Faculty Publications

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This collection includes faculty journal articles deposited per Rice's Open Access Policy and additional faculty work. Items found in this collection can also be found in the authors' departmental faculty publication collections.

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1,4-Dioxane-degrading consortia can be enriched from uncontaminated soils: prevalence of Mycobacterium and soluble di-iron monooxygenase genes
(Wiley, 2017) He, Ya; Mathieu, Jacques; da Silva, Marcio L.B.; Li, Mengyan; Alvarez, Pedro J.J.
Two bacterial consortia were enriched from uncontaminated soil by virtue of their ability to grow on 1,4-dioxane (dioxane) as a sole carbon and energy source. Their specific dioxane degradation rates at 30°C, pH = 7 (i.e. 5.7 to 7.1 g-dioxane per g-protein per day) were comparable to those of two dioxane-metabolizing archetypes: Pseudonocardia dioxanivoransCB1190 and Mycobacterium dioxanotrophicusPH-06. Based on 16S rRNA sequencing, Mycobacterium was the dominant genus. Acetylene inhibition tests suggest that dioxane degradation was mediated by monooxygenases. However, qPCR analyses targeting the tetrahydrofuran/dioxane monooxygenase gene (thmA/dxmA) (which is, to date, the only sequenced dioxane monooxygenase gene) were negative, indicating that other (as yet unknown) catabolic gene(s) were responsible. DNA sequence analyses also showed threefold to sevenfold enrichment of group 5 and group 6 soluble di-iron monooxygenase (SDIMO) genes relative to the original soil samples. Whereas biodegradation of trace levels of dioxane is a common challenge at contaminated sites, both consortia degraded dioxane at low initial concentrations (300 μg l−1) below detectable levels (5 μg l−1) in bioaugmented microcosms prepared with impacted groundwater. Overall, this work shows that dioxane-degrading bacteria (and the associated natural attenuation potential) exist even in some uncontaminated soils, and may be enriched to broaden bioaugmentation options for sites experiencing insufficient dioxane catabolic capacity.
1-bit Phase Shifters for Large-Antenna Full-Duplex mmWave Communications
(IEEE, 2020) da Silva, José Mairton Barros Jr.; Sabharwal, Ashutosh; Fodor, Gábor; Fischione, Carlo
Millimeter-wave using large-antenna arrays is a key technological component for the future cellular systems, where it is expected that hybrid beamforming along with quantized phase shifters will be used due to their implementation and cost efficiency. In this paper, we investigate the efficacy of full-duplex mmWave communication with hybrid beamforming using low-resolution phase shifters. We assume that the self-interference can be sufficiently cancelled by a combination of propagation domain and digital self-interference techniques, without any analog self-interference cancellation. We formulate the problem of joint self-interference suppression and downlink beamforming as a mixed-integer nonconvex joint optimization problem. We propose LowRes, a near-to-optimal solution using penalty dual decomposition. Numerical results indicate that LowRes using low-resolution phase shifters perform within 3% of the optimal solution that uses infinite phase shifter resolution. Moreover, even a single quantization bit outperforms half-duplex transmissions, respectively by 29% and 10% for both low and high residual self-interference scenarios, and for a wide range of practical antenna to radio-chain ratios. Thus, we conclude that 1-bit phase shifters suffice for full-duplex millimeter-wave communications, without requiring any additional new analog hardware.
1D to 3D Crossover of a Spin-Imbalanced Fermi Gas
(American Physical Society, 2016) Revelle, Melissa C.; Fry, Jacob A.; Olsen, Ben A.; Hulet, Randall G.; Rice Center for Quantum Materials
We have characterized the one-dimensional (1D) to three-dimensional (3D) crossover of a two-component spin-imbalanced Fermi gas of 6Li atoms in a 2D optical lattice by varying the lattice tunneling and the interactions. The gas phase separates, and we detect the phase boundaries using in situ imaging of the inhomogeneous density profiles. The locations of the phases are inverted in 1D as compared to 3D, thus providing a clear signature of the crossover. By scaling the tunneling rate t with respect to the pair binding energy εB, we observe a collapse of the data to a universal crossover point at a scaled tunneling value of ˜tc=0.025(7).
222Rn emanation measurements for the XENON1T experiment
(Springer Nature, 2021) XENON Collaboration
The selection of low-radioactive construction materials is of utmost importance for the success of low-energy rare event search experiments. Besides radioactive contaminants in the bulk, the emanation of radioactive radon atoms from material surfaces attains increasing relevance in the effort to further reduce the background of such experiments. In this work, we present the 222Rn emanation measurements performed for the XENON1T dark matter experiment. Together with the bulk impurity screening campaign, the results enabled us to select the radio-purest construction materials, targeting a 222Rn activity concentration of 10μBq/kg in 3.2t of xenon. The knowledge of the distribution of the 222Rn sources allowed us to selectively eliminate problematic components in the course of the experiment. The predictions from the emanation measurements were compared to data of the 222Rn activity concentration in XENON1T. The final 222Rn activity concentration of (4.5±0.1)μBq/kg in the target of XENON1T is the lowest ever achieved in a xenon dark matter experiment.
