Exploitation of the menshutkin reaction for the controlled assembly of halogen bonded architectures incorporating 1,2-diiodotetrafluorobenzene and 1,3,5-Triiodotrifluorobenzene

1,4-Diazabicyclo[2.2.2]octane (DABCO) forms well-defined co-crystals with 1,2-diiodotetrafluorobenzene (1,2-DITFB), [(1,2-DITFB)2DABCO], and 1,3,5-triiodotrifluorobenzene, [(1,3,5-TITFB)2DABCO]. Both systems exhibited lower-than-expected supramolecular connectivity, which inspired a search for polymorphs in alternative crystallization solvents. In dichloromethane solution, the Menshutkin reaction was found to occur, generating chloride anions and quaternary ammonium cations through the reaction between the solvent and DABCO. The controlled in situ production of chloride ions facilitated the crystallization of new halogen bonded networks, DABCO–CH2Cl[(1,2-DITFB)Cl] (zigzag X-bonded chains) and (DABCO–CH2Cl)3[(1,3,5-TITFB)2Cl3]·CHCl3 (2D pseudo-trigonal X-bonded nets displaying Borremean entanglement), propagating with charge-assisted C–I···Cl– halogen bonds. The method was found to be versatile, and substitution of DABCO with triethylamine (TEA) gave (TEA-CH2Cl)3[(1,2-DITFB)Cl3]·4(H2O) (mixed halogen bond hydrogen bond network with 2D supramolecular connectivity) and TEA-CH2Cl[(1,3,5-TITFB)Cl] (tightly packed planar trigonal nets). The co-crystals were typically produced in high yield and purity with relatively predictable supramolecular topology, particularly with respect to the connectivity of the iodobenzene molecules. The potential to use this synthetic methodology for crystal engineering of halogen bonded architectures is demonstrated and discussed.

Child's body in tree adds to Lockyer Valley death toll

"Two more bodies, including a that of child discovered in a tree, were retrieved in the Lockyer Valley at the weekend, reinforcing the grisly complexity of the search for the missing."

Adsorption thermodynamics and kinetics study for the self-assembly of 1,8,15,22-tetraaminophthalocyanatocobalt(II) on glassy carbon surface

Spontaneous adsorption of 1,8,15,22-tetraaminophthalocyanatocobalt(II) (4α-CoIITAPc) on glassy carbon (GC) electrode leads to the formation of a stable self-assembled monolayer (SAM). Since the SAM of 4α-CoIITAPc is redox active, its adsorption on GC electrode was followed by cyclic voltammetry. SAM of 4α-CoIITAPc on GC electrode shows two pairs of well-defined redox peaks corresponding to CoIII/CoII and CoIIIPc−1/CoIIIPc−2. The surface coverage (Γ) value, calculated by integrating the charge under CoII oxidation, was used to study the adsorption thermodynamics and kinetics of 4α-CoIITAPc on GC surface. Cyclic voltammetric studies show that the adsorption of 4α-CoIITAPc on GC electrode has reached the saturation coverage (Γs) within 3 h. The Γs value for the SAM of 4α-CoIITAPc on GC electrode was found to be 2.37 × 10−10 mol cm−2. Gibbs free energy (ΔGads) and adsorption rate constant (kad) for the adsorption of 4α-CoIITAPc on GC surface were found to be −16.76 kJ mol−1 and 7.1 M−1 s−1, respectively. The possible mechanism for the self-assembly of 4α-CoIITAPc on GC surface is through the addition of nucleophilic amines to the olefinic bond on the GC surface in addition to a meager contribution from π stacking. The contribution of π stacking was confirmed from the adsorption of unsubstituted phthalocyanatocobalt(II) (CoPc) on GC electrode. Raman spectra for the SAM of 4α-CoIITAPc on carbon surface shows strong stretching and breathing bands of Pc macrocycle, pyrrole ring and isoindole ring. Raman and CV studies suggest that 4α-CoIITAPc is adopting nearly a flat orientation or little bit tilted orientation.

