QuanAnts Machine: A Quantum Algorithm for Biomarker Discovery

The discovery of biomarker sets for a targeted pathway is a challenging problem in biomedical medicine, which is computationally prohibited on classical algorithms due to the massive search space. Here, I present a quantum algorithm named QuantAnts Machine to address the task. The proposed algorithm is a quantum analog of the classical Ant Colony Optimization (ACO). We create the mixture of multi-domain from genetic networks by representation theory, enabling the search of biomarkers from the multi-modality of the human genome. Although the proposed model can be generalized, we investigate the RAS-mutational activation in this work. To the end, QuantAnts Machine discovers rarely-known biomarkers in clinical-associated domain for RAS-activation pathway, including COL5A1, COL5A2, CCT5, MTSS1 and NCAPD2. Besides, the model also suggests several therapeutic-targets such as JUP, CD9, CD34 and CD74

Molecular characterization of the interaction between peripherin-2 and opsins in rod and cone photoreceptors

The tetraspanin peripherin-2 is a glyco-membrane protein exclusively expressed in the outer segments of rod and cone photoreceptors. Mutations in peripherin-2 are associated with retinal disorders characterized by Degeneration of rod or cone cells. Previous unpublished work identified peripherin-2 as a potential novel part of the protein complex comprising the B-subunit of the cyclic nucleotide-gated channel (CNGB1a and the light detector rhodopsin. In the first part of this study, using a combination of protein biochemical and FRET approaches in transfected HEK293 cells and in virally transduced murine rod outer segments, it could be demonstrated that peripherin-2 simultaneously binds to both, CNGB1a and rhodopsin. The interaction between peripherin-2 and rhodopsin was not described in previous studies. The binding domain mediating the peripherin-2/rhodopsin interaction could be narrowed down to the fourth transmembrane domain (TM4) of peripherin-2. Finally, the data revealed that the G266D point mutation in TM4 of peripherin-2 that is linked to a rod degenerative disease selectively disrupts the peripherin-2/rhodopsin interaction. To analyze if peripherin-2 also binds to cone opsins in the second part of this study, a similar experimental approach was conducted as used for the investigation of the peripherin-2/rhodopsin interaction. In this context, it was unveiled that peripherin-2 binds to both, short wavelength-and medium wavelength-sensitive cone opsin (S-opsin and M-opsin, respectively) in transfected HEK293 cells and in outer segments of transduced murine cones. Co-immunoprecipitation and quantitative FRET analysis revealed that binding of peripherin-2 to M-opsin was stronger than the peripherin-2/S-opsin interaction. This result was supported by transmission electron microscopy studies using gold particles coupled to opsin- and peripherin-2-specific antibodies. Finally, quantitative FRET analysis in transfected HEK293 cells and in transduced cone outer segments demonstrated that the V268I Point mutation in TM4 of peripherin-2 associated with a degenerative cone disease significantly attenuates the peripherin-2/M-opsin interaction. Taken together, this study provides a proof-of-principle for FRET-based analysis of protein-protein interactions in the outer segments of rod and cone photoreceptors. This approach led to the identification of hitherto unknown Protein complexes between peripherin-2 and opsins suggesting a novel physiological role of peripherin-2 in rods and cones. Finally, Analysis of disease-linked point mutations unveiled the molecular determinants of the peripherin-2/opsin interaction. These results might contribute to understanding the differential penetrance of certain point mutations in rods and cones

Ultra-large alignments using Phylogeny-aware Profiles

Many biological questions, including the estimation of deep evolutionary histories and the detection of remote homology between protein sequences, rely upon multiple sequence alignments (MSAs) and phylogenetic trees of large datasets. However, accurate large-scale multiple sequence alignment is very difficult, especially when the dataset contains fragmentary sequences. We present UPP, an MSA method that uses a new machine learning technique - the Ensemble of Hidden Markov Models - that we propose here. UPP produces highly accurate alignments for both nucleotide and amino acid sequences, even on ultra-large datasets or datasets containing fragmentary sequences. UPP is available at https://github.com/smirarab/sepp.Comment: Online supplemental materials and data are available at http://www.cs.utexas.edu/users/phylo/software/upp

Robust model predictive kinematic tracking control with terminal region for wheeled robotic systems

This paper addresses the nonlinear model predictive control (MPC) for wheeled mobile robots (WMRs) under external disturbance. The decoupling technique is utilized based on the non-holonomic constraint description for separating the WMR model. This method is able to achieve the under-actuated kinematic sub-system without disturbance and fully-actuated dynamic sub-system in presence of disturbance. Thanks to the decoupling technique, the disturbance is lumped into dynamic sub-system. The novelty lies in that the MPC-based tracking control with fixed initial point guarantees the stability based on a new establishment of terminal region and equivalent terminal controller. The feasibility problem is demonstrated to lead the tracking problem using theoretical analysis. Moreover, the control structure is inserted more the robust nonlinear dynamic controller. The effectiveness and advantages of the proposed control scheme are verified by numerical simulations using Yamip tool

Assessment of earthquake-induced ground liquefaction susceptibility for Hanoi city using geological and geomorphologic characteristics