25th Anniversary Article: Ordered Polymer Structures for the Engineering of Photons and Phonons
(Wiley, 2014) Lee, Jae-Hwang; Koh, Cheong Yang; Singer, Jonathan P.; Jeon, Seog-Jin; Maldovan, Martin; Stein, Ori; Thomas, Edwin L.
The engineering of optical and acoustic material functionalities via construction of ordered local and global architectures on various length scales commensurate with and well below the characteristic length scales of photons and phonons in the material is an indispensable and powerful means to develop novel materials. In the current mature status of photonics, polymers hold a pivotal role in various application areas such as light-emission, sensing, energy, and displays, with exclusive advantages despite their relatively low dielectric constants. Moreover, in the nascent field of phononics, polymers are expected to be a superior material platform due to the ability for readily fabricated complex polymer structures possessing a wide range of mechanical behaviors, complete phononic bandgaps, and resonant architectures. In this review, polymer-centric photonic and phononic crystals and metamaterials are highlighted, and basic concepts, fabrication techniques, selected functional polymers, applications, and emerging ideas are introduced.
25th Annual Computational Neuroscience Meeting: CNS-2016
(BioMed Central, 2016) Sharpee, Tatyana O.; Destexhe, Alain; Kawato, Mitsuo; Sekulić, Vladislav; Skinner, Frances K.; Wójcik, Daniel K.; Chintaluri, Chaitanya; Cserpán, Dorottya; Somogyvári, Zoltán; Kim, Jae K.; Kilpatrick, Zachary P.; Bennett, Matthew R.; Josić, Kresimir; Elices, Irene; Arroyo, David; Levi, Rafael; Rodriguez, Francisco B.; Varona, Pablo; Hwang, Eunjin; Kim, Bowon; Han, Hio-Been; Kim, Tae; McKenna, James T.; Brown, Ritchie E.; McCarley, Robert W.; Choi, Jee H.; Rankin, James; Popp, Pamela O.; Rinzel, John; Tabas, Alejandro; Rupp, André; Balaguer-Ballester, Emili; Maturana, Matias I.; Grayden, David B.; Cloherty, Shaun L.; Kameneva, Tatiana; Ibbotson, Michael R.; Meffin, Hamish; Koren, Veronika; Lochmann, Timm; Dragoi, Valentin; Obermayer, Klaus; Psarrou, Maria; Schilstra, Maria; Davey, Neil; Torben-Nielsen, Benjamin; Steuber, Volker; Ju, Huiwen; Yu, Jiao; Hines, Michael L.; Chen, Liang; Yu, Yuguo; Kim, Jimin; Leahy, Will; Shlizerman, Eli; Birgiolas, Justas; Gerkin, Richard C.; Crook, Sharon M.; Viriyopase, Atthaphon; Memmesheimer, Raoul-Martin; Gielen, Stan; Dabaghian, Yuri; DeVito, Justin; Perotti, Luca; Kim, Anmo J.; Fenk, Lisa M.; Cheng, Cheng; Maimon, Gaby; Zhao, Chang; Widmer, Yves; Sprecher, Simon; Senn, Walter; Halnes, Geir; Mäki-Marttunen, Tuomo; Keller, Daniel; Pettersen, Klas H.; Andreassen, Ole A.; Einevoll, Gaute T.; Yamada, Yasunori; Steyn-Ross, Moira L.; Alistair Steyn-Ross, D.; Mejias, Jorge F.; Murray, John D.; Kennedy, Henry; Wang, Xiao-Jing; Kruscha, Alexandra; Grewe, Jan; Benda, Jan; Lindner, Benjamin; Badel, Laurent; Ohta, Kazumi; Tsuchimoto, Yoshiko; Kazama, Hokto; Kahng, B.; Tam, Nicoladie D.; Pollonini, Luca; Zouridakis, George; Soh, Jaehyun; Kim, DaeEun; Yoo, Minsu; Palmer, S.E.; Culmone, Viviana; Bojak, Ingo; Ferrario, Andrea; Merrison-Hort, Robert; Borisyuk, Roman; Kim, Chang S.; Tezuka, Taro; Joo, Pangyu; Rho, Young-Ah; Burton, Shawn D.; Bard Ermentrout, G.; Jeong, Jaeseung; Urban, Nathaniel N.; Marsalek, Petr; Kim, Hoon-Hee; Moon, Seok-hyun; Lee, Do-won; Lee, Sung-beom; Lee, Ji-yong; Molkov, Yaroslav I.; Hamade, Khaldoun; Teka, Wondimu; Barnett, William H.; Kim, Taegyo; Markin, Sergey; Rybak, Ilya A.; Forro, Csaba; Dermutz, Harald; Demkó, László; Vörös, János; Babichev, Andrey; Huang, Haiping; Verduzco-Flores, Sergio; Dos Santos, Filipa; Andras, Peter; Metzner, Christoph; Schweikard, Achim; Zurowski, Bartosz; Roach, James P.; Sander, Leonard M.; Zochowski, Michal R.; Skilling, Quinton M.; Ognjanovski, Nicolette; Aton, Sara