keyword
MENU ▼
Read by QxMD icon Read
search

network inference

keyword
https://www.readbyqxmd.com/read/28806280/integrated-analysis-of-biopsies-from-inflammatory-bowel-disease-patients-identifies-saa1-as-a-link-between-mucosal-microbes-with-th17-and-th22-cells
#1
Mei San Tang, Rowann Bowcutt, Jacqueline M Leung, Martin J Wolff, Uma M Gundra, David Hudesman, Lisa B Malter, Michael A Poles, Lea Ann Chen, Zhiheng Pei, Antonio G Neto, Wasif M Abidi, Thomas Ullman, Lloyd Mayer, Richard A Bonneau, Ilseung Cho, Pʼng Loke
BACKGROUND: Inflammatory bowel diseases (IBD) are believed to be driven by dysregulated interactions between the host and the gut microbiota. Our goal is to characterize and infer relationships between mucosal T cells, the host tissue environment, and microbial communities in patients with IBD who will serve as basis for mechanistic studies on human IBD. METHODS: We characterized mucosal CD4 T cells using flow cytometry, along with matching mucosal global gene expression and microbial communities data from 35 pinch biopsy samples from patients with IBD...
August 9, 2017: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/28805692/real-time-rain-rate-evaluation-via-satellite-downlink-signal-attenuation-measurement
#2
Filippo Giannetti, Ruggero Reggiannini, Marco Moretti, Elisa Adirosi, Luca Baldini, Luca Facheris, Andrea Antonini, Samantha Melani, Giacomo Bacci, Antonio Petrolino, Attilio Vaccaro
We present the NEFOCAST project (named by the contraction of "Nefele", which is the Italian spelling for the mythological cloud nymph Nephele, and "forecast"), funded by the Tuscany Region, about the feasibility of a system for the detection and monitoring of precipitation fields over the regional territory based on the use of a widespread network of new-generation Eutelsat "SmartLNB" (smart low-noise block converter) domestic terminals. Though primarily intended for interactive satellite services, these devices can also be used as weather sensors, as they have the capability of measuring the rain-induced attenuation incurred by the downlink signal and relaying it on an auxiliary return channel...
August 12, 2017: Sensors
https://www.readbyqxmd.com/read/28802227/anti-inflammatory-effects-of-shufengjiedu-capsule-for-upper-respiratory-infection-via-the-erk-pathway
#3
Yanmei Li, Nianwei Chang, Yanqi Han, Mengge Zhou, Jie Gao, Yuanyuan Hou, Min Jiang, Tiejun Zhang, Gang Bai
BACKGROUND: Shufengjiedu Capsule (SFJD) is a type of Chinese traditional medicine compound for the treatment of acute upper respiratory tract infection. The present work aims to decipher the mechanism of SFJD. METHODS: In this study, we used target prediction and RNA sequence (RNA-Seq) based on transcriptome analysis to clarify the inflammation-eliminating mechanism of SFJD. Firstly, Pseudomonas aeruginosa (PAK) was used to induce acute lung injury in KM mice. After being treated by SFJD, the differently expressed genes were analyzed by RNA-Seq...
August 9, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28800327/analytical-strategy-to-prioritize-alzheimer-s-disease-candidate-genes-in-gene-regulatory-networks-using-public-expression-data
#4
Shweta Bagewadi Kawalia, Tamara Raschka, Mufassra Naz, Ricardo de Matos Simoes, Philipp Senger, Martin Hofmann-Apitius
Alzheimer's disease (AD) progressively destroys cognitive abilities in the aging population with tremendous effects on memory. Despite recent progress in understanding the underlying mechanisms, high drug attrition rates have put a question mark behind our knowledge about its etiology. Re-evaluation of past studies could help us to elucidate molecular-level details of this disease. Several methods to infer such networks exist, but most of them do not elaborate on context specificity and completeness of the generated networks, missing out on lesser-known candidates...
