Investigation on selection crystal behavior of a Ni3Al-based single crystal superalloy IC6SX

AbstractThe grain selection occurring during the solidification of a Ni3Al-base single crystal superalloy IC6SX prepared by spiral grain selection method was studied systematically. Results showed that the equiaxed grains were transformed into columnar grains within starter block and most of columnar grains then will be eliminated. The crystal were formed after the remained columnar grains were eliminated through preferred growth and coupling of spiral structure in Spiral grain selection. The results can explain the competitive growth mechanism of the spiral grain selection and can be used to optimize process design to lay an important foundation for improving preparation processes of single crystal superalloy

Reactive uptake coefficients for multiphase reactions determined by a dynamic chamber system

Dynamic flow-through chambers are frequently used to measure gas exchange rates between the atmosphere and biosphere on the Earth's surface such as vegetation and soils. Here, we explore the performance of a dynamic chamber system in determining the uptake coefficient γ of exemplary gases (O3 and SO2) on bulk solid-phase samples. After characterization of the dynamic chamber system, the derived γ is compared with that determined from a coated-wall flow tube system. Our results show that the dynamic chamber system and the flow tube method show a good agreement for γin the range of 10−8 to 10−3. The dynamic chamber technique can be used for liquid samples and real atmospheric aerosol samples without complicated coating procedures, which complements the existing techniques in atmospheric kinetic studies.</p

Even Visually Intact Cell Walls in Waterlogged Archaeological Wood Are Chemically Deteriorated and Mechanically Fragile : A Case of a 170 Year-Old Shipwreck

Structural and chemical deterioration and its impact on cell wall mechanics were investigated for visually intact cell walls (VICWs) in waterlogged archaeological wood (WAW). Cell wall mechanical properties were examined by nanoindentation without prior embedding. WAW showed more than 25% decrease of both hardness and elastic modulus. Changes of cell wall composition, cellulose crystallite structure and porosity were investigated by ATR-FTIR imaging, Raman imaging, wet chemistry, C-13-solid state NMR, pyrolysis-GC/MS, wide angle X-ray scattering, and N-2 nitrogen adsorption. VICWs in WAW possessed a cleavage of carboxyl in side chains of xylan, a serious loss of polysaccharides, and a partial breakage of beta -O-4 interlinks in lignin. This was accompanied by a higher amount of mesopores in cell walls. Even VICWs in WAW were severely deteriorated at the nanoscale with impact on mechanics, which has strong implications for the conservation of archaeological shipwrecks.Peer reviewe

Even Visually Intact Cell Walls in Waterlogged Archaeological Wood Are Chemically Deteriorated and Mechanically Fragile: A Case of a 170 Year-Old Shipwreck

Structural and chemical deterioration and its impact on cell wall mechanics were investigated for visually intact cell walls (VICWs) in waterlogged archaeological wood (WAW). Cell wall mechanical properties were examined by nanoindentation without prior embedding. WAW showed more than 25% decrease of both hardness and elastic modulus. Changes of cell wall composition, cellulose crystallite structure and porosity were investigated by ATR-FTIR imaging, Raman imaging, wet chemistry, 13C-solid state NMR, pyrolysis-GC/MS, wide angle X-ray scattering, and N2 nitrogen adsorption. VICWs in WAW possessed a cleavage of carboxyl in side chains of xylan, a serious loss of polysaccharides, and a partial breakage of β-O-4 interlinks in lignin. This was accompanied by a higher amount of mesopores in cell walls. Even VICWs in WAW were severely deteriorated at the nanoscale with impact on mechanics, which has strong implications for the conservation of archaeological shipwrecks

Phenotypic and transcriptional analysis of the osmotic regulator OmpR in Yersinia pestis

