Research Output 1973 2020

2020

An innovative multistage anaerobic hythane reactor (MAHR): Metabolic flux, thermodynamics and microbial functions

Si, B., Yang, H., Huang, S., Watson, J., Zhang, Y. & Liu, Z., Feb 1 2020, In : Water Research. 169, 115216.

Research output: Contribution to journalArticle

thermodynamics
Thermodynamics
Fluxes
Methane
Fermentation

Catalytic Microgelators for Decoupled Control of Gelation Rate and Rigidity of the Biological Gels

Hong, Y. T., Bregante, D. T., Lee, J. C. W., Seo, Y., Kim, D. H., Lee, Y. J., Schook, L. B., Jeon, H., Sung, H. J., Flaherty, D. W., Rogers, S. A. & Kong, H., Jan 10 2020, In : Journal of Controlled Release. 317, p. 166-180 15 p.

Research output: Contribution to journalArticle

Open Access
Thrombin
Gels
Thrombosis
Fibrin
Fibrinogen

Compact quantum dots for quantitative cytology

Le, P., Chitoor, S., Tu, C., Lim, S. J. & Smith, A. M., Jan 1 2020, Methods in Molecular Biology. Humana Press Inc., p. 147-158 12 p. (Methods in Molecular Biology; vol. 2064).

Research output: Chapter in Book/Report/Conference proceedingChapter

Quantum Dots
Nanoparticles
Cell Biology
Click Chemistry
Fluorescent Dyes

Computed tomography-guided additive manufacturing of Personalized Absorbable Gastrointestinal Stents for intestinal fistulae and perforations

Fathi, P., Capron, G., Tripathi, I., Misra, S., Ostadhossein, F., Selmic, L., Rowitz, B. & Pan, D., Jan 2020, In : Biomaterials. 228, 119542.

Research output: Contribution to journalArticle

3D printers
Intestinal Perforation
Intestinal Fistula
Stents
Tomography

Emerging molecular biology tools and strategies for engineering natural product biosynthesis

Xu, W., Klumbys, E., Ang, E. L. & Zhao, H., Jun 2020, In : Metabolic Engineering Communications. 10, e00108.

Research output: Contribution to journalReview article

Open Access
Molecular biology
Biosynthesis
Biological Products
Molecular Biology
Enzymes

Photosynthesis in the fleeting shadows: An overlooked opportunity for increasing crop productivity?

Wang, Y., Burgess, S. J., De Becker, E. & Long, S. P., Jan 6 2020, (Accepted/In press) In : The Plant Journal.

Research output: Contribution to journalArticle

Photosynthesis
Carbon
photosynthesis
Ribulose-Bisphosphate Carboxylase
ribulose-bisphosphate carboxylase

Photosynthetic efficiency and mesophyll conductance are unaffected in Arabidopsis thaliana aquaporin knock-out lines

Kromdijk, J., Głowacka, K. & Long, S. P., Jan 1 2020, In : Journal of experimental botany. 71, 1, p. 318-329 12 p.

Research output: Contribution to journalArticle

Open Access
Aquaporins
aquaporins
Chloroplasts
Arabidopsis
mesophyll

Probing cholesterol binding and translocation in P-glycoprotein

Thangapandian, S., Kapoor, K. & Tajkhorshid, E., Jan 1 2020, In : Biochimica et Biophysica Acta - Biomembranes. 1862, 1, 183090.

Research output: Contribution to journalArticle

P-Glycoprotein
Cholesterol
Amino Acids
Binding Sites
Molecular Dynamics Simulation

Revisiting Replication-Induced Transcription in Escherichia coli

Golding, I., Jan 1 2020, In : BioEssays. 42, 1, 1900193.

Research output: Contribution to journalComment/debate

The role of A-site ion on proton diffusion in perovskite oxides (ABO3)

Jing, Y. & Aluru, N. R., Jan 1 2020, In : Journal of Power Sources. 445, 227327.

Research output: Contribution to journalArticle

Perovskite
Oxides
Protons
Ions
Proton transfer
2019
Soybean oil
Soybean Oil
Soybean Proteins
Xylose
Lignin

13C-lutein is differentially distributed in tissues of an adult female rhesus macaque following a single oral administration: a pilot study

Jeon, S., Li, Q., Rubakhin, S. S., Sweedler, J. V., Smith, J. W., Neuringer, M., Kuchan, M. & Erdman, J. W., Jan 2019, In : Nutrition Research. 61, p. 102-108 7 p.

