites with comparable properties to their single-crystal counterparts could enable key advancements in the commercial production of perovskite-based technologies (e.g., direct X-ray/γ-ray detectors, scintillators, and nonlinear optics).

Simultaneous chromatography and electrophoresis: two-dimensional planar separations.

Single-dimension separations are routinely coupled in series to achieve two-dimensional separations, yet little has been done to simultaneously exploit multiple dimensions during separation. In this work, simultaneous chromatography and electrophoresis is introduced and evaluated for its potential to achieve two-dimensional separations. In simultaneous chromatography and electrophoresis, chromatography occurs via capillary action while an orthogonal electric field concurrently promotes electrophoresis in a second dimension. A novel apparatus with a dual solvent reservoir was designed to apply the concurrent electric field. Various compounds were used to characterize the apparatus and technique, i.e., vitamins, amino acids, and dyes. Improved separation is reported with equivalent analysis times in comparison to planar chromatography alone. The feasibility of simultaneously employing chromatography and electrophoresis in two dimensions is discussed.

Optometry-based general population survey of pupil ruff atrophy and ocular hypertension.

BACKGROUND: To evaluate and describe the pupil ruff changes and relationship to intraocular pressure, pseudoexfoliation syndrome and glaucoma status in an optometric population in New Zealand. DESIGN: Prospective cross-sectional survey of an optometric population. PARTICIPANTS: Six hundred and twenty subjects over 50 years old routinely attending the participating optometry practices. Exclusion criteria included previous intraocular surgery, ophthalmic laser, uveitis, angle closure and secondary glaucoma. METHODS: Multicentre study involving 11 optometry practices in the Wellington region, New Zealand. The pupillary ruff and associated gonioscopy findings of study participants were graded based on the previously published Pupil Ruff Atrophy grading system. Parameters evaluated include pupillary ruff absence and abnormality, pseudoexfoliation material and trabecular meshwork pigmentation. MAIN OUTCOME MEASURES: Correlations between intereye Pupil Ruff Atrophy grading differences and inter-eye intraocular pressure and cup:disc ratio differences. RESULTS: Six hundred and twenty subjects were included, with a mean age of 62.2 ± 9.1 years and mean intraocular pressure of 14.8 ± 3.4 mmHg. Four hundred and fourteen (66.8%) had bilateral pupil ruff changes and 12 (1.5%) had pseudoexfoliation. Inter-eye intraocular pressure asymmetry was significantly correlated with amount of missing pupillary ruff (r = 0.111; P = 0.022) and trabecular meshwork pigmentation (r = 0.147; P = 0.002). Inter-eye cup:disc ratio asymmetry was not correlated with any of the Pupil Ruff Atrophy grading parameters. CONCLUSIONS: Asymmetry of pupillary ruff absence and trabecular meshwork pigmentation was correlated with intraocular pressure asymmetry (but not with cup:disc ratio asymmetry) in a general optometric population setting in New Zealand.

Exfoliation procedure-dependent optical properties of solution deposited MoS2 films.

The development of high-precision large-area optical coatings and devices comprising low-dimensional materials hinges on scalable solution-based manufacturability with control over exfoliation procedure-dependent effects. As such, it is critical to understand the influence of technique-induced transition metal dichalcogenide (TMDC) optical properties that impact the design, performance, and integration of advanced optical coatings and devices. Here, we examine the optical properties of semiconducting MoS2 films from the exfoliation formulations of four prominent approaches: solvent-mediated exfoliation, chemical exfoliation with phase reconversion, redox exfoliation, and native redox exfoliation. The resulting MoS2 films exhibit distinct refractive indices (n), extinction coefficients (k), dielectric functions (ε1 and ε2), and absorption coefficients (α). For example, a large index contrast of Δn ≈ 2.3 is observed. These exfoliation procedures and related chemistries produce different exfoliated flake dimensions, chemical impurities, carrier doping, and lattice strain that influence the resulting optical properties. First-principles calculations further confirm the impact of lattice defects and doping characteristics on MoS2 optical properties. Overall, incomplete phase reconfiguration (from 1T to mixed crystalline 2H and amorphous phases), lattice vacancies, intraflake strain, and Mo oxidation largely contribute to the observed differences in the reported MoS2 optical properties. These findings highlight the need for controlled technique-induced effects as well as the opportunity for continued development of, and improvement to, liquid phase exfoliation methodologies. Such chemical and processing-induced effects present compelling routes to engineer exfoliated TMDC optical properties toward the development of next-generation high-performance mirrors, narrow bandpass filters, and wavelength-tailored absorbers.

