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IEEE Transactions on Nanobioscience

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https://www.readbyqxmd.com/read/28103559/exploring-the-missing-links-between-dietary-habits-and-diseases
#1
Malay Bhattacharyya, Soumi Maity, Sanghamitra Bandyopadhyay
Disease dietomics is an emerging area of systems biology that attempts to explore the connections between the dietary habits and diseases. Some of the topical studies highlight that foods might have different impacts over an organism either in progressing a disease (negative association) or in fighting against it (positive association). The association of foods with different diseases can be put together to build a network that might provide a global view of the entire system. Again, such disease-food networks might emerge in a more complex form while considering the disease subtypes individually...
January 16, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28092568/equivalent-discrete-time-channel-modeling-for-molecular-communication-with-emphasize-on-an-absorbing-receiver
#2
Martin Damrath, Sebastian Korte, Peter Hoeher
This paper introduces the equivalent discrete-time channel model (EDTCM) to the area of diffusion-based molecular communication (DBMC). Emphasize is on an absorbing receiver, which is based on the so-called first passage time concept. In the wireless communications community the EDTCM is well known. Therefore, it is anticipated that the EDTCM improves the accessibility of DBMC and supports the adaptation of classical wireless communication algorithms to the area of DBMC. Furthermore, the EDTCM has the capability to provide a remarkable reduction of computational complexity compared to random walk based DBMC simulators...
January 10, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28092570/identifying-epigenetic-biomarkers-using-maximal-relevance-and-minimal-redundancy-based-feature-selection-for-multi-omics-data
#3
Saurav Mallik, Tapas Bhadra, Ujjwal Maulik
Epigenetic Biomarker discovery is an important task in bioinformatics. In this article, we develop a new framework of identifying statistically significant epigenetic biomarkers using maximal-relevance and minimal-redundancy criterion based feature (gene) selection for multi-omics dataset. Firstly, we determine the genes that have both expression as well as methylation values, and follow normal distribution. Similarly, we identify the genes which consist of both expression and methylation values, but do not follow normal distribution...
January 9, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28092569/discovery-of-micrornas-and-transcription-factors-co-regulatory-modules-by-integrating-multiple-types-of-genomic-data
#4
Jiawei Luo, Gen Xiang, Chu Pan
It is well known that regulators known as microRNA (miRNA) and transcription factor (TF) have been found to play an important role in gene regulation. However, there are few researches of collaborative regulatory (co-regulatory) mechanism between miRNA and TF on system level (function level). Meanwhile, recent advances in high-throughput genomic technologies have enabled researchers to collect diverse large-scale genomic data, which can be used to study the co-regulatory mechanism between miRNA and TF. In this paper, we propose a novel method called SNCoNMF (Sparse Network regularized non-negative matrix factorization for Co-regulatory modules identification) which adopts multiple non-negative matrix factorization framework to identify co-regulatory modules including miRNAs, TFs and genes...
January 9, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28103195/the-enhancement-of-nasal-drug-absorption-from-powder-formulations-by-the-addition-of-sodium-carboxymethyl-cellulose
#5
Akiko Tanaka, Tomoyuki Furubayashi, Hitomi Yamasaki, Katsuko Takano, Mayuko Kawakami, Shunsuke Kimura, Daisuke Inoue, Hidemasa Katsumi, Toshiyasu Sakane, Akira Yamamoto
For nasal drug absorption, powder formulations can be expected to provide many advantages. The first aim of this study was to examine drug absorption following nasal administration of powder formulations in rats. Pharmaceutical excipients are typically added to most powder formulations. The second aim was to investigate the change in nasal drug absorption of powder formulations in the presence of sodium carboxymethyl cellulose (CMC-Na). Model drugs used were norfloxacin (NFX), warfarin (WF), and piroxicam (PXC)...
January 4, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28026780/hierarchically-micro-and-nanopatterned-topographical-cues-for-modulation-of-cellular-structure-and-function
#6
Hoon Seonwoo, Won-Gyu Bae, Sunho Park, Hong-Nam Kim, Kyoung Soon Choi, Ki Taek Lim, Hoon Hyun, Jin-Woo Kim, Jangho Kim, Jong Hoon Chung
Living cells receive biochemical and physical information from the surrounding microenvironment and respond to this information. Multiscale hierarchical substrates with micro- and nanogrooves have been shown to mimic the native extracellular matrix (ECM) better than conventional nanopatterned substrates; therefore, substrates with hierarchical topographical cues are considered suitable for investigating the role of physical factors in tissue functions. In this study, precisely controllable, multiscale hierarchical substrates that could mimic the micro- and nanotopography of complex ECMs were fabricated and used to culture various cell types, including fibroblasts, endothelial cells, osteoblasts, and human mesenchymal stem cells...
