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Feng Yan, Lili Liu, Tiffany R Walsh, Yu Gong, Patrick Z El-Khoury, Yanyan Zhang, Zihua Zhu, James J De Yoreo, Mark H Engelhard, Xin Zhang, Chun-Long Chen
In nature, specific biomolecules interacting with mineral precursors are responsible for the precise production of nanostructured inorganic materials that exhibit complex morphologies and superior performance. Despite advances in developing biomimetic approaches, the design rules for creating sequence-defined molecules that lead to the synthesis of inorganic nanomaterials with predictable complex morphologies are unknown. Herein we report the design of sequence-defined peptoids for controlled synthesis of highly branched plasmonic gold particles...
June 13, 2018: Nature Communications
M Jane Brennan, Sydney E Hollingshead, Jonathan J Wilker, Julie C Liu
Many protein-based materials, such as soy and mussel adhesive proteins, have been the subject of scientific and commercial interest. Recently, a variety of protein adhesives have been isolated from diverse sources such as insects, frogs and squid ring teeth. Many of these adhesives have similar amino acid compositions to elastomeric proteins such as elastin. Although elastin is widely investigated for a structural biomaterial, little work has been done to assess its adhesive potential. In this study, recombinant elastin-like polypeptides were created to probe the factors affecting adhesion strength...
May 2018: Royal Society Open Science
Harrison Ritz, Matthew R Nassar, Michael J Frank, Amitai Shenhav
To behave adaptively in environments that are noisy and nonstationary, humans and other animals must monitor feedback from their environment and adjust their predictions and actions accordingly. An understudied approach for modeling these adaptive processes comes from the engineering field of control theory, which provides general principles for regulating dynamical systems, often without requiring a generative model. The proportional-integral-derivative (PID) controller is one of the most popular models of industrial process control...
June 7, 2018: Journal of Cognitive Neuroscience
Arya A Das, Elizabeth Jacob
The ErbB signalling pathway has been studied extensively owing to its role in normal physiology and its dysregulation in cancer. Reverse engineering by mathematical models use the reductionist approach to characterize the network components. For an emergent, system-level view of the network, we propose a data analytics pipeline that can learn from the data generated by reverse engineering and use it to re-engineer the system with an agent-based approach. Data from a kinetic model that estimates the parameters by fitting to experiments on cell lines, were encoded into rules, for the interactions of the molecular species (agents) involved in biochemical reactions...
June 2018: Journal of Biosciences
Antoine Danchin, Christos Ouzounis, Taku Tokuyasu, Jean-Daniel Zucker
Science and engineering rely on the accumulation and dissemination of knowledge to make discoveries and create new designs. Discovery-driven genome research rests on knowledge passed on via gene annotations. In response to the deluge of sequencing big data, standard annotation practice employs automated procedures that rely on majority rules. We argue this hinders progress through the generation and propagation of errors, leading investigators into blind alleys. More subtly, this inductive process discourages the discovery of novelty, which remains essential in biological research and reflects the nature of biology itself...
May 28, 2018: Microbial Biotechnology
K Lange, A Brinker, M Nowak, C Zöllner, W Lauer
BACKGROUND: The Federal Institute for Drugs and Medical Devices (BfArM) was notified of an event in which it was not possible to sufficiently ventilate a patient suffering a severe asthma attack. It turned out that the ventilation pressures used by the device for pressure-controlled ventilation were below the values set by the user, which the user was not aware of. The ventilation pressures chosen by the user exceeded the preset alarm limits of the ventilator. This pressure and alarm management significantly differed from that of other ventilators used in the hospital...
May 25, 2018: Der Anaesthesist
Luca Ornigotti, Artem Ryabov, Viktor Holubec, Radim Filip
The trajectories of an overdamped particle in a highly unstable potential diverge so rapidly, that the variance of position grows much faster than its mean. A description of the dynamics by moments is therefore not informative. Instead, we propose and analyze local directly measurable characteristics, which overcome this limitation. We discuss the most probable particle position (position of the maximum of the probability density) and the local uncertainty in an unstable cubic potential, V(x)∼x^{3}, both in the transient regime and in the long-time limit...