J.; Zochowski, Michal; Wang, Sheng-Jun; Ouyang, Guang; Guang, Jing; Zhang, Mingsha; Michael Wong, K.Y.; Zhou, Changsong; Robinson, Peter A.; Sanz-Leon, Paula; Drysdale, Peter M.; Fung, Felix; Abeysuriya, Romesh G.; Rennie, Chris J.; Zhao, Xuelong; Choe, Yoonsuck; Yang, Huei-Fang; Mi, Yuanyuan; Lin, Xiaohan; Wu, Si; Liedtke, Joscha; Schottdorf, Manuel; Wolf, Fred; Yamamura, Yoriko; Wickens, Jeffery R.; Rumbell, Timothy; Ramsey, Julia; Reyes, Amy; Draguljić, Danel; Hof, Patrick R.; Luebke, Jennifer; Weaver, Christina M.; He, Hu; Yang, Xu; Ma, Hailin; Xu, Zhiheng; Wang, Yuzhe; Baek, Kwangyeol; Morris, Laurel S.; Kundu, Prantik; Voon, Valerie; Agnes, Everton J.; Vogels, Tim P.; Podlaski, William F.; Giese, Martin; Kuravi, Pradeep; Vogels, Rufin; Seeholzer, Alexander; Podlaski, William; Ranjan, Rajnish; Vogels, Tim; Torres, Joaquin J.; Baroni, Fabiano; Latorre, Roberto; Gips, Bart; Lowet, Eric; Roberts, Mark J.; de Weerd, Peter; Jensen, Ole; van der Eerden, Jan; Goodarzinick, Abdorreza; Niry, Mohammad D.; Valizadeh, Alireza; Pariz, Aref; Parsi, Shervin S.; Warburton, Julia M.; Marucci, Lucia; Tamagnini, Francesco; Brown, Jon; Tsaneva-Atanasova, Krasimira; Kleberg, Florence I.; Triesch, Jochen; Moezzi, Bahar; Iannella, Nicolangelo; Schaworonkow, Natalie; Plogmacher, Lukas; Goldsworthy, Mitchell R.; Hordacre, Brenton; McDonnell, Mark D.; Ridding, Michael C.; Zapotocky, Martin; Smit, Daniel; Fouquet, Coralie; Trembleau, Alain; Dasgupta, Sakyasingha; Nishikawa, Isao; Aihara, Kazuyuki; Toyoizumi, Taro; Robb, Daniel T.; Mellen, Nick; Toporikova, Natalia; Tang, Rongxiang; Tang, Yi-Yuan; Liang, Guangsheng; Kiser, Seth A.; Howard, James H.; Goncharenko, Julia; Voronenko, Sergej O.; Ahamed, Tosif; Stephens, Greg; Yger, Pierre; Lefebvre, Baptiste; Spampinato, Giulia L.B.; Esposito, Elric; et Olivier Marre, Marcel S.; Choi, Hansol; Song, Min-Ho; Chung, SueYeon; Lee, Dan D.; Sompolinsky, Haim; Phillips, Ryan S.; Smith, Jeffrey; Chatzikalymniou, Alexandra P.; Ferguson, Katie; Alex Cayco Gajic, N.; Clopath, Claudia; Angus Silver, R.; Gleeson, Padraig; Marin, Boris; Sadeh, Sadra; Quintana, Adrian; Cantarelli, Matteo; Dura-Bernal, Salvador; Lytton, William W.; Davison, Andrew; Li, Luozheng; Zhang, Wenhao; Wang, Dahui; Song, Youngjo; Park, Sol; Choi, Ilhwan; Shin, Hee-sup; Choi, Hannah; Pasupathy, Anitha; Shea-Brown, Eric; Huh, Dongsung; Sejnowski, Terrence J.; Vogt, Simon M; Kumar, Arvind; Schmidt, Robert; Van Wert, Stephen; Schiff, Steven J.; Veale, Richard; Scheutz, Matthias; Lee, Sang W.; Gallinaro, Júlia; Rotter, Stefan; Rubchinsky, Leonid L.; Cheung, Chung C.; Ratnadurai-Giridharan, Shivakeshavan; Shomali, Safura R.; Ahmadabadi, Majid N.; Shimazaki, Hideaki; Nader Rasuli, S.; Zhao, Xiaochen; Rasch, Malte J.; Wilting, Jens; Priesemann, Viola; Levina, Anna; Rudelt, Lucas; Lizier, Joseph T.; Spinney, Richard E.; Rubinov, Mikail; Wibral, Michael; Bak, Ji H.; Pillow, Jonathan; Zaho, Yuan; Park, Il M.; Kang, Jiyoung; Park, Hae-Jeong; Jang, Jaeson; Paik, Se-Bum; Choi, Woochul; Lee, Changju; Song, Min; Lee, Hyeonsu; Park, Youngjin; Yilmaz, Ergin; Baysal, Veli; Ozer, Mahmut; Saska, Daniel; Nowotny, Thomas; Chan, Ho K.; Diamond, Alan; Herrmann, Christoph S.; Murray, Micah M.; Ionta, Silvio; Hutt, Axel; Lefebvre, Jérémie; Weidel, Philipp; Duarte, Renato; Morrison, Abigail; Lee, Jung H.; Iyer, Ramakrishnan; Mihalas, Stefan; Koch, Christof; Petrovici, Mihai A.; Leng, Luziwei; Breitwieser, Oliver; Stöckel, David; Bytschok, Ilja; Martel, Roman; Bill, Johannes; Schemmel, Johannes; Meier, Karlheinz; Esler, Timothy B.; Burkitt, Anthony N.; Kerr, Robert R.; Tahayori, Bahman; Nolte, Max; Reimann, Michael W.; Muller, Eilif; Markram, Henry; Parziale, Antonio; Senatore, Rosa; Marcelli, Angelo; Skiker, K.; Maouene, M.; Neymotin, Samuel A.; Seidenstein, Alexandra; Lakatos, Peter; Sanger, Terence D.; Menzies, Rosemary J.; McLauchlan, Campbell; van Albada, Sacha J.; Kedziora, David J.; Neymotin, Samuel; Kerr, Cliff