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Genetic Network Inference Using Hierarchical Structure

Shuhei Kimura, Masato Tokuhisa, Mariko Okada-Hatakeyama
2016 Frontiers in Physiology  
Third, we use the hierarchical structure obtained to assign confidence values to all candidate regulations.  ...  Many methods for inferring genetic networks have been proposed, but the regulations they infer often include false-positives.  ...  obtained to assess the confidence values of the regulations.  ... 
doi:10.3389/fphys.2016.00057 pmid:26941653 pmcid:PMC4763037 fatcat:c24tq5mh6vftbgl5zwbugdfsdm

N6-Methyladenosine-Related Long Non-Coding RNAs Are Identified as a Potential Prognostic Biomarker for Lung Squamous Cell Carcinoma and Validated by Real-Time PCR

Wei Zhang, Qian Zhang, Zhefan Xie, Li Che, Tingting Xia, Xingdong Cai, Shengming Liu
2022 Frontiers in Genetics  
The m6A-related lncRNA prognostic markers (m6A-LPMs) were established using the least absolute shrinkage and selection operator (LASSO) Cox regression analysis.  ...  LUSC patients were divided into two subgroups (clusters 1 and 2) using principal component analysis. The expression of PD-L1 was lower in tumor tissues and cluster 2 of LUSC patients.  ...  ROC curves was used to assess the prognostic accuracy of this risk model.  ... 
doi:10.3389/fgene.2022.839957 pmid:35719401 pmcid:PMC9204524 fatcat:xwwrl6ie2rb6nmojdzrgwwanuu

An overview of methods of fine and ultrafine particle collection for physicochemical characterisation and toxicity assessments

Prashant Kumar, Gopinath Kalaiarasan, Alexandra E. Porter, Alessandra Pinna, Michał M. Kłosowski, Philip Demokritou, Kian Fan Chung, Chris Pain, D.K. Arvind, Rossella Arcucci, Ian M. Adcock, Claire Dilliway
2020 Science of the Total Environment  
We review the suitability of available instrumentation to collect the PM mass required for these assessments.  ...  An evaluation of methods and instrumentation used for airborne virus collection concludes that samplers operating cyclone sampling techniques (using centrifugal forces) are effective in collecting airborne  ...  Acknowledgements This work has been supported by the EPSRC funded project, Health assessment across biological length scales for personal pollution exposure and its mitigation (INHALE; Grant No.  ... 
doi:10.1016/j.scitotenv.2020.143553 pmid:33239200 fatcat:at3o5hug2jfwtjpg66amgwmajy

A single-cell transcriptome atlas of human early embryogenesis [article]

Yichi Xu, Tengjiao Zhang, Qin Zhou, Mengzhu Hu, Yao Qi, Yifang Xue, Lihui Wang, Zhirong Bao, Weiyang Shi
2021 bioRxiv   pre-print
Combined with data of other vertebrates, the rich information shed light on spatial patterning of axes, systemic temporal regulation of developmental progression and potential human-specific regulation  ...  Our study provides a compendium of early progenitor cells of human organs, which can serve as the root of lineage analysis in organogenesis.  ...  . ****, p value < 10 -7 ; ***, p value < 0.001 (Mann-Whitney U test). Fig. 5 . 5 Fig. 5. Systemic regulation in vertebrate embryogenesis.  ... 
doi:10.1101/2021.11.30.470583 fatcat:rxd3slb35fdtxpfuodphr34f3i

Transcriptome analysis reveals a ribosome constituents disorder involved in the RPL5 downregulated zebrafish model of Diamond-Blackfan anemia

Yang Wan, Qian Zhang, Zhaojun Zhang, Binfeng Song, Xiaomin Wang, Yingchi Zhang, Qiong Jia, Tao Cheng, Xiaofan Zhu, Anskar Yu-Hung Leung, Weiping Yuan, Haibo Jia (+1 others)
2016 BMC Medical Genomics  
By comparing with other DBA zebrafish models and processing functional coupling network, we identified some common regulated genes, lncRNAs and miRNAs, that might play important roles in development and  ...  The clinical phenotypes of DBA include failure of erythropoiesis, congenital anomalies and cancer predisposition.  ...  Confidence intervals for estimates of FPKM were calculated using a Bayesian inference method [49] .  ... 
doi:10.1186/s12920-016-0174-9 pmid:26961822 pmcid:PMC4785739 fatcat:4unimizek5hr5dbfgbp55z7shq