August 8, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28799926/daily-runoff-prediction-using-the-linear-and-non-linear-models
#5
Alireza Sharifi, Yagob Dinpashoh, Rasoul Mirabbasi
Runoff prediction, as a nonlinear and complex process, is essential for designing canals, water management and planning, flood control and predicting soil erosion. There are a number of techniques for runoff prediction based on the hydro-meteorological and geomorphological variables. In recent years, several soft computing techniques have been developed to predict runoff. There are some challenging issues in runoff modeling including the selection of appropriate inputs and determination of the optimum length of training and testing data sets...
August 2017: Water Science and Technology: a Journal of the International Association on Water Pollution Research
https://www.readbyqxmd.com/read/28798961/leaking-privacy-and-shadow-profiles-in-online-social-networks
#6
David Garcia
Social interaction and data integration in the digital society can affect the control that individuals have on their privacy. Social networking sites can access data from other services, including user contact lists where nonusers are listed too. Although most research on online privacy has focused on inference of personal information of users, this data integration poses the question of whether it is possible to predict personal information of nonusers. This article tests the shadow profile hypothesis, which postulates that the data given by the users of an online service predict personal information of nonusers...
August 2017: Science Advances
https://www.readbyqxmd.com/read/28797096/prediction-of-n-linked-glycosylation-sites-using-position-relative-features-and-statistical-moments
#7
Muhammad Aizaz Akmal, Nouman Rasool, Yaser Daanial Khan
Glycosylation is one of the most complex post translation modification in eukaryotic cells. Almost 50% of the human proteome is glycosylated as glycosylation plays a vital role in various biological functions such as antigen's recognition, cell-cell communication, expression of genes and protein folding. It is a significant challenge to identify glycosylation sites in protein sequences as experimental methods are time taking and expensive. A reliable computational method is desirable for the identification of glycosylation sites...
2017: PloS One
https://www.readbyqxmd.com/read/28797087/a-comparison-of-monte-carlo-based-bayesian-parameter-estimation-methods-for-stochastic-models-of-genetic-networks
#8
Inés P Mariño, Alexey Zaikin, Joaquín Míguez
We compare three state-of-the-art Bayesian inference methods for the estimation of the unknown parameters in a stochastic model of a genetic network. In particular, we introduce a stochastic version of the paradigmatic synthetic multicellular clock model proposed by Ullner et al., 2007. By introducing dynamical noise in the model and assuming that the partial observations of the system are contaminated by additive noise, we enable a principled mechanism to represent experimental uncertainties in the synthesis of the multicellular system and pave the way for the design of probabilistic methods for the estimation of any unknowns in the model...
2017: PloS One
https://www.readbyqxmd.com/read/28796610/deep-learning-markov-random-field-for-semantic-segmentation
#9
Ziwei Liu, Xiaoxiao Li, Ping Luo, Chen Change Loy, Xiaoou Tang
Semantic segmentation tasks can be well modeled by Markov Random Field (MRF). This paper addresses semantic segmentation by incorporating high-order relations and mixture of label contexts into MRF. Unlike previous works that optimized MRFs using iterative algorithm, we solve MRF by proposing a Convolutional Neural Network (CNN), namely Deep Parsing Network (DPN), which enables deterministic end-to-end computation in a single forward pass. Specifically, DPN extends a contemporary CNN to model unary terms and additional layers are devised to approximate the mean field (MF) algorithm for pairwise terms...
August 9, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28796604/dual-temporal-and-spatial-sparse-representation-for-inferring-group-wise-brain-networks-from-resting-state-fmri-dataset
#10
Junhui Gong, Xiaoyan Liu, Tianming Liu, Jiansong Zhou, Gang Sun, Juanxiu Tian
Recently, sparse representation has been successfully used to identify brain networks from task-based fMRI dataset. However, when using the strategy to analyze resting-state fMRI dataset, it is still a challenge to automatically infer the group-wise brain networks under consideration of group commonalities and subject-specific characteristics. In the paper, a novel method based on dual temporal and spatial sparse representation (DTSSR) is proposed to meet this challenge. Firstly, the brain functional networks with subject-specific characteristics are obtained via sparse representation with online dictionary learning for the fMRI time series (temporal domain) of each subject...