eMouseAtlas, EMAGE, and the spatial dimension of the transcriptome.

eMouseAtlas (www.emouseatlas.org) is a comprehensive online resource to visualise mouse development and investigate gene expression in the mouse embryo. We have recently deployed a completely redesigned Mouse Anatomy Atlas website (www.emouseatlas.org/emap/ema) that allows users to view 3D embryo reconstructions, delineated anatomy, and high-resolution histological sections. A new feature of the website is the IIP3D web tool that allows a user to view arbitrary sections of 3D embryo reconstructions using a web browser. This feature provides interactive access to very high-volume 3D images via a tiled pan-and-zoom style interface and circumvents the need to download large image files for visualisation. eMouseAtlas additionally includes EMAGE (Edinburgh Mouse Atlas of Gene Expression) (www.emouseatlas.org/emage), a freely available, curated online database of in situ gene expression patterns, where gene expression domains extracted from raw data images are spatially mapped into atlas embryo models. In this way, EMAGE introduces a spatial dimension to transcriptome data and allows exploration of the spatial similarity between gene expression patterns. New features of the EMAGE interface allow complex queries to be built, and users can view and compare multiple gene expression patterns. EMAGE now includes mapping of 3D gene expression domains captured using the imaging technique optical projection tomography. 3D mapping uses WlzWarp, an open-source software tool developed by eMouseAtlas.

EMAGE mouse embryo spatial gene expression database: 2010 update.

EMAGE (http://www.emouseatlas.org/emage) is a freely available online database of in situ gene expression patterns in the developing mouse embryo. Gene expression domains from raw images are extracted and integrated spatially into a set of standard 3D virtual mouse embryos at different stages of development, which allows data interrogation by spatial methods. An anatomy ontology is also used to describe sites of expression, which allows data to be queried using text-based methods. Here, we describe recent enhancements to EMAGE including: the release of a completely re-designed website, which offers integration of many different search functions in HTML web pages, improved user feedback and the ability to find similar expression patterns at the click of a button; back-end refactoring from an object oriented to relational architecture, allowing associated SQL access; and the provision of further access by standard formatted URLs and a Java API. We have also increased data coverage by sourcing from a greater selection of journals and developed automated methods for spatial data annotation that are being applied to spatially incorporate the genome-wide (approximately 19,000 gene) 'EURExpress' dataset into EMAGE.

Effective Optical Properties of Laterally Coalescing Monolayer MoS2.

Two-dimensional (2D) transition metal dichalcogenides (TMDCs) exhibit compelling dimension-dependent exciton-dominated optical behavior influenced by thickness and lateral quantum confinement effects. Thickness quantum confinement effects have been observed; however, experimental optical property assessment of nanoscale lateral dimension monolayer TMDCs is lacking. Here, we employ ex situ spectroscopic ellipsometry to evaluate laterally coalescing monolayer metalorganic chemical vapor deposited MoS2. A multisample analysis is used to constrain Bruggeman and Maxwell-Garnett effective medium approximations and the effective dielectric functions are derived for laterally coalesced and uncoalesced MoS2 films (∼10-94% surface coverage for ∼10-140 nm lateral grain sizes). This analysis demonstrates the ability to probe MoS2 optical exciton behavior at growth-relevant grain sizes in relation to chemical vapor nucleation density, ripening, and lateral growth conditions. Our analysis is pertinent toward expected in situ epitaxial 2D TMDC film growth metrology to enable the facile development of monolayer films with targeted process-dependent optical properties.

