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"Yu, Michael"
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An 88-line MATLAB code for the parameterized level set method based topology optimization using radial basis functions
This paper presents a compact and efficient 88-line MATLAB code for the parameterized level set method based topology optimization using radial basis functions (RBFs), which is applied to minimize the compliance of a two-dimensional linear elastic structure. This parameterized level set method using radial basis functions can maintain a relatively smooth level set function with an approximate re-initialization scheme during the optimization process. It also has less dependency on initial designs due to its capability in nucleation of new holes inside the material domain. The MATLAB code and simple modifications are explained in detail with numerical examples. The 88-line code included in the
appendix
is intended for educational purposes.
Journal Article
الصين في السنوات الثلاثين المقبلة
يتحدث هذا الكتاب عن الصين في السنوات الثلاثين المقبلة حيث أن نهوض الأمة الصينية حلم يراود الشعب الصيني منذ مائتي السنة ومحاولات تحقيقه تكررت خلال تلك الفترة مرات عدة وكانت تمنى مرة بالفشل وأخرى بنصف الفشل نصف النجاح لكن هذا الشعب كان يفيد في كل مرة من تجاربه إلى أن أفضت تجربته الأخيرة التي بدأت منذ ما يقرب من ثلاثين سنة إلى نجاح تام جعل الصين وهذه الدولة الأمة في طليعة دول العالم فما هي هذه التجربة؟ وماذا ستكون عليه الصين بعد ثلاثين عاما أخرى.
BOOK
Big 4 Office Size and Audit Quality
Larger offices of Big 4 auditors are predicted to have higher quality audits for SEC registrants due to greater in-house experience in administering such audits. We test this prediction by examining a sample of 6,568 U.S. firm-year observations for the period 2003–2005 and audited by 285 unique Big 4 offices. Results are consistent with larger offices providing higher quality audits. Specifically, larger offices are more likely to issue going-concern audit reports, and clients in larger offices evidence less aggressive earnings management behavior. These findings are robust to extensive controls for client risk factors and to controls for other auditor characteristics. While the evidence suggests audit quality is higher on average in larger Big 4 offices, we make no claims that audit quality is unacceptably low in smaller offices.
Journal Article
The art of music
\"The Art of music is a handsomely illustrated and rich interdisciplinary look at the mutual influence between music and the visual arts across cultures and eras. The book sheds new light on more familiar artists at the intersection of the visual and the musical, such as Wassily Kandinsky and Arnold Schoenberg, and presents new scholarship on less well-known examples in the arts of Asia, Africa, the Americas, and Europe, from antique pottery to contemporary video and sound art. Essays consider key works and themes such as synesthesia and other formal and theoretical crossovers, motifs of musicians, and performative and ritual functions of music, musical instruments, and art. With more than 250 color images illustrating works of art in diverse traditions, The Art of music offers enriching reading for scholars and general audiences alike\"-- Provided by publisher.
Book
The effect of smoking on chronic inflammation, immune function and blood cell composition
Smoking is the number one risk factor for cancer mortality but only 15–20% of heavy smokers develop lung cancer. It would, therefore, be of great benefit to identify those at high risk early on so that preventative measures can be initiated. To investigate this, we evaluated the effects of smoking on inflammatory markers, innate and adaptive immune responses to bacterial and viral challenges and blood cell composition. We found that plasma samples from 30 heavy smokers (16 men and 14 women) had significantly higher CRP, fibrinogen, IL-6 and CEA levels than 36 non-smoking controls. Whole blood samples from smokers, incubated for 7 h at 37 °C in the absence of any exogenous stimuli, secreted significantly higher levels of IL-8 and a number of other cytokines/chemokines than non-smokers. When challenged for 7 h with
E. coli,
whole blood samples from smokers secreted significantly lower levels of many inflammatory cytokines/chemokines. However, when stimulated with HSV-1, significantly higher levels of both PGE
2
and many cytokines/chemokines were secreted from smokers’ blood samples than from controls. In terms of blood cell composition, red blood cells, hematocrits, hemoglobin levels, MCV, MCH, MCHC, Pct and RDW levels were all elevated in smokers, in keeping with their compromised lung capacity. As well, total leukocytes were significantly higher, driven by increases in granulocytes and monocytes. In addition, smokers had lower NK cells and higher Tregs than controls, suggesting that smoking may reduce the ability to kill nascent tumor cells. Importantly, there was substantial person-to person variation amongst smokers with some showing markedly different values from controls and others showing normal levels of many parameters measured, indicating the former may be at significantly higher risk of developing lung cancer.