Research output: Contribution to journalArticle

Lutein
Macaca mulatta
Oral Administration
Tissue Distribution
Haplorhini

3D-Printed Hydrogel Composites for Predictive Temporal (4D) Cellular Organizations and Patterned Biogenic Mineralization

McCracken, J. M., Rauzan, B. M., Kjellman, J. C. E., Kandel, M. E., Liu, Y. H., Badea, A., Miller, L. A., Rogers, S. A., Popescu, G. & Nuzzo, R. G., Jan 10 2019, In : Advanced Healthcare Materials. 8, 1, 1800788.

Research output: Contribution to journalArticle

Ink
Hydrogel
Hydrogels
Scaffolds
Organizations

A 27-band snapshot hyperspectral imaging system for label-free tumor detection during image-guided surgery

Blair, S., Garcia, M., Konopka, C., Dobrucki, W. & Gruev, V., Jan 1 2019, Label-Free Biomedical Imaging and Sensing, LBIS 2019. Hayden, O. & Shaked, N. T. (eds.). SPIE, 108900G. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 10890).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Computer-Assisted Surgery
surgery
Imaging systems
Surgery
Labels

A Chalcogen-Bonding Cascade Switch for Planarizable Push–Pull Probes

Macchione, M., Goujon, A., Strakova, K., Humeniuk, H. V., Licari, G., Tajkhorshid, E., Sakai, N. & Matile, S., Oct 28 2019, In : Angewandte Chemie - International Edition. 58, 44, p. 15752-15756 5 p.

Research output: Contribution to journalArticle

Chalcogens
Switches
Supramolecular chemistry
Chemical stability
Molecular dynamics

A clinical trial of intraoperative near-infrared imaging to assess tumor extent and identify residual disease during anterior mediastinal tumor resection

Predina, J. D., Keating, J., Newton, A., Corbett, C., Xia, L., Shin, M., Frenzel Sulyok, L., Deshpande, C., Litzky, L., Nie, S., Kucharczuk, J. C. & Singhal, S., Mar 1 2019, In : Cancer. 125, 5, p. 807-817 11 p.

Research output: Contribution to journalArticle

Clinical Trials
Indocyanine Green
Neoplasms
Phrenic Nerve
Thymoma

A comparison of glenohumeral joint kinematics and muscle activation during standard and geared manual wheelchair mobility

Slavens, B. A., Jahanian, O., Schnorenberg, A. J. & Hsiao-Wecksler, E. T., Aug 2019, In : Medical Engineering and Physics. 70, p. 1-8 8 p.

Research output: Contribution to journalArticle

Shoulder Joint
Wheelchairs
Biomechanical Phenomena
Muscle
Kinematics

A comparison of mid-infrared spectral regions on accuracy of tissue classification

Mittal, S. & Bhargava, R., Apr 21 2019, In : Analyst. 144, 8, p. 2635-2642 8 p.

Research output: Contribution to journalArticle

Dermatoglyphics
Tissue
Infrared radiation
Pixels
Breast

A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data

Dinh, H. V., Suthers, P. F., Chan, S. H. J., Shen, Y., Xiao, T., Deewan, A., Jagtap, S. S., Zhao, H., Rao, C. V., Rabinowitz, J. D. & Maranas, C. D., Dec 2019, In : Metabolic Engineering Communications. 9, e00101.

Research output: Contribution to journalArticle

Open Access
Genomics
Genes
Yeasts
Genome
Basidiomycota

A computational model of feedback-mediated hematopoietic stem cell differentiation in vitro

Mahadik, B., Hannon, B. & Harley, B. A. C., Mar 2019, In : PloS one. 14, 3, e0212502.

Research output: Contribution to journalArticle

Open Access
Hematopoietic Stem Cells
Stem cells
cell differentiation
Cell Differentiation
Feedback

A connected cytoskeleton network generates axonal tension in embryonic: Drosophila

Fan, A., Joy, M. S. H. & Saif, T., Jan 1 2019, In : Lab on a chip. 19, 18, p. 3133-3139 7 p.

