Faculty of Arts and Science

Research Output 1960 2019

2019

1 H-decoupling and Isotopic Labeling for the Measurement of the Longitudinal Relaxation Time of Hyperpolarized 13 C-Methylenes in Choline Analogs

Uppala, S., Gamliel, A., Harris, T., Sosna, J., Gomori, J. M., Jerschow, A. & Katz-Brull, R., Jan 1 2019, In : Israel Journal of Chemistry.

Research output: Contribution to journalArticle

Choline
Relaxation time
Labeling
Protons
Polarization

Ab Initio Molecular Dynamics Study of Hydroxide Diffusion Mechanisms in Nanoconfined Structural Mimics of Anion Exchange Membranes

Zelovich, T., Long, Z., Hickner, M., Paddison, S. J., Bae, C. & Tuckerman, M., Feb 28 2019, In : Journal of Physical Chemistry C. 123, 8, p. 4638-4653 16 p.

Research output: Contribution to journalArticle

hydroxides
Anions
Molecular dynamics
Ion exchange
Negative ions
entropy
Free energy
Permittivity
Entropy
Proteins

A comparison of the prevalence of psychiatric disorders in Puerto Rico with the United States and the Puerto Rican population of the United States

Canino, G., Shrout, P., NeMoyer, A., Vila, D., Santiago, K. M., Garcia, P., Quiñones, A., Cruz, V. & Alegria, M., Jan 1 2019, (Accepted/In press) In : Social Psychiatry and Psychiatric Epidemiology.

Research output: Contribution to journalArticle

Puerto Rico
Psychiatry
social support
Hispanic Americans
Social Support

A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory

Athanasiadou, R., Neymotin, B., Brandt, N., Wang, W., Christiaen, L., Gresham, D. & Tranchina, D., Mar 1 2019, In : PLoS computational biology. 15, 3, p. e1006794

Research output: Contribution to journalArticle

Open Access
Statistical Models
statistical models
RNA
Spike
Calibration

A diverse range of factors affect the nature of neural representations underlying short-term memory

Orhan, A. E. & Ma, W. J., Feb 1 2019, In : Nature Neuroscience. 22, 2, p. 275-283 9 p.

Research output: Contribution to journalArticle

Short-Term Memory
Population
Neurons
Brain

A division of labor between power and phase coherence in encoding attention to stimulus streams

Tavano, A. & Poeppel, D., Jun 1 2019, In : NeuroImage. 193, p. 146-156 11 p.

Research output: Contribution to journalArticle

Reaction Time
Power (Psychology)

Advancing environmental exposure assessment science to benefit society

Caplin, A., Ghandehari, M., Lim, C., Glimcher, P. & Thurston, G., Dec 1 2019, In : Nature Communications. 10, 1, 1236.

Research output: Contribution to journalReview article

Open Access
Air Pollutants
Air Pollution
Environmental Exposure
Health
health

A Fragment Quantum Mechanical Method for Metalloproteins

Xu, M., He, X., Zhu, T. & Zhang, J., Jan 1 2019, (Accepted/In press) In : Journal of Chemical Theory and Computation.

Research output: Contribution to journalArticle

Metalloproteins
Potential energy
potential energy
fragments
Structural optimization

Altered steady state and activity-dependent de novo protein expression in fragile X syndrome

Bowling, H., Bhattacharya, A., Zhang, G., Alam, D., Lebowitz, J. Z., Bohm-Levine, N., Lin, D., Singha, P., Mamcarz, M., Puckett, R., Zhou, L., Aryal, S., Sharp, K., Kirshenbaum, K., Berry-Kravis, E., Neubert, T. A. & Klann, E., Dec 1 2019, In : Nature Communications. 10, 1, 1710.

Research output: Contribution to journalArticle

Open Access
Fragile X Syndrome
proteins
Blood
blood
mice

A matter of timing

Perry, M. W. & Desplan, C., Jan 1 2019, In : eLife. 8

Research output: Contribution to journalArticle

An asymmetrical president-in-power effect

Morisi, D., Jost, J. & Singh, V., May 1 2019, In : American Political Science Review. 113, 2, p. 614-620 7 p.

Research output: Contribution to journalArticle

president
asymmetry
polarization
legitimacy
ideology

An extended dual graph library and partitioning algorithm applicable to pseudoknotted RNA structures

Jain, S., Saju, S., Petingi, L. & Schlick, T., Jan 1 2019, In : Methods.

