Publications

In Press
Chenghe Guan, Ziming Li, Rahul Mehrotra, Michael Keith, and Abhinav Alakshendra. In Press. “Smart city interventions and green accessibility for urban migrants: Case studies of Patna and Mumbai in India.” Urban Planning International.Abstract
Post-colonial India has experienced rapid urbanization characterized by rural-urban migration and the prosperity of informal settlement in cities. However, urban planning and infrastructure development has paid little attention to the needs of walking accessibility for pedestrians, especially the urban poor and migrants. The goals of “Smart city”-oriented urban policy cover inclusiveness, accessibility, transparency, comfortable, safety, sustainable, etc. In order to find how such emerging policy intervention could help pedestrians, we illustrate non-motorized accessibility challenges and opportunities for migrants and urban poor in Patna and Mumbai through case studies at multiple scales and various aspects. We found that to fulfill the needs of pedestrians not only means providing them adequate facilities but also means embodying the idea of inclusiveness and users’ perceptions into practical methods for enhancing accessibility. Moreover, informality makes the vision of smart cities more complex in the two cities, which implies the significance to hearing the diverse grassroots opinions by applying “smart” governance concept as well as innovative technologies for collecting data of accessibility of different social groups. 
M. A. Mapalo, N. Robin, B. E. Boudinot, J. Ortega-Hernández, and P. A. Barden. In Press. “A tardigrade in Dominican amber.” Proceedings of the Royal Society B .
MM Krasnow. In Press. “Ultrasociality without group selection: possible, reasonable, and likely.” Behavioral & Brain Sciences.Abstract

Comment on The Economic Origins of Ultrasociality by Gowdy & Krall. 

