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Title: Phage probes couple to DNA relaxation dynamics to reveal universal behavior across scales and regimes
M13 phage are a novel microrheological probe that are sensitive to polymer relaxations, capturing DNA dynamics and revealing universal scaling behaviors across the unentangled and entangled regimes. more »« less
Akitaya, Hugo A.; Ballinger, Brad; Demaine, Erik D.; Hull, Thomas C.; Schmidt, Christiane
(, Proceedings of the 33rd Canadian Conference on Computational Geometry (CCCG 2021))
He, Meng; Sheehy, Don
(Ed.)
We introduce basic, but heretofore generally unexplored, problems in computational origami that are similar in style to classic problems from discrete and computational geometry. We consider the problems of folding each corner of a polygon P to a point p and folding each edge of a polygon P onto a line segment L that connects two boundary points of P and compute the number of edges of the polygon containing p or L limited by crease lines and boundary edges.
Abstract From microscaled capillaries to millimeter‐sized vessels, human vasculature spans multiple scales and cell types. The convergence of bioengineering, materials science, and stem cell biology has enabled tissue engineers to recreate the structure and function of different hierarchical levels of the vascular tree. Engineering large‐scale vessels aims to replace damaged arteries, arterioles, and venules and their routine application in the clinic may become a reality in the near future. Strategies to engineer meso‐ and microvasculature are extensively explored to generate models for studying vascular biology, drug transport, and disease progression as well as for vascularizing engineered tissues for regenerative medicine. However, bioengineering tissues for transplantation has failed to result in clinical translation due to the lack of proper integrated vasculature for effective oxygen and nutrient delivery. The development of strategies to generate multiscale vascular networks and their direct anastomosis to host vasculature would greatly benefit this formidable goal. In this review, design considerations and technologies for engineering millimeter‐, meso‐, and microscale vessels are discussed. Examples of recent state‐of‐the‐art strategies to engineer multiscale vasculature are also provided. Finally, key challenges limiting the translation of vascularized tissues are identified and perspectives on future directions for exploration are presented.
Mo, Tianchi; Bender, Michael A; Das, Rathish; Farach-Colton, Martin; Tench, David
(, ACM Transactions on Database Systems)
Recent work has investigated adaptive filters, which are filters that change their internal representation in response to queries that yield false positives. These include: (1) strongly adaptive filters, which guarantee a false-positive probability of at most ϵ for any query regardless of the history of prior queries, i.e., against adaptive adversaries, (2) support-optimal filters, which guarantee an average false-positive probability of at most ϵ over sufficiently large query sequences, when the adversary is oblivious, (3) other adaptive filters that change their representation and empirically perform better, but do not come with any specific provable guarantees beyond static filters. In this paper, we investigate the performance advantages that strongly adaptive filters offer on (non-adversarial) skewed query distributions, which are common in database applications. In our theoretical and experimental results, we model query distribution skewness with the Zipfian distribution with parameterz. We consider two strongly adaptive filters: the broom filter and the telescoping adaptive filter (TAF). We also consider two adaptive (but not strongly adaptive) filters: the adaptive cuckoo filter (ACF), and a non-adaptive rank-and-select quotient filter augmented with a cache of recent false positives, which we call the cache-augmented filter (CAF). We prove upper bounds on the false-positive rates of the broom filter, the TAF, and the CAF as a function of the Zipfian parameterzas the length of the query sequence tends to infinity. We provide an implementation of the broom filter, based on the (non-adaptive) rank-and-select quotient filter. We validate the above bounds experimentally on synthetic Zipfian query sequences on the broom filter, the TAF, and the CAF. Finally, we measure the observed false-positive rate of the broom filter, the TAF, the CAF, and the ACF on highly skewed real-world network trace data. We find that all adaptive filters achieved 1-2 orders of magnitude lower false-positive rates than non-adaptive filters. We further find that the broom filter and the TAF outperform the CAF only when the ratio of distinct negative queries to positive set size is high; otherwise, the CAF and the strongly adaptive filters yield similar false-positive rates.
DADARLAT, MARIUS
(, Revue Roumaine Mathematiques Pures Appliquees)
In this article, we survey recent results concerning non-stability of discrete groupswith respect to the operator norm. We focus on topological obstructions toperturbing almost representations of a discrete group Γ into unitary groups U(n)to true representations. Several natural notions of stability are discussed: localto-local stability, uniform-to-uniform stability, uniform-to-local stability, and C∗-stability.