August 9, 2017: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28796489/rational-modular-rna-engineering-based-on-in-vivo-profiling-of-structural-accessibility
#11
Abigail N Leistra, Paul Amador, Aishwarya Buvanendiran, Alex Moon-Walker, Lydia M Contreras
Bacterial small RNAs (sRNAs) have been established as powerful parts for controlling gene expression. However, development and application of engineered sRNAs has primarily focused on regulating novel synthetic targets. In this work, we demonstrate a rational modular RNA engineering approach that uses in vivo structural accessibility measurements to tune the regulatory activity of a multisubstrate sRNA for differential control of its native target network. Employing the CsrB global sRNA regulator as a model system, we use published in vivo structural accessibility data to infer the contribution of its local structures (substructures) to function and select a subset for engineering...
August 10, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28795686/hdl-and-atherosclerotic-cardiovascular-disease-genetic-insights-into-complex-biology
#12
REVIEW
Robert S Rosenson, H Bryan Brewer, Philip J Barter, Johan L M Björkegren, M John Chapman, Daniel Gaudet, Daniel Seung Kim, Eric Niesor, Kerry-Anne Rye, Frank M Sacks, Jean-Claude Tardif, Robert A Hegele
Plasma levels of HDL cholesterol (HDL-C) predict the risk of cardiovascular disease at the epidemiological level, but a direct causal role for HDL in cardiovascular disease remains controversial. Studies in animal models and humans with rare monogenic disorders link only particular HDL-associated mechanisms with causality, including those mechanisms related to particle functionality rather than cholesterol content. Mendelian randomization studies indicate that most genetic variants that affect a range of pathways that increase plasma HDL-C levels are not usually associated with reduced risk of cardiovascular disease, with some exceptions, such as cholesteryl ester transfer protein variants...
August 10, 2017: Nature Reviews. Cardiology
https://www.readbyqxmd.com/read/28794258/genetic-architecture-and-molecular-networks-underlying-leaf-thickness-in-desert-adapted-tomato
#13
Viktoriya Coneva, Margaret Frank, Maria A de Luis Balaguer, Mao Li, Rosangela Sozzani, Daniel H Chitwood
Thicker leaves allow plants to grow in water-limited conditions. However, our understanding of the genetic underpinnings of this highly functional leaf shape trait is poor. We used a custom-built confocal profilometer to directly measure leaf thickness in a set of introgression lines (ILs) derived from the desert tomato species Solanum pennellii, and identified quantitative trait loci (QTL). We report evidence of a complex genetic architecture of this trait and roles for both genetic and environmental factors...
August 9, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28793925/perturbed-human-sub-networks-by-fusobacterium-nucleatum-candidate-virulence-proteins
#14
Andreas Zanzoni, Lionel Spinelli, Shérazade Braham, Christine Brun
BACKGROUND: Fusobacterium nucleatum is a gram-negative anaerobic species residing in the oral cavity and implicated in several inflammatory processes in the human body. Although F. nucleatum abundance is increased in inflammatory bowel disease subjects and is prevalent in colorectal cancer patients, the causal role of the bacterium in gastrointestinal disorders and the mechanistic details of host cell functions subversion are not fully understood. RESULTS: We devised a computational strategy to identify putative secreted F...
August 10, 2017: Microbiome
https://www.readbyqxmd.com/read/28790372/coda-integrating-multi-level-context-oriented-directed-associations-for-analysis-of-drug-effects
#15
Hasun Yu, Jinmyung Jung, Seyeol Yoon, Mijin Kwon, Sunghwa Bae, Soorin Yim, Jaehyun Lee, Seunghyun Kim, Yeeok Kang, Dohoen Lee
In silico network-based methods have shown promising results in the field of drug development. Yet, most of networks used in the previous research have not included context information even though biological associations actually do appear in the specific contexts. Here, we reconstruct an anatomical context-specific network by assigning contexts to biological associations using protein expression data and scientific literature. Furthermore, we employ the context-specific network for the analysis of drug effects with a proximity measure between drug targets and diseases...