EMAGE--Edinburgh Mouse Atlas of Gene Expression: 2008 update.

EMAGE (http://genex.hgu.mrc.ac.uk/Emage/database) is a database of in situ gene expression patterns in the developing mouse embryo. Domains of expression from raw data images are spatially integrated into a set of standard 3D virtual mouse embryos at different stages of development, allowing data interrogation by spatial methods. Sites of expression are also described using an anatomy ontology and data can be queried using text-based methods. Here we describe recent enhancements to EMAGE which include advances in spatial search methods including: a refined local spatial similarity search algorithm, a method to allow global spatial comparison of patterns in EMAGE and subsequent hierarchical-clustering, and spatial searches across multiple stages of development. In addition, we have extended data access by the introduction of web services and new HTML-based search interfaces, which allow access to data that has not yet been spatially annotated. We have also started incorporating full 3D images of gene expression that have been generated using optical projection tomography (OPT).

Active Plasmonics and Active Chiral Plasmonics through Orientation-Dependent Multipolar Interactions.

While most active plasmonic efforts focus on responsive metamaterials to modulate optical response, we present a simple alternative based on applied orientation control that can likely be implemented for many passive plasmonic materials. Passive plasmonic motifs are simpler to prepare but cannot be altered postfabrication. We show that such systems can be easily manipulated through substrate orientation control to generate both active plasmonic and active chiral plasmonic responses. Using gold nanocrescents as our model platform, we demonstrate tuning of optical extinction from -21% to +36% at oblique incidence relative to normal incidence. Variation of substrate orientation in relation to incident polarization is also demonstrated to controllably switch chiroptical handedness (e.g., Δg = ± 0.55). These active plasmonic responses arise from the multipolar character of resonant modes. In particular, we correlate magnetoelectric and dipole-quadrupole polarizabilities with different light-matter orientation-dependence in both near- and far-field localized surface plasmon activity. Additionally, the attribution of far-field optical response to higher-order multipoles highlights the sensitivity offered by these orientation-dependent characterization techniques to probe the influence of localized electromagnetic field gradients on a plasmonic response. The sensitivity afforded by orientation-dependent optical characterization is further observed by the manifestation in both plasmon and chiral plasmon responses of unpredicted structural nanocrescent variance (e.g., left- and right-tip asymmetry) not physically resolved through topographical imaging.

Addressing Lameness in Farmed Animals: An Urgent Need to Achieve Compliance with EU Animal Welfare Law.

Lameness is the clinical manifestation of a range of painful locomotory conditions affecting many species of farmed animals. Although these conditions have serious consequences for animal welfare, productivity, and longevity, the prevention and treatment of lameness continue to receive insufficient attention in most farming sectors across the European Union (EU). In this paper, we outline the legislative framework that regulates the handling of lameness and other painful conditions in farmed animals in the EU. We briefly outline the current situation in different livestock farming sectors. Finally, we make the case for the introduction of regular on-farm monitoring of lameness and for the setting of alarm thresholds that should trigger corrective actions.

Protection of Dairy Cattle in the EU: State of Play and Directions for Policymaking from a Legal and Animal Advocacy Perspective.

With the exception of a detailed Directive for calves, the welfare of dairy cattle is not regulated by species-specific legislation in the European Union. Their basic protection falls under the provisions of Directive 98/58/EC, also known as the "General Farm Animals Directive". Article 3 of this Directive states: "Member States shall make provision to ensure that the owners or keepers take all reasonable steps to ensure the welfare of animals under their care and to ensure that those animals are not caused any unnecessary pain, suffering or injury". However, recent reports show that the welfare of dairy cows in the EU is not sufficiently monitored and that serious problems persist. Lameness, mastitis, cubicle design, flooring, cleanliness, and permanent tethering remain critical areas. We argue that, to demonstrate compliance with Article 3 of Directive 98/58, farmers and Member States should urgently address these issues. The increasing proportion of cows that are never allowed to graze and high milk yields are also reasons for concern and will need to be addressed as a matter of priority in future EU guides to good practice and, eventually, legislation.

