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https://www.readbyqxmd.com/read/28916180/interpreting-temporal-fluctuations-in-resting-state-functional-connectivity-mri
#1
REVIEW
Raphaël Liégeois, Timothy O Laumann, Abraham Z Snyder, Juan Zhou, B T Thomas Yeo
Resting-state functional connectivity is a powerful tool for studying human functional brain networks. Temporal fluctuations in functional connectivity, i.e., dynamic functional connectivity (dFC), are thought to reflect dynamic changes in brain organization and non-stationary switching of discrete brain states. However, recent studies have suggested that dFC might be attributed to sampling variability of static FC. Despite this controversy, a detailed exposition of stationarity and statistical testing of dFC is lacking in the literature...
September 12, 2017: NeuroImage
https://www.readbyqxmd.com/read/28916136/mathematical-basis-of-improved-protein-subfamily-classification-by-a-hmm-based-sequence-filter
#2
Siddhartha Kundu
Informative phylogenetic analysis is dependent on the presence of curated and annotated sequences. This may be complemented by the simultaneous availability of empirical data pertaining to their in vivo function. Confounding sequences, with their similarity to more than one functional cluster, can therefore, render any categorization ambiguous, subjective, and imprecise. Here, I analyze and discuss the development of a mathematical expression that can characterize a potential confounding protein sequence. Specifically, statistical descriptors of combinatorially arranged profile HMM scores are computed and evaluated...
September 12, 2017: Mathematical Biosciences
https://www.readbyqxmd.com/read/28902053/welcome-day-a-community-interprofessional-model-for-meeting-the-needs-of-migrant-workers
#3
Lora Wyss, Rosanna F Hess
Welcome Day, one specific day in the life of Hartville Migrant Ministry (HMM), a faith-based ministry in Ohio, illustrates the organization's vision, mission, and community collaboration. Migrant and seasonal farm workers, the Migrant Head Start program, HMM and Welcome Day, interprofessional collaboration, and Malone University School of Nursing faculty and students support are discussed. Programs and activities presented here could be reproduced in other communities.
October 2017: Journal of Christian Nursing: a Quarterly Publication of Nurses Christian Fellowship
https://www.readbyqxmd.com/read/28888060/unidirectional-growth-of-heavy-meromyosin-hmm-clusters-along-actin-filaments-revealed-by-real-time-fluorescence-microscopy
#4
Rika Hirakawa, Yusuke Nishikawa, Taro Q P Uyeda, Kiyotaka Tokuraku
Heavy meromyosin (HMM) forms clusters along actin filaments under low ATP concentrations. Here, we observed the growth of HMM clusters under low concentrations of ATP in real time using fluorescence microscopy. When actin filaments were loosely immobilized on positively charged lipid bilayers, clusters of HMM-GFP were readily formed. Time-lapse observation revealed that the clusters grew unidirectionally. When we used a mixture of actin filaments and copolymers of actin and acto-S1dC, a chimeric protein of actin and the myosin motor domain, HMM-GFP preferentially formed clusters along the copolymers...
September 9, 2017: Cytoskeleton
https://www.readbyqxmd.com/read/28878807/distribution-and-functionality-of-copy-number-variation-across-european-cattle-populations
#5
Maulik Upadhyay, Vinicus H da Silva, Hendrik-Jan Megens, Marleen H P W Visker, Paolo Ajmone-Marsan, Valentin A Bâlteanu, Susana Dunner, Jose F Garcia, Catarina Ginja, Juha Kantanen, Martien A M Groenen, Richard P M A Crooijmans
Copy number variation (CNV), which is characterized by large-scale losses or gains of DNA fragments, contributes significantly to genetic and phenotypic variation. Assessing CNV across different European cattle populations might reveal genetic changes responsible for phenotypic differences, which have accumulated throughout the domestication history of cattle as consequences of evolutionary forces that act upon them. To explore pattern of CNVs across European cattle, we genotyped 149 individuals, that represent different European regions, using the Illumina Bovine HD Genotyping array...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28874136/himme-using-genetic-patterns-as-a-proxy-for-genome-assembly-reliability-assessment
#6
Jordi Abante, Noushin Ghaffari, Charles D Johnson, Aniruddha Datta
BACKGROUND: The information content of genomes plays a crucial role in the existence and proper development of living organisms. Thus, tremendous effort has been dedicated to developing DNA sequencing technologies that provide a better understanding of the underlying mechanisms of cellular processes. Advances in the development of sequencing technology have made it possible to sequence genomes in a relatively fast and inexpensive way. However, as with any measurement technology, there is noise involved and this needs to be addressed to reach conclusions based on the resulting data...
