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RNA design rules from a massive open laboratory
Lee, Jeehyung,Kladwang, Wipapat,Lee, Minjae,Cantu, Daniel,Azizyan, Martin,Kim, Hanjoo,Limpaecher, Alex,Yoon, Sungroh,Treuille, Adrien,Das, Rhiju National Academy of Sciences 2014 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.111 No.6
<P>Self-assembling RNA molecules present compelling substrates for the rational interrogation and control of living systems. However, imperfect in silico models—even at the secondary structure level—hinder the design of new RNAs that function properly when synthesized. Here, we present a unique and potentially general approach to such empirical problems: the Massive Open Laboratory. The EteRNA project connects 37,000 enthusiasts to RNA design puzzles through an online interface. Uniquely, EteRNA participants not only manipulate simulated molecules but also control a remote experimental pipeline for high-throughput RNA synthesis and structure mapping. We show herein that the EteRNA community leveraged dozens of cycles of continuous wet laboratory feedback to learn strategies for solving in vitro RNA design problems on which automated methods fail. The top strategies—including several previously unrecognized negative design rules—were distilled by machine learning into an algorithm, EteRNABot. Over a rigorous 1-y testing phase, both the EteRNA community and EteRNABot significantly outperformed prior algorithms in a dozen RNA secondary structure design tests, including the creation of dendrimer-like structures and scaffolds for small molecule sensors. These results show that an online community can carry out large-scale experiments, hypothesis generation, and algorithm design to create practical advances in empirical science.</P>
Minjae Yoon,Chan Joo Lee,Sungha Park,Sang-Hak Lee 대한심장학회 2022 Korean Circulation Journal Vol.52 No.12
Background and Objectives: Some individuals exhibit discrepancies between risk classifications assessed using clinical factors and those obtained by vascular imaging. We aimed to evaluate whether statins provide clinical outcome benefits in patients classified as having low to moderate cardiovascular risk but with carotid plaque. Methods: This was a retrospective propensity score matching study. A total of 12,158 consecutive patients undergoing carotid ultrasound between January 2012 to February 2020 were screened. Individuals with low to moderate cardiovascular risk who were not currently recommended for statin therapy but had carotid plaques were included. Among 1,611 enrolled individuals, 806 (statin group: 403, control group: 403) were analyzed. The primary outcomes were major adverse cardiovascular and cerebrovascular events (MACCEs: cardiovascular death, myocardial infarction, coronary revascularization, and ischemic stroke or transient ischemic attack) and all-cause mortality. Results: During the median follow-up of 6.0 years, the incidence of MACCEs did not differ between the groups (6.1 and 5.7/1,000 person-years in the control and statin groups, respectively; adjusted hazard ratio [HR], 0.95; p=0.90). The incidence of all-cause mortality did not differ (3.9 and 3.9/1,000 person-years, respectively; adjusted HR, 1.02; p=0.97). Kaplan-Meier curves revealed similar rates of MACCEs (log-rank p=0.72) and all-cause mortality (log-rank p=0.99) in the 2 groups. Age and smoking were independent predictors of MACCEs. Subgroups exhibited no differences in clinical outcomes with statin use. Conclusions: Benefit of statin therapy was likely to be limited in low to moderate risk patients with carotid plaques. These results could guide physicians in clinical decision-making regarding cardiovascular prevention.
Lee, Minjae,Gibson, Harry W.,Kim, Taehoon,Colby, Ralph H.,Choi, U Hyeok American Chemical Society 2019 Macromolecules Vol.52 No.11
<P>The role of solvating polyethers on single-ion conduction and segmental dynamics is investigated for an amorphous main-chain polycation, polyviologen (PV), with two different [−(CH<SUB>2</SUB>)<SUB>6</SUB>- and −(CH<SUB>2</SUB>)<SUB>10</SUB>−] spacers and bis(trifluoromethylsulfonyl)imide (Tf<SUB>2</SUB>N<SUP>-</SUP>) counteranions and its blends with three polyethers: 18-crown-6 (18C6), 30-crown-10 (30C10), or poly(ethylene glycol) dimethyl ether 1000. Compared to the neat PV, the addition of polyethers steps up the ion rearrangement (α<SUB>2</SUB>) and segmental motion (α), both processes following the Vogel temperature dependence, consistent with a reduction in the glass-transition temperature (<I>T</I><SUB>g</SUB>) and fragility due to the plasticization by the polyether. An electrode polarization model is used to determine the number density of simultaneously conducting ions and their mobilities. Incorporating polyethers lowers the activation energy of simultaneously conducting Tf<SUB>2</SUB>N<SUP>-</SUP> ions so that the counteranion’s participation in the blends in the ion conduction is more than 4 times higher than that of the unplasticized PV. This is consistent with an increase in the static dielectric constant (ε<SUB>s</SUB>). The maximum enhancement in ε<SUB>s</SUB> is observed in the 30C10 blend with ε<SUB>s</SUB> = 54, whereas the blend with 18C6 having a relatively smaller cavity size shows a value ε<SUB>s</SUB> = 24, similar to that of the neat PV (ε<SUB>s</SUB> = 21). This suggests that 30C10 may be large enough to wrap both pyridiniums in the viologen repeat unit, promoting the dissociation of viologen-Tf<SUB>2</SUB>N ion pairs, thereby creating separated ion pairs with a larger dipole. The plasticization and complexation play a significant role in directly boosting ionic conductivity (σ<SUB>DC</SUB>) of the single-ion conducting PV blends by ∼10 times over the whole temperature range measured.</P> [FIG OMISSION]</BR>
Angular Change and Secondary Stress in Main Cables of Suspension Bridges
Minjae Lee,Ho-Kyung Kim 한국강구조학회 2016 International Journal of Steel Structures Vol.16 No.2
Three basic cable equations are proposed for evaluating the deflected shape of the main cables of suspension bridges subject to angular changes near the saddles of the main towers as well as the cable bands. The secondary stress on the tensioned parallel wires can be estimated via the combined use of the three basic cable equations that take into account the free and/or friction slip between wires as a function of the lateral restraints by cable bands and wrapping wires. A series of laboratory loading tests were carried out for a parallel wire strand to validate the proposed procedure. The proposed method was also applied to the Yi Sun-sin Bridge to demonstrate the level of secondary stress in parallel wires and to identify the factors that have an impact on the secondary stress in the completed stage as well as during the construction phase. The residual tension of the wrapping wire, which impacts the frictional resistance between wires of the main cable, was measured from field tests. The evaluated secondary stress was found to exceed 10% of the tensile strength of the wires. The findings reported herein also confirm that the distance between the tower saddle and the first cable band is a critical factor for secondary stress. Based on the experimental validation and application to an actual bridge, the proposed approach, despite being based on simplified formulations, is demonstrated to be useful in predicting the secondary stress that develops in parallel wire cables.