Developing atom probe tomography for unique nanoscale insights into biomaterials

Bone provides structure and support for vertebrates, and it is the largest ion exchanger in the body to maintain homeostasis. Bone is a complex and heterogeneous composite material mainly composed of inorganic phases (mineral), organic phases (collagen, non-collagenous proteins), and water. Understanding the spatial structure and chemical composition of bone across different length scales is of great significance for elucidating its biomineralization mechanism, mechanical support, bone pathological treatment, and bone scaffold development. However, the simultaneous characterization of structure and chemical information of bone at the nanoscale presents many limitations, especially the exploration of 3D spatial structure and the mapping of low atomic mass elements. Among the many synthetic bone substitutes, bioactive glasses (BG) are an attractive candidate with applications in critical bone damage repair, as they stimulate biological responses that favor bone formation and angiogenesis. However, previously it has been difficult to develop an amorphous BG that combines a 3D porous structure with a strong biological activity because conventional BG easily crystallizes during processing. The crystallization of bioactive glass limits the dissolution rate of the material and therefore slows down the surface reactivity, leading to a decrease in scaffold bioactivity and bone regeneration capabilities. In recent years, a new amorphous 3D strontium-containing BG (pSrBG) scaffold was developed by adding strontium to increase the bioactivity of BG. Prior characterization of this material showed a scaffold with a near-perfect bone contact without fibrous tissue coverage, and that it supports nearly exclusively lamellar bone repair, similar to normal and functional bone. Besides, strontium was detected in new form bone and plasma after 21 days of transplantation in vivo, indicating that strontium successfully diffused as the material dissolved. However, due to the detection limits of conventional characterization techniques, it was not possible to specify the precise locality of released ions, and hence, it is not clear whether the locally achievable strontium concentration at the interface exceeds the medically acceptable range. Furthermore, the mechanism of Sr uptake into the bone and bone repair remains inconclusive. Atom probe tomography (APT) is a 3D microscopy characterization technique with a unique combination of high spatial and chemical resolution, which can be used to characterize this new type of biomaterial, animal bone, and the interface between material and bone. The work in this thesis presents the enabling preliminary development of APT techniques prior to this interface analysis. The synthetic bone material and porcine trabecular bone were investigated and characterised using APT. The challenges and corresponding countermeasures of biomaterials for APT sample preparation and experiments are outlined. The influence of various experimental parameters such as temperature, detection rate, laser pulse energy, and pulse frequency on the data quality by the LEAP-5000XR is explored and discussed. To this end, optimal operating conditions of APT were investigated and selected for two strontium-containing bioactive glass particles, the pSrBG scaffold, and porcine trabecular bone. The structure, including the spatial distribution of collagen and mineral phases, and their chemical composition were analyzed at the atomic level within the porcine trabecular bone. The challenges and limitations of APT in reconstruction analysis and quantitative chemical composition measurements of biomaterials are addressed. This study demonstrates that APT has the unique capacity to identify and characterize significant compositional variations in nanoscale volumes within individual bone phases that may provide new insights into the further development and demonstration of the potential of APT in exploring the spatial structure and chemical composition of bones. It also provides the basis for advancing knowledge in APT research at the interface of pSrBG and bone

Product-based Neural Networks for User Response Prediction

Predicting user responses, such as clicks and conversions, is of great importance and has found its usage in many Web applications including recommender systems, web search and online advertising. The data in those applications is mostly categorical and contains multiple fields; a typical representation is to transform it into a high-dimensional sparse binary feature representation via one-hot encoding. Facing with the extreme sparsity, traditional models may limit their capacity of mining shallow patterns from the data, i.e. low-order feature combinations. Deep models like deep neural networks, on the other hand, cannot be directly applied for the high-dimensional input because of the huge feature space. In this paper, we propose a Product-based Neural Networks (PNN) with an embedding layer to learn a distributed representation of the categorical data, a product layer to capture interactive patterns between inter-field categories, and further fully connected layers to explore high-order feature interactions. Our experimental results on two large-scale real-world ad click datasets demonstrate that PNNs consistently outperform the state-of-the-art models on various metrics.Comment: 6 pages, 5 figures, ICDM201

Nonlinear dynamics study of a high-temperature rotor-bearing-seal system in gas turbine

