8 At 40 K and 1.01 bar, xenon hydrate adopts a type I clathrate structure in which the polyhedral T-cages and D-cages are 82 % and 80 % occupied (overall 3.87 mol kg -1 Xe, 51 wt. %) with average Xe–O distances of 4.26 Å and 3.86 Å, respectively. In Xe-loaded CC3, the closest atoms from the CC3 molecule form analogous, polyhedral organic cages around the xenon guest (Supplementary Information, Table S1). The shortest contact distances between the cage molecule and xenon guests are comparable with the xenon hydrate cages: the average Xe···phenyl ring centroid distance for the cage cavity is 4.22 Å, while short Xe···H contacts with a mean distance of 3.75 Å are present in the window cavity. The volumetric density of enclathrated xenon in CC3 close to saturation is 0.31 g cm -3 . This is lower than in xenon hydrate (0.85 g cm -3 ) but CC3, unlike the hydrate, is stable to removal of the xenon guest, and retains a preorganised host structure that can capture xenon at low partial gas pressures. The structure of CC3-R Kr-loaded at 9.8 bar was determined by analogous in situ PXRD experiments (Supplementary Information, Section 2). This structure indicates that the krypton atoms are hosted in the cage cavity and cage window sites, with a decreased overall occupancy with respect to the xenon-loaded CC3 structure of 2.1±0.1 Kr atoms per cage (1.63 mol kg -1 , 13 wt. %), reflecting the much lower simulated and measured affinity of Kr for CC3 (Fig. 2c,d).
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In principle, the development of computational methods for structure and property prediction o ﬀ ers the potential for the in silico design of functional materials. Here, we evaluate the crystal energy landscapes of a series of porous organic cages, for which small changes in chemical structure lead to completely di ﬀ erent crystal packing arrangements and, hence, porosity. The di ﬀ erences in crystal packing are not intuitively obvious from the molecular structure, and hence qualitative approaches to crystal engineering have limited scope for designing new materials. We ﬁ nd that the crystal structures and the resulting porosity of these molecular crystals can generally be predicted in silico , such that computational screening of similar compounds should be possible. The computational predictability of organic cage crystal packing is demonstrated by the subsequent discovery, during screening of crystallisation conditions, of the lowest energy predicted structure for one of the cages.
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Metal-organic frameworks (MOFs) have received considerable attention over the last decade due to their interesting pore structures, chemical diversity, and potential applications in various fields such as gas storage, separation, shape/size selectivity, catalysis, sensors and drug delivery. 13 MOFs have extended crystalline structures, containing metal clusters and organic ligands. One-, two- and three- dimensional structures (1D, 2D and 3D, respectively) are formed by linking metal sites and organic ligands, where the dimensionality can be controlled by the connectivity and geometry of the secondary building blocks. More importantly, due to the large number of choices of both metal clusters and organic linkers, the number of potential structures of MOFs is vast. The concept of ‘reticular chemistry’ was proposed by Yaghi and O’Keeffe to design and construct porous MOFs materials by using secondary building units (SBUs). 14 A large number of topologies results from linking various molecular ligands and metal clusters. By choosing appropriate building blocks and synthetic methods, MOFs with well-defined pore sizes, shapes and functionalities can be formed that result in desired properties. One of most well-known 3D MOFs is MOF-5, consisting of zinc clusters and 1,4 benzenedicarboxylate (BDC) that generate a cubic extended porous structure reported by the Yaghi group that can be used for hydrogen storage. 15 MOF-5 adsorbs 22.5 mmol g -1 (4.5 wt %) H 2 at 78 K and 20 bar. A number of analogues of MOF-5,
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er relative pressure, and the desorption hysteresis, suggests some mesoporous character that cannot be rationalized by the crystal structures. This is explained by pronounced cracking of the CC2β crystals during desolvation (Fig. 4). Cracking of the crystals upon desolvation was not generally observed for our other imine cages and polymorphs, and certainly not to this extent. However, for CC2β, this fracturing seems to be unavoidable, even with very slow drying. This is because of the relatively strong directing interaction between the cages and the dioxane molecules, combined with anisotropic chang- es in the crystal lattice parameters (Table 1). Nevertheless, the CC2β material remains polycrystalline after desolvation (100 °C, dynamic vacuum, 16 hours), and the structure deter- mined from PXRD shows that the window-to-window pack- ing motif and orthorhombic Fddd symmetry is conserved in the desolvated material (Fig. 5). In the solvate, the dimeric cage moiety is slightly expanded to accommodate one dioxane
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Results showed that when the CC1α structure was optimised, there was a small volume contraction upon optimisation, with the greatest effect in the a-axis of a - 1.22 % shift. For CC1β, the a and b directions were equivalent since the cages pack hexagonally in the a,b plane (see Figure 3.13). On minimisation, the hexagonal symmetry was slightly distorted since the a-vector (-1.49 %) contraction was around 0.5 % greater than that in the b-direction (-0.97 %). In contrast the NPT MD simulations give an isotropic expansion from the experimental data. A similar effect was seen for the CC2 structure: in this case there was an hexagonal arrangement in the ab plane but the cages were not close packed, as seen with CC1β, but rather arranged to form 1-D channels in the  direction (refer to Figure 3.13c). This gives CC2 the lowest density of these cage structures. CC3 shows the smallest deviation in both the optimised (0.90 %) and MD simulations (-0.72 %). This was likely to be down to the cubic close packing of the system, with the functionalised vertices most likely holding the systems shape. Figure 3.13d shows that the differences in cell parameters between experimental data and optimisation calculations were small (less than 2 %), with the NPT MD results reproducing experiment to within 1 % for all of the structures used in the fitting procedure.