Neurotransmitters are small molecules involved in neuronal signaling and can also serve as stress biomarkers.1Their abnormal levels have been also proposed to be indicative of several neurological diseases such as Alzheimer’s disease, Parkinson’s disease, Huntington disease, among others. Hence, measuring their levels is highly important for early diagnosis, therapy, and disease prognosis. In this work, we investigate facile functionalization methods to tune and enhance sensitivity of printed graphene sensors to neurotransmitters. Sensors based on direct laser scribing and screen-printed graphene ink are studied. These printing methods offer ease of prototyping and scalable fabrication at low cost. The effect of functionalization of laser induced graphene (LIG) by electrodeposition and solution-based deposition of TMDs (molybdenum disulfide2and tungsten disulfide) and metal nanoparticles is studied. For different processing methods, electrochemical characteristics (such as electrochemically active surface area: ECSA and heterogenous electron transfer rate: k0) are extracted and correlated to surface chemistry and defect density obtained respectively using X-ray photoelectron spectroscopy (XPS) and Raman spectroscopy. These functionalization methods are observed to directly impact the sensitivity and limit of detection (LOD) of the graphene sensors for the studied neurotransmitters. For example, as compared to bare LIG, it is observed that electrodeposition of MoS2on LIG improves ECSA by 3 times and k0by 1.5 times.3Electrodeposition of MoS2also significantly reduces LOD of serotonin and dopamine in saliva, enabling detection of their physiologically relevant concentrations (in pM-nM range). In addition, chemical treatment of LIG sensors is carried out in the form of acetic acid treatment. Acetic acid treatment has been shown previously to improve C-C bonds improving the conductivity of LIG sensors.4In our work, in particular, acetic acid treatment leads to larger improvement of LOD of norepinephrine compared to MoS2electrodeposition. In addition, we investigate the effect of plasma treatment to tune the sensor response by modifying the defect density and chemistry. For example, we find that oxygen plasma treatment of screen-printed graphene ink greatly improves LOD of norepinephrine up to three orders of magnitude, which may be attributed to the increased defects and oxygen functional groups on the surface as evident by XPS measurements. Defects are known to play a key role in enhancing the sensitivity of 2D materials to surface interactions, and have been explored in tuning/enhancing the sensor sensitivity.5Building on our previous work,3we apply a custom machine learning-based data processing method to further improve that sensitivity and LOD, and also to automatically benchmark different molecule-material pairs. Future work includes expanding the plasma chemistry and conditions, studying the effect of precursor mixture in laser-induced solution-based functionalization, and understanding the interplay between molecule-material system. Work is also underway to improve the machine learning model by using nonlinear learning models such as neural networks to improve the sensor sensitivity, selectivity, and robustness. ReferencesA. J. Steckl, P. Ray, (2018), doi:10.1021/acssensors.8b00726.Y. Lei, D. Butler, M. C. Lucking, F. Zhang, T. Xia, K. Fujisawa, T. Granzier-Nakajima, R. Cruz-Silva, M. Endo, H. Terrones, M. Terrones, A. Ebrahimi,Sci. Adv.6, 4250–4257 (2020).V. Kammarchedu, D. Butler, A. Ebrahimi,Anal. Chim. Acta.1232, 340447 (2022).H. Yoon, J. Nah, H. Kim, S. Ko, M. Sharifuzzaman, S. C. Barman, X. Xuan, J. Kim, J. Y. Park,Sensors Actuators B Chem.311, 127866 (2020).T. Wu, A. Alharbi, R. Kiani, D. Shahrjerdi,Adv. Mater.31, 1–12 (2019).
Safi_Samghabadi, Farshad, Marfai, Juexin, Cueva, Camyla, Aporvari, Mehdi, Neill, Philip, Chabi, Maede, Robertson-Anderson, Rae M, and Conrad, Jacinta C. Phage probes couple to DNA relaxation dynamics to reveal universal behavior across scales and regimes. Retrieved from https://par.nsf.gov/biblio/10632161. Soft Matter 21.5 Web. doi:10.1039/D4SM01150C.
Safi_Samghabadi, Farshad, Marfai, Juexin, Cueva, Camyla, Aporvari, Mehdi, Neill, Philip, Chabi, Maede, Robertson-Anderson, Rae M, & Conrad, Jacinta C. Phage probes couple to DNA relaxation dynamics to reveal universal behavior across scales and regimes. Soft Matter, 21 (5). Retrieved from https://par.nsf.gov/biblio/10632161. https://doi.org/10.1039/D4SM01150C
Safi_Samghabadi, Farshad, Marfai, Juexin, Cueva, Camyla, Aporvari, Mehdi, Neill, Philip, Chabi, Maede, Robertson-Anderson, Rae M, and Conrad, Jacinta C.
"Phage probes couple to DNA relaxation dynamics to reveal universal behavior across scales and regimes". Soft Matter 21 (5). Country unknown/Code not available: RSC. https://doi.org/10.1039/D4SM01150C.https://par.nsf.gov/biblio/10632161.
@article{osti_10632161,
place = {Country unknown/Code not available},
title = {Phage probes couple to DNA relaxation dynamics to reveal universal behavior across scales and regimes},
url = {https://par.nsf.gov/biblio/10632161},
DOI = {10.1039/D4SM01150C},
abstractNote = {M13 phage are a novel microrheological probe that are sensitive to polymer relaxations, capturing DNA dynamics and revealing universal scaling behaviors across the unentangled and entangled regimes.},
journal = {Soft Matter},
volume = {21},
number = {5},
publisher = {RSC},
author = {Safi_Samghabadi, Farshad and Marfai, Juexin and Cueva, Camyla and Aporvari, Mehdi and Neill, Philip and Chabi, Maede and Robertson-Anderson, Rae M and Conrad, Jacinta C},
}
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