C.; Suter, Benjamin A.; Shepherd, Gordon M.G.; Ryu, Juhyoung; Lee, Sang-Hun; Lee, Joonwon; Lee, Hyang J.; Lim, Daeseob; Wang, Jisung; Lee, Heonsoo; Jung, Nam; Anh Quang, Le; Maeng, Seung E.; Lee, Tae H.; Lee, Jae W.; Park, Chang-hyun; Ahn, Sora; Moon, Jangsup; Choi, Yun S.; Kim, Juhee; Jun, Sang B.; Lee, Seungjun; Lee, Hyang W.; Jo, Sumin; Jun, Eunji; Yu, Suin; Goetze, Felix; Lai, Pik-Yin; Kim, Seonghyun; Kwag, Jeehyun; Jang, Hyun J.; Filipović, Marko; Reig, Ramon; Aertsen, Ad; Silberberg, Gilad; Bachmann, Claudia; Buttler, Simone; Jacobs, Heidi; Dillen, Kim; Fink, Gereon R.; Kukolja, Juraj; Kepple, Daniel; Giaffar, Hamza; Rinberg, Dima; Shea, Steven; Koulakov, Alex; Bahuguna, Jyotika; Tetzlaff, Tom; Kotaleski, Jeanette H.; Kunze, Tim; Peterson, Andre; Knösche, Thomas; Kim, Minjung; Kim, Hojeong; Park, Ji S.; Yeon, Ji W.; Kim, Sung-Phil; Kang, Jae-Hwan; Lee, Chungho; Spiegler, Andreas; Petkoski, Spase; Palva, Matias J.; Jirsa, Viktor K.; Saggio, Maria L.; Siep, Silvan F.; Stacey, William C.; Bernar, Christophe; Choung, Oh-hyeon; Jeong, Yong; Lee, Yong-il; Kim, Su H.; Jeong, Mir; Lee, Jeungmin; Kwon, Jaehyung; Kralik, Jerald D.; Jahng, Jaehwan; Hwang, Dong-Uk; Kwon, Jae-Hyung; Park, Sang-Min; Kim, Seongkyun; Kim, Hyoungkyu; Kim, Pyeong S.; Yoon, Sangsup; Lim, Sewoong; Park, Choongseok; Miller, Thomas; Clements, Katie; Ahn, Sungwoo; Ji, Eoon H.; Issa, Fadi A.; Baek, JeongHun; Oba, Shigeyuki; Yoshimoto, Junichiro; Doya, Kenji; Ishii, Shin; Mosqueiro, Thiago S.; Strube-Bloss, Martin F.; Smith, Brian; Huerta, Ramon; Hadrava, Michal; Hlinka, Jaroslav; Bos, Hannah; Helias, Moritz; Welzig, Charles M.; Harper, Zachary J.; Kim, Won S.; Shin, In-Seob; Baek, Hyeon-Man; Han, Seung K.; Richter, René; Vitay, Julien; Beuth, Frederick; Hamker, Fred H.; Toppin, Kelly; Guo, Yixin; Graham, Bruce P.; Kale, Penelope J.; Gollo, Leonardo L.; Stern, Merav; Abbott, L.F.; Fedorov, Leonid A.; Giese, Martin A.; Ardestani, Mohammad H.; Faraji, Mohammad J.; Preuschoff, Kerstin; Gerstner, Wulfram; van Gendt, Margriet J.; Briaire, Jeroen J.; Kalkman, Randy K.; Frijns, Johan H.M.; Lee, Won H.; Frangou, Sophia; Fulcher, Ben D.; Tran, Patricia H.P.; Fornito, Alex; Gliske, Stephen V.; Lim, Eugene; Holman, Katherine A.; Fink, Christian G.; Kim, Jinseop S.; Mu, Shang; Briggman, Kevin L.; Sebastian Seung, H.; Wegener, Detlef; Bohnenkamp, Lisa; Ernst, Udo A.; Devor, Anna; Dale, Anders M.; Lines, Glenn T.; Edwards, Andy; Tveito, Aslak; Hagen, Espen; Senk, Johanna; Diesmann, Markus; Schmidt, Maximilian; Bakker, Rembrandt; Shen, Kelly; Bezgin, Gleb; Hilgetag, Claus-Christian; van Albada, Sacha J.; Sun, Haoqi; Sourina, Olga; Huang, Guang-Bin; Klanner, Felix; Denk, Cornelia; Glomb, Katharina; Ponce-Alvarez, Adrián; Gilson, Matthieu; Ritter, Petra; Deco, Gustavo; Witek, Maria A.G.; Clarke, Eric F.; Hansen, Mads; Wallentin, Mikkel; Kringelbach, Morten L.; Vuust, Peter; Klingbeil, Guido; De Schutter, Erik; Chen, Weiliang; Zang, Yunliang; Hong, Sungho; Takashima, Akira; Zamora, Criseida; Gallimore, Andrew R.; Goldschmidt, Dennis; Manoonpong, Poramate; Karoly, Philippa J.; Freestone, Dean R.; Soundry, Daniel; Kuhlmann, Levin; Paninski, Liam; Cook, Mark; Lee, Jaejin; Fishman, Yonatan I.; Cohen, Yale E.; Roberts, James A.; Cocchi, Luca; Sweeney, Yann; Lee, Soohyun; Jung, Woo-Sung; Kim, Youngsoo; Jung, Younginha; Song, Yoon-Kyu; Chavane, Frédéric; Soman, Karthik; Muralidharan, Vignesh; Srinivasa Chakravarthy, V.; Shivkumar, Sabyasachi; Mandali, Alekhya; Pragathi Priyadharsini, B.; Mehta, Hima; Davey, Catherine E.; Brinkman, Braden A.W.; Kekona, Tyler; Rieke, Fred; Buice, Michael; De Pittà, Maurizio; Berry, Hugues; Brunel, Nicolas; Breakspear, Michael; Marsat, Gary; Drew, Jordan; Chapman, Phillip D.; Daly, Kevin C.; Bradle, Samual P.; Seo, Sat B.; Su, Jianzhong; Kavalali, Ege T.; Blackwell, Justin; Shiau, LieJune; Buhry, Laure; Basnayake, Kanishka; Lee, Sue-Hyun; Levy, Brandon A.; Baker, Chris I; Leleu, Timothée; Philips, Ryan T.; Chhabria, Karishma