Tumorigenicity assessment of cell therapy products: the need for global consensus and points to consider

Y. Sato, H. Bando, M. Di Piazza, G. Gowing, C. Herberts, S. Jackman, G. Leoni, S. Libertini, T. MacLachlan, J.W. McBlane, L. Pereira Mouriès, M. Sharpe (+4 others)
2019 Cytotherapy  
We discuss the value of those approaches, in particular the limitations of in vivo methods, and comment on challenges and future directions.  ...  In such circumstances, the developers of cell therapy products may have conducted various tumorigenicity tests and consulted with regulators in respective countries.  ...  Mercedes Serabian (US Food and Drug Administration, CBER OTAT) for her leadership as co-chair of the HESI CT-TRACS Committee (2016, 2017) and her valuable expert input in the discussions leading to this  ... 
doi:10.1016/j.jcyt.2019.10.001 pmid:31711733 fatcat:laljer5fx5fe3oafzpl7moktx4

Distributed optimization in wireless sensor networks: an island-model framework

Giovanni Iacca
2013 Soft Computing - A Fusion of Foundations, Methodologies and Applications  
Such a system might be used, for example, to implement advanced network features like distributed modelling, self-optimizing protocols, and anomaly detection, to name a few.  ...  We perform extensive tests of different DOWSN configurations on a benchmark made up of continuous optimization problems; we analyze the influence of the network parameters (number of nodes, inter-node  ...  Acknowledgements INCAS 3 is co-funded by the Province of Drenthe, the Municipality of Assen, the European Fund for Regional Development and the Ministry of Economic Affairs, Peaks in the Delta.  ... 
doi:10.1007/s00500-013-1091-x fatcat:ytaallpusbcm7kqncbhpxfyspq

BNC1 regulates cell heterogeneity in human pluripotent stem cell derived-epicardium

Laure Gambardella, Sophie A. McManus, Victoria Moignard, Derya Sebukhan, Agathe Delaune, Simon Andrews, William G. Bernard, Maura A. Morrison, Paul R. Riley, Berthold Göttgens, Nicolas Gambardella Le Novère, Sanjay Sinha
2019 Development  
Network inference methods using transcriptomic data from the different cell lineages derived from the hPSC-epi delivered a core transcriptional network organised around WT1, TCF21 and BNC1.  ...  This study unveils a list of epicardial regulators and is a step towards engineering subpopulations of epicardial cells with selective biological activities.  ...  Network inference Following the conclusions of the DREAM5 challenge's analysis (Marbach et al., 2012) , we used a combination of methods based on different algorithms to infer regulatory networks.  ... 
doi:10.1242/dev.174441 pmid:31767620 pmcid:PMC6955213 fatcat:qcrucqmbp5fgtc7hbvfphqjdtq

Data-driven modelling of a gene regulatory network for cell fate decisions in the growing limb bud

M. Uzkudun, L. Marcon, J. Sharpe
2015 Molecular Systems Biology  
This network reveals a new model of PD regulation which we call the "crossover model", because the proximal morphogen (RA) controls the distal boundary of Hoxa11, while conversely the distal morphogens  ...  Secondly, we use reverse-engineering to test how different gene regulatory networks can interpret the opposing gradients of fibroblast growth factors (FGF) and retinoic acid (RA) to pattern the PD markers  ...  Acknowledgements We thank Nadia Mercader and Miguel Torres for sharing their WMISH data on Hoxa11 and Hoxa13, and for many useful discussions about PD patterning, and Andreea Munteanu and Xavier Diego  ... 
doi:10.15252/msb.20145882 pmid:26174932 pmcid:PMC4547844 fatcat:k32kc43usfd4ro5mlaklthgvda

Mutations in Bcl9 and Pygo genes cause congenital heart defects by tissue-specific perturbation of Wnt/β-catenin signaling [article]