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A solution of 1,3,5-triformylbenzene (3.75 g, 23.13 mmol) in dichloromethane (1150 mL) was added drop-wise over 48 hours (ca.0.4 mL/min) via pressure equalizing dropping funnel to a solution of ethylenediamine (2.08 g, 34.69 mmol) in dichloromethane (850 mL) in a 2- litre 3-necked round bottom flask cooled in an ice bath. The stirring rate used was 400 rpm. After complete addition, the reaction was allowed to stir for another 24 hours at room temperature. The solution was then filtered through filter paper (loss of solid to filter paper was 0.030 g). The solvent was removed from the filtrate via rotary evaporation (temperature of the water bath maintained below 20 °C) and the crude product was re-dissolved in chloroform (100 mL) and the solution re-filtered. The residue in the filter paper was washed with chloroform (50 mL). The two fractions of the organic filtrate were combined and the solvent removed under vacuum on a rotary evaporator (temperature of the water bath maintained below 20 °C) to give the product as a beige powder.
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POCs have proven to be an effective and fascinating approach towards the synthesis of porous materials consisting of discrete organic molecules. The recent major advances that have been made in their preparation are due to the application of dynamic covalent chemistry. Under certain conditions, this exploits reversible covalent bond formation to achieve the most thermodynamically stable product. 56 This means that even once the initial products are formed, changing the reaction environment can result in an adjustment in their distribution towards the isolation of a single product. 57 By utilising this approach, POC molecules consisting of covalent bonds may be prepared, typically requiring the use of simple starting materials and proceeding in one step and in high yields. It is therefore a very powerful and adaptable tool. It has enabled a large number of POC molecules to be synthesised over the past few years, with many remaining shape-persistent upon desolvation and exhibiting BET surface areas to rival those of extended porous frameworks and networks. 58 The majority of POCs synthesised to date rely on the formation of an imine bond through the reaction of a primary amine and an aldehyde, 59 although more recently, boronate ester methodologies have also been shown to be a promising route towards their preparation. 60
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focuses on the preparation of structurally analogous assemblies that are instead bridged by metallic linkers. The design principles remain the same, in that the constructs gained feature similarly well-defined and hydrophobic internal voids, although now com- paratively larger, which greatly increases the scope for potential application. An attractive feature of coordination cages over their organic counterparts is that they are formed via metal-mediated self-assembly, which tends to minimize the multistep syntheses that are necessary to prepare similarly-sized organic cages and allows for their formation with relative ease. Whilst true, this statement neither accounts for serendipity, nor the fortuitous discoveries that it often aﬀords. 26
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site is found to be the most reactive site. One can conclude that the surface reactivity of the mono hydro- genation fullerene cages is increased with increasing the number of pentagon-pentagon fusion, agrees with the previous observation . Therefore, the less the cone angle, the larger the curvature and the highest reactive site. Result in the localized carbon atom at three pentagons has the highest reactive site, while the localized car- bon atom at three hexagons has the lowest reactive site.
On the third day following release, all the females were removed from the cages and put in 30 × 30 × 30 cm cages for blood feeding for 30 min on each of 2 consecutive days on fresh bovine blood. All blood-fed females were kept for three days after the last blood meal for egging en masse. The females were allowed to lay eggs for two consecutive days. Each day, newly laid eggs were collected, rinsed and allowed to hatch over two days. The sterility rate was then assessed by counting the number of hatched eggs under a stereomicroscope. To assess the insemination state of fe- males, spermathecae were dissected under a stereomicro- scope and the presence/absence of spermatozoa was observed at 400X magnification.