2D material integrated macroporous electrodes for Li-ion batteries
(Royal Society of Chemistry, 2017) Gullapalli, Hemtej; Kalaga, Kaushik; Vinod, Soumya; Rodrigues, Marco-Tulio F.; George, Antony; Ajayan, Pulickel M.
Three-dimensionally structured architectures are known to improve the performance of electrodes used in Li ion battery systems. In addition, integration of select 2D materials into 3D structures, for enhancing both electrical conductivity and electrochemical activity, will prove advantageous. Here a scalable one-step chemical vapor deposition technique is demonstrated for the controlled etching and simultaneous graphene growth on stainless steel substrates resulting in a 3D micro-mesh architecture that is ideal for high rate/high capacity electrodes; the graphene coated 3D stainless steel current collector is used with an MoS2 electrode material for demonstrating high stability and rate capacity in Li-ion batteries.
3-Dimensional spatially organized PEG-based hydrogels for an aortic valve co-culture model
(Elsevier, 2015) Puperi, Daniel S.; Balaoing, Liezl R.; O'Connell, Ronan W.; West, Jennifer L.; Grande-Allen, K. Jane
Physiologically relevant inﾠvitro models are needed to study disease progression and to develop and screen potential therapeutic interventions for disease. Heart valve disease, in particular, has no early intervention or non-invasive treatment because there is a lack of understanding the cellular mechanisms which lead to disease. Here, we establish a novel, customizable synthetic hydrogel platform that can be used to study cell-cell interactions and the factors which contribute to valve disease. Spatially localized cell adhesive ligands bound in the scaffold promote cell growth and organization of valve interstitial cells and valve endothelial cells in 3D co-culture. Both cell types maintained phenotypes, homeostatic functions, and produced zonally localized extracellular matrix. This model extends the capabilities of inﾠvitro research by providing a platform to perform direct contact co-culture with cells in their physiologically relevant spatial arrangement.
3D bioprinting: improving in vitro models of metastasis with heterogeneous tumor microenvironments
(The Company of Biologists, 2017) Albritton, Jacob L.; Miller, Jordan S.
Even with many advances in treatment over the past decades, cancer still remains a leading cause of death worldwide. Despite the recognized relationship between metastasis and increased mortality rate, surprisingly little is known about the exact mechanism of metastatic progression. Currently available in vitro models cannot replicate the three-dimensionality and heterogeneity of the tumor microenvironment sufficiently to recapitulate many of the known characteristics of tumors in vivo. Our understanding of metastatic progression would thus be boosted by the development of in vitro models that could more completely capture the salient features of cancer biology. Bioengineering groups have been working for over two decades to create in vitro microenvironments for application in regenerative medicine and tissue engineering. Over this time, advances in 3D printing technology and biomaterials research have jointly led to the creation of 3D bioprinting, which has improved our ability to develop in vitro models with complexity approaching that of the in vivo tumor microenvironment. In this Review, we give an overview of 3D bioprinting methods developed for tissue engineering, which can be directly applied to constructing in vitro models of heterogeneous tumor microenvironments. We discuss considerations and limitations associated with 3D printing and highlight how these advances could be harnessed to better model metastasis and potentially guide the development of anti-cancer strategies.