Claudio Cantu, Anastasia Felker, Dario Zimmerli, Elena Chiavacci, Elena Maria Cabello, Lucia Kirchgeorg, Tomas Valenta, George Hausmann, Jorge Ripoll, Natalie Vilain, Michel Aguet, Konrad Basler (+1 others)
2018 bioRxiv   pre-print
Genetic alterations in human BCL9 genes have repeatedly been found in congenital heart disease (CHD) with as-of-yet unclear causality.  ...  Here, combining zebrafish and mouse genetics, we document tissue-specific functions in canonical Wnt signaling for BCL9 and Pygo proteins during heart development.  ...  Haitao Ji for chemical compounds, the ZBM at UZH for imaging support, and the members of the Mosimann and Basler labs for constructive input.  ... 
doi:10.1101/249680 fatcat:jrt4edlyzzewhggqwjcgpnweq4

Genome-wide association study results for educational attainment aid in identifying genetic heterogeneity of schizophrenia [article]

Vikas Bansal, Marina Mitjans, Casper A. P. Burik, Richard Karlsson Linner, Aysu Okbay, Cornelius A. Rietveld, Martin Begemann, Stefan Bonn, Stephan Ripke, Ronald de Vlaming, Michel G. Nivard, Hannelore Ehrenreich (+1 others)
2017 bioRxiv   pre-print
Instead, several genes seem to have pleiotropic effects on EA and SZ, but without a clear pattern of sign concordance. Genetic heterogeneity of SZ contributes to this finding.  ...  We investigated possible causes of this counterintuitive finding using genome-wide association study results for EA and SZ (N = 443,581) and a replication cohort (1,169 controls; 1,067 cases) with deeply  ...  In all models, the P values of the coefficients were very similar to the ones obtained by LPM.  ... 
doi:10.1101/114405 fatcat:rczy3n45cfffzh7tdq3tdq3nxa

Distribution Of Macrophages In The Gastrointestinal Tract Of Horses

2017 Equine Veterinary Education  
However, in many cases the likely identity can be inferred from crossspecies mapping, with further confidence derived from the pattern of expression.  ...  From this list, using Log2 fold change (log2 fc) values of ≥ 1.5 or ≤ 1.5 with p < 0.02 a list of upregulated and down regulated genes was generated.  ... 
doi:10.1111/eve.13_12792 fatcat:ufjce3yc5nckvap7ulrmr6364m

7th European Conference on Schizophrenia Research: Time for precision medicine?

2019 European Archives of Psychiatry and Clinical Neuroscience  
The costs for publication were fully covered by delegates' payments of registration fees.  ...  For each patient, the rCBF values in L-SMA [-9; ? 10; ? 60] and L-LPM[-46; -12; ? 43] were converted in t-values by being compared to 37 controls.  ...  In the present study, we investigate the impact of common genetic variants of NOS1AP on the cortical WM network using fMRI.  ... 
doi:10.1007/s00406-019-01045-6 fatcat:4tbfk4p4yngqto7uxhrdczle54

The Effects of Old and New Media on Children's Weight

Agne Suziedelyte
2012 Social Science Research Network  
To address the endogeneity of children's media use, I use the child fixed effects and correlated random effects models. I find no evidence that media use contributes to weight gain among children.  ...  The Child Development Supplement to the Panel Study of Income Dynamics is used for the analysis.  ...  The findings of these studies cannot be used, however, to draw causal inferences, because the endogeneity of media use is not addressed.  ... 
doi:10.2139/ssrn.2140985 fatcat:fjfdudqggvc63duapsgdy5sy4m

Review on Valve Stiction. Part I: From Modeling to Smart Diagnosis

Riccardo di Capaci, Claudio Scali
2015 Processes  
In parallel, Miao and Seborg [15] developed a technique using a decay ratio index of the autocorrelation coefficients of the control error.  ...  Once single/multiple significant oscillations have been identified, the hard following step is to assess the sources of these malfunctions.  ...  Similarly, PDF of the first derivative of the error signal is used for self-regulating processes. Kano et al.  ... 
doi:10.3390/pr3020422 fatcat:cuqtoaur3rch5ctxo4em6kfe6m
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