Research output: Contribution to journalArticle

Libraries
RNA
Topology
Nucleic Acid Databases
Graph theory
Authoritarianism
Anger
authoritarianism
anger
Fear
Linguistics
autism
infant
pragmatics
Language

Author Correction: Testing the key assumption of heritability estimates based on genome-wide genetic relatedness (Journal of Human Genetics, (2014), 59, 6, (342-345), 10.1038/jhg.2014.14)

Conley, D., Siegal, M., Domingue, B. W., Harris, K. M., McQueen, M. B. & Boardman, J. D., Jan 1 2019, In : Journal of Human Genetics.

Research output: Contribution to journalComment/debate

Open Access
Medical Genetics
Genome
Surveys and Questionnaires

Author Correction: c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont (Nature, (2018), 554, 7692, (373-377), 10.1038/nature25500)

Xu, M., Pokrovskii, M., Ding, Y., Yi, R., Au, C., Harrison, O. J., Galan, C., Belkaid, Y., Bonneau, R. & Littman, D. R., Feb 21 2019, In : Nature. 566, 7744, p. E7

Research output: Contribution to journalComment/debate

Regulatory T-Lymphocytes

BAR-based optimum adaptive steered MD for configurational sampling

Wang, X., Tu, X., Deng, B., Zhang, J. & Sun, Z., Jan 1 2019, In : Journal of Computational Chemistry.

Research output: Contribution to journalArticle

Surface mount technology
Sampling
Adaptive Sampling
Free energy
Adaptive Method

Bidirectional sliding of two parallel microtubules generated by multiple identical motors

Allard, J., Doumic, M., Mogilner, A. & Oelz, D., Jan 1 2019, In : Journal of Mathematical Biology.

Research output: Contribution to journalArticle

Microtubules
microtubules
Continuous-time Markov Process
Molecular Motor
Markov Chains

Biomimetic Approach Toward Enterocin and Deoxyenterocin

Rizzo, A., Mayer, R. J. & Trauner, D., Feb 1 2019, In : Journal of Organic Chemistry. 84, 3, p. 1162-1175 14 p.

Research output: Contribution to journalArticle

Biomimetics
Biological Products
Polyketides
Ketones
Discrete Fourier transforms

Body Mass Index in Multiple Sclerosis modulates ceramide-induced DNA methylation and disease course

Castro, K., Ntranos, A., Amatruda, M., Petracca, M., Kosa, P., Chen, E. Y., Morstein, J., Trauner, D., Watson, C. T., Kiebish, M. A., Bielekova, B., Inglese, M., Katz Sand, I. & Casaccia, P., Jan 1 2019, In : EBioMedicine.

Research output: Contribution to journalArticle

Open Access
Ceramides
DNA Methylation
Multiple Sclerosis
Body Mass Index
Genes

Brief, daily meditation enhances attention, memory, mood, and emotional regulation in non-experienced meditators

Basso, J. C., McHale, A., Ende, V., Oberlin, D. J. & Suzuki, W., Jan 1 2019, In : Behavioural Brain Research. 356, p. 208-220 13 p.

Research output: Contribution to journalArticle

Meditation
Webcasts
Exercise Test
Control Groups
Short-Term Memory

Bringing close others to the emergency department for an acute coronary event is associated with increased patient perception of threat

Cornelius, T., Meli, L., Thorson, K. R., Chang, B. P., Edmondson, D. & West, T., Jan 1 2019, In : General Hospital Psychiatry. 56, p. 42-49 8 p.

Research output: Contribution to journalArticle

Acute Coronary Syndrome
Post-Traumatic Stress Disorders
Hospital Emergency Service
Medication Adherence
Checklist

Choice-Related Activity during Visual Slant Discrimination in Macaque CIP But Not V3A

Elmore, L. C., Rosenberg, A., DeAngelis, G. C. & Angelaki, D., Mar 1 2019, In : eNeuro. 6, 2

Research output: Contribution to journalArticle

Open Access
Macaca
Neurons
Haplorhini
Discrimination (Psychology)

Combining Iteration-Free Polarization with Large Time Step Stochastic-Isokinetic Integration

Albaugh, A., Tuckerman, M. & Head-Gordon, T., Apr 9 2019, In : Journal of Chemical Theory and Computation. 15, 4, p. 2195-2205 11 p.