Postural responses following a rotational support surface perturbation, following knee joint replacement: frontal plane rotations.

Total knee arthroplasty (TKA) is associated with altered sensory and motor functions of the knee which may impair balance control when standing and walking. This study examined the organization of electromyographic and kinematic postural responses to frontal plane support surface rotations, after TKA. Eight TKA patients and nine control participants volunteered. Patients demonstrated changes in onset latency of rectus femoris and gluteus medius, and in amplitude of muscle activity in tibialis anterior, gastrocnemius, rectus femoris, and gluteus medius, for both perturbation directions, and for both the surgical and sound limbs. Peak knee joint angular velocity was reduced among the patients for both perturbation directions and both the surgical and sound limbs, and patients demonstrated greater peak center of mass displacement. The CNS appears to alter the response to postural perturbation of both lower limbs, based on the reduced capacities of the surgical limb. Impaired detection of the valgus-varus loading of the knee joints may lead to the changes in muscle activity and resultant kinematics. Clinically, these findings are relevant in understanding that fully recovered TKA patients may continue to demonstrate balance impairments, and that balance training during physical rehabilitation may be advantageous to these patients.

EMAGE: a spatial database of gene expression patterns during mouse embryo development.

EMAGE (http://genex.hgu.mrc.ac.uk/Emage/database) is a freely available, curated database of gene expression patterns generated by in situ techniques in the developing mouse embryo. It is unique in that it contains standardized spatial representations of the sites of gene expression for each gene, denoted against a set of virtual reference embryo models. As such, the data can be interrogated in a novel and abstract manner by using space to define a query. Accompanying the spatial representations of gene expression patterns are text descriptions of the sites of expression, which also allows searching of the data by more conventional text-based methods.

Organization of postural responses following a rotational support surface perturbation, after TKA: sagittal plane rotations.

Proprioceptive dysfunction, related to osteoarthritis and total knee arthroplasty (TKA) may be related to changes in gait, and may result in balance impairment. This study examined the organization of postural responses to rotational support surface perturbations after TKA. Eight TKA patients and nine control participants volunteered. EMG was collected bilaterally from lower limb muscles. Kinematic data were collected using an OPTOTRAK system. The temporal pattern of muscle activation was preserved in both the surgical and sound limbs of the patient groups, while muscle activation amplitude was reduced. Knee joint angular displacement was reduced in both limbs among patients. COM displacement was not different. Patients demonstrated a different method in recovering posture control following a postural perturbation. Bilateral changes appear to reflect a simplification in the organization of the motor response, in response to the needs of the injured, or previously injured limb.

Personal characteristics, cooking at home and shopping frequency influence consumption.

This study examines how the consumption of fruits and vegetables is affected by home cooking habits and shopping patterns, including distance to patronized stores and frequency of shopping, in two low-income predominantly African American urban neighborhoods in New Orleans, Louisiana. In-person interviews were conducted in 2013 with 901 adult residents who identified themselves as the primary household shopper. Respondents were asked where and how often they shopped and answered a food frequency questionnaire. Addresses were geocoded and distances to the stores where respondents shopped were calculated. Multivariable logistic regression was used to examine the relationship between food consumption and personal factors, neighborhood factors and shopping habits. Consumption of daily servings of fresh produce increased by 3% for each additional trip to a grocery store, by 76% for shopping at a farmer's market, and by 38% for preparing food at home. Each additional trip to a convenience store increased the frequency of consumption of chips, candy and pastries by 3%. The distance from residence to the type of store patronized was not associated with consumption of produce or chips, candy or pastries. Shopping at full-service grocery stores, farmer's markets and cooking at home were positively associated with the consumption of fresh produce while shopping at convenience stores was associated with increased consumption of chips, candy and pastries. These findings are useful for designing programmatic interventions to increase fresh fruit and vegetable consumption among residents in low-income urban communities.