Most of the major faults in gas turbines often originate from the rotor shaft. Some of these faults could result to misalignment, imbalance, crack, rub-impact and eccentricity. This study analyzes nonlinear factors such as lube-film surge and thermal-stress. Seal and bearing quality significantly affect the performance of a rotor system. The nonlinear dynamic characteristics of a high-temperature rotor–bearing–seal coupled system are investigated. Dynamic trajectories, Poincaré maps, frequency spectra diagrams are used to analyze the features of the rotor-bearing-seal coupled system in terms of various parameters. Several nonlinear phenomena in the high-temperature rotor–bearing–seal coupled system, such as periodic, double-periodic, multi-periodic, and quasi-periodic motion are investigated. Through these curves and the program, the dynamic characteristics of gas turbine rotors could be easily and accurately calculated. To validate this method, the critical speed of a real rotor of an actual gas turbine was calculated by means of the program and curves. The results are consistent with the measured data and may contribute to further understanding the nonlinear dynamics of the high-temperature rotor-bearing-seal coupled system

Mussel-Inspired Carboxymethyl Chitosan Hydrogel Coating of Titanium Alloy with Antibacterial and Bioactive Properties

Infection-related titanium implant failure rates remain exceedingly high in the clinic. Functional surface coating represents a very promising strategy to improve the antibacterial and bioactive properties of titanium alloy implants. Here, we describe a novel bioactive surface coating that consists of a mussel-inspired carboxymethyl chitosan hydrogel loaded with silver nanoparticles (AgNPs) to enhance the bioactive properties of the titanium alloy. The preparation of hydrogel is based on gallic acid grafted carboxymethyl chitosan (CMCS-GA) catalyzed by DMTMM (4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride). To build a firm bonding between the hydrogel and titanium alloy plate, a polydopamine layer was introduced onto the surface of the titanium alloy. With HRP/H2O2 catalysis, CMCS-GA can simply form a firm gel layer on the titanium alloy plate through the catechol groups. The surface properties of titanium alloy were characterized by scanning electron microscope (SEM), X-ray photoelectron spectroscopy (XPS), and water contact angle. Silver nanoparticles were loaded into the gel layer by in situ reduction to enhance the antibacterial properties. In vitro antibacterial and cell viability experiments showed that the AgNPs-loaded Ti-gel possesses excellent antibacterial properties and did not affect the proliferation of rabbit mesenchymal stem cells (MSCs)

PDGF Upregulates Mcl-1 Through Activation of β-Catenin and HIF-1α-Dependent Signaling in Human Prostate Cancer Cells

BACKGROUND: Aberrant platelet derived growth factor (PDGF) signaling has been associated with prostate cancer (PCa) progression. However, its role in the regulation of PCa cell growth and survival has not been well characterized. METHODOLOGY/PRINCIPAL FINDINGS: Using experimental models that closely mimic clinical pathophysiology of PCa progression, we demonstrated that PDGF is a survival factor in PCa cells through upregulation of myeloid cell leukemia-1 (Mcl-1). PDGF treatment induced rapid nuclear translocation of β-catenin, presumably mediated by c-Abl and p68 signaling. Intriguingly, PDGF promoted formation of a nuclear transcriptional complex consisting of β-catenin and hypoxia-inducible factor (HIF)-1α, and its binding to Mcl-1 promoter. Deletion of a putative hypoxia response element (HRE) within the Mcl-1 promoter attenuated PDGF effects on Mcl-1 expression. Blockade of PDGF receptor (PDGFR) signaling with a pharmacological inhibitor AG-17 abrogated PDGF induction of Mcl-1, and induced apoptosis in metastatic PCa cells. CONCLUSIONS/SIGNIFICANCE: Our study elucidated a crucial survival mechanism in PCa cells, indicating that interruption of the PDGF-Mcl-1 survival signal may provide a novel strategy for treating PCa metastasis

Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta)

<p>Abstract</p> <p>Background</p> <p>Rhesus macaques are the most widely utilized nonhuman primate model in biomedical research. Previous efforts have validated fewer than 900 single nucleotide polymorphisms (SNPs) in this species, which limits opportunities for genetic studies related to health and disease. Extensive information about SNPs and other genetic variation in rhesus macaques would facilitate valuable genetic analyses, as well as provide markers for genome-wide linkage analysis and the genetic management of captive breeding colonies.</p> <p>Results</p> <p>We used the available rhesus macaque draft genome sequence, new sequence data from unrelated individuals and existing published sequence data to create a genome-wide SNP resource for Indian-origin rhesus monkeys. The original reference animal and two additional Indian-origin individuals were resequenced to low coverage using SOLiD™ sequencing. We then used three strategies to validate SNPs: comparison of potential SNPs found in the same individual using two different sequencing chemistries, and comparison of potential SNPs in different individuals identified with either the same or different sequencing chemistries. Our approach validated approximately 3 million SNPs distributed across the genome. Preliminary analysis of SNP annotations suggests that a substantial number of these macaque SNPs may have functional effects. More than 700 non-synonymous SNPs were scored by Polyphen-2 as either possibly or probably damaging to protein function and these variants now constitute potential models for studying functional genetic variation relevant to human physiology and disease.</p> <p>Conclusions</p> <p>Resequencing of a small number of animals identified greater than 3 million SNPs. This provides a significant new information resource for rhesus macaques, an important research animal. The data also suggests that overall genetic variation is high in this species. We identified many potentially damaging non-synonymous coding SNPs, providing new opportunities to identify rhesus models for human disease.</p

