The microwell-mesh: A novel device and protocol for the high throughput manufacturing of cartilage microtissues

Microwell platforms are frequently described for the efficient and uniform manufacture of 3-dimensional (3D) multicellular microtissues. Multiple partial or complete medium exchanges can displace microtissues from discrete microwells, and this can result in either the loss of microtissues from culture, or microtissue amalgamation when displaced microtissues fall into common microwells. Herein we describe the first microwell platform that incorporates a mesh to retain microtissues within discrete microwells; the microwell-mesh. We show that bonding a nylon mesh with an appropriate pore size over the microwell openings allows single cells to pass through the mesh into the microwells during the seeding process, but subsequently retains assembled microtissues within discrete microwells. To demonstrate the utility of this platform, we used the microwell-mesh to manufacture hundreds of cartilage microtissues, each formed from 5 × 10(3) bone marrow-derived mesenchymal stem/stromal cells (MSC). The microwell-mesh enabled reliable microtissue retention over 21-day cultures that included multiple full medium exchanges. Cartilage-like matrix formation was more rapid and homogeneous in microtissues than in conventional large diameter control cartilage pellets formed from 2 × 10(5) MSC each. The microwell-mesh platform offers an elegant mechanism to retain microtissues in microwells, and we believe that this improvement will make this platform useful in 3D culture protocols that require multiple medium exchanges, such as those that mimic specific developmental processes or complex sequential drug exposures.

Pyroxene thermometry of rhyolite lavas of the Bruneau–Jarbidge eruptive center, Central Snake River Plain

The Bruneau–Jarbidge eruptive center of the central Snake River Plain in southern Idaho, USA produced multiple rhyolite lava flows with volumes of <10 km³ to 200 km³ each from ~11.2 to 8.1 Ma, most of which follow its climactic phase of large-volume explosive volcanism, represented by the Cougar Point Tuff, from 12.7 to 10.5 Ma. These lavas represent the waning stages of silicic volcanism at a major eruptive center of the Yellowstone hotspot track. Here we provide pyroxene compositions and thermometry results from several lavas that demonstrate that the demise of the silicic volcanic system was characterized by sustained, high pre-eruptive magma temperatures (mostly ≥950 °C) prior to the onset of exclusively basaltic volcanism at the eruptive center. Pyroxenes display a variety of textures in single samples, including solitary euhedral crystals as well as glomerocrysts, crystal clots and annealed microgranular inclusions of pyroxene ±magnetite± plagioclase. Pigeonite and augite crystals are unzoned, and there are no detectable differences in major and minor element compositions according to textural variety — mineral compositions in the microgranular inclusions and crystal clots are identical to those of phenocrysts in the host lavas. In contrast to members of the preceding Cougar Point Tuff that host polymodal glass and mineral populations, pyroxene compositions in each of the lavas are characterized by single rather than multiple discrete compositional modes. Collectively, the lavas reproduce and extend the range of Fe–Mg pyroxene compositional modes observed in the Cougar Point Tuff to more Mg-rich varieties. The compositionally homogeneous populations of pyroxene in each of the lavas, as well as the lack of core-to-rim zonation in individual crystals suggest that individual eruptions each were fed by compositionally homogeneous magma reservoirs, and similarities with the Cougar Point Tuff suggest consanguinity of such reservoirs to those that supplied the polymodal Cougar Point Tuff. Pyroxene thermometry results obtained using QUILF equilibria yield pre-eruptive magma temperatures of 905 to 980 °C, and individual modes consistently record higher Ca content and higher temperatures than pyroxenes with equivalent Fe–Mg ratios in the preceding Cougar Point Tuff. As is the case with the Cougar Point Tuff, evidence for up-temperature zonation within single crystals that would be consistent with recycling of sub- or near-solidus material from antecedent magma reservoirs by rapid reheating is extremely rare. Also, the absence of intra-crystal zonation, particularly at crystal rims, is not easily reconciled with cannibalization of caldera fill that subsided into pre-eruptive reservoirs. The textural, compositional and thermometric results rather are consistent with minor re-equilibration to higher temperatures of the unerupted crystalline residue from the explosive phase of volcanism, or perhaps with newly generated magmas from source materials very similar to those for the Cougar Point Tuff. Collectively, the data suggest that most of the pyroxene compositional diversity that is represented by the tuffs and lavas was produced early in the history of the eruptive center and that compositions across this range were preserved or duplicated through much of its lifetime. Mineral compositions and thermometry of the multiple lavas suggest that unerupted magmas residual to the explosive phase of volcanism may have been stored at sustained, high temperatures subsequent to the explosive phase of volcanism. If so, such persistent high temperatures and large eruptive magma volumes likewise require an abundant and persistent supply of basalt magmas to the lower and/or mid-crust, consistent with the tectonic setting of a continental hotspot.