In this paper, the earthquake-induced liquefaction susceptibility of Hanoi city is assessed using the recent published geological and geomorphologic data. A combination of classification methods based on the distribution of sedimentary deposits proposed by Youd and Perkins (1978) and geomorphologic units proposed by Iwasaki (1982) was applied. The subsurface lithology and geomorphologic maps were combined in a GIS platform for assessing the liquefaction susceptibility of Hanoi city.The resulting map shows that the liquefaction hazard of Hanoi city classified into four categories: high, moderate, low liquefaction potential and not likely areas. In the most of Hanoi area, the ground liquefaction potentials are moderate. The high liquefaction likely areas spread along the river beds and around the lake areas. The not likely and low liquefaction potential areas are observed mainly in the northwest and northeast of the study region such as Chanchim, Soc Son, and Bavi mountains. The present map can help the scientists, engineers, and planners to have the general information on regional liquefaction potential of the Hanoi city. ReferencesBird JF, Bommer JJ, 2004b. Earthquake Losses due to Ground Failure. Submitted to Engineering Geology, 75(2), 147-179.Bird Juliet F, Bommer Julian J., 2004a. Evaluating earthquake losses due to ground failure and identifying their relative contribution (Paper no. 3156). In Proceedings of the 13th world conference on earthquake engineering, Vancouver, B.C., Canada, august 1-6.Bui Van Duan, Nguyen Cong Thang, Nguyen Van Vuong, Pham Dinh Nguyen, 2013. The magnitude of the largest possible earthquake in the Muong La-Bac Yen fault zone. J. Sci. of the Earth, 35(1), 53-59.Dao Dinh Bac, Dang Van Bao, 2010. Geomorphologic characteristics, the ancient river beds system of the capital city and their values to the development of the Thang Long - Hanoi. International Workshop commemorating the 1000 years of Thang Long, Hanoi. Vietnam national University, Hanoi.Ganapathy, G. P., Rajawat, A. S., 2012. Evaluation of liquefaction potential hazard of Chennai city, India: using geological and geomorphological characteristics. Natural hazards, 64(2), 1717-1729.Goyal, A., Sinha, R., Chaudhari, M. and Jaiswal, K., 2001. Performance of Reinforced Concrete Buildings in Ahmedabad during Bhuj Earthquake January 26, 2001. Workshop on Recent Earthquakes of Chamoli and Bhuj: Volume I, Roorkee, India, May 24-26.Iwasaki, T., Tokida, K., Tatsuoka, F., Watanabe, S., Yasuda, S., Sato, H., 1982. Microzonation for soil liquefaction potential using simplified methods. In Proceedings of the 3rd international conference on microzonation, Seattle, 3, 1310-1330.Kuribayashi E., Tatsuoka, F., 1975. Brief review of liquefaction during earthquake in Japan,” Soils and Foundations, 15(4), 81-92.Lew M, Naeim F, Huang SC, Lam HK, Carpenter LD, 2000. Geotechnical and geological effects of the 21 September 1999 Chi-Chi earthquake, Taiwan. Structural Design of Tall Buildings, 9, 89-106.National Research Council, 1985. Ishihara 1985. Liquefaction of Soils During Earthquake, National Academy press, 240, p.34. Nguyen Hong Phuong (Project Manager), 2002. Study of seismic risk of Hanoi city. Project code 01C-04/09-2001-2. Institute for Marine Geology and Geophysics, VAST.Nguyen Hong Phuong (Project Manager), 2007. Application of GIS technology to Development of a model for seismic risk analysis for Hanoi city. Institute for Marine Geology and Geophysics, VAST.Nguyen Hong Phuong (Project Manager), 2014.  Estimation of Site Effects and Assessment of Urban Seismic Risk for Hanoi city. National Scientific Research Project Final report, Institute of Geophysics, VAST.Nguyen Hong Phuong and Pham The Truyen, 2014. Probabilistic seismic hazard assessment for South Central Vietnam. J. Sci. of the Earth, 36(4), 451-461.Phan Trong Trinh, Hoang Quang Vinh, Nguyen Van Huong, Ngo Van Liem, 2013. Active fault segmentation and seismic hazard in Hoa Binh reservoir, Vietnam. Cent. Eur. J. Geosci, 5(2), 223-235.Phan Trong Trinh, Ngo Van Liem, Nguyen Van Huong, Hoang Quang Vinh, Bui Van Thom, Bui Thi Thao, Mai Thanh Tan, Nguyen Hoang, 2012. Late Quaternary tectonics and seismotectonics along the Red River fault zone, North Vietnam. Earth-Science Reviews 114, 224-235.Susumu Yasuda, Nozomu Yoshida, Hiroyoshi Kiku, Hidenori Abo, and Masato Uda, 2001. Analyses of Liquefaction-Induced Deformation of Grounds and Structures by a Simple Method (March 26). International Conferences on Recent Advances in Geotechnical Earthquake Engineering and Soil Dynamics, p.27. http://scholarsmine.mst.edu/icrageesd/04icrageesd/session04/27.Updike, R. G., Egan, J. A., Moriwaki, Y., Idriss, I. M., Moses, T. L., 1988. A model for earthquake-induced translatory landslides in Quaternary sediments. Geological Society of America Bulletin, 100(5), 783-792.Vu Thanh Tam (Project Manager), 2014. Study and propose a reasonable threshold for preventing the subsidence caused by ground water exploitation, pilot application for downtown area of the Hanoi city. Final report of the Scientific research and technology development Project, National Center for water resource planning and investigation. Ministry of Natural Resources and Environment.Youd T. L., 1993. Liquefaction, ground failure and consequent damage during the 22 April 1991 Costa Rica earthquake. Abridged from EERI Proceedings: U.S. Costa Rica Workshop, http://nisee.berkeley.edu/costarica/Youd T. L., and Hoose S.N., 1977.  Liquefaction Susceptibility and Geologic Setting, Proceedings, 6th World Conference on Earthquake Engineering, New Delhi, India, 6, 37-42.Youd T. L., and Perkins D. M., 1978. Mapping liquefaction-induced ground failure potential. Journal of the Geotechnical Engineering Division, ASCE, 104, GT4, 433-446