3D Covalent Organic Frameworks with Interpenetrated pcb Topology Based on 8-Connected Cubic Nodes
(American Chemical Society, 2022) Shan, Zhen; Wu, Miaomiao; Zhu, Dongyang; Wu, Xiaowei; Zhang, Kan; Verduzco, Rafael; Zhang, Gen
The connectivity of building units for 3D covalent organic frameworks (COFs) has long been primarily 4 and 6, which have severely curtailed the structural diversity of 3D COFs. Here we demonstrate the successful design and synthesis of a porphyrin based, 8-connected building block with cubic configuration, which could be further reticulated into an unprecedented interpenetrated pcb topology by imine condensation with linear amine monomers. This study presents the first case of high-connectivity building units bearing 8-connected cubic nodes, thus greatly enriching the topological possibilities of 3D COFs.
3D Macroporous Solids from Chemically Cross-linked Carbon Nanotubes
(Wiley, 2014) Ozden, Sehmus; Narayanan, Tharangattu N.; Tiwary, Chandra S.; Dong, Pei; Hart, Amelia H.C.; Vajtai, Robert; Ajayan, Pulickel M.
Suzuki reaction for covalently interconnected 3D carbon nanotube (CNT) architectures is reported. The synthesis of 3D macroscopic solids made of CNTs covalently connected via Suzuki cross-coupling, a well-known carbon-carbon covalent bond forming reaction in organic chemistry, is scalable. The resulting solid has a highly porous, interconnected structure of chemically cross-linked CNTs. Its use for the removal of oil from contaminated water is demonstrated.
3D printed fiber optic faceplates by custom controlled fused deposition modeling
(Optical Society of America, 2018) Wang, Ye; Gawedzinski, John; Pawlowski, Michal E.; Tkaczyk, Tomasz S.
A 3D printing technique for manufacturing air-clad coherent fiber optic faceplates is presented. The custom G-code programming is implemented on a fused deposition modeling (FDM) desktop printer to additively draw optical fibers using high-transparency thermoplastic filaments. The 3D printed faceplate consists of 20000 fibers and achieves spatial resolution 1.78 LP/mm. Transmission loss and crosstalk are characterized and compared among the faceplates printed from four kinds of transparent filaments as well as different faceplate thicknesses. The printing temperature is verified by testing the transmission of the faceplates printed under different temperatures. Compared with the conventional stack-and-draw fabrication, the FDM 3D printing technique simplifies the fabrication procedure. The ability to draw fibers with arbitrary organization, structure and overall shape provides additional degree of freedom to opto-mechanical design. Our results indicate a promising capability of 3D printing as the manufacturing technology for fiber optical devices.
3D Shear Velocity Structure of the Caribbean—Northwestern South America Subduction Zone From Ambient Noise and Ballistic Rayleigh Wave Tomography
(Wiley, 2024) Miao, Wenpei; Cornthwaite, John; Levander, Alan; Niu, Fenglin; Schmitz, Michael; Li, Guoliang; Dionicio, Viviana; Prieto, German
The Caribbean-South America subduction zone is a flat subduction zone, with Laramide-style thick-skinned uplifts occurring in the Merida Andes, Sierra de Perija Range, and Santa Marta Massif. Geodetic measurements and historical seismicity show this region is storing strain energy and is capable of a mega-thrust earthquake (M ≥ 8.0). Previous seismic investigations of the lithosphere and upper mantle in this area are either very large scale, very local, or only peripheral to this area; therefore, details of the Caribbean plate subduction geometry beneath the Maracaibo block remain unclear. In this study, we used a new data set acquired by the Caribbean-Merida Andes seismic experiment (CARMA), which comprised 65 temporary broadband stations and 44 permanent stations from the Colombian and Venezuelan national seismic networks. We jointly inverted ambient noise Rayleigh wave Z/H ratios, phase velocities in the 8–30 s band and ballistic Rayleigh wave phase velocities in 30–80 s band to construct a 3-D S-wave velocity model in the area between 75°–65°W and 5°–12°N. The 3-D model reveals a general increase in crust thickness from the trench to the southeast. An anomalous area is the Lake Maracaibo, which is underlaid by the thinnest crystalline crust in the region. This observation may indicate that the Maracaibo block is experiencing a contortion deformation within the crust. We also identified a high velocity anomaly above the subducting Caribbean slab, likely representing a detached piece of eclogitized Caribbean large igneous province from the base of the Maracaibo block. Additionally, our Vs model clearly indicates a slab tear within the subducted Caribbean slab, approximately beneath the Oca-Ancon Fault.
3D tissue-engineered model of Ewing's sarcoma
(Elsevier, 2014) Lamhamedi-Cherradi, Salah-Eddine; Santoro, Marco; Ramammoorthy, Vandhana; Menegaz, Brian A.; Bartholomeusz, Geoffrey; Iles, Lakesla R.; Amin, Hesham M.; Livingston, J. Andrew; Mikos, Antonios G.; Ludwig, Joseph A.
