computer

Publications and Patents

Our achievements and aspirations spring in many ways from faculty members’ creativity, talent, and dedication in scholarship, teaching, and professional service. Recent faculty research and scholarship projects are listed below.

Publications

 2016

Zhao L, Chunmei Ma, Limi Mao, Lingyu Tang, Kam-biu Liu, Yu Zhang, Huayu Lu, Shuang-Ye Wu (accepted) Investigation of peat sediments from the Daiyun Mountain in the southeast China: late Holocene vegetation, climate and human impacts. Submitted to The Holocene

Jia, Xin, Shuangwen Yi, Yonggang Sun, Shuang-Ye Wu & Huayu Lu. (accepted) Spatial and temporal variations in prehistoric human settlement and their influencing factors on the south bank of the Xar Maron River, Northeast China. Frontiers of Earth Science.

Jia, X, Yonggang Sun, Lin Wang, Wenfeng Sun, Zhijun Zhao, Wenbo Huang, Huayu Lu, Wu, S (accepted) "The transition of human subsistence strategies in relation to climate change during the Bronze Age in the West Liao River Basin, Northeast China". The Holocene

An, W., Hou, S., Zhang, W., Wang, Y., Liu, Y., Wu, S., and Pang, H. (2016) Significant recent warming over the northern Tibetan Plateau from ice core δ18O records, Clim. Past, 12, 1-11, www.clim-past.net/12/1/2016/; doi:10.5194/cp-12-1-2016, 2016.

D. Murrugarra, A. Veliz-Cuba, B. Aguilar, and R. Laubenbacher. Identification of control targets of Boolean molecular network models via computational algebra. Submitted.

“Synthesis, characterization and DNA binding activity of PtCl2[DMSO][N4[N-3(4-pyridylmethyl)thymidine]]” Jun Chen, Kaiyu Li, Shawn Swavey, Kevin M. Church. Inorganica Chimica Acta, 2016, 444, 76-80.

“Synthesis, spectroscopic, and electrochemical studies of bis-ruthenium (II) polypyridyl complexes bridged by dipyrromethenes” Shawn Swavey, David Ireland, Emily Irwin, Jacob Counts. Inorganica Chimica Acta, 2016, accepted.

“A Ruthenium(II) Polypyridyl Nucleoside as a Potential Photodynamic Therapy Agent” Jun Chen, Kaiyu Li, Shawn Swavey, Kevin M. Church ChemistrySelect, 4, 2016, 1-6.

“Dipyrromethenes from solvent-free reactions and their BODIPY Analogs: Synthesis, Optical, Electrochemical, and Theoretical Studies” Shawn Swavey, Michael Coladepietro, Aliah Burbayea, European Journal of Organic Chemistry, 2016, accepted.

“Photoreactions of DNA with a bimetallic ruthenium(II) polypyridyl complex bridged by an organic chromophore” Shawn Swavey, Mengyu Wang, Nathaniel Lundy, Jamie Allen. Inorganica Chimica Acta, 2016, accepted.

2015

Xuefeng Sun, Yinghua Li, Xiaobo Feng, Chengqiu Lu, Shuangwen Yi, Huayu Lua, Shejiang Wang, Shuang-Ye Wu (2015) Pedostratigraphy of eolian deposition near Yunxian Man site on the Hanjiang River terraces at Yunxian Basin, central China. Quaternary International, http://dx.doi.org/10.1016/j.quaint.2015.05.034

An, W., Hou, S., Zhang, W., Wang, Y., Liu, Y., Wu, S., and Pang, H. (2015) Significant recent warming over the northern Tibetan Plateau from ice core δ18O records, Clim. Past Discuss., 11, 2701-2728, doi:10.5194/cpd-11-2701-2015, 2015.

Shi JF, Lu HY, Li JB, Shi SY, Wu S-Y, Hou XY, Li LL. (2015) Tree-ring based February-April precipitation reconstruction for the lower reaches of the Yangtze River, southeastern China. Global and Planetary Change. DOI: 10.1016/j.gloplacha.2015.05.006 

Wu, Y and Wu S-Y* (2015) Changing Characteristics of Precipitation in China during 1951-2013, International Journal of Climatology. DOI: 10.1002/joc.4432

Wu, S-Y (2015) “Changing characteristics of precipitation in the conterminous USA”, Climatic Change. DOI:10.1007/s10584-015-1453-8

Tang, Yanying, Hongxi Pang, Wangbin Zhang, Yaju Li, Shuang-Ye Wu, Shugui Hou (2015) Effects of changes in moisture source and the upstream rainout on stable isotopes in summer precipitation — a case study in Nanjing, East China. Hydrol. Earth Syst. Sci. 19, 4293-4306, 2015. doi:10.5194/hess-19-4293-2015

Davis, JG, Chapman, JI, Wu, S-Y, McEwan, RW. (2015) Spatiotemporal Dynamics of Coarse Woody Debris in an Old-Growth Temperate Deciduous Forest. Forest Sciences 61(2): 680-688. http://dx.doi.org/10.5849/forsci.14-156 

Veliz-Cuba, A. Hirning, A. Atanas, F. Hussain, F. Vancia, and K. Josic, and M. Bennett. Sources of Variability in a Synthetic Gene Oscillator, PLoS Comput Biol 11 (12), 2015.