Reconfiguring Guangzhou identity – a study of place and locality on Sina Weibo

This thesis investigates the role of Chinese microblogging platform Sina Weibo in how the people of Guangzhou understand and negotiate their sense of locality. The geo-identity approach used in this thesis opens up a new approach to explore the complex power relationships that structure our society in and through digital media. It finds that although the Chinese government is trying to orchestrate a homogeneous sense of national belonging, Weibo is constantly reinforcing people's awareness of and identification with the local. The findings show that as new communication technologies and practices reconfigure people's daily experience and social lives, they redefine our sense of self and belonging.

Mapping bound plasmon propagation on a nanoscale stripe waveguide using quantum dots: Influence of spacer layer thickness

In this paper we image the highly confined long range plasmons of a nanoscale metal stripe waveguide using quantum emitters. Plasmons were excited using a highly focused 633 nm laser beam and a specially designed grating structure to provide stronger incoupling to the desired mode. A homogeneous thin layer of quantum dots was used to image the near field intensity of the propagating plasmons on the waveguide. We observed that the photoluminescence is quenched when the QD to metal surface distance is less than 10 nm. The optimised spacer layer thickness for the stripe waveguides was found to be around 20 nm. Authors believe that the findings of this paper prove beneficial for the development of plasmonic devices utilising stripe waveguides.

Mixture models of nucleotide sequence evolution that account for heterogeneity in the substitution process across sites and across lineages

Molecular phylogenetic studies of homologous sequences of nucleotides often assume that the underlying evolutionary process was globally stationary, reversible, and homogeneous (SRH), and that a model of evolution with one or more site-specific and time-reversible rate matrices (e.g., the GTR rate matrix) is enough to accurately model the evolution of data over the whole tree. However, an increasing body of data suggests that evolution under these conditions is an exception, rather than the norm. To address this issue, several non-SRH models of molecular evolution have been proposed, but they either ignore heterogeneity in the substitution process across sites (HAS) or assume it can be modeled accurately using the distribution. As an alternative to these models of evolution, we introduce a family of mixture models that approximate HAS without the assumption of an underlying predefined statistical distribution. This family of mixture models is combined with non-SRH models of evolution that account for heterogeneity in the substitution process across lineages (HAL). We also present two algorithms for searching model space and identifying an optimal model of evolution that is less likely to over- or underparameterize the data. The performance of the two new algorithms was evaluated using alignments of nucleotides with 10 000 sites simulated under complex non-SRH conditions on a 25-tipped tree. The algorithms were found to be very successful, identifying the correct HAL model with a 75% success rate (the average success rate for assigning rate matrices to the tree's 48 edges was 99.25%) and, for the correct HAL model, identifying the correct HAS model with a 98% success rate. Finally, parameter estimates obtained under the correct HAL-HAS model were found to be accurate and precise. The merits of our new algorithms were illustrated with an analysis of 42 337 second codon sites extracted from a concatenation of 106 alignments of orthologous genes encoded by the nuclear genomes of Saccharomyces cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, S. castellii, S. kluyveri, S. bayanus, and Candida albicans. Our results show that second codon sites in the ancestral genome of these species contained 49.1% invariable sites, 39.6% variable sites belonging to one rate category (V1), and 11.3% variable sites belonging to a second rate category (V2). The ancestral nucleotide content was found to differ markedly across these three sets of sites, and the evolutionary processes operating at the variable sites were found to be non-SRH and best modeled by a combination of eight edge-specific rate matrices (four for V1 and four for V2). The number of substitutions per site at the variable sites also differed markedly, with sites belonging to V1 evolving slower than those belonging to V2 along the lineages separating the seven species of Saccharomyces. Finally, sites belonging to V1 appeared to have ceased evolving along the lineages separating S. cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, and S. bayanus, implying that they might have become so selectively constrained that they could be considered invariable sites in these species.