Assembly and disassembly of temporary public spaces : establishing the theoretical needs

Contemporary cities no longer offer the same types of permanent environments that we planned for in the latter part of the twentieth century. Our public spaces are increasingly temporary, transient, and ephemeral. The theories, principles and tactics with which we designed these spaces in the past are no longer appropriate. We need a new theory for understanding the creation, use, and reuse of temporary public space. Moe than a theory, we need new architectural tactics or strategies that can be reliably employed to create successful temporary public spaces. This paper will present ongoing research that starts that process through critical review and technical analysis of existing and historic temporary public spaces. Through the analysis of a number of public spaces, that were either designed for temporary use or became temporary through changing social conditions, this research identifies the tactics and heuristics used in such projects. These tactics and heuristics are then analysed to extract some broader principles for the design of temporary public space. The theories of time related building layers, a model of environmental sustainability, and the recycling of social meaning, are all explored. The paper will go on to identify a number of key questions that need to be explored and addressed by a theory for such developments: How can we retain social meaning in the fabric of the city and its public spaces while we disassemble it and recycle it into new purposes? What role will preservation have in the rapidly changing future; will exemplary temporary spaces be preserved and thereby become no longer temporary? Does the environmental advantage of recycling materials, components and spaces outweigh the removal or social loss of temporary public space? This research starts to identify the knowledge gaps and proposes a number of strategies for making public space in the age of temporary, recyclable, and repurposing of our urban infrastructure; a way of creating lighter, cheaper, quicker, and temporary interventions.

Molecular camouflage : making use of protecting groups to control the self-assembly of inorganic janus particles onto metal–chalcogenide nanotubes by Pearson Hardness

Hard and soft: Binding of inorganic Pt@Fe3O4 Janus particles to WS2 nanotubes through their Pt or Fe3O4 domains is governed by the difference in Pearson hardness: the soft Pt block has a higher sulfur affinity than the harder magnetite face; thus the binding proceeds preferentially through the Pt face. This binding preference can be reversed by masking the Pt face with an organic protecting group.

Perturbed Lignification Impacts Tree Growth in Hybrid Poplar-A Function of Sink Strength, Vascular Integrity, and Photosynthetic Assimilation

The effects of reductions in cell wall lignin content, manifested by RNA interference suppression of coumaroyl 3'-hydroxylase, on plant growth, water transport, gas exchange, and photosynthesis were evaluated in hybrid poplar trees (Populus alba 3 grandidentata). The growth characteristics of the reduced lignin trees were significantly impaired, resulting in smaller stems and reduced root biomass when compared to wild-type trees, as well as altered leaf morphology and architecture. The severe inhibition of cell wall lignification produced trees with a collapsed xylem phenotype, resulting in compromised vascular integrity, and displayed reduced hydraulic conductivity and a greater susceptibility to wall failure and cavitation. In the reduced lignin trees, photosynthetic carbon assimilation and stomatal conductance were also greatly reduced, however, shoot xylem pressure potential and carbon isotope discrimination were higher and water-use efficiency was lower, inconsistent with water stress. Reductions in assimilation rate could not be ascribed to increased stomatal limitation. Starch and soluble sugars analysis of leaves revealed that photosynthate was accumulating to high levels, suggesting that the trees with substantially reduced cell wall lignin were not carbon limited and that reductions in sink strength were, instead, limiting photosynthesis.

A model-framed evaluation of elephant effects on tree and fire dynamics in African savannas

There is a concern that high densities of elephants in southern Africa could lead to the overall reduction of other forms of biodiversity. We present a grid-based model of elephant-savanna dynamics, which differs from previous elephant-vegetation models by accounting for woody plant demographics, tree-grass interactions, stochastic environmental variables (fire and rainfall), and spatial contagion of fire and tree recruitment. The model projects changes in height structure and spatial pattern of trees over periods of centuries. The vegetation component of the model produces long-term tree-grass coexistence, and the emergent fire frequencies match those reported for southern African savannas. Including elephants in the savanna model had the expected effect of reducing woody plant cover, mainly via increased adult tree mortality, although at an elephant density of 1.0 elephant/km2, woody plants still persisted for over a century. We tested three different scenarios in addition to our default assumptions. (1) Reducing mortality of adult trees after elephant use, mimicking a more browsing-tolerant tree species, mitigated the detrimental effect of elephants on the woody population. (2) Coupling germination success (increased seedling recruitment) to elephant browsing further increased tree persistence, and (3) a faster growing woody component allowed some woody plant persistence for at least a century at a density of 3 elephants/km2. Quantitative models of the kind presented here provide a valuable tool for exploring the consequences of management decisions involving the manipulation of elephant population densities. © 2005 by the Ecological Society of America.