Evaluation of an injectable hydrogel and polymethyl methacrylate in restoring mechanics to compressively fractured spine motion segments.

BACKGROUND CONTEXT: Compressive fracture can produce profound changes to the mechanical profile of a spine segment. Minimally invasive repair has the potential to restore both function and structural integrity to an injured spine. Use of both hydrogels to address changes to the disc, combined with polymethyl methacrylate (PMMA) to address changes to the vertebral body, has the potential to facilitate repair. PURPOSE: The purpose of this investigation was to determine if the combined use of hydrogel injection and PMMA could restore the mechanical profile of an axially injured spinal motion segment. STUDY DESIGN: This is a basic science study evaluating a combination of hydrogel injection and vertebroplasty on restoring mechanics to compressively injured porcine spine motion segments. METHODS: Fourteen porcine spine motion segments were subject to axial compression until fracture using a dynamic servohydraulic testing apparatus. Rotational and compressive stiffness was measured for each specimen under the following conditions: initial undamaged, fractured, fatigue loading under compression, hydrogel injection, PMMA injection, and fatigue loading under compression. Group 1 received hydrogel injection followed by PMMA injection, whereas Group 2 received PMMA injection followed by hydrogel injection. This study was funded under a Natural Sciences and Engineering Research Council of Canada discovery grant. RESULTS: PMMA injection was found to alter the compressive stiffness properties of axially injured spine motion segments, restoring values from Groups 1 and 2 to 89.3%±29.3% and 81%±27.9% of initial values respectively. Hydrogel injection was found to alter the rotational stiffness properties, restoring specimens in Groups 1 and 2 to 151.5%±81% and 177.2%±54.9% of initial values respectively. Prolonged restoration of function was not possible, however, after further fatigue loading. CONCLUSIONS: Using this repair technique, replication of the mechanism of injury appears to cause a rapid deterioration in function of the motion segments. Containment of the hydrogel appears to be an issue with large breaches in the end plate, as it is posited to migrate into the cancellous bone of the vertebral body. Future work should attempt to evaluate methods in fully sealing the disc space.

EMAP and EMAGE: a framework for understanding spatially organized data.

The Edinburgh MouseAtlas Project (EMAP) is a time-series of mouse-embryo volumetric models. The models provide a context-free spatial framework onto which structural interpretations and experimental data can be mapped. This enables collation, comparison, and query of complex spatial patterns with respect to each other and with respect to known or hypothesized structure. The atlas also includes a time-dependent anatomical ontology and mapping between the ontology and the spatial models in the form of delineated anatomical regions or tissues. The models provide a natural, graphical context for browsing and visualizing complex data. The Edinburgh Mouse Atlas Gene-Expression Database (EMAGE) is one of the first applications of the EMAP framework and provides a spatially mapped gene-expression database with associated tools for data mapping, submission, and query. In this article, we describe the underlying principles of the Atlas and the gene-expression database, and provide a practical introduction to the use of the EMAP and EMAGE tools, including use of new techniques for whole body gene-expression data capture and mapping.

EMAGE: Electronic Mouse Atlas of Gene Expression.

The EMAGE (Electronic Mouse Atlas of Gene Expression) database (http://www.emouseatlas.org/emage) allows users to perform on-line queries of mouse developmental gene expression. EMAGE data are represented spatially using a framework of 3D mouse embryo models, thus allowing uniquely spatial queries to be carried out alongside more traditional text-based queries. This spatial representation of the data also allows a comparison of spatial similarity between the expression patterns. The data are mapped to the models by a team of curators using bespoke mapping software, and the associated meta-data are curated for accuracy and completeness. The data contained in EMAGE are gathered from three main sources: from the published literature, through large-scale screens and collaborations, and via direct submissions from researchers. There are a variety of ways to query the EMAGE database via the on-line search interfaces, as well as via direct computational script-based queries. EMAGE is a free, on-line, community resource funded by the Medical Research Council, UK.