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Functional mapping

Guangxin Yao, Shuanggang Hu, Lu Yu, Yanfei Ru, Charlie Degui Chen, Qiang Liu, Yonglian Zhang
As an important nuclear hormone receptor, estrogen receptor alpha (ERα), which is encoded by Esr1 gene, regulates the expression of hundreds of genes in a stimulus-specific, temporal and tissue-specific fashion, mainly by binding to specific DNA sequences-estrogen response elements (EREs). As an important estrogen target tissue in males, the function of the efferent ductules relies on the presence of the ERα protein, but the underlying regulatory mechanisms are poorly illustrated. In this study, genome-wide ERα-binding sites in mouse efferent ductules were mapped by ChIP-seq...
June 22, 2017: Endocrinology
Peter Marx, Peter Antal, Bence Bolgar, Gyorgy Bagdy, Bill Deakin, Gabriella Juhasz
Comorbidity patterns have become a major source of information to explore shared mechanisms of pathogenesis between disorders. In hypothesis-free exploration of comorbid conditions, disease-disease networks are usually identified by pairwise methods. However, interpretation of the results is hindered by several confounders. In particular a very large number of pairwise associations can arise indirectly through other comorbidity associations and they increase exponentially with the increasing breadth of the investigated diseases...
June 23, 2017: PLoS Computational Biology
Baochang Zhangm, Yun Yangm, Chen Chen, Linlin Yang, Jungong Han, Ling Shao
Human action recognition is an important yet challenging task. This paper presents a low-cost descriptor called 3D Histograms of Texture (3DHoTs) to extract discriminant features from a sequence of depth maps. 3DHoTs are derived from projecting depth frames onto three orthogonal Cartesian planes, i.e., the frontal, side and top planes, and thus compactly characterize the salient information of a specific action, on which texture features are calculated to represent the action. Besides this fast feature descriptor, a new multi-class boosting classifier (MBC) is also proposed to efficiently exploit different kinds of features in a unified framework for action classification...
June 21, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
Zhengjue Wang, Yinghua Wang, Hongwei Liu, Hao Zhang
In this paper, we propose a new discriminative non-linear dictionary learning approach, called correlation constrained structured kernel KSVD, for object recognition. The objective function for dictionary learning contains a reconstructive term and a discriminative term. In the reconstructive term, signals are implicitly non-linearly mapped into a space, where a structured kernel dictionary, each sub-dictionary of which lies in the span of the mapped signals from the corresponding class, is established. In the discriminative term, by analyzing the classification mechanism, the correlation constraint is proposed in kernel form, constraining the correlations between different discriminative codes, and restricting the coefficient vectors to be transformed into a feature space, where the features are highly correlated inner-class and nearly independent between-classes...
June 21, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
Hoda S Hashemi, Hassan Rivaz
A critical step in quasi-static ultrasound elastography is estimation of time-delay between two frames of radiofrequency (RF) data that are obtained while the tissue is undergoing deformation. This paper presents a novel technique for timedelay estimation (TDE) of all samples of RF data simultaneously, thereby exploiting all the information in RF data for TDE. A nonlinear cost function that incorporates similarity of RF data intensity and prior information of displacement continuity is formulated. Optimization of this function involves searching for TDE of all samples of the RF data, rendering the optimization intractable with conventional techniques given that the number of variables can be approximately one million...
June 21, 2017: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
T Guaratini, L G P Feitosa, D B Silva, N P Lopes, J L C Lopes, R Vessecchi
Alkaloids from plants of the genus Erythrina display important biological activities, including anxiolytic action. Characterization of these alkaloids by mass spectrometry (MS) has contributed to the construction of a spectral library, has improved understanding of their structures, and has supported the proposal of fragmentation mechanisms in light of density functional calculations (DFT). In this study, we have used low- and high-resolution MS(n) analyses to investigate the fragmentation patterns of erythrinian alkaloids; we have employed the B3LYP/6-31+G(d,p) model to obtain their reactive sites...