September 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28869811/hidden-markov-model-analysis-reveals-the-advantage-of-analytic-eye-movement-patterns-in-face-recognition-across-cultures
#7
Tim Chuk, Kate Crookes, William G Hayward, Antoni B Chan, Janet H Hsiao
It remains controversial whether culture modulates eye movement behavior in face recognition. Inconsistent results have been reported regarding whether cultural differences in eye movement patterns exist, whether these differences affect recognition performance, and whether participants use similar eye movement patterns when viewing faces from different ethnicities. These inconsistencies may be due to substantial individual differences in eye movement patterns within a cultural group. Here we addressed this issue by conducting individual-level eye movement data analysis using hidden Markov models (HMMs)...
September 1, 2017: Cognition
https://www.readbyqxmd.com/read/28867956/meggasense-the-metagenome-genome-annotated-sequence-natural-language-search-engine-a-platform-for-%C3%A2-the-construction-of-sequence-data-warehouses
#8
Ranko Gacesa, Jurica Zucko, Solveig K Petursdottir, Elisabet Eik Gudmundsdottir, Olafur H Fridjonsson, Janko Diminic, Paul F Long, John Cullum, Daslav Hranueli, Gudmundur O Hreggvidsson, Antonio Starcevic
The MEGGASENSE platform constructs relational databases of DNA or protein sequences. The default functional analysis uses 14 106 hidden Markov model (HMM) profiles based on sequences in the KEGG database. The Solr search engine allows sophisticated queries and a BLAST search function is also incorporated. These standard capabilities were used to generate the SCATT database from the predicted proteome of Streptomyces cattleya. The implementation of a specialised metagenome database (AMYLOMICS) for bioprospecting of carbohydrate-modifying enzymes is described...
June 2017: Food Technology and Biotechnology
https://www.readbyqxmd.com/read/28852755/intelligent-identification-of-multi-level-nanopore-signatures-for-accurate-detection-of-cancer-biomarkers
#9
Jian-Hua Zhang, Xiu-Ling Liu, Zheng-Li Hu, Yi-Lun Ying, Yi-Tao Long
To achieve accurate detection of cancer biomarkers with nanopore sensors, the precise recognition of multi-level current blockage events (signature) is a pivotal problem. However, it remains rather a challenge to identify the multi-level current blockages of target biomarkers in nanopore experiments, especially for the nanopore analysis of serum samples. In this work, we combined a modified DBSCAN (Density-Based Spatial Clustering of Applications with Noise) algorithm with the Viterbi training algorithm of the hidden Markov model (HMM) to achieve intelligent retrieval of multi-level current signatures from microRNA in serum samples...
August 30, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28840939/viruses-in-cancers-among-the-immunosuppressed
#10
Laila Sara Arroyo Mühr, Zurab Bzhalava, Maria Hortlund, Camilla Lagheden, Sara Nordqvist Kleppe, Davit Bzhalava, Emilie Hultin, Joakim Dillner
Most cancer forms known to be caused by viruses are increased among the immunosuppressed, but several cancer forms without established viral etiology are also increased, notably non-melanoma skin carcinoma (NMSC). We followed all 13429 solid organ transplantation patients in Sweden for cancer occurrence after transplantation. We requested these tumor specimens and sequenced the first 89 specimens received (62 NMSCs, 27 other cancers). The sequences were analyzed for viruses based on two bioinformatics algorithms (paracel-blast (sensitive for detection of known viruses) and hidden Markov model (HMM; sensitive for distantly related viruses))...