Dbh+ catecholaminergic cardiomyocytes contribute to the structure and function of the cardiac conduction system in murine heart

The heterogeneity of functional cardiomyocytes arises during heart development, which is essential to the complex and highly coordinated cardiac physiological function. Yet the biological and physiological identities and the origin of the specialized cardiomyocyte populations have not been fully comprehended. Here we report a previously unrecognised population of cardiomyocytes expressing Dbhgene encoding dopamine beta-hydroxylase in murine heart. We determined how these myocytes are distributed across the heart by utilising advanced single-cell and spatial transcriptomic analyses, genetic fate mapping and molecular imaging with computational reconstruction. We demonstrated that they form the key functional components of the cardiac conduction system by using optogenetic electrophysiology and conditional cardiomyocyte Dbh gene deletion models. We revealed their close relationship with sympathetic innervation during cardiac conduction system formation. Our study thus provides new insights into the development and heterogeneity of the mammalian cardiac conduction system by revealing a new cardiomyocyte population with potential catecholaminergic endocrine function

Bos taurus genome assembly

We present here the assembly of the bovine genome. The assembly method combines the BAC plus WGS local assembly used for the rat and sea urchin with the whole genome shotgun (WGS) only assembly used for many other animal genomes including the rhesus macaque. The assembly process consisted of multiple phases: First, BACs were assembled with BAC generated sequence, then subsequently in combination with the individual overlapping WGS reads. Different assembly parameters were tested to separately optimize the performance for each BAC assembly of the BAC and WGS reads. In parallel, a second assembly was produced using only the WGS sequences and a global whole genome assembly method. The two assemblies were combined to create a more complete genome representation that retained the high quality BAC-based local assembly information, but with gaps between BACs filled in with the WGS-only assembly. Finally, the entire assembly was placed on chromosomes using the available map information. Over 90% of the assembly is now placed on chromosomes. The estimated genome size is 2.87 Gb which represents a high degree of completeness, with 95% of the available EST sequences found in assembled contigs. The quality of the assembly was evaluated by comparison to 73 finished BACs, where the draft assembly covers between 92.5 and 100% (average 98.5%) of the finished BACs. The assembly contigs and scaffolds align linearly to the finished BACs, suggesting that misassemblies are rare. Genotyping and genetic mapping of 17,482 SNPs revealed that more than 99.2% were correctly positioned within the Btau_4.0 assembly, confirming the accuracy of the assembly. The biological analysis of this bovine genome assembly is being published, and the sequence data is available to support future bovine research

Somatic mutations affect key pathways in lung adenocarcinoma

Determining the genetic basis of cancer requires comprehensive analyses of large collections of histopathologically well- classified primary tumours. Here we report the results of a collaborative study to discover somatic mutations in 188 human lung adenocarcinomas. DNA sequencing of 623 genes with known or potential relationships to cancer revealed more than 1,000 somatic mutations across the samples. Our analysis identified 26 genes that are mutated at significantly high frequencies and thus are probably involved in carcinogenesis. The frequently mutated genes include tyrosine kinases, among them the EGFR homologue ERBB4; multiple ephrin receptor genes, notably EPHA3; vascular endothelial growth factor receptor KDR; and NTRK genes. These data provide evidence of somatic mutations in primary lung adenocarcinoma for several tumour suppressor genes involved in other cancers - including NF1, APC, RB1 and ATM - and for sequence changes in PTPRD as well as the frequently deleted gene LRP1B. The observed mutational profiles correlate with clinical features, smoking status and DNA repair defects. These results are reinforced by data integration including single nucleotide polymorphism array and gene expression array. Our findings shed further light on several important signalling pathways involved in lung adenocarcinoma, and suggest new molecular targets for treatment.National Human Genome Research InstituteWe thank A. Lash, M.F. Zakowski, M.G. Kris and V. Rusch for intellectual contributions, and many members of the Baylor Human Genome Sequencing Center, the Broad Institute of Harvard and MIT, and the Genome Center at Washington University for support. This work was funded by grants from the National Human Genome Research Institute to E.S.L., R.A.G. and R.K.W.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62885/1/nature07423.pd

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead