Modelling DNA Origami Self-Assembly at the Domain Level

We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each staple is associated with a free-energy change that depends on staple sequence, the possibility of coaxial stacking with neighbouring domains, and the entropic cost of constraining the scaffold by inserting staple crossovers. A rigorous thermodynamic model is difficult to implement as a result of the complex, multiply connected geometry of the scaffold: we present a solution to this problem for planar origami. Coaxial stacking and entropic terms, particularly when loop closure exponents are taken to be larger than those for ideal chains, introduce interactions between staples. These cooperative interactions lead to the prediction of sharp assembly transitions with notable hysteresis that are consistent with experimental observations. We show that the model reproduces the experimentally observed consequences of reducing staple concentration, accelerated cooling and absent staples. We also present a simpler methodology that gives consistent results and can be used to study a wider range of systems including non-planar origami

Deep learning-based parameter mapping for joint relaxation and diffusion tensor MR Fingerprinting

Magnetic Resonance Fingerprinting (MRF) enables the simultaneous quantification of multiple properties of biological tissues. It relies on a pseudo-random acquisition and the matching of acquired signal evolutions to a precomputed dictionary. However, the dictionary is not scalable to higher-parametric spaces, limiting MRF to the simultaneous mapping of only a small number of parameters (proton density, T1 and T2 in general). Inspired by diffusion-weighted SSFP imaging, we present a proof-of-concept of a novel MRF sequence with embedded diffusion-encoding gradients along all three axes to efficiently encode orientational diffusion and T1 and T2 relaxation. We take advantage of a convolutional neural network (CNN) to reconstruct multiple quantitative maps from this single, highly undersampled acquisition. We bypass expensive dictionary matching by learning the implicit physical relationships between the spatiotemporal MRF data and the T1, T2 and diffusion tensor parameters. The predicted parameter maps and the derived scalar diffusion metrics agree well with state-of-the-art reference protocols. Orientational diffusion information is captured as seen from the estimated primary diffusion directions. In addition to this, the joint acquisition and reconstruction framework proves capable of preserving tissue abnormalities in multiple sclerosis lesions

Cyclooxygenase-2 overexpression is common in serrated and non-serrated colorectal adenoma, but uncommon in hyperplastic polyp and sessile serrated polyp/adenoma

<p>Abstract</p> <p>Background</p> <p>Cyclooxygenase-2 (COX-2, <it>PTGS2</it>) plays an important role in colorectal carcinogenesis. COX-2 overexpression in colorectal cancer is inversely associated with microsatellite instability (MSI) and the CpG island methylator phenotype (CIMP). Evidence suggests that MSI/CIMP+ colorectal cancer may arise through the serrated tumorigenic pathway through various forms of serrated neoplasias. Therefore, we hypothesized that COX-2 may play a less important role in the serrated pathway.</p> <p>Methods</p> <p>By immunohistochemistry, we assessed COX-2 expression in 24 hyperplastic polyps, 7 sessile serrated polyp/adenomas (SSA), 5 mixed polyps with SSA and adenoma, 27 traditional serrated adenomas, 515 non-serrated adenomas (tubular adenoma, tubulovillous adenoma and villous adenoma), 33 adenomas with intramucosal carcinomas, 96 adenocarcinomas with serration (corkscrew gland) and 111 adenocarcinomas without serration.</p> <p>Results</p> <p>Strong (2+) COX-2 overexpression was more common in non-serrated adenomas (28% = 143/515) than in hyperplastic polyps (4.2% = 1/24, p = 0.008) and serrated polyps (7 SSAs and 5 mixed polyps) (0% = 0/12, p = 0.04). Furthermore, any (1+/2+) COX-2 overexpression was more frequent in non-serrated adenomas (60% = 307/515) than in hyperplastic polyps (13% = 3/24, p < 0.0001) and serrated polyps (SSAs and mixed polyps) (25% = 3/12, p = 0.03). Traditional serrated adenomas and non-serrated adenomas showed similar frequencies of COX-2 overexpression. Regardless of serration, COX-2 overexpression was frequent (~85%) in colorectal adenocarcinomas. Tumor location was not significantly correlated with COX-2 overexpression, although there was a trend towards higher frequencies of COX-2 overexpression in distal tumors (than proximal tumors) among hyperplastic polyps, SSAs, mixed polyps, traditional serrated adenomas and adenocarcinomas.</p> <p>Conclusion</p> <p>COX-2 overexpression is infrequent in hyperplastic polyp, SSA and mixed polyp with SSA and adenoma, compared to non-serrated and serrated adenoma. COX-2 overexpression becomes more frequent as tumors progress to higher grade neoplasias. Our observations suggest that COX-2 may play a less significant role in the serrated pathway of tumorigenesis; however, COX-2 may still play a role in later stage of the serrated pathway.</p