<p>Abstract</p> <p>Background</p> <p>The osmotic regulator OmpR in <it>Escherichia coli </it>regulates differentially the expression of major porin proteins OmpF and OmpC. In <it>Yersinia enterocolitica </it>and <it>Y. pseudotuberculosis</it>, OmpR is required for both virulence and survival within macrophages. However, the phenotypic and regulatory roles of OmpR in <it>Y. pestis </it>are not yet fully understood.</p> <p>Results</p> <p><it>Y. pestis </it>OmpR is involved in building resistance against phagocytosis and controls the adaptation to various stressful conditions met in macrophages. The <it>ompR </it>mutation likely did not affect the virulence of <it>Y. pestis </it>strain 201 that was a human-avirulent enzootic strain. The microarray-based comparative transcriptome analysis disclosed a set of 224 genes whose expressions were affected by the <it>ompR </it>mutation, indicating the global regulatory role of OmpR in <it>Y. pestis</it>. Real-time RT-PCR or <it>lacZ </it>fusion reporter assay further validated 16 OmpR-dependent genes, for which OmpR consensus-like sequences were found within their upstream DNA regions. <it>ompC</it>, <it>F</it>, <it>X</it>, and <it>R </it>were up-regulated dramatically with the increase of medium osmolarity, which was mediated by OmpR occupying the target promoter regions in a tandem manner.</p> <p>Conclusion</p> <p>OmpR contributes to the resistance against phagocytosis or survival within macrophages, which is conserved in the pathogenic yersiniae. <it>Y. pestis </it>OmpR regulates <it>ompC</it>, <it>F</it>, <it>X</it>, and <it>R </it>directly through OmpR-promoter DNA association. There is an inducible expressions of the pore-forming proteins OmpF, C, and × at high osmolarity in <it>Y. pestis</it>, in contrast to the reciprocal regulation of them in <it>E. coli</it>. The main difference is that <it>ompF </it>expression is not repressed at high osmolarity in <it>Y. pestis</it>, which is likely due to the absence of a promoter-distal OmpR-binding site for <it>ompF</it>.</p

Regulatory effects of cAMP receptor protein (CRP) on porin genes and its own gene in Yersinia pestis

<p>Abstract</p> <p>Background</p> <p>The cAMP receptor protein (CRP) is a global bacterial regulator that controls many target genes. The CRP-cAMP complex regulates the <it>ompR-envZ </it>operon in <it>E. coli </it>directly, involving both positive and negative regulations of multiple target promoters; further, it controls the production of porins indirectly through its direct action on <it>ompR-envZ</it>. Auto-regulation of CRP has also been established in <it>E. coli</it>. However, the regulation of porin genes and its own gene by CRP remains unclear in <it>Y. pestis</it>.</p> <p>Results</p> <p><it>Y. pestis </it>employs a distinct mechanism indicating that CRP has no regulatory effect on the <it>ompR-envZ </it>operon; however, it stimulates <it>ompC </it>and <it>ompF </it>directly, while repressing <it>ompX</it>. No transcriptional regulatory association between CRP and its own gene can be detected in <it>Y. pestis</it>, which is also in contrast to the fact that CRP acts as both repressor and activator for its own gene in <it>E. coli</it>. It is likely that <it>Y. pestis </it>OmpR and CRP respectively sense different signals (medium osmolarity, and cellular cAMP levels) to regulate porin genes independently.</p> <p>Conclusion</p> <p>Although the CRP of <it>Y. pestis </it>shows a very high homology to that of <it>E. coli</it>, and the consensus DNA sequence recognized by CRP is shared by the two bacteria, the <it>Y. pestis </it>CRP can recognize the promoters of <it>ompC</it>, <it>F</it>, and <it>X </it>directly rather than that of its own gene, which is different from the relevant regulatory circuit of <it>E. coli</it>. Data presented here indicate a remarkable remodeling of the CRP-mediated regulation of porin genes and of its own one between these two bacteria.</p

FastPop: a rapid principal component derived method to infer intercontinental ancestry using genetic data.

BACKGROUND: Identifying subpopulations within a study and inferring intercontinental ancestry of the samples are important steps in genome wide association studies. Two software packages are widely used in analysis of substructure: Structure and Eigenstrat. Structure assigns each individual to a population by using a Bayesian method with multiple tuning parameters. It requires considerable computational time when dealing with thousands of samples and lacks the ability to create scores that could be used as covariates. Eigenstrat uses a principal component analysis method to model all sources of sampling variation. However, it does not readily provide information directly relevant to ancestral origin; the eigenvectors generated by Eigenstrat are sample specific and thus cannot be generalized to other individuals. RESULTS: We developed FastPop, an efficient R package that fills the gap between Structure and Eigenstrat. It can: 1, generate PCA scores that identify ancestral origins and can be used for multiple studies; 2, infer ancestry information for data arising from two or more intercontinental origins. We demonstrate the use of FastPop using 2318 SNP markers selected from the genome based on high variability among European, Asian and West African (African) populations. We conducted an analysis of 505 Hapmap samples with European, African or Asian ancestry along with 19661 additional samples of unknown ancestry. The results from FastPop are highly consistent with those obtained by Structure across the 19661 samples we studied. The correlations of the results between FastPop and Structure are 0.99, 0.97 and 0.99 for European, African and Asian ancestry scores, respectively. Compared with Structure, FastPop is more efficient as it finished ancestry inference for 19661 samples in 16 min compared with 21-24 h required by Structure. FastPop also provided scores based on SNP weights so the scores of reference population can be applied to other studies provided the same set of markers are used. We also present application of the method for studying four continental populations (European, Asian, African, and Native American). CONCLUSIONS: We developed an algorithm that can infer ancestries on data involving two or more intercontinental origins. It is efficient for analyzing large datasets. Additionally the PCA derived scores can be applied to multiple data sets to ensure the same ancestry analysis is applied to all studies