Research output: Contribution to journalArticle

iteration
self consistent fields
Molecular dynamics
Polarization
Potential energy surfaces

Comparative Epigenomics Reveals that RNA Polymerase II Pausing and Chromatin Domain Organization Control Nematode piRNA Biogenesis

Beltran, T., Barroso, C., Birkle, T. Y., Stevens, L., Schwartz, H. T., Sternberg, P. W., Fradin, H., Gunsalus, K., Piano, F., Sharma, G., Cerrato, C., Ahringer, J., Martínez-Pérez, E., Blaxter, M. & Sarkies, P., Mar 25 2019, In : Developmental Cell. 48, 6, p. 793-810.e6

Research output: Contribution to journalArticle

Open Access
RNA Polymerase II
Epigenomics
Small Interfering RNA
Chromatin
Caenorhabditis elegans

Compartmentalized Nanoreactors for One-Pot Redox-Driven Transformations

Qu, P., Kuepfert, M., Jockusch, S. & Weck, M., Jan 1 2019, In : ACS Catalysis. p. 2701-2706 6 p.

Research output: Contribution to journalArticle

Nanoreactors
Micelles
Alcohols
Ketones
Catalysts

Computational analysis for residue-specific CDK2-inhibitor bindings

Yang, Y. P., He, L. P., Bao, J. X., Qi, Y. F. & Zhang, J., Feb 1 2019, In : Chinese Journal of Chemical Physics. 32, 1, p. 134-142 9 p.

Research output: Contribution to journalArticle

Open Access
Cyclin-Dependent Kinase 2
inhibitors
Free energy
cancer
Cells
Impulsive Behavior
Psychiatry
Health
behavior disorders
Risk-Taking

Concise Asymmetric Synthesis of Kweichowenol A

Konrad, D. B., Kicin, B. & Trauner, D., Jan 1 2019, In : Synlett. 30, 4, p. 383-386 4 p.

Research output: Contribution to journalArticle

Open Access
Biological Products
Oxygenation
3-hydroxybutanal
cyclohexene

Contributions of crust proteins to spore surface properties in Bacillus subtilis

Shuster, B., Khemmani, M., Abe, K., Huang, X., Nakaya, Y., Maryn, N., Buttar, S., Gonzalez, A. N., Driks, A., Sato, T. & Eichenberger, P., Jan 1 2019, In : Molecular Microbiology.

Research output: Contribution to journalArticle

Surface Properties
Bacillus subtilis
Spores
Hydrophobic and Hydrophilic Interactions
Polysaccharides

Coordination of neural patterning in the Drosophila visual system

Courgeon, M. & Desplan, C., Jun 1 2019, In : Current Opinion in Neurobiology. 56, p. 153-159 7 p.

Research output: Contribution to journalReview article

Neuropil
Drosophila
Gene Expression

Copy Number Variation in Domestication

Lye, Z. N. & Purugganan, M., Jan 1 2019, In : Trends in Plant Science.

Research output: Contribution to journalReview article

domestication
mutation
genetic variation
animals
genes

Cortical double-opponent cells and human color perception

Shapley, R., Nunez, V. & Gordon, J., Dec 1 2019, In : Current Opinion in Behavioral Sciences. 30, p. 1-7 7 p.

Research output: Contribution to journalReview article

Color Perception
Color
Visual Cortex
Neurons

Cross-species hybridization and the origin of North African date palms

Flowers, J., Hazzouri, K. M., Gros-Balthazard, M., Mo, Z., Koutroumpa, K., Perrakis, A., Ferrand, S., Khierallah, H. S. M., Fuller, D. Q., Aberlenc, F., Fournaraki, C. & Purugganan, M., Jan 29 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 5, p. 1651-1658 8 p.

Research output: Contribution to journalArticle

Middle East
Northern Africa
Population
Genome
Phoeniceae
Molecular Dynamics Simulation
Principal Component Analysis

DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks

Cao, H., Wang, J., He, L., Qi, Y. & Zhang, J., Apr 22 2019, In : Journal of Chemical Information and Modeling. 59, 4, p. 1508-1514 7 p.

Research output: Contribution to journalArticle

neural network
Neural networks
Proteins
engineering
determinants

Determination of binding affinities of 3-Hydroxy-3-Methylglutaryl Coenzyme A reductase inhibitors from free energy calculation

Sun, Z., Wang, X. & Zhang, J., May 16 2019, In : Chemical Physics Letters. 723, p. 1-10 10 p.

Research output: Contribution to journalArticle

coenzymes
inhibitors
Free energy
affinity
Enthalpy

Developmental evidence for a link between the inherence bias in explanation and psychological essentialism

Sutherland, S. L. & Cimpian, A., Jan 1 2019, In : Journal of Experimental Child Psychology. 177, p. 265-281 17 p.