Founder p.Arg 446* mutation in the PDHX gene explains over half of cases with congenital lactic acidosis in Roma children

Investigation of 31 of Roma patients with congenital lactic acidosis (CLA) from Bulgaria identified homozygosity for the R446* mutation in the PDHX gene as the most common cause of the disorder in this ethnic group. It accounted for around 60% of patients in the study and over 25% of all CLA cases referred to the National Genetic Laboratory in Bulgaria. The detection of a homozygous patient from Hungary and carriers among population controls from Romania and Slovakia suggests a wide spread of the mutation in the European Roma population. The clinical phenotype of the twenty R446* homozygotes was relatively homogeneous, with lactic acidosis crisis in the first days or months of life as the most common initial presentation (15/20 patients) and delayed psychomotor development and/or seizures in infancy as the leading manifestations in a smaller group (5/20 patients). The subsequent clinical picture was dominated by impaired physical growth and a very consistent pattern of static cerebral palsy-like encephalopathy with spasticity and severe to profound mental retardation seen in over 80% of cases. Most patients had a positive family history. We propose testing for the R446* mutation in PDHX as a rapid first screening in Roma infants with metabolic acidosis. It will facilitate and accelerate diagnosis in a large proportion of cases, allow early rehabilitation to alleviate the chronic clinical course, and prevent further affected births in high-risk families.

Raman spectroscopy techniques for detection of energetic materials at high and low concentration

This thesis presents the development of a rapid, sensitive and reproducible spectroscopic method for the detection of TNT in forensic and environmental applications. Simple nano sensors prepared by cost effective methods were utilized as sensitive platforms for the detection of TNT by surface enhanced Raman spectroscopy. The optimization of the substrate and the careful selection of a suitable recognition molecule contributed to the significant improvements of sensitive and selective targeting over current detection methods. The work presented in this thesis paves the way for effective detection and monitoring of explosives residues in law enforcement and environmental health applications.

Fine mapping and replication of genetic risk Loci in primary sclerosing cholangitis

Background and aims. Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease characterized by progressive inflammation and fibrosis of the bile ducts eventually leading to biliary cirrhosis. Recent genetic studies in PSC have identified associations at 2q13, 2q35, 3p21, 4q27, 13q31 and suggestive association at 10p15. The aim of this study was to further characterize and refine the genetic architecture of PSC. Methods. We analyzed previously reported associated SNPs at four of these non-HLA loci and 59 SNPs tagging the IL-2/IL-21 (4q27) and IL2RA (10p15) loci in 992 UK PSC cases and 5162 healthy UK controls. Results. The most associated SNPs identified were rs3197999 (3p21 (MST1), p = 1.9 × 10 -6, OR A vs G = 1.28, 95% CI (1.16-1.42)); rs4147359 (10p15 (IL2RA), p = 2.6 × 10 -4, OR A vs G = 1.20, 95% CI (1.09-1.33)) and rs12511287 (4q27 (IL-2/IL-21), p = 3.0 × 10 -4, OR A vs T = 1.21, 95% CI (1.09-1.35)). In addition, we performed a meta-analysis for selected SNPs using published summary statistics from recent studies. We observed genome-wide significance for rs3197999 (3p21 (MST1), P combined = 3.8 × 10 -12) and rs4147359 (10p15 (IL2RA), P combined = 1.5 × 10 -8). Conclusion. We have for the first time confirmed the association of PSC with genetic variants at 10p15 (IL2RA) locus at genome-wide significance and replicated the associations at MST1 and IL-2/IL-21 loci in a large homogeneous UK population. These results strongly implicate the role of IL-2/IL2RA pathway in PSC and provide further confirmation of MST1 association. © Informa Healthcare.