Despite longstanding reliance upon monolayer culture for studying cancer cells, and numerous advantages from both a practical and experimental standpoint, a growing body of evidence suggests that more complex three-dimensional (3D) models are necessary to properly mimic many of the critical hallmarks associated with the oncogenesis, maintenance and spread of Ewing's sarcoma (ES), the second most common pediatric bone tumor. And as clinicians increasingly turn to biologically-targeted therapies that exert their effects not only on the tumor cells themselves, but also on the surrounding extracellular matrix, it is especially important that preclinical models evolve in parallel to reliably measure antineoplastic effects and possible mechanisms of de novo and acquired drug resistance. Herein, we highlight a number of innovative methods used to fabricate biomimetic ES tumors, encompassing both the surrounding cellular milieu and the extracellular matrix (ECM), and suggest potential applications to advance our understanding of ES biology, preclinical drug testing, and personalized medicine.
3D touchless multiorder reflection structural color sensing display
(American Association for the Advancement of Science, 2020) Kang, Han Sol; Han, Sang Won; Park, Chanho; Lee, Seung Won; Eoh, Hongkyu; Baek, Jonghyeok; Shin, Dong-Gap; Park, Tae Hyun; Huh, June; Lee, Hyungsuk; Kim, Dae-Eun; Ryu, Du Yeol; Thomas, Edwin L.; Koh, Won-Gun; Park, Cheolmin
The development of a lightweight, low-power, user-interactive three-dimensional (3D) touchless display in which a human stimulus can be detected and simultaneously visualized in noncontact mode is of great interest. Here, we present a user-interactive 3D touchless sensing display based on multiorder reflection structural colors (SCs) of a thin, solid-state block copolymer (BCP) photonic crystal (PC). Full-visible-range SCs are developed in a BCP PC consisting of alternating lamellae, one of which contains a chemically cross-linked, interpenetrated hydrogel network. The absorption of a nonvolatile ionic liquid into the domains of the interpenetrated network allows for further manipulation of SC by using multiple-order photonic reflections, giving rise to unprecedented visible SCs arising from reflective color mixing. Furthermore, by using a hygroscopic ionic liquid ink, a printable 3D touchless interactive display is created where 3D position of a human finger is efficiently visualized in different SCs as a function of finger-to-display distance.
3D Ultrastructure of the Cochlear Outer Hair Cell Lateral Wall Revealed By Electron Tomography
(Frontiers, 2019) Triffo, William Jeffrey; Palsdottir, Hildur; Song, Junha; Morgan, David Gene; McDonald, Kent L.; Auer, Manfred; Raphael, Robert M.
Outer Hair Cells (OHCs) in the mammalian cochlea display a unique type of voltage-induced mechanical movement termed electromotility, which amplifies auditory signals and contributes to the sensitivity and frequency selectivity of mammalian hearing. Electromotility occurs in the OHC lateral wall, but it is not fully understood how the supramolecular architecture of the lateral wall enables this unique form of cellular motility. Employing electron tomography of high-pressure frozen and freeze-substituted OHCs, we visualized the 3D structure and organization of the membrane and cytoskeletal components of the OHC lateral wall. The subsurface cisterna (SSC) is a highly prominent feature, and we report that the SSC membranes and lumen possess hexagonally ordered arrays of particles. We also find the SSC is tightly connected to adjacent actin filaments by short filamentous protein connections. Pillar proteins that join the plasma membrane to the cytoskeleton appear as variable structures considerably thinner than actin filaments and significantly more flexible than actin-SSC links. The structurally rich organization and rigidity of the SSC coupled with apparently weaker mechanical connections between the plasma membrane (PM) and cytoskeleton reveal that the membrane-cytoskeletal architecture of the OHC lateral wall is more complex than previously appreciated. These observations are important for our understanding of OHC mechanics and need to be considered in computational models of OHC electromotility that incorporate subcellular features.
4 Ezra and 2 Baruch: Literary Composition and Oral Performance in First-Century Apocalyptic Literature
(the Society of Biblical Literature, 2012) Henze, Matthias
Students of 4 Ezra and 2 Baruch have long noticed numerous thematic, generic, and linguistic parallels that exist between them. Both texts were written in the late first or possibly the early second century C.E., most likely in the land of Israel. The composition of both works was triggered by the Roman destruction of Jerusalem in the year 70 C.E., as both texts are, in essence, elaborate responses to the host of challenges posted by the Roman aggression. Both stories are set fictitiously during the Babylonian destruction of Jerusalem in the sixth century B.C.E. 4 Ezra and 2 Baruch are Jewish apocalypses of the historical type, and both make extensive use of the same set of literary genres, such as prophetic dialogue, prayer, public speech, and the symbolic dream vision. Neither author reveals his identity by instead chooses to write pseudonymously in the voice of a biblical scribe of the exilic and early postexilic period: Ezra, who returned the Torah to Jerusalem, and Baruch, the scribe of Jeremiah. What drives the momentum forward is a continuous revelatory dialogue between the seer and God, or God's interpreting angel. By the end of each book both seers have undergone a remarkable transformation, from skeptic to consoler, ideal community leader, and latter-day Moses.