Research output: Contribution to journalArticle

Cytoskeleton
Drosophila
Axons
Neurons
Stiffness

A continuing career in biocatalysis: Frances H. Arnold

Fasan, R., Jennifer Kan, S. B. & Zhao, H., Nov 1 2019, In : ACS Catalysis. 9, 11, p. 9775-9788 14 p.

Research output: Contribution to journalArticle

Enzymes
Biocatalysts
Catalysis
Biocatalysis

Activate capture and digital counting (AC + DC) assay for protein biomarker detection integrated with a self-powered microfluidic cartridge

Che, C., Li, N., Long, K. D., Aguirre, M. Á., Canady, T. D., Huang, Q., Demirci, U. & Cunningham, B. T., Jan 1 2019, In : Lab on a chip. 19, 23, p. 3943-3953 11 p.

Research output: Contribution to journalArticle

Microfluidics
Biomarkers
Antibodies
Assays
Gold

Activation of silent biosynthetic gene clusters using transcription factor decoys

Wang, B., Guo, F., Dong, S. H. & Zhao, H., Feb 1 2019, In : Nature chemical biology. 15, 2, p. 111-114 4 p.

Research output: Contribution to journalArticle

Multigene Family
Transcription Factors
Oxazoles
Peptide Synthases
Polyketide Synthases

Advancing point-of-care diagnostics of metabolites through engineering semisynthetic proteins

Zhang, J. J. & Lu, Y., Apr 2019, In : Clinical Chemistry. 65, 4, p. 507-509 3 p.

Research output: Contribution to journalReview article

Point-of-Care Systems
Protein Engineering
Metabolites
Proteins

Advancing the Fields of Measurement Science with Partnerships and Awards

Sweedler, J. V., Apr 2 2019, In : Analytical chemistry. 91, 7, 1 p.

Research output: Contribution to journalEditorial

A fully automated, faster noise rejection approach to increasing the analytical capability of chemical imaging for digital histopathology

Gupta, S., Mittal, S., Kajdacsy-Balla, A., Bhargava, R. & Bajaj, C., Apr 2019, In : PloS one. 14, 4, e0205219.

Research output: Contribution to journalArticle

Open Access
histopathology
Noise
image analysis
Imaging techniques
Signal to noise ratio

A gelatin hydrogel to study endometrial angiogenesis and trophoblast invasion

Zambuto, S. G., Clancy, K. B. H. & Harley, B. A., Oct 6 2019, In : Interface Focus. 9, 5, 20190016.

Research output: Contribution to journalArticle

Hydrogel
Endothelial cells
Trophoblasts
Gelatin
Hydrogels

A gene cluster for taurine sulfur assimilation in an anaerobic human gut bacterium

Xing, M., Wei, Y., Hua, G., Li, M., Nanjaraj Urs, A. N., Wang, F., Hu, Y., Zhai, W., Liu, Y., Ang, E. L., Zhao, H. & Zhang, Y., Aug 15 2019, In : Biochemical Journal. 476, 15, p. 2271-2279 9 p.

Research output: Contribution to journalArticle

Taurine
Multigene Family
Sulfur
Bacteria
Genes

Allosteric Interactions in Human Cytochrome P450 CYP3A4: The Role of Phenylalanine 213

Denisov, I. G., Grinkova, Y. V., Nandigrami, P., Shekhar, M., Tajkhorshid, E. & Sligar, S. G., Mar 12 2019, In : Biochemistry. 58, 10, p. 1411-1422 12 p.

Research output: Contribution to journalArticle

Cytochrome P-450 CYP3A
Phenylalanine
Cytochrome P-450 Enzyme System
Progesterone
Carbamazepine

Anaerobic conversion of the hydrothermal liquefaction aqueous phase: Fate of organics and intensification with granule activated carbon/ozone pretreatment

Si, B., Yang, L., Zhou, X., Watson, J., Tommaso, G., Chen, W. T., Liao, Q., Duan, N., Liu, Z. & Zhang, Y., Jan 1 2019, In : Green Chemistry. 21, 6, p. 1305-1318 14 p.

Research output: Contribution to journalArticle

Ozone
Liquefaction
liquefaction
Activated carbon
activated carbon

Analysis of high Mg-incorporation into GaN via PAMBE modulation doping and molecular dynamics simulations

Ismail, F. H., Landi, M., Kelly, F. P. & Kim, K., Jan 1 2019.