August 25, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28813877/capture-learning-and-classification-of-upper-extremity-movement-primitives-in-healthy-controls-and-stroke-patients
#11
Jorge Guerra, Jasim Uddin, Dawn Nilsen, James Mclnerney, Ammarah Fadoo, Isirame B Omofuma, Shatif Hughes, Sunil Agrawal, Peter Allen, Heidi M Schambra
There currently exist no practical tools to identify functional movements in the upper extremities (UEs). This absence has limited the precise therapeutic dosing of patients recovering from stroke. In this proof-of-principle study, we aimed to develop an accurate approach for classifying UE functional movement primitives, which comprise functional movements. Data were generated from inertial measurement units (IMUs) placed on upper body segments of older healthy individuals and chronic stroke patients. Subjects performed activities commonly trained during rehabilitation after stroke...
July 2017: IEEE ... International Conference on Rehabilitation Robotics: [proceedings]
https://www.readbyqxmd.com/read/28807860/hidden-markov-modeling-of-frequency-following-responses-to-mandarin-lexical-tones
#12
Fernando Llanos, Zilong Xie, Bharath Chandrasekaran
BACKGROUND: The frequency-following response (FFR) is a scalp-recorded electrophysiological potential reflecting phase-locked activity from neural ensembles in the auditory system. The FFR is often used to assess the robustness of subcortical pitch processing. Due to low signal-to-noise ratio at the single-trial level, FFRs are typically averaged across thousands of stimulus repetitions. Prior work using this approach has shown that subcortical encoding of linguistically-relevant pitch patterns is modulated by long-term language experience...
August 12, 2017: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/28771616/quantification-of-transplant-derived-circulating-cell-free-dna-in-absence-of-a-donor-genotype
#13
Eilon Sharon, Hao Shi, Sandhya Kharbanda, Winston Koh, Lance R Martin, Kiran K Khush, Hannah Valantine, Jonathan K Pritchard, Iwijn De Vlaminck
Quantification of cell-free DNA (cfDNA) in circulating blood derived from a transplanted organ is a powerful approach to monitoring post-transplant injury. Genome transplant dynamics (GTD) quantifies donor-derived cfDNA (dd-cfDNA) by taking advantage of single-nucleotide polymorphisms (SNPs) distributed across the genome to discriminate donor and recipient DNA molecules. In its current implementation, GTD requires genotyping of both the transplant recipient and donor. However, in practice, donor genotype information is often unavailable...
August 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28766669/broadband-room-temperature-strong-coupling-between-quantum-dots-and-metamaterials
#14
Chaitanya Indukuri, Ravindra Kumar Yadav, J K Basu
Herein, we report the first demonstration of room temperature enhanced light-matter coupling in the visible regime for metamaterials using cooperative coupled quasi two dimensional quantum dot assemblies located at precise distances from the hyperbolic metamaterial (HMM) templates. The non-monotonic variation of the magnitude of strong coupling, manifested in terms of strong splitting of the photoluminescence of quantum dots, can be explained in terms of enhanced LDOS near the surface of such metamaterials as well as the plasmon mediated super-radiance of closely spaced quantum dots (QDs)...
August 17, 2017: Nanoscale
https://www.readbyqxmd.com/read/28744863/classification-of-changes-occurring-in-lung-patient-during-radiotherapy-using-relative-%C3%AE-analysis-and-hidden-markov-models
#15
Nicolas Varfalvy, Ophelie Piron, Marc François Cyr, Anne Dagnault, Louis Archambault
PURPOSE: to present a new automated patient classification method based on relative gamma analysis and hidden Markov models (HMM) to identify patients undergoing important anatomical changes during radiation therapy. METHODS: daily EPID images of every treatment field were acquired for 52 patients treated for lung cancer. In addition, CBCT were acquired on a regular basis. Gamma analysis was performed relative to the first fraction given that no significant anatomical change was observed on the CBCT of the first fraction compared to the planning CT...