Research output: Contribution to journalArticle

Psychology

Developmental perspectives on risky and impulsive choice

Rosenbaum, G. M. & Hartley, C., Feb 18 2019, In : Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 374, 1766, 1 p.

Research output: Contribution to journalArticle

Risk-Taking
Impulsive Behavior
Choice Behavior
Behavioral Economics
adolescence

Diastereoselectivities in Reductions of α-Alkoxy Ketones Are Not Always Correlated to Chelation-Induced Rate Acceleration

Bartolo, N. D., Hornstein, A. L., Zhao, A. Y. & Woerpel, K., Jan 1 2019, In : Synthesis (Germany). 51, 1, p. 296-302 7 p.

Research output: Contribution to journalArticle

Chelation
Ketones
Reducing Agents
Reducing agents
Organometallics

Did I do that? Detecting a perturbation to visual feedback in a reaching task

Gaffin-Cahn, E., Hudson, T. E. & Landy, M., Jan 1 2019, In : Journal of vision. 19, 1, p. 1-18 18 p., 5.

Research output: Contribution to journalArticle

Sensory Feedback
Proprioception
Aptitude

Directing voluntary temporal attention increases fixational stability

Denison, R. N., Yuval-Greenberg, S. & Carrasco-Queijeiro, M., Jan 9 2019, In : Journal of Neuroscience. 39, 2, p. 353-363 11 p.

Research output: Contribution to journalArticle

Eye Movements
Visual Perception
Task Performance and Analysis
Inhibition (Psychology)

Directions for research and training in plant omics: Big Questions and Big Data

Argueso, C. T., Assmann, S. M., Birnbaum, K., Chen, S., Dinneny, J. R., Doherty, C. J., Eveland, A. L., Friesner, J., Greenlee, V. R., Law, J. A., Marshall-Colón, A., Mason, G. A., O'Lexy, R., Peck, S. C., Schmitz, R. J., Song, L., Stern, D., Varagona, M. J., Walley, J. W. & Williams, C. M., Apr 1 2019, In : Plant Direct. 3, 4, e00133.

Research output: Contribution to journalArticle

Open Access
training (plants)
Education
plant biology
Research
Arabidopsis

Discoidin-domain receptor coordinates cell-matrix adhesion and collective polarity in migratory cardiopharyngeal progenitors

Bernadskaya, Y. Y., Brahmbhatt, S., Gline, S. E., Wang, W. & Christiaen, L., Dec 1 2019, In : Nature Communications. 10, 1, 57.

Research output: Contribution to journalArticle

Cell-Matrix Junctions
polarity
adhesion
Adhesion
Light trailers

Distance-dependent memory for pictures and words

Amit, E., Rim, S. Y., Halbeisen, G., Cohen Priva, U., Stephan, E. & Trope, Y., Apr 1 2019, In : Journal of Memory and Language. 105, p. 119-130 12 p.

Research output: Contribution to journalArticle

Data storage equipment
Psychology
Labels
experiment
Episodic Memory

Dorsal hippocampal damage disrupts the auditory context-dependent attenuation of taste neophobia in mice

Grau-Perales, A. B., Levy, E. R. J., Fenton, A. & Gallo, M., Jan 1 2019, In : Neurobiology of Learning and Memory. 157, p. 121-127 7 p.

Research output: Contribution to journalArticle

Hippocampus
N-Methylaspartate
Rodentia
Learning
Brain

Dynamics of aesthetic experience are reflected in the default-mode network

Belfi, A. M., Vessel, E. A., Brielmann, A., Isik, A. I., Chatterjee, A., Leder, H., Pelli, D. & Starr, G. G., Mar 1 2019, In : NeuroImage. 188, p. 584-597 14 p.

Research output: Contribution to journalArticle

Esthetics
Art
Reward
Research
Neuroimaging

EBprotV2: A Perseus Plugin for Differential Protein Abundance Analysis of Labeling-Based Quantitative Proteomics Data

Koh, H. W. L., Zhang, Y., Vogel, C. & Choi, H., Feb 1 2019, In : Journal of Proteome Research. 18, 2, p. 748-752 5 p.

Research output: Contribution to journalArticle

Proteomics
Labeling
Peptides
Proteins
Labels

Editorial overview: Particle system shape change and response

Sacanna, S., Spicer, P. & Velikov, K. P., Jan 1 2019, In : Current Opinion in Colloid and Interface Science.

Research output: Contribution to journalEditorial