Research output: Contribution to conferencePaper

Molecular dynamics
Doping (additives)
Modulation
Computer simulation
Secondary ion mass spectrometry

Analysis of Paper-Based Colorimetric Assays with a Smartphone Spectrometer

Woodburn, E. V., Long, K. D. & Cunningham, B. T., Jan 15 2019, In : IEEE Sensors Journal. 19, 2, p. 508-514 7 p., 8494768.

Research output: Contribution to journalArticle

Smartphones
Spectrometers
Assays
strip
Cameras

An efficient gene knock-in strategy using 5′-modified double-stranded DNA donors with short homology arms

Yu, Y., Guo, Y., Tian, Q., Lan, Y., Yeh, H., Zhang, M., Tasan, I., Jain, S. & Zhao, H., Dec 23 2019, (Accepted/In press) In : Nature chemical biology.

Research output: Contribution to journalArticle

Gene Knock-In Techniques
Ribonucleoproteins
Neoplastic Stem Cells
HEK293 Cells
DNA

A network of phosphatidylinositol 4,5-bisphosphate binding sites regulates gating of the Ca2+-activated Cl channel ANO1 (TMEM16A)

Yu, K., Jiang, T., Cui, Y. Y., Tajkhorshid, E. & Criss Hartzell, H., Jan 1 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 40, p. 19952-19962 11 p.

Research output: Contribution to journalArticle

Open Access
Molecular Dynamics Simulation
Phosphatidylinositols
Binding Sites
Mutagenesis
Fluids and Secretions

An extended bacterial reductive pyrimidine degradation pathway that enables nitrogen release from β-alanine

Yin, J., Wei, Y., Liu, D., Hu, Y., Lu, Q., Lui Ang, E., Zhao, H. & Zhang, Y., Jan 1 2019, In : Journal of Biological Chemistry. 294, 43, p. 15662-15671 10 p.

Research output: Contribution to journalArticle

Alanine
Nitrogen
Degradation
Bacteria
Uracil

An extra copy of the β-glucosidase gene improved the cellobiose fermentation capability of an engineered Saccharomyces cerevisiae strain

Kim, H. J., Lee, W. H., Turner, T. L., Kwak, S. & Jin, Y. S., Oct 1 2019, In : 3 Biotech. 9, 10, 367.

Research output: Contribution to journalArticle

Glucosidases
Cellobiose
cellobiose
glucosidases
Fermentation

A NIR Light Gated DNA Nanodevice for Spatiotemporally Controlled Imaging of MicroRNA in Cells and Animals

Zhao, J., Chu, H., Zhao, Y., Lu, Y. & Li, L., May 1 2019, In : Journal of the American Chemical Society. 141, 17, p. 7056-7062 7 p.

Research output: Contribution to journalArticle

MicroRNAs
Animals
DNA
Imaging techniques
Light

Anodized/etched and dis treated ti surfaces to promote bone formation

Mesa, A., Montes, R., Patiño, E., Alzate, J. F., Civantos, A., Balcázar, N., Pavón, J. J. & Allain, J. P., Jan 1 2019, Society for Biomaterials Annual Meeting and Exposition 2019: The Pinnacle of Biomaterials Innovation and Excellence - Transactions of the 42nd Annual Meeting. Society for Biomaterials, 1 p. (Transactions of the Annual Meeting of the Society for Biomaterials and the Annual International Biomaterials Symposium; vol. 40).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Osteogenesis
Bone Morphogenetic Protein 2
Bone
Titanium
Hazardous Waste

Anomalous scaling of flexural phonon damping in nanoresonators with confined fluid

De, S. & Aluru, N. R., Dec 1 2019, In : Microsystems and Nanoengineering. 5, 1, 2.

Research output: Contribution to journalArticle

Damping
damping
scaling
Fluids
fluids

A novel technique for in situ uniaxial tests of self-assembled soft biomaterials

Elhebeary, M., Emon, M. A. B., Aydin, O. & Saif, M. T. A., Jan 1 2019, In : Lab on a chip. 19, 7, p. 1153-1161 9 p.

Research output: Contribution to journalArticle

Biocompatible Materials
Biomaterials
Tissue
Collagen
Electric Stimulation

A pathway for isethionate dissimilation in Bacillus krulwichiae

Tong, Y., Wei, Y., Hu, Y., Ang, E. L., Zhao, H. & Zhang, Y., Jan 1 2019, In : Applied and environmental microbiology. 85, 15, e00793-19.