March 2018: Physical Review. E
Rakesh S Engineer, Seth R Podolsky, Baruch S Fertel, Purva Grover, Heather Jimenez, Erin L Simon, Courtney M Smalley
INTRODUCTION: The American College of Emergency Physicians embarked on the "Choosing Wisely" campaign to avoid computed tomographic (CT) scans in patients with minor head injury who are at low risk based on validated decision rules. We hypothesized that a Pediatric Mild Head Injury Care Path could be developed and implemented to reduce inappropriate CT utilization with support of a clinical decision support tool (CDST) and a structured parent discussion tool. METHODS: A quality improvement project was initiated for 9 weeks to reduce inappropriate CT utilization through 5 interventions: (1) engagement of leadership, (2) provider education, (3) incorporation of a parent discussion tool to guide discussion during the emergency department (ED) visit between the parent and the provider, (4) CDST embedded in the electronic medical record, and (5) importation of data into the note to drive compliance...
May 15, 2018: Pediatric Emergency Care
Tingting Wang, Zhen Xie
Basic biological research and biomedical applications often require studying the multiple interactions between genes or proteins while multiplex RNA interference (RNAi) technology is still challenging in mammalian cells. In mammalian genomes, the natural microRNA (miRNA) clusters, of which the miRNAs often share similar expression patterns and target diverse genes, would provide a potential multiplex RNAi scaffold. Based on the natural pri-miR-155 precursor, we have developed and characterized a multiplex RNAi method by engineering synthetic miRNA clusters, among which the maturation and function of individual miRNA precursors are independent of their positions in the cluster...
2018: Methods in Molecular Biology
Emily Freed, Jacob Fenster, Sharon L Smolinski, Julie Walker, Calvin A Henard, Ryan Gill, Carrie A Eckert
The realization of a sustainable bioeconomy requires our ability to understand and engineer complex design principles for the development of platform organisms capable of efficient conversion of cheap and sustainable feedstocks (e.g. sunlight, CO2 , non-food biomass) to biofuels and bioproducts at sufficient titers and costs. For model microbes such as E. coli, advances in DNA reading and writing technologies are driving adoption of new paradigms for engineering biological systems. Unfortunately, microbes with properties of interest for the utilization of cheap and renewable feedstocks such as photosynthesis, autotrophic growth, and cellulose degradation have very few, if any, genetic tools for metabolic engineering...
May 11, 2018: Biotechnology and Bioengineering
Jeffrey Ian Lipton, Robert MacCurdy, Zachary Manchester, Lillian Chin, Daniel Cellucci, Daniela Rus
In nature, repeated base units produce handed structures that selectively bond to make rigid or compliant materials. Auxetic tilings are scale-independent frameworks made from repeated unit cells that expand under tension. We discovered how to produce handedness in auxetic unit cells that shear as they expand by changing the symmetries and alignments of auxetic tilings. Using the symmetry and alignment rules that we developed, we made handed shearing auxetics that tile planes, cylinders, and spheres. By compositing the handed shearing auxetics in a manner inspired by keratin and collagen, we produce both compliant structures that expand while twisting and deployable structures that can rigidly lock...
May 11, 2018: Science
Hélder Pereira, Duarte Andre Sousa, António Cunha, Renato Andrade, J Espregueira-Mendes, J Miguel Oliveira, Rui L Reis
In recent times, the field of tissue engineering and regenerative medicine (TERM) has considerably increased the extent of therapeutic strategies for clinical application in orthopedics. However, TERM approaches have its rules and requirements, in the respect of the biologic response of each tissue and bioactive agents which need to be considered, respected, and subject of ongoing studies. Different medical devices/products have been prematurely available on the market and used in clinics with limited success...
2018: Advances in Experimental Medicine and Biology
Jeroen S de Bruin, Klaus-Peter Adlassnig, Harald Leitich, Andrea Rappelsberger
BACKGROUND: Evidence-based clinical guidelines have a major positive effect on the physician's decision-making process. Computer-executable clinical guidelines allow for automated guideline marshalling during a clinical diagnostic process, thus improving the decision-making process. OBJECTIVES: Implementation of a digital clinical guideline for the prevention of mother-to-child transmission of hepatitis B as a computerized workflow, thereby separating business logic from medical knowledge and decision-making...