Journal Article
Structure-material integrated design by level sets
This paper proposes a structure-material integrated design method in the framework of level sets. A two-scale optimization is performed, where not only is the structural configuration optimized, but the effective properties of the constituent material are also designed by optimizing the configuration of the periodically-arranged microstructures. In this way, the approach can simultaneously generate optimized material distribution patterns as well as optimized materials. Due to the fact that the level set method produces material-void solutions only, the obtained material is uniformly distributed over the material regions of the structure in a strict sense. Three numerical examples are presented to validate the proposed method. The obtained optimal solutions illustrate that whether to design material cells or to optimize structural configurations to achieve the best structural performance would be problem dependent, and thus further demonstrate the necessity and validity of the integrated design scheme.
Journal Article
Molecular level detection and localization of mechanical damage in collagen enabled by collagen hybridizing peptides
Mechanical injury to connective tissue causes changes in collagen structure and material behaviour, but the role and mechanisms of molecular damage have not been established. In the case of mechanical subfailure damage, no apparent macroscale damage can be detected, yet this damage initiates and potentiates in pathological processes. Here, we utilize collagen hybridizing peptide (CHP), which binds unfolded collagen by triple helix formation, to detect molecular level subfailure damage to collagen in mechanically stretched rat tail tendon fascicle. Our results directly reveal that collagen triple helix unfolding occurs during tensile loading of collagenous tissues and thus is an important damage mechanism. Steered molecular dynamics simulations suggest that a likely mechanism for triple helix unfolding is intermolecular shearing of collagen α-chains. Our results elucidate a probable molecular failure mechanism associated with subfailure injuries, and demonstrate the potential of CHP targeting for diagnosis, treatment and monitoring of tissue disease and injury.
Collagen denaturation is thought to occur during tissue mechanical damage, but its role in damage initiation is still unclear. Here, the authors use a collagen hybridizing peptide to provide insights into the molecular mechanisms leading to collagen unfolding during tendon mechanical stretch.
Journal Article
Metabolic independence drives gut microbial colonization and resilience in health and disease
Background
Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge.
Results
Here we use fecal microbiota transplantation (FMT) as an in natura experimental model to investigate the association between metabolic independence and resilience in stressed gut environments. Our genome-resolved metagenomics survey suggests that FMT serves as an environmental filter that favors populations with higher metabolic independence, the genomes of which encode complete metabolic modules to synthesize critical metabolites, including amino acids, nucleotides, and vitamins. Interestingly, we observe higher completion of the same biosynthetic pathways in microbes enriched in IBD patients.
Conclusions
These observations suggest a general mechanism that underlies changes in diversity in perturbed gut environments and reveal taxon-independent markers of “dysbiosis” that may explain why widespread yet typically low-abundance members of healthy gut microbiomes can dominate under inflammatory conditions without any causal association with disease.
Journal Article
Conserved transcription factors promote cell fate stability and restrict reprogramming potential in differentiated cells
Defining the mechanisms safeguarding cell fate identity in differentiated cells is crucial to improve 1) - our understanding of how differentiation is maintained in healthy tissues or altered in a disease state, and 2) - our ability to use cell fate reprogramming for regenerative purposes. Here, using a genome-wide transcription factor screen followed by validation steps in a variety of reprogramming assays (cardiac, neural and iPSC in fibroblasts and endothelial cells), we identified a set of four transcription factors (ATF7IP, JUNB, SP7, and ZNF207 [AJSZ]) that robustly opposes cell fate reprogramming in both lineage and cell type independent manners. Mechanistically, our integrated multi-omics approach (ChIP, ATAC and RNA-seq) revealed that AJSZ oppose cell fate reprogramming by 1) - maintaining chromatin enriched for reprogramming TF motifs in a closed state and 2) - downregulating genes required for reprogramming. Finally, KD of AJSZ in combination with MGT overexpression, significantly reduced scar size and improved heart function by 50%, as compared to MGT alone post-myocardial infarction. Collectively, our study suggests that inhibition of barrier to reprogramming mechanisms represents a promising therapeutic avenue to improve adult organ function post-injury.
Transdifferentiation has been proposed as an approach for regenerative medicine, but the mechanisms that safeguard cell identity are not well established. Here they identify transcription factors that oppose transdifferentiation and show that knockdown of these genes improves recovery after myocardial infarction.
Journal Article