An Activity Coordination System

Engineering and Applied Science

Molecular dynamics simulations and coupled nucleotide substitution experiments indicate the nature of A·A base pairing and a putative structure of the coralyne-induced homo-adenine duplex

Coralyne is an alkaloid drug that binds homo-adenine DNA (and RNA) oligonucleotides more tightly than it does Watson–Crick DNA. Hud’s laboratory has shown that poly(dA) in the presence of coralyne forms an anti-parallel duplex, however attempts to determine the structure by NMR spectroscopy and X-ray crystallography have been unsuccessful. Assuming adenine–adenine hydrogen bonding between the two poly(dA) strands, we constructed 40 hypothetical homo-(dA) anti-parallel duplexes and docked coralyne into the six most favorable duplex structures. The two most stable structures had trans glycosidic bonds, but distinct pairing geometries, i.e. either Watson–Crick Hoogsteen (transWH) or Watson–Crick Watson–Crick (transWW) with stability of transWH > transWW. To narrow down the possibilities, 7-deaza adenine base substitutions (dA→7) were engineered into homo-(dA) sequences. These substitutions significantly reduced the thermal stability of the coralyne-induced homo-(dA) structure. These experiments strongly suggest the involvement of N7 in the coralyne-induced A·A base pairs. Moreover, due to the differential effect on melting as a function of the location of the dA→7 mutations, these results are consistent with the N1–N7 base pairing of the transWH pairs. Together, the simulation and base substitution experiments predict that the coralyne-induced homo-(dA) duplex structure adopts the transWH geometry

Mass casualty events: what to do as the dust settles?

Care during mass casualty events (MCE) has improved during the last 15 years. Military and civilian collaboration has led to partnerships which augment the response to MCE. Much has been written about strategies to deliver care during an MCE, but there is little about how to transition back to normal operations after an event. A panel discussion entitled The Day(s) After: Lessons Learned from Trauma Team Management in the Aftermath of an Unexpected Mass Casualty Event at the 76th Annual American Association for the Surgery of Trauma meeting on September 13, 2017 brought together a cadre of military and civilian surgeons with experience in MCEs. The events described were the First Battle of Mogadishu (1993), the Second Battle of Fallujah (2004), the Bagram Detention Center Rocket Attack (2014), the Boston Marathon Bombing (2013), the Asiana Flight 214 Plane Crash (2013), the Baltimore Riots (2015), and the Orlando Pulse Night Club Shooting (2016). This article focuses on the lessons learned from military and civilian surgeons in the days after MCEs

Kinesiology Tape: A Descriptive Survey of Healthcare Professionals in the United States

# Background The existing body of kinesiology tape (KT) research reveals inconsistent results which challenges the efficacy of the intervention. Understanding professional beliefs and KT clinical application might provide insight for future research and development of evidence-based guidelines. # Purpose The purpose of this study was to survey and document the beliefs and clinical application methods of KT among healthcare professionals in the United States. # Design Cross-sectional survey study. # Methods A 30-question online survey was emailed to members of the National Athletic Trainers Association, Academy of Orthopedic Physical Therapy, and American Academy of Sports Physical Therapy. Professionals were also informed through a recruitment post in different private healthcare Facebook groups. # Results One thousand and eighty-three respondents completed the survey. Most respondents used KT for post-injury treatment (74%), pain modulation (67%), and neuro-sensory feedback (60%). Most believed that KT stimulates skin mechanoreceptors (77%), improve local circulation (69%), and modulates pain (60%). Some respondents believed KT only created a placebo effect (40%) and use it for such therapeutic purposes (58%). Most used a standard uncut roll (67%) in black (71%) or beige (66%). Most respondents did not use any specialty pre-cut tape (83%), infused tape (99.54%), or a topical analgesic with tape (65%). The most common tape tension lengths used by respondents were 50% tension (47%) and 25% (25%) tension. Patient reported outcomes (80%) were the most common clinical measures. Most respondents provided skin prep (64%) and tape removal (77%) instructions. Some did not provide any skin prep (36%) or tape removal (23%) instruction. The average recommended times to wear KT were two to three days (60%). The maximum times ranged from two to five days (81%). # Conclusion This survey provides insight into how professionals use KT and highlights the gap between research and practice. Future research should address these gaps to better determine evidence-based guidelines. # Level of Evidence

An Ontology Pattern for Oceanographic Cruises: Towards an Oceanographer\u27s Dream of Integrated Knowledge Discovery

EarthCube is a major effort of the National Science Foundation to establish a next-generation knowledge architecture for the broader geosciences. Data storage, retrieval, access, and reuse are central parts of this new effort. Currently, EarthCube is organized around several building blocks and research coordination networks. OceanLink is a semantics enabled building block that aims at improving data retrieval and reuse via ontologies, Semantic Web technologies, and Linked Data for the ocean sciences. Cruises, in the sense of research expeditions, are central events for ocean scientists. Consequently, information about these cruises and the involved vessels has to be shared and made retrievable. For example, the ability to find cruises in the vicinity of physiographic features of interest, e.g., a hydrothermal vent field or a fracture zone, is of primary interest for oceanographers. In this paper, we use a design pattern-centric strategy to engineer ontologies for OceanLink. We provide a formal axiomatization of the introduced patterns and ontologies using the Web Ontology Language, explain design choices, discuss the re-usability of our models, and provide lessons learned for the future geo-ontologies

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

It is well recognized that base sequence exerts a significant influence on the properties of DNA and plays a significant role in protein–DNA interactions vital for cellular processes. Understanding and predicting base sequence effects requires an extensive structural and dynamic dataset which is currently unavailable from experiment. A consortium of laboratories was consequently formed to obtain this information using molecular simulations. This article describes results providing information not only on all 10 unique base pair steps, but also on all possible nearest-neighbor effects on these steps. These results are derived from simulations of 50–100 ns on 39 different DNA oligomers in explicit solvent and using a physiological salt concentration. We demonstrate that the simulations are converged in terms of helical and backbone parameters. The results show that nearest-neighbor effects on base pair steps are very significant, implying that dinucleotide models are insufficient for predicting sequence-dependent behavior. Flanking base sequences can notably lead to base pair step parameters in dynamic equilibrium between two conformational sub-states. Although this study only provides limited data on next-nearest-neighbor effects, we suggest that such effects should be analyzed before attempting to predict the sequence-dependent behavior of DNA