Parallel streaming signature EM-tree: A clustering algorithm for web scale applications

The proliferation of the web presents an unsolved problem of automatically analyzing billions of pages of natural language. We introduce a scalable algorithm that clusters hundreds of millions of web pages into hundreds of thousands of clusters. It does this on a single mid-range machine using efficient algorithms and compressed document representations. It is applied to two web-scale crawls covering tens of terabytes. ClueWeb09 and ClueWeb12 contain 500 and 733 million web pages and were clustered into 500,000 to 700,000 clusters. To the best of our knowledge, such fine grained clustering has not been previously demonstrated. Previous approaches clustered a sample that limits the maximum number of discoverable clusters. The proposed EM-tree algorithm uses the entire collection in clustering and produces several orders of magnitude more clusters than the existing algorithms. Fine grained clustering is necessary for meaningful clustering in massive collections where the number of distinct topics grows linearly with collection size. These fine-grained clusters show an improved cluster quality when assessed with two novel evaluations using ad hoc search relevance judgments and spam classifications for external validation. These evaluations solve the problem of assessing the quality of clusters where categorical labeling is unavailable and unfeasible.

High-throughput bone and cartilage micropellet manufacture, followed by assembly of micropellets into biphasic osteochondral tissue

Engineered biphasic osteochondral tissues may have utility in cartilage defect repair. As bone-marrow-derived mesenchymal stem/stromal cells (MSC) have the capacity to make both bone-like and cartilage-like tissues, they are an ideal cell population for use in the manufacture of osteochondral tissues. Effective differentiation of MSC to bone-like and cartilage-like tissues requires two unique medium formulations and this presents a challenge both in achieving initial MSC differentiation and in maintaining tissue stability when the unified osteochondral tissue is subsequently cultured in a single medium formulation. In this proof-of-principle study, we used an in-house fabricated microwell platform to manufacture thousands of micropellets formed from 166 MSC each. We then characterized the development of bone-like and cartilage-like tissue formation in the micropellets maintained for 8–14 days in sequential combinations of osteogenic or chondrogenic induction medium. When bone-like or cartilage-like micropellets were induced for only 8 days, they displayed significant phenotypic changes when the osteogenic or chondrogenic induction medium, respectively, was swapped. Based on these data, we developed an extended 14-day protocol for the pre-culture of bone-like and cartilage-like micropellets in their respective induction medium. Unified osteochondral tissues were formed by layering 12,000 osteogenic micropellets and 12,000 chondrogenic micropellets into a biphasic structure and then further culture in chondrogenic induction medium. The assembled tissue was cultured for a further 8 days and characterized via histology. The micropellets had amalgamated into a continuous structure with distinctive bone-like and cartilage-like regions. This proof-of-concept study demonstrates the feasibility of micropellet assembly for the formation of osteochondral-like tissues for possible use in osteochondral defect repair.

A Monte-Carlo tree search in argumentation

Monte-Carlo Tree Search (MCTS) is a heuristic to search in large trees. We apply it to argumentative puzzles where MCTS pursues the best argumentation with respect to a set of arguments to be argued. To make our ideas as widely applicable as possible, we integrate MCTS to an abstract setting for argumentation where the content of arguments is left unspecified. Experimental results show the pertinence of this integration for learning argumentations by comparing it with a basic reinforcement learning.

Micromorphology and anatomy of leaves of Syzygium floribundum (Myrtaceae: Syzygieae), a rainforest tree endemic to eastern Australia

Although species of Syzygium are abundant components of the rainforests in Queensland and New South Wales, little is known about the anatomy of the Australian taxa. Here we describe the foliar anatomy and micromorphology of Syzygium floribundum (syn: Waterhousea floribunda) using standard protocols for scanning electron microscopy (SEM) and light microscopy. Syzygium floribundum possesses dorsiventral leaves with cyclo-staurocytic stomata, single epidermis, internal phloem, rhombus-shaped calcium oxalate crystals and complex-open midrib. In general, leaf anatomical and micromorphological characters are common with some species of the tribe Syzygieae. However, this particular combination of leaf characters has not been reported in a species of the genus. The anatomy of the species is typical of mesophytic taxa.

