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Pedro Fonseca, Niek den Teuling, Xi Long, Ronald M Aarts
To compare conditional random fields (CRF), hidden Markov models (HMMs) and Bayesian linear discriminants (LDs) for cardiorespiratory sleep stage classification on a five-class sleep staging task (Wake/N1/N2/N3/REM), to explore the benefit of incorporating time information in the classification and to evaluate the feasibility of sleep staging on obstructive sleep apnea (OSA) patients.
 Approach: The classifiers with and without time information were evaluated with 10-fold cross-validation on five-, four- (Wake/N1+N2/N3/REM) and three-class (Wake/NREM/REM) classification tasks using a data set comprising 443 night-time polysomnography (PSG) recordings of 231 participants (180 healthy participants, 100 of which with a 'regular' sleep architecture, and 51 participants previously diagnosed with OSA)...
April 5, 2018: Physiological Measurement
Bartosz Janaszek, Marcin Kieliszczyk, Anna Tyszka-Zawadzka, Paweł Szczepański
In this paper we demonstrate a new class of anisotropic 1D hyperbolic metamaterials (HMMs) possessing multiresonant dispersion characteristics. With the help of an EMT-based model, we analyze HMMs with unit cells composed of layers characterized by various plasma frequencies, revealing multiple resonance transitions corresponding to the critical absorptions points. In particular, we show that relative locations of plasma frequencies of constituent materials and the unit cell's geometry determine the type of dispersion characteristics as well as spectral locations of critical absorption points...
March 20, 2018: Applied Optics
Shaodan Zhou, Jiaqi Tang, Bo Jia, Yunkai Lü
Activators regenerated by electron transfer-atom transfer radical polymerization (ARGET-ATRP) was applied to the continuous grafting of polybasic polymers and poly(ethylene glycol) (PEG) brushes on the surface of the magnetic microspheres (MMs). At first, the MMs were coated with silica gel, modified by amino group, and then 2-bromoisobutyryl bromide was grafted on the surface of MMs. After that, the hydrophilic polymer brushes magnetic microspheres (HMMs) were prepared by polymerization on the surface of the MMs...
February 8, 2018: Se Pu, Chinese Journal of Chromatography
Shanshan Ren, Koen Bertels, Zaid Al-Ars
GATK HaplotypeCaller (HC) is a popular variant caller, which is widely used to identify variants in complex genomes. However, due to its high variants detection accuracy, it suffers from long execution time. In GATK HC, the pair-HMMs forward algorithm accounts for a large percentage of the total execution time. This article proposes to accelerate the pair-HMMs forward algorithm on graphics processing units (GPUs) to improve the performance of GATK HC. This article presents several GPU-based implementations of the pair-HMMs forward algorithm...
2018: Evolutionary Bioinformatics Online
Joel A Boyd, Ben J Woodcroft, Gene W Tyson
Large-scale metagenomic datasets enable the recovery of hundreds of population genomes from environmental samples. However, these genomes do not typically represent the full diversity of complex microbial communities. Gene-centric approaches can be used to gain a comprehensive view of diversity by examining each read independently, but traditional pairwise comparison approaches typically over-classify taxonomy and scale poorly with increasing metagenome and database sizes. Here we introduce GraftM, a tool that uses gene specific packages to rapidly identify gene families in metagenomic data using hidden Markov models (HMMs) or DIAMOND databases, and classifies these sequences using placement into pre-constructed gene trees...
March 19, 2018: Nucleic Acids Research
Kolla Rajasekhar, Kapilkumar Mehta, Thimmaiah Govindaraju
Amyloid beta (Aβ) aggregation is the key trait responsible for the pathological devastation caused by Alzheimer's disease (AD). Among the various pathways of multifaceted toxicity exhibited by Aβ aggregates in neuronal cells, generation of reactive oxygen species (ROS) by Aβ-CuII complex and mitochondrial damage are prominent. Aβ interferes with mitochondrial transport channels, causing mitochondrial dysfunction. Herein, we present nontoxic hybrid multifunctional modulators (HMMs, TGR86-88) developed by integrating the structural and functional features of the metal chelating aggregation modulator, clioquinol (Clq) and the antioxidant epigallocatechin gallate (EGCG)...
