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IEEE Transactions on Nanobioscience

Guilherme Soares, Andri Prsspero, Marcos Calabresi, Diego Rodrigues, Lums Simoes, Caio Quini, Ronaldo Matos, Leonardo Pinto, Ailton Sousa-, Andris Bakuzis, Paulo Mancera, Jose Miranda
In this paper, the application of a technique to evaluate in vivo biodistribution of magnetic nanoparticles (MNP) is addressed: the Multichannel AC Biosusceptometry System (MC-ACB). It allows real-time assessment of magnetic nanoparticles in both bloodstream clearance and liver accumulation, where a complex network of inter-related cells is responsible for MNP uptake. Based on the acquired MC-ACB images, we propose a mathematical model to help understand the distribution and accumulation pharmacokinetics of MNP...
April 18, 2019: IEEE Transactions on Nanobioscience
Mi Li, Ning Xi, Yuechao Wang, Lianqing Liu
Hydrogels designed by biomimetism and bioinspiration have been considered as a promising biomaterial for biomedical applications due to their biocompatible characteristics. Though biomimetic or bioinspired hydrogels have been widely studied by biochemical analysis, so far the detailed organizations and properties of native natural hydrogels are still not fully understood. The advent of atomic force microscopy (AFM) provides a potent tool for probing the biological samples in their living states with nanometer spatial resolution, which offers new possibilities for addressing the biological and material issues at the nanoscale...
April 12, 2019: IEEE Transactions on Nanobioscience
Radu Paul Mihail, Gongbo Liang, Nathan Jacobs
Rheumatoid arthritis (RA) is an autoimmune disease whose common manifestation involves the slow destruction of joint tissue, damage that is visible in a radiograph. Over time, this damage causes pain and loss of functioning which depends, to some extent, on the spatial deformation induced by the joint damage. Building an accurate model of the current deformation and predicting potential future deformations is an important component of treatment planning. Unfortunately, this is currently a time consuming and labor intensive manual process...
April 12, 2019: IEEE Transactions on Nanobioscience
Yiran Wang, Adam Noel, Nan Yang
A novel a priori Monte Carlo (APMC) algorithm is proposed to accurately simulate the molecules absorbed at spherical receiver(s) with low computational complexity in diffusion-based molecular communication (MC) systems. It is demonstrated that the APMC algorithm achieves high simulation efficiency since by using this algorithm, the fraction of molecules absorbed for a relatively large time step length precisely matches the analytical result. Therefore, the APMC algorithm overcomes the shortcoming of the existing refined Monte Carlo (RMC) algorithm which enables accurate simulation for a relatively small time step length only...
April 11, 2019: IEEE Transactions on Nanobioscience
Canjia Li, Yingfei Sun, Ben He, Le Sun
Precision Medicine (PM) is regarded as an information retrieval (IR) task, in which biomedical articles containing treatment information about specific diseases or genetic variants are retrieved in response to patient record, aiming at providing medical evidence to the point-of-care. In existing PM approaches, manual keywords such as "treatment" and "therapy" are considered direct indicators of treatment information, and are thereby introduced to expand the original query. However, the common medical concepts that are implicitly related to treatment (such as "oncogene", "tumor"), and differ the relevant documents from the non-relevant ones, are yet to be utilized...
April 9, 2019: IEEE Transactions on Nanobioscience
Chen Lin, Sheng Ni, Yun Liang, Xiangxiang Zeng, Xiangrong Liu
The prediction of Drug-Target Interaction (DTI) is an important research direction in bioinformatics as it greatly shortens the development cycle of new drugs. State-of-theart computational methods for DTI prediction adopt a binary classification framework, i.e. a known DTI is positive while an unknown DTI is negative. Two severe problems occur in such a framework: (1) the number of negative samples is overwhelming; (2) a negative instance can not rule out the existence of the drugtarget interaction. Instead of treating unknown DTIs as negative instances in previous work, in this paper, we assume the unknown DTIs are missing labels...
April 9, 2019: IEEE Transactions on Nanobioscience
Boshu Ru, Dingcheng Li, Yueqi Hu, Lixia Yao
Serendipitous drug usage refers to the unexpected relief of comorbid diseases or symptoms when taking a medication for a different known indication. Historically, serendipity has contributed significantly to identifying many new drug indications. If patient-reported serendipitous drug usage in social media could be computationally identified, it could help generate and validate drug-repositioning hypotheses. We investigated deep neural network models for mining serendipitous drug usage from social media. We used the word2vec algorithm to construct wordembedding features from drug reviews posted in a WebMD patient forum...