June 23, 2017: Journal of Mass Spectrometry: JMS
Marion Carrier, Michael Windt, Bernhard Ziegler, Jörn Appelt, Bodo Saake, Dietrich Meier, Anthony Bridgwater
The transformation of lignocellulosic biomass into bio-based commodity chemicals is technically possible. Among thermochemical processes, fast pyrolysis, a relatively mature technology that has now reached the commercial level, produces a high yield of an organic-rich liquid stream. Despite the recent efforts in elucidating the degradation paths of biomass pyrolysis, the selectivity and recovery rates of bio-compounds remain low. In an attempt to clarify the general degradation scheme of biomass fast pyrolysis and provide a quantitative insight, this study has combined the use of fast pyrolysis micro-reactors, spectrometric techniques and mixtures of unlabelled and Carbon-13 enriched materials...
June 23, 2017: ChemSusChem
Wei Zhai, Yin Sun, Changcheng Guo, Guanghui Hu, Mingchao Wang, Jiayi Zheng, WanYing Lin, Qingbo Huang, Gonghui Li, Junhua Zheng, Chawnshang Chang
While the androgen receptor (AR) might promote renal cell carcinoma (RCC) initiation and progression, the molecular mechanisms involved remain largely unclear. Here, we discovered the novel LncRNA-SARCC, which was suppressed and associated with better prognosis in RCC. Preclinical studies using multiple RCC cells and in vivo mouse model indicated that LncRNA-SARCC could attenuate RCC cell invasion, migration and proliferation in vitro and in vivo. Mechanistically, LncRNA-SARCC bound and destabilized AR protein with an inhibition of AR function, which led to transcriptionally de-repress miR-143-3p expression, thus inhibition of its downstream signals including AKT, MMP-13, K-RAS and P-ERK...
June 23, 2017: Cell Death and Differentiation
Lindsay A Wills, Xiaohui Qu, I-Ya Chang, Thomas J L Mustard, Douglas A Keszler, Kristin A Persson, Paul Ha-Yeon Cheong
The characterization of water-based corrosion, geochemical, environmental and catalytic processes rely on the accurate depiction of stable phases in a water environment. The process is aided by Pourbaix diagrams, which map the equilibrium solid and solution phases under varying conditions of pH and electrochemical potential. Recently, metastable or possibly stable nanometric aqueous clusters have been proposed as intermediate species in non-classical nucleation processes. Herein, we describe a Group Additivity approach to obtain Pourbaix diagrams with full consideration of multimeric cluster speciation from computations...
June 15, 2017: Nature Communications
Anna Lesniak, Izabela Herman-Sucharska, Małgorzata Klimek, Paulina Karcz, Anna Kubatko-Zielińska, Magdalena Nitecka, Grażyna Dutkowska, Bożena Romanowska-Dixon, Przemko Kwinta
PURPOSE: The main aim of the study was to evaluate which factors affect the long-time visual function in preterm children, whether it is prematurity or retinopathy of prematurity or perhaps disturbances in the visual pathway. MATERIALS AND METHODS: Fifty-eight children with mean birth weight 1016 g (range 520-1500 g) were evaluated at mean age 48 months (range 42-54 months). All children underwent magnetic resonance imaging (MRI) studies, visual evoked potentials (VEPs), and the Developmental Test of Visual Perception (DTVP)...
June 2017: Indian Journal of Ophthalmology
Sam Ellis, Andrew J Reader
Positron emission tomography (PET) is frequently used to monitor functional changes that occur over extended time scales, for example in longitudinal oncology PET protocols that include routine clinical follow-up scans to assess the efficacy of a course of treatment. In these contexts PET datasets are currently reconstructed into images using single-dataset reconstruction methods. Inspired by recently proposed joint PET-MR reconstruction methods, we propose to reconstruct longitudinal datasets simultaneously by using a joint penalty term in order to exploit the high degree of similarity between longitudinal images...