March 20, 2018: ACS Chemical Neuroscience
Florian Eggenhofer, Ivo L Hofacker, Rolf Backofen, Christian Höner Zu Siederdissen
Summary: A standard method for the identification of novel RNAs or proteins is homology search via probabilistic models. One approach relies on the definition of families, which can be encoded as covariance models (CMs) or Hidden Markov Models (HMMs). While being powerful tools, their complexity makes it tedious to investigate them in their (default) tabulated form. This specifically applies to the interpretation of comparisons between multiple models as in family clans. The Covariance model visualization tools (CMV) visualize CMs or HMMs to: I) Obtain an easily interpretable representation of HMMs and CMs; II) Put them in context with the structural sequence alignments they have been created from; III) Investigate results of model comparisons and highlight regions of interest...
March 15, 2018: Bioinformatics
Xianglian Song, Zizhuo Liu, Yuanjiang Xiang, Koray Aydin
Most of hyperbolic metamaterials (HMMs) investigated to date are based on isotropic materials resulting in uniaxial HMMs in which dielectric permittivities perpendicular to the propagation direction are the same. Using an anisotropic material constituent to form a HMM is a promising research direction providing opportunities to control the dielectric permittivity in all three directions independently. Herein, we propose and theoretically demonstrate novel biaxial HMMs composed of multilayer stacks of few-layer black phosphorus (BP) and Au thin films...
March 5, 2018: Optics Express
Dylan Lu, Haoliang Qian, Kangwei Wang, Hao Shen, Feifei Wei, Yunfeng Jiang, Eric E Fullerton, Paul K L Yu, Zhaowei Liu
Semiconductor quantum well (QW) light-emitting diodes (LEDs) have limited temporal modulation bandwidth of a few hundred MHz due to the long carrier recombination lifetime. Material doping and structure engineering typically leads to incremental change in the carrier recombination rate, whereas the plasmonic-based Purcell effect enables dramatic improvement for modulation frequency beyond the GHz limit. By stacking Ag-Si multilayers, the resulting hyperbolic metamaterials (HMMs) have shown tunability in the plasmonic density of states for enhancing light emission at various wavelengths...
March 7, 2018: Advanced Materials
Lu Wang, Shilong Li, Biran Zhang, Yuzhou Qin, Ziao Tian, Yangfu Fang, Yonglei Li, Zhaowei Liu, Yongfeng Mei
We demonstrate hyperbolic metamaterials (HMMs) on curved surface for an efficient outcoupling of non-radiative modes, which lead to an enhanced spontaneous emission. Those high-wavevector plasmonic modes can propagate along the curved structure and emit into the far-field, realizing a directional light emission with maximal fluorescent intensity. Detailed simulations disclose a high Purcell factor and a spatial power distribution in the curved HMM, which agrees with the experimental result. Our work presents remarkable enhancing capability in both Purcell factor and emission intensity, which could suggest unique structure design in metamaterials for potential application in e...
February 13, 2018: ACS Applied Materials & Interfaces
Mai Higuchi, Junichi Takahara
Hyperbolic metamaterials (HMMs) show great promise in photonics applications because their unconventional open isofrequency surface permits enlargement of wavenumbers without limitation. Although optical behaviors in HMMs can be macroscopically described by theoretical calculations with the effective medium approximation (EMA), neglect of microscopic phenomena in each layer leads to discrepancies from exact numerical results. We clarify the origin of bulk propagating waves in HMMs and we show that they can be classified into two modes: long- and short-range surface-plasmon-based coupled modes (LRSP and SRSP, respectively)...
January 22, 2018: Optics Express
Kirubin Pillay, Anneleen Dereymaeker, Katrien Jansen, Gunnar Naulaers, Sabine Van Huffel, Maarten De Vos
<i>Objective</i>. We develop a method for automated four-state sleep classification of preterm and term-born babies at term-age of 38-40 weeks postmenstrual age (the age since the last menstrual cycle of the mother) using multichannel Electroencephalogram (EEG) recordings. At this critical age, EEG differentiates from broader Quiet Sleep (QS) and Active Sleep (AS) stages to four, more complex states, and the quality and timing of this differentiation is indicative of the level of brain development...
January 30, 2018: Journal of Neural Engineering
Jingheng Cai, Ming Ouyang, Kai Kang, Xinyuan Song
Cocaine is a type of drug that functions to increase the availability of the neurotransmitter dopamine in the brain. However, cocaine dependence or abuse is highly related to an increased risk of psychiatric disorders and deficits in cognitive performance, attention, and decision-making abilities. Given the chronic and persistent features of drug addiction, the progression of abstaining from cocaine often evolves across several states, such as addiction to, moderate dependence on, and swearing off cocaine. Hidden Markov models (HMMs) are well suited to the characterization of longitudinal data in terms of a set of unobservable states, and have increasingly been used to uncover the dynamic heterogeneity in progressive diseases or activities...