Partial epilepsy syndrome in a Gypsy family linked to 5q31.3-q32

PURPOSE The restricted genetic diversity and homogeneous molecular basis of Mendelian disorders in isolated founder populations have rarely been explored in epilepsy research. Our long-term goal is to explore the genetic basis of epilepsies in one such population, the Gypsies. The aim of this report is the clinical and genetic characterization of a Gypsy family with a partial epilepsy syndrome. METHODS Clinical information was collected using semistructured interviews with affected subjects and informants. At least one interictal electroencephalography (EEG) recording was performed for each patient and previous data obtained from records. Neuroimaging included structural magnetic resonance imaging (MRI). Linkage and haplotype analysis was performed using the Illumina IVb Linkage Panel, supplemented with highly informative microsatellites in linked regions and Affymetrix SNP 5.0 array data. RESULTS We observed an early-onset partial epilepsy syndrome with seizure semiology strongly suggestive of temporal lobe epilepsy (TLE), with mild intellectual deficit co-occurring in a large proportion of the patients. Psychiatric morbidity was common in the extended pedigree but did not cosegregate with epilepsy. Linkage analysis definitively excluded previously reported loci, and identified a novel locus on 5q31.3-q32 with an logarithm of the odds (LOD) score of 3 corresponding to the expected maximum in this family. DISCUSSION The syndrome can be classified as familial temporal lobe epilepsy (FTLE) or possibly a new syndrome with mild intellectual deficit. The linked 5q region does not contain any ion channel-encoding genes and is thus likely to contribute new knowledge about epilepsy pathogenesis. Identification of the mutation in this family and in additional patients will define the full phenotypic spectrum.

The influence of the gas environment on morphology and chemical composition of surfaces micro-machined with a femtosecond laser

We investigated the influence of different gas environments on the fabrication of surfaces, homogeneously covered with equally sized and spaced micro-structures. Two types of structures have been successfully micro-machined with a femtosecond laser on titanium surfaces in various atmospheres. The surface chemistry of samples machined in oxygen and helium shows TiO2, while machining in nitrogen leads to an additional share of TiN. The actual surface structure was found to vary significantly as a function of the gas environment. We found that the ablated particles and their surface triggered two consecutive events: The optical properties of the gas environment became non-isotropic which then led to the pulse intensity being redistributed throughout the cross section of the laser beam. Additionally, the effective intensity was further reduced for TiN surfaces due to TiN's high reflectivity. Thus, the settings for the applied raster-scanning machining method had to be adjusted for each gas environment to produce comparable structures. In contrast to previous studies, where only noble gases were found suitable to produce homogeneous patches, we obtained them in an oxygen environment.

Feasibility of autologous bone marrow mesenchymal stem cell-derived extracellular matrix scaffold for cartilage tissue engineering

Extracellular matrix (ECM) materials are widely used in cartilage tissue engineering. However, the current ECM materials are unsatisfactory for clinical practice as most of them are derived from allogenous or xenogenous tissue. This study was designed to develop a novel autologous ECM scaffold for cartilage tissue engineering. The autologous bone marrow mesenchymal stem cell-derived ECM (aBMSC-dECM) membrane was collected and fabricated into a three-dimensional porous scaffold via cross-linking and freeze-drying techniques. Articular chondrocytes were seeded into the aBMSC-dECM scaffold and atelocollagen scaffold, respectively. An in vitro culture and an in vivo implantation in nude mice model were performed to evaluate the influence on engineered cartilage. The current results showed that the aBMSC-dECM scaffold had a good microstructure and biocompatibility. After 4 weeks in vitro culture, the engineered cartilage in the aBMSC-dECM scaffold group formed thicker cartilage tissue with more homogeneous structure and higher expressions of cartilaginous gene and protein compared with the atelocollagen scaffold group. Furthermore, the engineered cartilage based on the aBMSC-dECM scaffold showed better cartilage formation in terms of volume and homogeneity, cartilage matrix content, and compressive modulus after 3 weeks in vivo implantation. These results indicated that the aBMSC-dECM scaffold could be a successful novel candidate scaffold for cartilage tissue engineering.

The impact of wall shear stress and pressure drop on the stability of the atherosclerotic plaque

Rupture of vulnerable atheromatous plaque in the carotid and coronary arteries often leads to stroke and heart attack respectively. The mechanism of blood flow and plaque rupture in stenotic arteries is still not fully understood. A three dimensional rigid wall model was solved under steady state conditions and unsteady conditions by assuming a time-varying inlet velocity profile to investigate the relative importance of axial forces and pressure drops in arteries with asymmetric stenosis. Flow-structure interactions were investigated for the same geometry and the results were compared with those retrieved with the corresponding 2D cross-section structural models. The Navier-Stokes equations were used as the governing equations for the fluid. The tube wall was assumed hyperelastic, homogeneous, isotropic and incompressible. The analysis showed that the three dimensional behavior of velocity, pressure and wall shear stress is in general very different from that predicted by cross-section models. Pressure drop across the stenosis was found to be much higher than shear stress. Therefore, pressure may be the more important mechanical trigger for plaque rupture other than shear stress, although shear stress is closely related to plaque formation and progression.