July 26, 2017: Medical Physics
https://www.readbyqxmd.com/read/28742155/acceleration-of-the-sliding-movement-of-actin-filaments-with-the-use-of-a-non-motile-mutant-myosin-in-in-vitro-motility-assays-driven-by-skeletal-muscle-heavy-meromyosin
#16
Kohei Iwase, Masateru Tanaka, Keiko Hirose, Taro Q P Uyeda, Hajime Honda
We examined the movement of an actin filament sliding on a mixture of normal and genetically modified myosin molecules that were attached to a glass surface. For this purpose, we used a Dictyostelium G680V mutant myosin II whose release rates of Pi and ADP were highly suppressed relative to normal myosin, leading to a significantly extended life-time of the strongly bound state with actin and virtually no motility. When the mixing ratio of G680V mutant myosin II to skeletal muscle HMM (heavy myosin) was 0.01%, the actin filaments moved intermittently...
2017: PloS One
https://www.readbyqxmd.com/read/28726751/an-adaptive-feature-learning-model-for-sequential-radar-high-resolution-range-profile-recognition
#17
Xuan Peng, Xunzhang Gao, Yifan Zhang, Xiang Li
This paper proposes a new feature learning method for the recognition of radar high resolution range profile (HRRP) sequences. HRRPs from a period of continuous changing aspect angles are jointly modeled and discriminated by a single model named the discriminative infinite restricted Boltzmann machine (Dis-iRBM). Compared with the commonly used hidden Markov model (HMM)-based recognition method for HRRP sequences, which requires efficient preprocessing of the HRRP signal, the proposed method is an end-to-end method of which the input is the raw HRRP sequence, and the output is the label of the target...
July 20, 2017: Sensors
https://www.readbyqxmd.com/read/28718051/coronary-heart-disease-preoperative-gesture-interactive-diagnostic-system-based-on-augmented-reality
#18
Yi-Bo Zou, Yi-Min Chen, Ming-Ke Gao, Quan Liu, Si-Yu Jiang, Jia-Hui Lu, Chen Huang, Ze-Yu Li, Dian-Hua Zhang
Coronary heart disease preoperative diagnosis plays an important role in the treatment of vascular interventional surgery. Actually, most doctors are used to diagnosing the position of the vascular stenosis and then empirically estimating vascular stenosis by selective coronary angiography images instead of using mouse, keyboard and computer during preoperative diagnosis. The invasive diagnostic modality is short of intuitive and natural interaction and the results are not accurate enough. Aiming at above problems, the coronary heart disease preoperative gesture interactive diagnostic system based on Augmented Reality is proposed...
August 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/28710494/near-infrared-surface-enhanced-raman-scattering-based-on-star-shaped-gold-silver-nanoparticles-and-hyperbolic-metamaterial
#19
Chih-Hsien Lai, Guo-An Wang, Tsung-Kai Ling, Tzyy-Jiann Wang, Po-Kai Chiu, Yuan-Fong Chou Chau, Chih-Ching Huang, Hai-Pang Chiang
It is desirable to extend the surface-enhanced Raman scattering (SERS) from the conventionally used visible range into the infrared region, because the fluorescence background is lower in the long-wavelength regime. To do this, it is important to have a SERS substrate suitable for infrared operation. In this work, we report the near infrared SERS operation based on the substrates employing star-shaped gold/silver nanoparticles and hyperbolic metamaterial (HMM) structure. We first fabricate the SERS substrate in which nanoparticles are separated from a silver film by a thin dielectric layer...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28666322/svm-dependent-pairwise-hmm-an-application-to-protein-pairwise-alignments
#20
Gabriele Orlando, Daniele Raimondi, Taushif Khan, Tom Lenaerts, Wim Vranken
Motivation: Methods able to provide reliable protein alignments are crucial for many bioinformatics applications. In the last years many different algorithms have been developed and various kinds of information, from sequence conservation to secondary structure, have been used to improve the alignment performances. This is especially relevant for proteins with highly divergent sequences. However, recent works suggest that different features may have different importance in diverse protein classes and it would be an advantage to have more customizable approaches, capable to deal with different alignment definitions...
June 28, 2017: Bioinformatics
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