Research output: Contribution to journalArticle

Bacillus (bacteria)
Bacillus
Bacteria
bacterium
bacteria

Approximating the Ideal Observer and Hotelling Observer for Binary Signal Detection Tasks by Use of Supervised Learning Methods

Zhou, W., Li, H. & Anastasio, M. A., Oct 2019, In : IEEE transactions on medical imaging. 38, 10, p. 2456-2468 13 p., 8691467.

Research output: Contribution to journalArticle

Signal detection
Supervised learning
Statistics
Learning
Medical imaging

Aqueous acid-based synthesis of lead-free tin halide perovskites with near-unity photoluminescence quantum efficiency

Wang, A., Guo, Y., Zhou, Z., Niu, X., Wang, Y., Muhammad, F., Li, H., Zhang, T., Wang, J., Nie, S. & Deng, Z., Jan 1 2019, In : Chemical Science. 10, 17, p. 4573-4579 7 p.

Research output: Contribution to journalArticle

Open Access
Tin
Quantum efficiency
Photoluminescence
Acids
Quantum yield

Are we approaching a water ceiling to maize yields in the United States?

Delucia, E. H., Chen, S., Guan, K., Peng, B., Li, Y., Gomez-Casanovas, N., Kantola, I. B., Bernacchi, C., Huang, Y., Long, S. P. & Ort, D. R., Jun 18 2019, In : Ecosphere. 10, 6, e02773.

Research output: Contribution to journalArticle

Open Access
maize
corn
vapor pressure
water
water use efficiency

A rotifer-derived paralytic compound prevents transmission of schistosomiasis to a mammalian host

Gao, J., Yang, N., Lewis, F. A., Yau, P., Collins, J. J., Sweedler, J. V. & Newmark, P. A., Jan 1 2019, In : PLoS biology. 17, 10, e3000485.

Research output: Contribution to journalArticle

Open Access
schistosomiasis
Schistosoma
Schistosomiasis
Rotifera
Cercaria

A small-molecule competitive inhibitor of phosphatidic acid binding by the AAA+ protein NSF/Sec18 blocks the SNARE-priming stage of vacuole fusion

Sparks, R. P., Arango, A. S., Starr, M. L., Aboff, Z. L., Hurst, L. R., Rivera-Kohr, D. A., Zhang, C., Harnden, K. A., Jenkins, J. L., Guida, W. C., Tajkhorshid, E. & Fratti, R. A., Jan 1 2019, In : Journal of Biological Chemistry. 294, 46, p. 17168-17185 18 p.

Research output: Contribution to journalReview article

Open Access
N-Ethylmaleimide-Sensitive Proteins
SNARE Proteins
Phosphatidic Acids
Vacuoles
Carrier Proteins

A subtype of oral, laryngeal, esophageal, and lung, squamous cell carcinoma with high levels of TrkB-T1 neurotrophin receptor mRNA

Zhou, Y., Sinha, S., Schwartz, J. L. & Adami, G. R., Jun 20 2019, In : BMC Cancer. 19, 1, 607.

Research output: Contribution to journalArticle

Open Access
Nerve Growth Factor Receptors
Squamous Cell Carcinoma
Lung
Messenger RNA
Neoplasms
Open Access
Acoustics
Tomography
Computer-Assisted Image Processing
Multimodal Imaging
Surveys and Questionnaires

Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism

Singharoy, A., Maffeo, C., Delgado-Magnero, K. H., Swainsbury, D. J. K., Sener, M., Kleinekathöfer, U., Vant, J. W., Nguyen, J., Hitchcock, A., Isralewitz, B., Teo, I., Chandler, D. E., Stone, J. E., Phillips, J. C., Pogorelov, T. V., Mallus, M. I., Chipot, C., Luthey-Schulten, Z., Tieleman, D. P., Hunter, C. N. & 3 others, Tajkhorshid, E., Aksimentiev, A. & Schulten, K., Nov 14 2019, In : Cell. 179, 5, p. 1098-1111.e23

Research output: Contribution to journalArticle

Chromatophores
Energy conversion
Energy Metabolism
Phenotype
Atoms