Rank regression for analyzing ordinal qualitative data for treatment comparison

Ordinal qualitative data are often collected for phenotypical measurements in plant pathology and other biological sciences. Statistical methods, such as t tests or analysis of variance, are usually used to analyze ordinal data when comparing two groups or multiple groups. However, the underlying assumptions such as normality and homogeneous variances are often violated for qualitative data. To this end, we investigated an alternative methodology, rank regression, for analyzing the ordinal data. The rank-based methods are essentially based on pairwise comparisons and, therefore, can deal with qualitative data naturally. They require neither normality assumption nor data transformation. Apart from robustness against outliers and high efficiency, the rank regression can also incorporate covariate effects in the same way as the ordinary regression. By reanalyzing a data set from a wheat Fusarium crown rot study, we illustrated the use of the rank regression methodology and demonstrated that the rank regression models appear to be more appropriate and sensible for analyzing nonnormal data and data with outliers.

Thermal conductivity of a new carbon nanotube analog: The diamond nanothread

Based on the non-equilibrium molecular dynamics simulations, we have studied the thermal conductivities of a novel ultra-thin one-dimensional carbon nanomaterial - diamond nanothread (DNT). Unlike single-wall carbon nanotube (CNT), the existence of the Stone-Wales transformations in DNT endows it with richer thermal transport characteristics. There is a transition from wave-dominated to particle-dominated transport region, which depends on the length of poly-benzene rings. However, independent of the transport region, strong length dependence in thermal conductivity is observed in DNTs with different lengths of poly-benzene ring. The distinctive SW characteristic in DNT provides more degrees of freedom to tune the thermal conductivity not found in the homogeneous structure of CNT. Therefore, DNT is an ideal platform to investigate various thermal transport mechanisms at the nanoscale. Its high tunability raises the potential to design DNTs for different applications, such as thermal connection and temperature management.

Copper-doped mesoporous silica nanospheres, a promising immunomodulatory agent for inducing osteogenesis

The application of mesoporous silica nanospheres (MSNs) loaded with drugs/growth factors to induce osteogenic differentiation of stem cells has been trialed by a number of researchers recently. However, limitations such as high cost, complex fabrication and unintended side effects from supraphysiological concentrations of the drugs/growth factors represent major obstacles to any potential clinical application in the near term. In this study we reported an in situ one-pot synthesis strategy of MSNs doped with hypoxia-inducing copper ions and systematically evaluated the nanospheres by in vitro biological assessments. The Cu-containing mesoporous silica nanospheres (Cu-MSNs) had uniform spherical morphology (∼100 nm), ordered mesoporous channels (∼2 nm) and homogeneous Cu distribution. Cu-MSNs demonstrated sustained release of both silicon (Si) and Cu ions and controlled degradability. The Cu-MSNs were phagocytized by immune cells and appeared to modulate a favorable immune environment by initiating proper pro-inflammatory cytokines, inducing osteogenic/angiogenic factors and suppressing osteoclastogenic factors by the immune cells. The immune microenvironment induced by the Cu-MSNs led to robust osteogenic differentiation of bone mesenchymal stem cells (BMSCs) via the activation of Oncostation M (OSM) pathway. These results suggest that the novel Cu-MSNs could be used as an immunomodulatory agent with osteostimulatory capacity for bone regeneration/therapy application. Statement of significance In order to stimulate both osteogenesis and angiogenesis of stem cells for further bone regeneration, a new kind of hypoxia-inducing copper doped mesoporous silica nanospheres (Cu-MSNs) were prepared via one-pot synthesis. Biological assessments under immune environment which better reflect the in vivo response revealed that the nanospheres possessed osteostimulatory capacity and had potential as immunomodulatory agent for bone regeneration/therapy application. The strategy of introducing controllable amount of therapeutic ions instead of loading expensive drugs/growth factors in mesoporous silica nanosphere provides new options for bioactive nanomaterial functionalization.