December 1, 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/27913355/hierarchically-micro-and-nanopatterned-topographical-cues-for-modulation-of-cellular-structure-and-function
#7
Hoon Seonwoo, Won-Gyu Bae, Sunho Park, Hong-Nam Kim, Kyoung Soon Choi, Ki Taek Lim, Hoon Hyun, Jin-Woo Kim, Jangho Kim, Jong Hoon Chung
Living cells receive biochemical and physical information from the surrounding microenvironment and respond to this information. Multiscale hierarchical substrates with micro- and nanogrooves have been shown to mimic the native extracellular matrix (ECM) better than conventional nanopatterned substrates; therefore, substrates with hierarchical topographical cues are considered suitable for investigating the role of physical factors in tissue functions. In this study, precisely controllable, multiscale hierarchical substrates that could mimic the micro- and nanotopography of complex ECMs were fabricated and used to culture various cell types, including fibroblasts, endothelial cells, osteoblasts, and human mesenchymal stem cells...
December 1, 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/27913356/a-framework-for-integrating-multiple-biological-networks-to-predict-microrna-disease-associations
#8
Wei Peng, Wei Lan, Zeng Yu, Jianxin Wang, Yi Pan
MicroRNAs have close relationship with human diseases. Therefore, identifying disease related MicroRNAs plays an important role in disease diagnosis, prognosis and therapy. However, designing an effective computational method which can make good use of various biological resources and correctly predict the associations between MicroRNA and disease is still a big challenge. Previous researchers have pointed out that there are complex relationships among microRNAs, diseases and environment factors. There are inter-relationships between microRNAs, diseases or environment factors based on their functional similarity or phenotype similarity or chemical structure similarity and so on...
November 29, 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/27893398/probabilistic-inference-on-multiple-normalized-genome-wide-signal-profiles-with-model-regularization
#9
Ka-Chun Wong, Chengbin Peng, Shankai Yan, Cheng Liang
Understanding genome-wide protein-DNA interactions forms the basis for further focused studies. In particular, the chromatin immunoprecipitation (ChIP) with sequencing (ChIPSeq) technology can enable us to measure the genome-wide occupancy of DNA-binding protein of interest in vivo. Multiple ChIP-Seq runs thus inherent the potential for us to decipher the combinatorial interactions among multiple DNA-binding proteins. To handle those multiple genome-wide runs, we propose to integrate regularized regression functions (i...
November 21, 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/27875228/performance-evaluation-and-optimal-detection-of-relay-assisted-diffusion-based-molecular-communication-with-drift
#10
Nooshin Tavakkoli, Paeiz Azmi, Nader Mokari
In this paper, we consider a decode-and-forward (DF) relay-assisted diffusion-based molecular communication system inside one of the blood vessels of a human body with positive drift from transmitter to receiver. We use the normal approximation to the distribution of the number of received molecules and derive a closed-form expression for the end-toend bit error probability of the system. We then propose an optimization problem that aims at minimizing the bit error probability of the system and solve it at the receiver nanomachine by an algorithm based on the bisection method to determine the optimal detection threshold...
November 16, 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/27849548/an-end-to-end-model-of-plant-pheromone-channel-for-long-range-molecular-communications
#11
Bige Deniz Unluturk, Ian Akyildiz
A new track in molecular communication is using pheromones which can scale up the range of diffusion-based communication from meters to meters and enable new applications requiring long range. Pheromone communication is the emission of molecules in the air which trigger behavioral or physiological responses in receiving organisms. The objective of this paper is to introduce a new end-to-end model which incorporates pheromone behavior with communication theory for plants. The proposed model includes both the transmission and reception processes as well as the propagation channel...
November 11, 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28092503/propagation-modeling-and-analysis-of-molecular-motors-in-molecular-communication
#12
Youssef Chahibi, Ian F Akyildiz, Ilangko Balasingham
Molecular motor networks (MMNs) are networks constructed from molecular motors to enable nanomachines to perform coordinated tasks of sensing, computing, and actuation at the nano- and micro- scales. Living cells are naturally enabled with this same mechanism to establish point-to-point communication between different locations inside the cell. Similar to a railway system, the cytoplasm contains an intricate infrastructure of tracks, named microtubules, interconnecting different internal components of the cell...
December 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28092502/capacity-evaluation-of-a-quantum-based-channel-in-a-biological-context
#13
Valeria Loscri, Anna Maria Vegni
Nanotechnology, as enabler of the miniaturization of devices in a scale ranging from 1 to few hundreds of nm , represents a viable solution for " alternative" communication paradigms that could be effective in complex networked systems, as body area networks. Traditional communication paradigms are not effective in the context of joint body and nano-networked systems, for several reasons, and then novel approaches have been investigated such as nanomechanical, electromagnetic, acoustic, molecular, etc. On the other hand, quantum phenomena represent a natural direction for developing nanotechnology, since it has to be considered as a new scale where new phenomena can occur and can be exploited for information purpose...
December 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28092501/parallel-molecular-distributed-detection-with-brownian-motion
#14
Uri Rogers, Min-Sung Koh
This paper explores the in vivo distributed detection of an undesired biological agent's (BAs) biomarkers by a group of biological sized nanomachines in an aqueous medium under drift. The term distributed, indicates that the system information relative to the BAs presence is dispersed across the collection of nanomachines, where each nanomachine possesses limited communication, computation, and movement capabilities. Using Brownian motion with drift, a probabilistic detection and optimal data fusion framework, coined molecular distributed detection, will be introduced that combines theory from both molecular communication and distributed detection...