Substrate effects in the supramolecular assembly of 1,3,5-benzene tricarboxylic acid on graphite and graphene

The behavior of small molecules on a surface depends critically on both molecule–substrate and intermolecular interactions. We present here a detailed comparative investigation of 1,3,5-benzene tricarboxylic acid (trimesic acid, TMA) on two different surfaces: highly oriented pyrolytic graphite (HOPG) and single-layer graphene (SLG) grown on a polycrystalline Cu foil. On the basis of high-resolution scanning tunnelling microscopy (STM) images, we show that the epitaxy matrix for the hexagonal TMA chicken wire phase is identical on these two surfaces, and, using density functional theory (DFT) with a non-local van der Waals correlation contribution, we identify the most energetically favorable adsorption geometries. Simulated STM images based on these calculations suggest that the TMA lattice can stably adsorb on sites other than those identified to maximize binding interactions with the substrate. This is consistent with our net energy calculations that suggest that intermolecular interactions (TMA–TMA dimer bonding) are dominant over TMA–substrate interactions in stabilizing the system. STM images demonstrate the robustness of the TMA films on SLG, where the molecular network extends across the variable topography of the SLG substrates and remains intact after rinsing and drying the films. These results help to elucidate molecular behavior on SLG and suggest significant similarities between adsorption on HOPG and SLG.

The rapid manufacture of uniform composite multicellular-biomaterial micropellets, their assembly into macroscopic organized tissues, and potential applications in cartilage tissue engineering

We and others have published on the rapid manufacture of micropellet tissues, typically formed from 100-500 cells each. The micropellet geometry enhances cellular biological properties, and in many cases the micropellets can subsequently be utilized as building blocks to assemble complex macrotissues. Generally, micropellets are formed from cells alone, however when replicating matrix-rich tissues such as cartilage it would be ideal if matrix or biomaterials supplements could be incorporated directly into the micropellet during the manufacturing process. Herein we describe a method to efficiently incorporate donor cartilage matrix into tissue engineered cartilage micropellets. We lyophilized bovine cartilage matrix, and then shattered it into microscopic pieces having average dimensions < 10 μm diameter; we termed this microscopic donor matrix "cartilage dust (CD)". Using a microwell platform, we show that ~0.83 μg CD can be rapidly and efficiently incorporated into single multicellular aggregates formed from 180 bone marrow mesenchymal stem/stromal cells (MSC) each. The microwell platform enabled the rapid manufacture of thousands of replica composite micropellets, with each micropellet having a material/CD core and a cellular surface. This micropellet organization enabled the rapid bulking up of the micropellet core matrix content, and left an adhesive cellular outer surface. This morphological organization enabled the ready assembly of the composite micropellets into macroscopic tissues. Generically, this is a versatile method that enables the rapid and uniform integration of biomaterials into multicellular micropellets that can then be used as tissue building blocks. In this study, the addition of CD resulted in an approximate 8-fold volume increase in the micropellets, with the donor matrix functioning to contribute to an increase in total cartilage matrix content. Composite micropellets were readily assembled into macroscopic cartilage tissues; the incorporation of CD enhanced tissue size and matrix content, but did not enhance chondrogenic gene expression.

Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus)

Striped catfish (Pangasianodon hypophthalmus) is a commercially important freshwater fish used in inland aquaculture in the Mekong Delta, Vietnam. The culture industry is facing a significant challenge however from saltwater intrusion into many low topographical coastal provinces across the Mekong Delta as a result of predicted climate change impacts. Developing genomic resources for this species can facilitate the production of improved culture lines that can withstand raised salinity conditions, and so we have applied high-throughput Ion Torrent sequencing of transcriptome libraries from six target osmoregulatory organs from striped catfish as a genomic resource for use in future selection strategies. We obtained 12,177,770 reads after trimming and processing with an average length of 97 bp. De novo assemblies were generated using CLC Genomic Workbench, Trinity and Velvet/Oases with the best overall contig performance resulting from the CLC assembly. De novo assembly using CLC yielded 66,451 contigs with an average length of 478 bp and N50 length of 506 bp. A total of 37,969 contigs (57%) possessed significant similarity with proteins in the non-redundant database. Comparative analyses revealed that a significant number of contigs matched sequences reported in other teleost fishes, ranging in similarity from 45.2% with Atlantic cod to 52% with zebrafish. In addition, 28,879 simple sequence repeats (SSRs) and 55,721 single nucleotide polymorphisms (SNPs) were detected in the striped catfish transcriptome. The sequence collection generated in the current study represents the most comprehensive genomic resource for P. hypophthalmus available to date. Our results illustrate the utility of next-generation sequencing as an efficient tool for constructing a large genomic database for marker development in non-model species.