August 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28779869/functional-integration-of-complex-mirna-networks-in-central-and-peripheral-lesion-and-axonal-regeneration
#16
REVIEW
M Ghibaudi, M Boido, A Vercelli
New players are emerging in the game of peripheral and central nervous system injury since their physiopathological mechanisms remain partially elusive. These mechanisms are characterized by several molecules whose activation and/or modification following a trauma is often controlled at transcriptional level. In this scenario, microRNAs (miRNAs/miRs) have been identified as main actors in coordinating important molecular pathways in nerve or spinal cord injury (SCI). miRNAs are small non-coding RNAs whose functionality at network level is now emerging as a new level of complexity...
August 2, 2017: Progress in Neurobiology
https://www.readbyqxmd.com/read/28778080/using-molecular-functional-networks-to-manifest-connections-between-obesity-and-obesity-related-diseases
#17
Jialiang Yang, Jing Qiu, Kejing Wang, Lijuan Zhu, Jingjing Fan, Deyin Zheng, Xiaodi Meng, Jiasheng Yang, Lihong Peng, Yu Fu, Dahan Zhang, Shouneng Peng, Haiyun Huang, Yi Zhang
Obesity is a primary risk factor for many diseases such as certain cancers. In this study, we have developed three algorithms including a random-walk based method OBNet, a shortest-path based method OBsp and a direct-overlap method OBoverlap, to reveal obesity-disease connections at protein-interaction subnetworks corresponding to thousands of biological functions and pathways. Through literature mining, we also curated an obesity-associated disease list, by which we compared the methods. As a result, OBNet outperforms other two methods...
July 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28776616/what-can-be-inferred-from-moir%C3%A3-patterns-a-case-study-of-trimesic-acid-monolayers-on-graphite
#18
Saskia Spitzer, Oliver Helmle, Oliver Ochs, Joshua Horsley, Natalia Martsinovich, Wolfgang M Heckl, Markus Lackinger
Self-assembly of benzene-1,3,5-tricarboxylic acid (trimesic acid - TMA) monolayers at the alkanoic acid-graphite interface is revisited. Even though this archetypal model system for hydrogen bonded porous networks is particularly well studied, the analysis of routinely observed superperiodic contrast modulations known as moiré patterns lags significantly behind. Fundamental questions remain unanswered such as, are moiré periodicity and orientation always the same, i.e. is exclusively only one specific moiré pattern observed? What are the geometric relationships (superstructure matrices) between moiré, TMA, and graphite lattices? What affects the moiré pattern formation? Is there any influence from solvent, concentration, or thermal treatment? These basic questions are addressed via scanning tunneling microscopy experiments at the liquid-solid interface, revealing a variety of different moiré patterns...
August 4, 2017: Faraday Discussions
https://www.readbyqxmd.com/read/28772240/dynamic-response-and-transfer-function-of-social-systems-a-neuro-inspired-model-of-collective-human-activity-patterns
#19
Ilias N Lymperopoulos
The interaction of social networks with the external environment gives rise to non-stationary activity patterns reflecting the temporal structure and strength of exogenous influences that drive social dynamical processes far from an equilibrium state. Following a neuro-inspired approach, based on the dynamics of a passive neuronal membrane, and the firing rate dynamics of single neurons and neuronal populations, we build a state-of-the-art model of the collective social response to exogenous interventions. In this regard, we analyze online activity patterns with a view to determining the transfer function of social systems, that is, the dynamic relationship between external influences and the resulting activity...
July 14, 2017: Neural Networks: the Official Journal of the International Neural Network Society
https://www.readbyqxmd.com/read/28772189/learning-abstract-visual-concepts-via-probabilistic-program-induction-in-a-language-of-thought
#20
Matthew C Overlan, Robert A Jacobs, Steven T Piantadosi
The ability to learn abstract concepts is a powerful component of human cognition. It has been argued that variable binding is the key element enabling this ability, but the computational aspects of variable binding remain poorly understood. Here, we address this shortcoming by formalizing the Hierarchical Language of Thought (HLOT) model of rule learning. Given a set of data items, the model uses Bayesian inference to infer a probability distribution over stochastic programs that implement variable binding...
July 31, 2017: Cognition
keyword
keyword
30315
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"