The Atlantic salmon (Salmo salar L.) used in the study had been selectively inbred for 7–10 generations (see Johnston et al., 2003b). Eggs from 360 families were incubated at ~8.3°C until hatching and were then transferred to tanks and freshwater sea cages as described previously using standard commercial procedures (see Johnston et al., 2003b). The fish were branded, and 504 fish were individually PIT tagged (passive integrated transponder; supplied by Fish Eagle Co., Gloucester, UK) prior to seawater transfer. Smolts were stocked into four steel construction cages with a 12·mm mesh cube net of 5·m×5·m×5·m at the Loch Eil (56°49′ N 5°07′ W) trial site [Marine Harvest Scotland Ltd, Edinburgh, UK] on 17–18 April 2000. Each cage was stocked with 600 smolts, representing a random selection of the available fish. Fish were fed to satiety using an automatic feeding system (AKVAsmart Ltd, Glasgow, UK) as previously described (Johnston et al., 2003b). The diet was a standard commercial ration (Ecolife ® )
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Time-series clustering requires the definition of a clustering algorithm, a dissimilarity mea- sure, a representative cluster centroid, and a cluster evaluation step . It is not possible to know in advance what will be the best clustering approach for a given data set. To investigate the different partitions of cages and find which provide the best fit to the data, we apply several clustering algorithm configurations, for a total of 9 approaches, with cluster evaluation using 7 cluster evaluation indices, and a final step investigating cluster stability. In some cases, we expect clustering results to be consistent across different configurations, which may be an indi- cation of clustering patterns in sea lice counts. However, given the unique behaviour of each algorithm and the inherent stochasticity in some of the methods, cluster membership would be expected to show variation between methods and even across random repetitions within the same method. Where cluster membership differs from total concordance within a specific method, stability is indicated to be ‘partial’ so as to contrast this with methods which result in largely identical membership and indicate highly stable clusters. However, it can be the case that two methods both result in stable clusters but that their membership differs between methods; this lack of stability is more problematic and indicates that treatment of one or more variables, or their use in the estimated distance metric is leading to inconsistent outcomes, making interpretation more challenging.
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Postoperative external immobilization is often required when stand-alone devices are used. However, we did not observe any case of cage extrusion in our study popula- tion. This may be due to the surface structure of the cages, which either feature teeth (PEEK) or are coated with Plasmapore W and use a fixation ring (TTN). Some surgeons advocate rigid internal fixation and cervical immobilization postoperatively to prevent graft migration and nonunion and to enhance fusion [40,41]. The out- comes of rigid plate fixation have been equivocal to sur- gery without internal fixation in some studies [42-44]. In degenerative spondylosis the application of an internal fixation or a collar does not seem to influence the clinical or radiological outcome in a negative manner .
The measurement of magnetic susceptibility of polycrystalline samples described in the previous chapter has provided information concerning fine details of the electronic structure of encapsulated transition metal ions in the solid state. It was felt desirable also to measure magnetic properties in solution to ascertain whether intermolecular interactions were influencing the magnetism and whether alternative conformations of the cages might be adopted; i . e ., whether the ligand field might be modified by relaxing distortions imposed by lattice forces. The information obtained from such magnetic studies can be reinforced by measurements of optical spectra of these cages in solution w h ich provide complementary data on electron configuration and ligand field parameters.
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Cleaner shrimp in both tropical and temperate environments are known to prey on the ectoparasites of fishes (see Vaughan et al. 2016 for species), but it is likely that only the gregarious species, like L. vit- tata, would offer any meaningful benefit to aquacul- ture, as individuals of these species naturally occur together in groups, unlike the pair- forming species which are intolerant of additional conspecifics (Wong & Michiels 2011). L. vittata has a natural distribution extending throughout the Indo-Pacific (Palomares & Pauly 2018), which includes the major marine aqua- culture producing nations. It is currently cultured commercially in Australia for the ornamental trade and has the potential for large-scale development. L. vittata may also be effective against other fish ecto- parasites in aquaculture. In our recent laboratory trials (Vaughan et al. 2018), L. vittata was effective at re ducing and consuming the benthic stages of the cilio phoran ectoparasite Cryptocaryon irritans Brown, 1951, and the cocoons of the marine leech Zey lani cobdella arugamensis de Silva, 1963. Its effi- ciency against these and other ectoparasites remains to be tested under farm conditions. However, cleaner shrimp biocontrol models may offer a solution to sym- patric infestations, which are often a reality in aqua- culture. Cleaner shrimp and other shrimp species should therefore continue to be explored for a future role in aquaculture biocontrol, as originally proposed by Becker & Grutter (2004). Hints of the success of using shrimp in biocontrol already exist in the litera- ture; Rhyncho cinetes typus has been used to reduce net biofouling of scallop cages in Chile (Dumont et al. 2009), while the experimental field trial use of the native freshwater shrimp Macrobrachium vollen- hoveni (Herklots, 1857) in parts of the Senegal River reduced the prevalence of human schistosomiasis by predation on the snail intermediate host (Sokolow et al. 2015).