2018: Studies in Health Technology and Informatics
Sarah Haßdenteufel, Nicholas Johnson, Adrienne W Paton, James C Paton, Stephen High, Richard Zimmermann
Protein transport into the mammalian endoplasmic reticulum (ER) is mediated by the heterotrimeric Sec61 channel. The signal recognition particle (SRP) and TRC systems and Sec62 have all been characterized as membrane-targeting components for small presecretory proteins, whereas Sec63 and the lumenal chaperone BiP act as auxiliary translocation components. Here, we report the transport requirements of two natural, small presecretory proteins and engineered variants using semipermeabilized human cells after the depletion of specific ER components...
May 1, 2018: Cell Reports
Kang Wang, Ye Chen, Xiangjun Gong, Jianlong Xia, Junpeng Zhao, Lei Shen
Biomaterials are often engineered with nanostructured surfaces to control interactions with proteins and thus regulate their biofunctions. However, the mechanism of how nanostructured surfaces resist or attract proteins together with the underlying design rules remains poorly understood at a molecular level, greatly limiting attempts to develop high-performance biomaterials and devices through the rational design of nanostructures. Here, we study the dynamics of nonspecific protein adsorption on block copolymer nanostructures of varying adhesive domain areas in a resistant matrix...
May 1, 2018: Physical Chemistry Chemical Physics: PCCP
Haogang Cai, James Muller, David Depoil, Viveka Mayya, Michael P Sheetz, Michael L Dustin, Shalom J Wind
Elucidating the rules for receptor triggering in cell-cell and cell-matrix contacts requires precise control of ligand positioning in three dimensions. Here, we use the T cell receptor (TCR) as a model and subject T cells to different geometric arrangements of ligands, using a nanofabricated single-molecule array platform. This comprises monovalent TCR ligands anchored to lithographically patterned nanoparticle clusters surrounded by mobile adhesion molecules on a supported lipid bilayer. The TCR ligand could be co-planar with the supported lipid bilayer (2D), excluding the CD45 transmembrane tyrosine phosphatase, or elevated by 10 nm on solid nanopedestals (3D), allowing closer access of CD45 to engaged TCR...
April 30, 2018: Nature Nanotechnology
Zi Wang, Dali Wang, Chengcheng Li, Yichi Xu, Husheng Li, Zhirong Bao
Motivation: Cell movement in the early phase of C. elegans development is regulated by a highly complex process in which a set of rules and connections are formulated at distinct scales. Previous efforts have demonstrated that agent-based, multi-scale modeling systems can integrate physical and biological rules and provide new avenues to study developmental systems. However, the application of these systems to model cell movement is still challenging and requires a comprehensive understanding of regulatory networks at the right scales...
April 25, 2018: Bioinformatics
Dani Setiawan, Jeffrey Brender, Yang Zhang
Protein function is determined by protein structure which is in turn determined by the corresponding protein sequence. If the rules that cause a protein to adopt a particular structure are understood, it should be possible to refine or even redefine the function of a protein by working backwards from the desired structure to the sequence. Automated protein design attempts to calculate the effects of mutations computationally with the goal of more radical or complex transformations than are accessible by experimental techniques...
April 25, 2018: Expert Opinion on Drug Discovery
Diana Baumgärtel, Corinna Mielke, Reinhold Haux
The use of decision support systems for smart homes can provide attractive solutions for challenges that have arisen in the Health Care System due to ageing of society. In order to provide an overview of current research projects in this field, a systematic literature review was performed according to the PRISMA approach. The aims of this work are to provide an overview of current research projects and to update a similar study from 2012. The literature search engines IEEE Xplore and PubMed were used. 23 papers were included...
2018: Studies in Health Technology and Informatics
Félix Musil, Sandip De, Jack Yang, Joshua E Campbell, Graeme M Day, Michele Ceriotti
Molecular crystals play an important role in several fields of science and technology. They frequently crystallize in different polymorphs with substantially different physical properties. To help guide the synthesis of candidate materials, atomic-scale modelling can be used to enumerate the stable polymorphs and to predict their properties, as well as to propose heuristic rules to rationalize the correlations between crystal structure and materials properties. Here we show how a recently-developed machine-learning (ML) framework can be used to achieve inexpensive and accurate predictions of the stability and properties of polymorphs, and a data-driven classification that is less biased and more flexible than typical heuristic rules...
February 7, 2018: Chemical Science
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