Vijay Janapa Reddi, Meeta Gupta, Glenn Holloway, Michael D Smith, Gu-Yeon Wei, and David Brooks. In Press. “Voltage emergency prediction”.
Hyoun Kyu Cho, Scott Mahlke, Farrukh Hijaz, Qingchuan Shi, Omer Khan, Mostafa Farahani, Amirali Baniasadi, Dr Michigan, Ron Dreslinski, Ram Krishnamurthy, and others. In Press. “Workshop on Near-threshold Computing (WNTC)”.
K. Schoonderwoerd and W.E. Friedman. In Press. “Zygotic dormancy underlies prolonged seed development in Franklinia alatamaha (Theaceae): a most unusual case of reproductive phenology in angiosperms. .” Botanical Journal of the Linnean Society.
In Preparation
N. Ranc, P. R. Moorcroft, F. Ossi, and F. Cagnacci. In Preparation. “Memory drives foraging decisions in a large wild mammal: evidence from a field experiment.” Proceedings of the National Academy of Sciences.
Tim Johnson, Glenn Adelson, and Bouffard A. In Preparation. “My Title.” In Conference ABC. Athens, GA. Publisher's Version
Dan Cabral. In Preparation. “Test Pub,” 65, 4, Pp. 23-25.
Submitted
Josiah Blackmore. Submitted. “Portuguese Scenes of the Senses, Medieval and Early Modern.” Edited by Ryan Giles. Beyond Sight: Smell, Taste, Touch and Hearing in Iberian Literatures and Cultures, Pp. 1200-1750.
Emily R Hager, Olivia S. Harringmeyer, T. Brock Wooldridge, Shunn Theingi, Jacob T. Gable, Sade McFadden, Beverly Neugeboren, Kyle M. Turner, and Hopi E. Hoekstra. Submitted. “A chromosomal inversion drives evolution of multiple adaptive traits in deermice.” bioRxiv.Abstract
A long-standing question in evolutionary biology is how differences in multiple traits can evolve quickly and be maintained together during local adaptation. Using forest and prairie ecotypes in deer mice, which differ in both tail length and coat color, we discovered a 41 Mb chromosomal inversion that is strongly linked to variation in both traits. The inversion maintains highly divergent loci in strong linkage disequilibrium and likely originated ~170 kya, long before the forest-prairie divergence ~10 kya. Consistent with a role in local adaptation, inversion frequency is associated with phenotype and habitat across both a local transect and the species range. Still, although eastern and western forest subspecies share similar phenotypes, the inversion isabsent in eastern North America. This work highlights the significance of inversion polymorphisms for the establishment and maintenance of multiple locally adaptive traits in mammals, and demonstrates that, even within a species, parallel phenotypes may evolve through non-parallel genetic mechanisms.
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Xiaoyao Liang, Gu-Yeon Wei, and David Brooks. Submitted. “Combating process variations”.
Yanmin Zhang, Sourav Chowdhury, Joao Rodrigues, and Eugene Shakhnovich. Submitted. “Development of Antibacterial Compounds That Block Evolutionary Pathways to Resistance.” arXiv:2011.01098 [q-bio]. Publisher's VersionAbstract
Antibiotic resistance is a worldwide challenge. A potential approach to block resistance is to simultaneously inhibit WT and known escape variants of the target bacterial protein. Here we applied an integrated computational and experimental approach to discover compounds that inhibit both WT and trimethoprim (TMP) resistant mutants of E. coli dihydrofolate reductase (DHFR). We identified a novel compound (CD15-3) that inhibits WT DHFR and its TMP resistant variants L28R, P21L and A26T with IC50 50-75 micromoles against WT and TMP-resistant strains. Resistance to CD15-3 was dramatically delayed compared to TMP in in vitro evolution. Whole genome sequencing of CD15-3 resistant strains showed no mutations in the target folA locus. Rather, gene duplication of several efflux pumps gave rise to weak (about twofold increase in IC50) resistance against CD15-3. Altogether, our results demonstrate the promise of strategy to develop evolution drugs - compounds which block evolutionary escape routes in pathogens.
Sergio Delgado. Submitted. “Objetos relacionais y la educación de los sentidos en Lygia Clark.” Cuadernos de Literatura.
Alfred W. Crompton, Catherine Musinsky, José F. Bonaparte, Bhart-Anjan Bhullar, and Tomasz Owerkowicz. Submitted. “Evolution of the mammalian fauces region and the origin of suckling.” Journal of Mammalian Evolution.Abstract
Suckling in therian mammals requires synchronous activity in the tensor veli palatini, palatoglossus, mylohyoideus and intrinsic tongue muscles that close the fauces. These muscles draw the dorsal surface of the tongue against a tensed soft palate to form a seal between the oral cavity and oropharynx. Depressing the tongue in front of the seal induces negative pressure and draws milk into the oral cavity. To trace the origin of fauces region in mammals, we studied serial sections of a pouch young marsupial and CT scans of non-mammalian cynodonts, ictidosaurs, mammaliaforms, and extant mammals.In Late Triassic ictidosaurs (Brasilitherium) and mammaliaforms, the origin of a medial slip of the reptilian posterior pterygoideus migrated to the lateral surface of the pterygopalatine boss that supported the lateral edge of a non-muscular soft palate. Suckling arose in early mammals after fibers of this slip migrated into the soft palate to form the tensor veli palatini, and the palatoglossus separated from the pharyngeal constrictors. The added stress on the pterygopalatine boss led to the addition of a hamulus. Once the transverse process of the pterygoid was lost, the lateral posterior pterygoideus differentiated to form the medial pterygoid. Monotreme ancestors modified the fauces region to break down invertebrates between keratinized pads on the posterior tongue and under the ventral surface of a long palatine. They lost the tensor veli palatini and palatoglossus and lack the ability to suckle.
Sergio Delgado. Submitted. “Fascination, or Enlightenment in the Age of Neon Light: The Case of Concrete Poetry in Brazil.” October.
Tong Wang, Haipeng Gong, and EugeneI. Shakhnovich. Submitted. “Improved fragment-based movement with LRFragLib for all-atom Ab initio protein folding.” arXiv preprint arXiv:1906.05785. Publisher's VersionAbstract
Fragment-based assembly has been widely used in Ab initio protein folding simulation which can effectively reduce the conformational space and thus accelerate sampling. The efficiency of fragment-based movement as well as the quality of fragment library determine whether the folding process can lead the free energy landscape to the global minimum and help the protein to reach near-native folded state. We designed an improved fragment-based movement, "fragmove", which substituted multiple backbone dihedral angles in every simulation step. This movement strategy was derived from the fragment library generated by LRFragLib, an effective fragment detection algorithm using logistic regression model. We show in replica exchange Monte Carlo (REMC) simulation that "fragmove", when compared with a set of existing movements in REMC, shows significant improved ability at increasing secondary and tertiary predicted model accuracy by 11.24% and 17.98%, respectively and reaching energy minima decreased by 5.72%. Our results demonstrate that this improved movement is more powerful to guide proteins faster to low energy regions of conformational space and promote folding efficiency and predicted model accuracy.
EM Wolkovich, S Allesina, KL Cottingham, JC Moore, and C de Mazancourt. Submitted. “Linking the green and brown worlds: The prevalence and effect of multi-channel feeding in food webs.” Ecology.
Sergio Delgado. Submitted. “Lygia Clark: At Home With Objects.” Journal of Latin American Cultural Studies.
Eugene Serebryany, Sourav Chowdhury, Nicki E. Watson, Arthur McClelland, and EugeneI. Shakhnovich. Submitted. “A Native Chemical Chaperone in the Human Eye Lens.” arXiv:2012.09805 [q-bio]. Publisher's VersionAbstract
Cataract is one of the most prevalent protein aggregation disorders and still the biggest cause of vision loss worldwide. The human lens, in its core region, lacks turnover of any cells or cellular components; it has therefore evolved remarkable mechanisms for resisting protein aggregation for a lifetime. We now report that one such mechanism relies on an unusually abundant metabolite, myo-inositol, to suppress light-scattering aggregation of lens proteins. We quantified aggregation suppression by in vitro turbidimetry and characterized both macroscopic and microscopic mechanisms of myo-inositol action using negative-stain electron microscopy, differential scanning fluorometry, and a thermal scanning Raman spectroscopy apparatus. Given recent metabolomic evidence that it is dramatically depleted in human cataractous lenses compared to age-matched controls, we suggest that maintaining or restoring healthy levels of myo-inositol in the lens may be a simple, safe, and widely available strategy for reducing the global burden of cataract.

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