December 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28092500/a-model-of-a-synthetic-biological-communication-interface-between-mammalian-cells-and-mechatronic-systems
#15
Keith C Heyde, Warren C Ruder
The creation of communication interfaces between abiotic and biotic systems represents a significant research challenge. In this work, we design and model a system linking the biochemical signaling pathways of mammalian cells to the actions of a mobile robotic prosthesis. We envision this system as a robotic platform carrying an optically monitored bioreactor that harbors mammalian cells. The cellular, optical signal is captured by an onboard fluorescent microscope and converted into an electronic signal. We first present a design for the overall cell-robot system, with a specific focus on the design of the synthetic gene networks needed for the system...
December 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28092499/nanoparticles-for-sirna-based-gene-silencing-in-tumor-therapy
#16
Anish Babu, Ranganayaki Muralidharan, Narsireddy Amreddy, Meghna Mehta, Anupama Munshi, Rajagopal Ramesh
Gene silencing through RNA interference (RNAi) has emerged as a potential strategy in manipulating cancer causing genes by complementary base-pairing mechanism. Small interfering RNA (siRNA) is an important RNAi tool that has found significant application in cancer therapy. However due to lack of stability, poor cellular uptake and high probability of loss-of-function due to degradation, siRNA therapeutic strategies seek safe and efficient delivery vehicles for in vivo applications. The current review discusses various nanoparticle systems currently used for siRNA delivery for cancer therapy, with emphasis on liposome based gene delivery systems...
December 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28060709/the-enhancement-of-nasal-drug-absorption-from-powder-formulations-by-the-addition-of-sodium-carboxymethyl-cellulose
#17
Akiko Tanaka, Tomoyuki Furubayashi, Hitomi Yamasaki, Katsuko Takano, Mayuko Kawakami, Shunsuke Kimura, Daisuke Inoue, Hidemasa Katsumi, Toshiyasu Sakane, Akira Yamamoto
For nasal drug absorption, powder formulations can be expected to provide many advantages. The first aim of this study was to examine drug absorption following nasal administration of powder formulations in rats. Pharmaceutical excipients are typically added to most powder formulations. The second aim was to investigate the change in nasal drug absorption of powder formulations in the presence of sodium carboxymethyl cellulose (CMC-Na). Model drugs used were norfloxacin (NFX), warfarin (WF), and piroxicam (PXC)...
December 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/27959817/chemical-and-biological-sensing-using-diatom-photonic-crystal-biosilica-with-in-situ-growth-plasmonic-nanoparticles
#18
Xianming Kong, Kenny Squire, Erwen Li, Paul LeDuff, Gregory L Rorrer, Suning Tang, Bin Chen, Christopher P McKay, Rafael Navarro-Gonzalez, Alan X Wang
In this paper, we described a new type of bioenabled nano-plasmonic sensors based on diatom photonic crystal biosilica with in-situ growth silver nanoparticles and demonstrated label-free chemical and biological sensing based on surface-enhanced Raman scattering (SERs) from complex samples. Diatoms are photosynthetic marine micro-organisms that create their own skeletal shells of hydrated amorphous silica, called frustules, which possess photonic crystal-like hierarchical micro- & nanoscale periodic pores. Our research shows that such hybrid plasmonic-biosilica nanostructures formed by cost-effective and eco-friendly bottom-up processes can achieve ultra-high limit of detection for medical applications, food sensing, water/air quality monitoring and geological/space research...
December 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/27925592/enzyme-free-scalable-dna-digital-design-techniques-a-review
#19
Aby K George, Harpreet Singh
With the recent developments in DNA nanotechnology, DNA has been used as the basic building block for the design of nanostructures, autonomous molecular motors, various devices, and circuits. DNA is considered as a possible candidate for replacing silicon for designing digital circuits in a near future, especially in implantable medical devices, because of its parallelism, computational powers, small size, light weight, and compatibility with bio-signals. The research in DNA digital design is in early stages of development, and electrical and computer engineers are not much attracted towards this field...
December 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/27875229/rapid-detection-of-protein-kinase-on-capacitive-sensing-platforms
#20
Rohit Chand, Dawoon Han, Yong-Sang Kim
In this study, we developed a capacitive sensor for the one-step and label-free detection of protein kinase A (PKA) enzyme. Metal-insulator-semiconductor (MIS) and electrolyte-insulator-semiconductor (EIS) are a simple electronic transducer, which allows efficient detection of the target analyte. For this reason, we performed a comparative sensing of PKA on the MIS and EIS capacitive sensor. The PKA-specific aptamer was used for the one-step detection. For the immobilization of thiolated aptamer, the MIS sensor contained a thin gold layer, whereas the EIS sensor had a self-aligned monolayer of gold nanoparticles...
December 2016: IEEE Transactions on Nanobioscience
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