4500-year paleohurricane record from the Western Gulf of Mexico, Coastal Central TX, USA
(Elsevier, 2024) Monica, Sarah B.; Wallace, Davin J.; Wallace, Elizabeth J.; Du, Xiaojing; Dee, Sylvia G.; Anderson, John B.
Texas receives the second-highest number of tropical cyclone (TC) landfalls per year in the United States. At present, long-term TC projections from climate models remain uncertain due to the short and biased nature of Atlantic TC observations. Sediment archives of past storms can help extend the observational record of TC strikes over the past few millennia. When a TC makes landfall along the central Texas coast, coastal downwelling channels and storm currents transport and deposit coarse sediment to a zone of rapid accumulation along the shelf, known as the Texas Mud Blanket (TMB). This “backwash” process results in expansive storm deposits along the shelf, making this region ideal for paleotempestological reconstructions. Here, we present two sediment cores, located approximately 6 km southeast of Matagorda Island (TX), that collectively yield a ∼4500-year paleohurricane record. 210Pb and 137Cs are utilized in conjunction with radiocarbon ages to produce high-resolution Bayesian age models. One-centimeter interval grain size analyses are used to identify TC deposits. Two-centimeter interval X-Ray Fluorescence (XRF) is used as an additional measure to verify depositional mechanisms in this shelf environment. We define an intense paleohurricane event threshold through statistical analysis of mean grain size data. The sediment-derived TC record is correlated to Palmer Drought Severity Index (PDSI) data from Paleo Hydrodynamics Data Assimilation (PHYDA) to bolster our interpretation of the TC record, revealing a coupled relationship between PDSI and TCs since ∼300 yr BP. Over the ∼4500-year period, 24 intense TCs were recorded in the sediment record, yielding a long-term annual landfall probability of ∼0.53%. Additionally, comparisons between other TC records within the Atlantic establish a relationship between enhanced TC activity in the Western Gulf of Mexico (GOM) and TCs formed in the Caribbean Sea.
A 2-D simulation study on CO2ﾠsoluble surfactant for foam enhanced oil recovery
(Elsevier, 2019) Zeng, Yongchao; Farajzadeh, Rouhi; Biswal, Sibani L.; Hirasaki, George J.
This paper probes the transport of CO2ﾠsoluble surfactant for foaming in porous media. We numerically investigate the effect of surfactant partitioning between the aqueous phase and the gaseous phase on foam transport for subsurface applications when the surfactant is injected in the CO2ﾠphase. A 2-D reservoir simulation is developed to quantify the effect of surfactant partition coefficient on the displacement conformance and CO2ﾠsweep efficiency. A texture-implicit local-equilibrium foam model is embedded to describe how the partitioning of surfactant between water and CO2ﾠaffects the CO2ﾠfoam mobility control when surfactant is injected in the CO2ﾠphase. We conclude that when surfactant has approximately equal affinity to both the CO2ﾠand the water, the transport of surfactant is in line with the gas propagation and therefore the sweep efficiency is maximized. Too high affinity to water (small partition coefficient) results in surfactant retardation whereas too high affinity to CO2ﾠ(large partition coefficient) leads to weak foam and insufficient mobility reduction. This work sheds light upon the design of water-alternating-gas-plus-surfactant-in-gas (WAGﾠ+ﾠS) process to improve the conventional foam process with surfactant-alternating-gas (SAG) injection mode during which significant amount of surfactant could possibly drain down by gravity before CO2ﾠslugs catch up to generate foam in situ the reservoir.
A 3D inﾠvitro model of patient-derived prostate cancer xenograft for controlled interrogation of inﾠvivo tumor-stromal interactions
(Elsevier, 2016) Fong, Eliza L.S.; Wan, Xinhai; Yang, Jun; Morgado, Micaela; Mikos, Antonios G.; Harrington, Daniel Anton; Navone, Nora M.; Farach-Carson, Mary C.
Patient-derived xenograft (PDX) models better represent human cancer than traditional cell lines. However, the complex in vivo environment makes it challenging to employ PDX models to investigate tumor-stromal interactions, such as those that mediate prostate cancer (PCa) bone metastasis. Thus, we engineered a defined three-dimensional (3D) hydrogel system capable of supporting the co-culture of PCa PDX cells and osteoblastic cells to recapitulate the PCa-osteoblast unit within the bone metastatic microenvironment in vitro. Our 3D model not only maintained cell viability but also preserved the typical osteogenic phenotype of PCa PDX cells. Additionally, co-culture cellularity was maintained over that of either cell type cultured alone, suggesting that the PCa-osteoblast cross-talk supports PCa progression in bone, as is hypothesized to occur in patients with prostatic bone metastasis. Strikingly, osteoblastic cells co-cultured with PCa PDX tumoroids organized around the tumoroids, closely mimicking the architecture of PCa metastases in bone. Finally, tumor-stromal signaling mediated by the fibroblast growth factor axis tightly paralleled that in the in vivo counterpart. Together, these findings indicate that this 3D PCa PDX model recapitulates important pathological properties of PCa bone metastasis, and validate the use of this model for controlled and systematic interrogation of complex in vivo tumor-stromal interactions.

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