April 4, 2019: IEEE Transactions on Nanobioscience
Libo Huang, Bingo Wing-Kuen Ling, Ruichu Cai, Yan Zeng, Jiong He, Yao Chen
In recent years, the signal processing opportunities with the multi-channel recording and the high precision detection provided by the development of new extracellular multielectrodes are increasing. Hence, designing new spike sorting algorithms are both attractive and challenging. These algorithms are used to distinguish the individual neurons' activity from the dense and simultaneously recorded neural action potentials with high accuracy. However, since the overlapping phenomenon often inevitably arises in the recorded data, they are not accurate enough in practical situations especially when the noise level is high...
April 4, 2019: IEEE Transactions on Nanobioscience
Jiahui Qiu, Yangming Zhou, Qi Wang, Tong Ruan, Ju Gao
Clinical named entity recognition (CNER) is a fundamental and crucial task for clinical and translation research. In recent years, deep learning methods have achieved significant success in CNER tasks. However, these methods depend greatly on recurrent neural networks (RNNs), which maintain a vector of hidden activations that are propagated through time, thus causing too much time to train models. In this paper, we propose a residual dilated convolutional neural network with conditional random field (RD-CNN-CRF) for the Chinese CNER, which makes the model asynchronous in computation and thus speeding up the training period dramatically...
April 1, 2019: IEEE Transactions on Nanobioscience
Urooj Ainuddin, Muhammad Khurram, S M Rezaul Hasan
The lysis-lysogeny switch in E. coli due to infection from lambda phage has been extensively studied and explained by scientists of molecular biology. The bacterium either survives with the viral strand of Deoxyribonucleic acid (DNA), or dies producing hundreds of viruses for propagation of infection. Many proteins transcribed after infection by λ phage take part in determining the fate of the bacterium, but two proteins that play a key role in this regard are the cI and cro dimers, that are transcribed off the viral DNA...
April 1, 2019: IEEE Transactions on Nanobioscience
Tao Jiang, Yilei Fu, Bo Liu, Yadong Wang
Novel sequence insertion (NSI) is an essential category of genome structural variations (SVs), which represents DNA segments absent from the reference genome assembly. It has important biological functions and strong correlation with phenotypes and diseases. The rapid development of long-read sequencing technologies provides the opportunities to discover NSIs more sensitively, since the much longer reads are helpful for the assembly and location of the novel sequences. However, most of state-of-the-art long-read based SV detection approaches are in generic design to detect various kinds of SVs, and they are either not suited to detect NSIs or computationally expensive...
April 1, 2019: IEEE Transactions on Nanobioscience
Shuai Huang, Lin Lin, Hao Yan, Juan Xu, Fuqiang Liu
Molecular communication (MC) is a promising paradigm for conveying information in nanonetworks where small particles like molecules are the carriers of information. In this paper, we investigate a special communication scenario where the MC system consists of a pair of mobile transmitter and receiver nanomachines. Both of them move randomly in a free diffusion manner. Due to the randomness generated by the motion of nanomachines and particle counting noise, the received signal at the receiver nanomachine, i...
March 27, 2019: IEEE Transactions on Nanobioscience
Nasibeh Rady Raz, Mohammad-R Akbarzadeh-T
Cooperative navigation and swarm decision making take center stage in a broad range of distributed applications with high environmental and measurement uncertainties. Here, we propose a Fuzzy Carotid Body-inspired Nanonetwork (FCBN) of autonomous nanomachines as a swarm computational framework for cooperative navigation and decision making at the nanoscale. The carotid body is a complex sensory system in animals that triggers the global breathing decision based on locally sensed data. Similarly, each nanomachine senses relevant local data and uses a Local Fuzzy Inference System (LFIS) to determine a local environmental trigger that, along with triggers of other nanomachines, collectively estimate the overall environmental state and the appropriate course of action by the nanonetwork...
March 21, 2019: IEEE Transactions on Nanobioscience
Benjamin E Noren, Rajib K Shaha, Alan T Stenquist, Carl P Frick, John S Oakey
Advancements in the microfabrication of soft materials have enabled the creation of increasingly sophisticated functional synthetic tissue structures for a myriad of tissue engineering applications. A challenge facing the field is mimicking the complex microarchitecture necessary to recapitulate proper morphology and function of many endogenous tissue constructs. This study describes the creation of PEGDA hydrogel microenvironments (microgels) that maintain a high level of viability at single cell patterning scales and can be integrated into composite scaffolds with tunable modulus...