Offender Theme Analyses in a Crime Narrative: An Applied Approach

There is a great deal of research on the structure of narrative and its mode, and on the narrative positioning and counter positioning of the actor in legal and social contexts. In offender narratives, personal experiences are embedded for observation and analysis of particular realities that contextualize a disposition of the perpetrator being ‘an undergoer’ rather than an ‘effector’ of actions. This is evaluated in the shift from a narrated action to a speaker utterance in prospection and also in anticipation of the criminal act. Using ‘grammatical logic’, it is also possible to demonstrate how the crucial event (the crime) is not a cause, but an effect of a personal theme that encapsulates pattern of circumstances when the narrative outcome in criminal narrative becomes the product of its discursive practices. This is the ‘story of intentionality’ (my term) in crime narratives, characteristically embedded within the 1st the story of crime, the 2nd is the story of investigation [14, 20]. Using techniques from functional grammar and critical stylistics for discourse analysis, I intend to show an effective approach for the search of offender theme that underlies an act of crime. These disciplines provide the analyst with the linguistic material to analyse intersentential cohesion in a chain of semantically linked sentences (in written or spoken discourse) that explore the ways in which things are ‘made to look’ in the structure and functions of the English language. As a case study, I am using an offender narrative from Tony Parker’s book Life After Life: Interviews with Twelve Murderers (1990) showing an effective approach for the search of personal themes underlying the act of crime. Offender theme analyses are also valuable for evaluating the changing nature or development of offender characteristics pre or post crime

Identification, extraction, and application of orange peel color extracts for silk fabric coloration

Under-utilized orange peel waste contains natural colorants that might be used for textile dyeing. Research into orange peel waste as natural colorants provides benefits for both the agricultural and fashion industry with a creative and sustainable solution. This research performed the extraction of colorants from the orange peel as plant dyes and investigated their potential dyeing capability of silk fabrics. With full factorial analysis, we determined the optimal extraction conditions by comparing 100 % ethanol, 70 % ethanol, and water, aiming to achieve the highest absorbance for the extracted solution. Conditions obtained with the best performance include an extraction temperature of 60 °C, an extraction time of 120 min, and a material-to-liquor ratio of 1:20 (wt/vol) for both 100 % and 0 % ethanol. To attain the highest K/S values on textiles with orthogonal experimental design, the optimal dyeing profiles of silk fabrics with water solution were found to be 100 °C, 60 min, pH 3, and Liquid Ratio of 1:15. Colorfastness results of crocking, washing, and sunlight are in favor of the usage of orange peel color extracts for textile application

Sleep and Breathing … and Cancer?

Sleep, like eating and breathing, is an essential part of the daily life cycle. Although the science is still emerging, sleep plays an important role in immune, cardiovascular, and neurocognitive function. Despite its great importance, nearly 40% of U.S. adults experience problems with sleep ranging from insufficient total sleep time, trouble initiating or maintaining sleep (Insomnia), circadian rhythm disorders, sleep-related movement disorders, and sleep-related breathing disorders such as obstructive sleep apnea (OSA). Herein, we discuss new evidence that suggests that sleep may also affect carcinogenesis. Specifically, we review recent epidemiologic data suggesting links between cancer and OSA. As OSA is a common, underdiagnosed, and undertreated condition, this has public health implications. Intriguing animal model data support a link between cancer and sleep/OSA, although mechanisms are not yet clear. Leaders in the fields of sleep medicine, pulmonology, and oncology recently met to review and discuss these data, as well as to outline future directions of study. We propose a multidisciplinary, three-pronged approach to studying the associations between cancer and sleep, utilizing mutually interactive epidemiologic studies, preclinical models, and early-phase clinical trials. Cancer Prev Res; 9(11); 821-7. ©2016 AACR

Growing the Field of Health Impact Assessment in the United States: An Agenda for Research and Practice

Health impact assessment (HIA) methods are used to evaluate the impact on health of policies and projects in community design, transportation planning, and other areas outside traditional public health concerns. At an October 2004 workshop, domestic and international experts explored issues associated with advancing the use of HIA methods by local health departments, planning commissions, and other decisionmakers in the United States. Workshop participants recommended conducting pilot tests of existing HIA tools, developing a database of health impacts of common projects and policies, developing resources for HIA use, building workforce capacity to conduct HIAs, and evaluating HIAs. HIA methods can influence decisionmakers to adjust policies and projects to maximize benefits and minimize harm to the public’s health