Leyendecker et al. (2001b) revealed significant interactions between genotype and housing sys- tem (battery cages, aviary and intensive free-range housing). Both layer lines (white egg Lohmann LSL and brown egg Lohmann Tradition) differed in their ability to be used in alternative housing systems. Comparing egg quality traits from different hous- ing systems did not reveal an explicit advantage of one housing system. Both layer lines exhibited higher Haugh units in the aviary. Eggshell thickness was higher in the intensive free-range system for both layer lines, and eggshell density only for the Lohmann Tradition. The Lohmann Tradition hens laid eggs with similar shell thickness and density. Yolk weight increased in battery cages for both layer lines. The highest grade of yolk colour was found out in the free-range system for LSL hens and in battery cages for Lohmann Tradition hens. The results of this study clearly demonstrated that layer line specific reactions were to be expected in
Both measurements of cage sizes from DLS and EM suggest that mutating clathrin boxes in epsin alters the way that the protein promotes assembly with slight differences in the observations made from the different techniques. EM measurements indicate that all clathrin box mutants are able to assemble clathrin with a distribution similar to WT epsin. This would suggest that the linkage hypothesis for assembly is incorrect i.e. that epsin links together triskelia via the clathrin box motifs to promote assembly. However, as discussed in Chapter 4 (see section 4.6.2) measuring cage size by EM biases the measurements to ‘cage like’ particles due to it being unfeasible to measure the size of amorphous aggregates or cage intermediates. The data is therefore a reflection of the size distribution of the ‘measurable’ fraction of the sample and does not take into account the actual number of each particle size. Given the large size of an EM grid and random variations in concentration and protein staining/fixing across the grid it would not be feasible to get an accurate value for the true number of different cage/particle sizes. Despite this it was observed that (in the areas imaged) that the clathrin box epsin mutants produced fewer cages for the given concentration than compared to WT epsin. The Δ257 and Δ480 mutants were intermediate in cage number where as with the DKO mutant it was more difficult to find cages to measure. Despite the qualitative nature of these statements this observation ties in with the observed DLS results and allows us to draw some inferences as to epsin promotion of clathrin assembly.
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selected based on their detail and relevance to the topic of cage design; both clinical and laboratory studies were included. Laboratory studies comparing cage designs and materials that were controlled and reliable were uti- lised to inform theoretical advantages of specific designs. The inclusion criteria of clinical studies were prospective and retrospective designss with patients requiring ACDF in the treatment of degenerative cervical disease, patient cohorts larger than 30 individual pati, implanting cages filled with allograft with or without anterior plating. Exclusion criteria included studies with non-degenerative disease cohorts, using additional proteins to promote fusion and ossification, or those that did not report on fusion rates, clinical outcomes and/or complication rates. In addition, the search was extended by manually search- ing the reference sections of relevant articles; this added 12 publications (See Additional file 2: Table S1).
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The concentration of gel forming subcomponents was found to affect the stability of the hydrogels (ESI Section 1.3). When 10 wt% of the components of cage 2 were mixed, gelation was slowed, requiring 5 minutes for the aqueous solution to be- come immobile upon inversion. When 5 wt% of building blocks were used, only viscous purple solutions were observed with no evidence of gel formation. When 15 wt% samples were prepared in which 4-aminophenyl-2-sulfonic acid (12 equiv.) was used in place of 4,4´-diaminobiphenyl-2,2´- disulphonic acid (6 equiv.), no gelation was observed and only a viscous purple solution was obtained. These building blocks would be expected to lead to the formation of threefold cross- links around mononuclear iron(II)-tris(pyridylimine) centers, but we infer that a higher degree of cross-linking is required to form a stable hydrogel. The relatively high concentration of gel-forming subcomponents required to form stable gels com- pared to related hydrogelators is attributed to the use of short polymer chains. This high concentration is desirable for providing a high loading of cages within the gels for use in guest binding.
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After purification, crystals of each of the dodecaamide cages were grown via layering with various solvent mixtures. The structures derived from single crystal X-ray diffraction (SCXRD) are shown in Fig. 2. For SCXRD analysis, the crystals were removed from solution and placed immediately in protective oil before mounting at 100 K on the diffractometer. When exposing the crystals to air at ambient temperatures, RCC1a, RCC1c and RCC1d rapidly lose their solvent content and become X-ray amorphous in the process. Only single crystals of RCC1b were stable in air under these conditions. Some of the solvent molecules (CHCl 3 ) in RCC1b and RCC1c are