March 15, 2019: IEEE Transactions on Nanobioscience
Zhongliang Jiang, Rajib Shaha, Kun Jiang, Ralph McBride, Carl Frick, John Oakey
Controlled cell delivery has shown some promising outcomes compared with traditional cell delivery approaches over the past decades, and strategies focused on optimization or engineering of controlled cell delivery have been intensively studied. In this report, we demonstrate the fabrication of a 3D printed hydrogel scaffold infused with degradable PEGPLA/NB composite hydrogel core for controlled cell delivery with improved cell viability and facile tunability. The 3D printed poly(ethylene glycol) diacrylate (PEGDA) scaffold with specifically designed architectures can provide mechanical support while allowing bidirectional diffusion of small molecules, thus permitting structural integrity and long-term cell viability...
March 15, 2019: IEEE Transactions on Nanobioscience
Adam Wang, Doohwan Jung, Jongseok Park, Gregory Junek, Hua Wang
Electrochemical interfaces with low-impedance, high biocompatibility, and long-term stability are of paramount importance for microelectrode arrays (MEAs) widely used in numerous cellular sensing/stimulation applications, e.g., brain interface, electroceuticals, neuroprosthetics, drug discovery, chemical screening, and fundamental biological research. This is increasingly critical since sensing/actuations at sub-cellular resolution necessitate ultra-miniaturized electrodes, which exhibit exacerbated electrochemical interfaces, especially on interfacial impedance...
March 15, 2019: IEEE Transactions on Nanobioscience
Craig L Miller, Gavin Stafford, Nathan Sigmon, Jordon A Gilmore
This work characterizes the use of the emerging solution blow spinning technique to create conductive carbon nanotube-PLA composite nanofibers. Poly(lactic acid) (PLA) and multi-walled Carbon nanotubes (MWCNT) were combined in various solvents to produce conductive fiber mats. Additionally, the authors were able to tune the conductivity of the fiber mats by modifying the MWCNT concentration. Conductive fiber mats were able to reach conductivity values as high as 474 S/cm which is approximately more than 2x higher than the ubiquitous Germanium...
March 15, 2019: IEEE Transactions on Nanobioscience
Joseph Lee, Michael Nolan, Hoseon Lee
In this paper a cell quantitation system is proposed based on a new microfluidic solenoid design. The design is simulated in COMSOL and a scaled version of the prototype is built and the induced voltage due to the passage of a magnetic material is measured using a low-noise amplifier and converted to a digital signal using a DSP chip. Simulation results show approximately 16 nV induced voltage across the solenoid and the measurement results for a scaled version of the solenoid outputs 125 mV peak voltage. A microfluidic fabrication process demonstrates a successful prototype of a microfluidic solenoid...
March 15, 2019: IEEE Transactions on Nanobioscience
Rachel S Zoll, Craig B Schindler, Travis L Massey, Daniel S Drew, Michel M Maharbiz, Kristofer S J Pister
Microwire and microelectrode arrays used for cortical neural recording typically consist of tens to hundreds of recording sites, but often only a fraction of these sites are in close enough proximity to firing neurons to record singleunit activity. Recent work has demonstrated precise, depthcontrollable mechanisms for the insertion of single neural recording electrodes, but these methods are mostly only capable of inserting electrodes which elicit adverse biological response. We present an electrostatic-based actuator capable of inserting individual carbon fiber microelectrodes which elicit minimal to no adverse biological response...
March 15, 2019: IEEE Transactions on Nanobioscience
Silvan Staufert, Harun Torlakcik, Salvador Pane, Christofer Hierold
Parylene-C is a frequently used polymeric thinfilm coating in medical applications and is known for its excellent biocompatibility and flexible deposition process. However, its use in long-term implants is limited due to its poor adhesion to metals in liquid environments. In this work we present a strategy to anchor Parylene-C to medical grade titanium (Ti) by means of nanostructuring the Ti substrates surface prior to Parylene coating. We observe that, after aging in physiological salt solution for 3 days, Parylene coating lose their adhesion to bare titanium surfaces...
March 15, 2019: IEEE Transactions on Nanobioscience
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