Design of a genetic muller C-element

Journal ArticleSynthetic biology uses engineering principles to design circuits out of genetic materials that are inserted into bacteria to perform various tasks. While synthetic combinational Boolean logic gates have been constructed, there are many open issues in the design of sequential logic gates. One such gate common in most asynchronous circuits is the Muller C-element, which is used to synchronize multiple independent processes. This paper proposes a novel design for a genetic Muller C-element using transcriptional regulatory elements. The design of a genetic Muller C-element enables the construction of virtually any asynchronous circuit from genetic material. There are, however, many issues that complicate designs with genetic materials. These complications result in modifications being required to the normal digital design procedure. This paper presents two designs that are logically equivalent to a Muller C-element. Mathematical analysis and stochastic simulation, however, show that only one functions reliably

Enhanced Performance in Polymer Light Emmiting Diode by Using Ultra-thin Conductive Films as the Buffer Layer

The ultra-thin nanocomposite films based on the nano-crystal TiO$_{2}$ (TiO$_{2}$-nc) or multi-walled carbon nano-tube (MWCNTs) were prepared and used as the buffer layers in the fabrication of the organic light-emitting diodes (OLEDs). The injection efficiency of the hole and electron was improved by inserting an ultra-thin buffer layer between the electrodes and emissive layer. The turn-on voltage of the device with the buffer layers was lowered from 4 to 2.5V, and the current density was increased from 0.3 to 0.7~mA/mm$^{2}$, in comparison with the device without such a buffer layer. These devices showed a high efficiency and good stability

Molecular characterization of the interaction between peripherin-2 and opsins in rod and cone photoreceptors

The tetraspanin peripherin-2 is a glyco-membrane protein exclusively expressed in the outer segments of rod and cone photoreceptors. Mutations in peripherin-2 are associated with retinal disorders characterized by Degeneration of rod or cone cells. Previous unpublished work identified peripherin-2 as a potential novel part of the protein complex comprising the B-subunit of the cyclic nucleotide-gated channel (CNGB1a and the light detector rhodopsin. In the first part of this study, using a combination of protein biochemical and FRET approaches in transfected HEK293 cells and in virally transduced murine rod outer segments, it could be demonstrated that peripherin-2 simultaneously binds to both, CNGB1a and rhodopsin. The interaction between peripherin-2 and rhodopsin was not described in previous studies. The binding domain mediating the peripherin-2/rhodopsin interaction could be narrowed down to the fourth transmembrane domain (TM4) of peripherin-2. Finally, the data revealed that the G266D point mutation in TM4 of peripherin-2 that is linked to a rod degenerative disease selectively disrupts the peripherin-2/rhodopsin interaction. To analyze if peripherin-2 also binds to cone opsins in the second part of this study, a similar experimental approach was conducted as used for the investigation of the peripherin-2/rhodopsin interaction. In this context, it was unveiled that peripherin-2 binds to both, short wavelength-and medium wavelength-sensitive cone opsin (S-opsin and M-opsin, respectively) in transfected HEK293 cells and in outer segments of transduced murine cones. Co-immunoprecipitation and quantitative FRET analysis revealed that binding of peripherin-2 to M-opsin was stronger than the peripherin-2/S-opsin interaction. This result was supported by transmission electron microscopy studies using gold particles coupled to opsin- and peripherin-2-specific antibodies. Finally, quantitative FRET analysis in transfected HEK293 cells and in transduced cone outer segments demonstrated that the V268I Point mutation in TM4 of peripherin-2 associated with a degenerative cone disease significantly attenuates the peripherin-2/M-opsin interaction. Taken together, this study provides a proof-of-principle for FRET-based analysis of protein-protein interactions in the outer segments of rod and cone photoreceptors. This approach led to the identification of hitherto unknown Protein complexes between peripherin-2 and opsins suggesting a novel physiological role of peripherin-2 in rods and cones. Finally, Analysis of disease-linked point mutations unveiled the molecular determinants of the peripherin-2/opsin interaction. These results might contribute to understanding the differential penetrance of certain point mutations in rods and cones