Genetic Interaction Analysis Among Oncogenesis-Related Genes Revealed Novel Genes and Networks in Lung Cancer Development

The development of cancer is driven by the accumulation of many oncogenesis-related genetic alterationsand tumorigenesis is triggered by complex networks of involved genes rather than independent actions. To explore the epistasis existing among oncogenesis-related genes in lung cancer development, we conducted pairwise genetic interaction analyses among 35,031 SNPs from 2027 oncogenesis-related genes. The genotypes from three independent genome-wide association studies including a total of 24,037 lung cancer patients and 20,401 healthy controls with Caucasian ancestry were analyzed in the study. Using a two-stage study design including discovery and replication studies, and stringent Bonferroni correction for multiple statistical analysis, we identified significant genetic interactions between SNPs in RGL1:RAD51B (OR=0.44, p value=3.27x10-11 in overall lung cancer and OR=0.41, p value=9.71x10-11 in non-small cell lung cancer), SYNE1:RNF43 (OR=0.73, p value=1.01x10-12 in adenocarcinoma) and FHIT:TSPAN8 (OR=1.82, p value=7.62x10-11 in squamous cell carcinoma) in our analysis. None of these genes have been identified from previous main effect association studies in lung cancer. Further eQTL gene expression analysis in lung tissues provided information supporting the functional role of the identified epistasis in lung tumorigenesis. Gene set enrichment analysis revealed potential pathways and gene networks underlying molecular mechanisms in overall lung cancer as well as histology subtypes development. Our results provide evidence that genetic interactions between oncogenesis-related genes play an important role in lung tumorigenesis and epistasis analysis, combined with functional annotation, provides a valuable tool for uncovering functional novel susceptibility genes that contribute to lung cancer development by interacting with other modifier genes

Deep-Learning-Enabled Fast Optical Identification and Characterization of Two-Dimensional Materials

Advanced microscopy and/or spectroscopy tools play indispensable role in nanoscience and nanotechnology research, as it provides rich information about the growth mechanism, chemical compositions, crystallography, and other important physical and chemical properties. However, the interpretation of imaging data heavily relies on the "intuition" of experienced researchers. As a result, many of the deep graphical features obtained through these tools are often unused because of difficulties in processing the data and finding the correlations. Such challenges can be well addressed by deep learning. In this work, we use the optical characterization of two-dimensional (2D) materials as a case study, and demonstrate a neural-network-based algorithm for the material and thickness identification of exfoliated 2D materials with high prediction accuracy and real-time processing capability. Further analysis shows that the trained network can extract deep graphical features such as contrast, color, edges, shapes, segment sizes and their distributions, based on which we develop an ensemble approach topredict the most relevant physical properties of 2D materials. Finally, a transfer learning technique is applied to adapt the pretrained network to other applications such as identifying layer numbers of a new 2D material, or materials produced by a different synthetic approach. Our artificial-intelligence-based material characterization approach is a powerful tool that would speed up the preparation, initial characterization of 2D materials and other nanomaterials and potentially accelerate new material discoveries

Identification of Susceptibility Pathways for the Role of Chromosome 15q25.1 in Modifying Lung Cancer Risk

Genome-wide association studies (GWAS) identified the chromosome 15q25.1 locus as a leading susceptibility region for lung cancer. However, the pathogenic pathways, through which susceptibility SNPs within chromosome 15q25.1 affects lung cancer risk, have not been explored. We analyzed three cohorts with GWAS data consisting 42,901 individuals and lung expression quantitative trait loci (eQTL) data on 409 individuals to identify and validate the underlying pathways and to investigate the combined effect of genes from the identified susceptibility pathways. The KEGG neuroactive ligand receptor interaction pathway, two Reactome pathways, and 22 Gene Ontology terms were identified and replicated to be significantly associated with lung cancer risk, with P values less than 0.05 and FDR less than 0.1. Functional annotation of eQTL analysis results showed that the neuroactive ligand receptor interaction pathway and gated channel activity were involved in lung cancer risk. These pathways provide important insights for the etiology of lung cancer