March 2018: Multivariate Behavioral Research
Hui-Ju Kao, Shun-Long Weng, Kai-Yao Huang, Fergie Joanda Kaunang, Justin Bo-Kai Hsu, Chien-Hsun Huang, Tzong-Yi Lee
BACKGROUND: Carbonylation, which takes place through oxidation of reactive oxygen species (ROS) on specific residues, is an irreversibly oxidative modification of proteins. It has been reported that the carbonylation is related to a number of metabolic or aging diseases including diabetes, chronic lung disease, Parkinson's disease, and Alzheimer's disease. Due to the lack of computational methods dedicated to exploring motif signatures of protein carbonylation sites, we were motivated to exploit an iterative statistical method to characterize and identify carbonylated sites with motif signatures...
December 21, 2017: BMC Systems Biology
Kenko Fujii, Gauthier Gras, Antonino Salerno, Guang-Zhong Yang
While minimally invasive surgery offers great benefits in terms of reduced patient trauma, bleeding, as well as faster recovery time, it still presents surgeons with major ergonomic challenges. Laparoscopic surgery requires the surgeon to bimanually control surgical instruments during the operation. A dedicated assistant is thus required to manoeuvre the camera, which is often difficult to synchronise with the surgeon's movements. This article introduces a robotic system in which a rigid endoscope held by a robotic arm is controlled via the surgeon's eye movement, thus forgoing the need for a camera assistant...
February 2018: Medical Image Analysis
Lukas Zimmermann, Andrew Stephens, Seung-Zin Nam, David Rau, Jonas Kübler, Marko Lozajic, Felix Gabler, Johannes Söding, Andrei N Lupas, Vikram Alva
The MPI Bioinformatics Toolkit ( is a free, one-stop web service for protein bioinformatic analysis. It currently offers 34 interconnected external and in-house tools, whose functionality covers sequence similarity searching, alignment construction, detection of sequence features, structure prediction, and sequence classification. This breadth has made the Toolkit an important resource for experimental biology and for teaching bioinformatic inquiry. Recently, we replaced the first version of the Toolkit, which was released in 2005 and had served around 2...
December 16, 2017: Journal of Molecular Biology
Wisnu Wiradhany, Mark R Nieuwenstein
In the original article, the number of HMMs and LMMs who took part in the first study was reported to have been 13and 10, respectively (p. 2624).
February 2018: Attention, Perception & Psychophysics
Ananth Prakash, Matt Jeffryes, Alex Bateman, Robert D Finn
Protein sequence similarity search is one of the most commonly used bioinformatics methods for identifying evolutionarily related proteins. In general, sequences that are evolutionarily related share some degree of similarity, and sequence-search algorithms use this principle to identify homologs. The requirement for a fast and sensitive sequence search method led to the development of the HMMER software, which in the latest version (v3.1) uses a combination of sophisticated acceleration heuristics and mathematical and computational optimizations to enable the use of profile hidden Markov models (HMMs) for sequence analysis...
December 8, 2017: Current Protocols in Bioinformatics
Tong Liu, Zhuo-Qian Liang
This article proposes a lightweight biometric sensing system using ubiquitous narrowband radio frequency (RF) links for path-dependent walker classification. The fluctuated received signal strength (RSS) sequence generated by human motion is used for feature representation. To capture the most discriminative characteristics of individuals, a three-layer RF sensing network is organized for building multiple sampling links at the most common heights of upper limbs, thighs, and lower legs. The optimal parameters of sensing configuration, such as the height of link location and number of fused links, are investigated to improve sensory data distinctions among subjects, and the experimental results suggest that the synergistic sensing by using multiple links can contribute a better performance...
December 5, 2017: Sensors
Mai Desouky, Ahmed M Mahmoud, Mohamed A Swillam
Noble Metals such as Gold and Silver demonstrated for mid IR metamaterials have suffered many obstacles such as: high losses and lack of tunability. The application of doped semiconductors has allowed overcoming the tunability restriction, besides, possessing lower losses as compared to metals. In addition, doped semiconductors have small magnitude of negative real permittivity which is required to realize mid IR Hyperbolic Metamaterials (HMMs). We theoretically demonstrate super focusing based on an all Semiconductor planar HMM using InAs heterostructure...
November 10, 2017: Scientific Reports
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