A. Veliz-Cuba, Z. Kilpatrick, and K. Josic. Stochastic models of evidence accumulation in changing environments. Accepted, SIAM Review, 2015.

A. Veliz-Cuba, H. Shouval, K. Josic, and Z. Kilpatrick. Neural networks that learn the precise timing of event sequences. Journal of Computational Neuroscience, 39 (3): 235-254, 2015.

A. Veliz-Cuba, B. Aguilar, and R. Laubenbacher. Dimension Reduction of Large Sparse AND-NOT Network Models. Electronic Notes in Theoretical Computer Science, 316: 83-95, 2015.

Hippo Growth Control Pathway and Organ Size I Waghmare, S Verghese, M Kango‐Singh. eLS Published Online: 14 MAY 2015 DOI: 10.1002/9780470015902.a0026054

Drosophila C-terminal Src kinase regulates growth via the Hippo signaling pathway. HJ Kwon, I Waghmare, S Verghese, A Singh, A Singh, M Kango-Singh 2015. Developmental biology 397 (1), 67-76

The Hippo pathway effector Yki downregulates Wg signaling to promote retinal differentiation in the Drosophila eye. E Wittkorn, A Sarkar, K Garcia, M Kango-Singh, A Singh 2015. Development 142 (11), 2002-2013

Luby, A.O.; Breitner, E.K.; Comfort, K.K. Preliminary protein corona formation stabilizes gold nanoparticles and improves deposition efficiency. Appl. Nanosci. 2015, DOI 10.1007/s13204-015-0501-z.

Breitner, E.K.; Husain, S.M,; Comfort, K.K. The Role of Biological Fluid and Dynamic Flow in the Behavior and Cellular Interactions of Gold Nanoparticles. J. Nanobiotechnol. 2015, 13:56.

Hussain, S.M.; Warheit, D.B.; Ng, S.P.; Comfort, K.K.; Grabinski, C.M.; Braydich-Stolle, L.K. At the Crossroads of Nanotoxicology in vitro: Past Achievements and Current Challenges. Invited Review. Toxicological Sciences 2015, 147, 5-16.

“Monometallic Europium, Terbium, and Neodymium Complexes formed from the Bridging Ligand 2,3-bis(2-pyridyl)pyrazine: Crystal Structure and Temperature Dependent Luminescent Properties” Shawn Swavey, Albert Fratini, Jasminder Grewal, Austin Hutchinson. Inorganica Chimica Acta, 2015, 428, 27-31.

“Photoinduced Interactions of Supramolecular Ruthenium(II) Complexes with Plasmid DNA: Synthesis, Spectroscopic, Electrochemical, and DNA Photocleavage Studies” Shawn Swavey, Madeleine DeBeer, Kaiyu Li Inorganic Chemistry, 2015, 54, 3139-3147.

“A Dimetallic Osmium(II) Complex as a Potential Phototherapeutic Agent: Binding and Photocleavage Studies with Plasmid DNA” Shawn Swavey and Kaiyu Li. European Journal of Inorganic Chemistry, 2015, 33, 5551-5555.

“Bimetallic ruthenium(II) bridged by a dypyrromethene chromophore: DNA binding and light driven reactions within the photodynamic therapy window” Shawn Swavey and Mengyu Wang. Inorganic Chemistry Communications, 2015, 61, 228-230.

2014

Chen Y, Lu H*, Zhang E, Zhang H, Xua Z, Yi S, Wu S-Y. (2014) Test stable carbon isotopic composition of soil organic matters as a proxy indicator of past precipitation: study of the sand fields in northern China. Quaternary International (2014) http://dx.doi.org/10.1016/j.quaint.2014.10.062

Zhang L., Fan J, Chen Q and Wu S-Y (2014) Reconstruction of the Hirnantian (Late Ordovician) palaeotopography in the Upper Yangtze region, South China, Estonian Journal of Earth Sciences 63(4): 329-334.

Wu, S-Y, Miller, AI (2014) “The shortest distance between two points isn’t always a great circle: getting around land masses in the calibration of marine geodisparity.” Paleobiology, 40(3), 2014, pp. 428–439.

Boyle, JT, Sheets, HD, Wu, S-Y, Goldman, D, Melchin, MJ, Cooper, RA, Sadler PM, Mitchell CE. (2014) A Reexamination of the contributions of biofacies and geographic range to extinction risk in Ordovician graptolites. GFF, 136:1, 38-41, DOI: 10.1080/11035897.2013.861864

A. Veliz-Cuba, A. Kumar, and K. Josic. Piecewise linear and Boolean models of chemical reaction networks. Bulletin of Mathematical Biology, 76(12):2945-2984, 2014.

A. Veliz-Cuba, B. Aguilar, F. Hinkelmann, and R. Laubenbacher. Steady state analysis of Boolean molecular network models via model reduction and computational algebra. BMC Bioinformatics 15:221, 2014.

A. Veliz-Cuba, D. Murrugarra, and R. Laubenbacher. Structure and Dynamics of Acyclic Networks. Discrete Event Dynamic Systems, 24(4): 647-658, 2014.

Toxicity and localization studies of a potential photodynamic therapy agent in Drosophila. J Yoho, C Stroh, S Swavey, M Kango‐Singh 2014. Genesis 52 (4), 309-314

Intercellular cooperation and competition in brain cancers: Lessons from Drosophila and human Studies. I Waghmare, A Roebke, M Minata, M Kango-Singh, I Nakano 2014. Stem cells translational medicine, sctm. 2014-0086

Braydich-Stolle, L.K.; Breitner, E.K.; Comfort, K.K.; Schlager J.J.; Hussain, S.M. Dynamic Characterization of Silver Nanoparticles in Physiological Fluids: Toxicological Implications. Langmuir, 2014, 30, 15309-15316.

Comfort, K.K.; Maurer, E.I.; Hussain, S.M. Slow Release of Ions from Internalized Silver Nanoparticles Modifies the Epidermal Growth Factor Signaling Response. Colloids and Surfaces B: Biointerfaces. 2014, 123, 136-142.

Comfort, K.K.; Braydich-Stolle, L.K.; Maurer, E.I.; Hussain, S.M. Less is More: In Vitro Chronic, Low-Level Nanomaterial Exposure Provides a More Meaningful Toxicity Assessment. ACS Nano 2014, 8, 3260-3271.

“A Bis-Ruthenated Porphyrin Capable of Plasmid DNA Photocleavage within the Photodynamic Therapy Window” Shawn Swavey and Dale Wilson Inorganica Chimica Acta, 2014, 426, 45-49.

2013

DeBrosse, M.C.; K.K. Comfort, E.A. Untener, D.A. Comfort, S.M. Hussain. (2013) High aspect ratio gold nanorods displayed augmented cellular internalization and surface chemistry mediated cytotoxicity. Materials Science and Engineering C. 33(7):4094 – 4100. http://dx.doi.org/10.1016/j.msec.2013.05.056

Untener, E.A.; K.K. Comfort, E.I. Maurer, C.M. Grabinski, D.A. Comfort, S.M. Hussain. (2013) Tannic acid coated gold nanorods demonstrate a distinctive form of endosomal uptake and unique distribution within cells. ACS Applied Materials & Interfaces 5(17):8366 – 8373. DOI: 10.1021/am402848q

Stacy, B.M.; K.K. Comfort, D.A. Comfort; S.M. Hussain. (2013) In Vitro Identification of Gold Nanorods through Hyperspectral Imaging. Plasmonics 8:1235 – 1240. doi: 10.1007/s11468-013-9538-6

Kim, S.S.; C.L. Hisey, Z. Kuang, D.A. Comfort, B.L. Farmer, R.R. Naik. (2013) The effect of single wall carbon nanotube metallicity on genomic DNA-mediated chirality enrichment. Nanoscale 5:4931.

Book Chapters

Beagle, J. K. (2015) Benzotriazole-mediated Synthesis of Nitrogen-containing Heterocycles. (Invited Review) In: Topics in Heterocyclic Chemistry, Monbaliu, J. C.; Ed. Springer, Germany doi:10.1007/7081_2015_178

Patents

UD-587: Zn PHPTMP - New Cationic Water Soluble Porphyrin with Anti-Resistant Properties. Co-inventors: Shawn Swavey, Ph.D. and Jayne Robinson, Ph.D. (applied for August 2014)

UD–524 (US Patent # 8,551,456): Combination Therapy and Methods for Treating Bacterial Biofilms. Co-Inventors: Jayne Robinson Ph.D. and Tracy Collins Ph.D.