June 23, 2017: Physics in Medicine and Biology
Tomaz Podlesnikar, Victoria Delgado, Jeroen J Bax
The left ventricular (LV) remodeling process associated with significant valvular heart disease (VHD) is characterized by an increase of myocardial interstitial space with deposition of collagen and loss of myofibers. These changes occur before LV systolic function deteriorates or the patient develops symptoms. Cardiovascular magnetic resonance (CMR) permits assessment of reactive fibrosis, with the use of T1 mapping techniques, and replacement fibrosis, with the use of late gadolinium contrast enhancement...
June 22, 2017: International Journal of Cardiovascular Imaging
Fatemeh Javadi-Zarnaghi, Claudia Höbartner
Practical application of enzymatic nucleic acids has received more attention in recent years. Understanding the mechanism of catalysis and availability of information on potentials and limitations of these enzymes expands their application scope. A general approach for characterization of functional macromolecules including enzymatic nucleic acids is to perturb a specific set of condition and to follow the perturbation effect by biophysical and biochemical methods. This chapter reviews several perturbation strategies for functional nucleic acids, including deletion, mutation, and modifications of backbone and nucleobases, and consequent kinetic analysis, spectroscopic investigations, and probing assays...
June 23, 2017: Advances in Biochemical Engineering/biotechnology
Hussain Bahbahani, Abdulfatai Tijjani, Christopher Mukasa, David Wragg, Faisal Almathen, Oyekanmi Nash, Gerald N Akpa, Mary Mbole-Kariuki, Sunir Malla, Mark Woolhouse, Tad Sonstegard, Curtis Van Tassell, Martin Blythe, Heather Huson, Olivier Hanotte
The East African Shorthorn Zebu (EASZ) cattle are ancient hybrid between Asian zebu × African taurine cattle preferred by local farmers due to their adaptability to the African environment. The genetic controls of these adaptabilities are not clearly understood yet. Here, we genotyped 92 EASZ samples from Kenya (KEASZ) with more than 770,000 SNPs and sequenced the genome of a pool of 10 KEASZ. We observe an even admixed autosomal zebu × taurine genomic structure in the population. A total of 101 and 165 candidate regions of positive selection, based on genome-wide SNP analyses (meta-SS, Rsb, iHS, and ΔAF) and pooled heterozygosity (Hp) full genome sequence analysis, are identified, in which 35 regions are shared between them...
2017: Frontiers in Genetics
Muhammad Hanam Hamid, Lina Rozano, Wee Chien Yeong, Janna Ong Abdullah, Noor Baity Saidi
Mitogen-activated protein kinase 4 (MPK4) interacts with the (Mitogen-activated protein kinase kinase kinase 1) MEKK1/ Mitogenactivated protein kinase kinase 1 (MKK1)/ Mitogen-activated protein kinase kinase 2 (MKK2) complex to affect its function in plant development or against pathogen attacks. The KEGG (Kyoto Encyclopedia of Genes and Genomes) network analysis of Arabidopsis thaliana revealed close interactions between those four genes in the same plant-pathogen interaction pathway, which warrants further study of these genes due to their evolutionary conservation in different plant species...
2017: Bioinformation
A C Aschenbrenner, K Bassler, M Brondolin, L Bonaguro, P Carrera, K Klee, T Ulas, J L Schultze, M Hoch
There is an enormous need to make better use of the ever increasing wealth of publicly available genomic information and to utilize the tremendous progress in computational approaches in the life sciences. Transcriptional regulation of protein-coding genes is a major mechanism of controlling cellular functions. However, the myriad of transcription factors potentially controlling transcription of any given gene makes it often difficult to quickly identify the biological relevant transcription factors. Here, we report on the identification of Hnf4a as a major transcription factor of the so far unstudied DnaJ heat shock protein family (Hsp40) member C22 (Dnajc22)...
June 22, 2017: Scientific Reports
Wei Eric Wang, Liangpeng Li, Xuewei Xia, Wenbin Fu, Qiao Liao, Cong Lan, Dezhong Yang, Hongmei Chen, Rongchuan Yue, Cindy S Zeng, Lin Zhou, Bin Zhou, Dayue D Duan, Xiongwen Chen, Steven R Houser, Chunyu Zeng
Background -Adult mammalian hearts have a limited ability to generate new cardiomyocytes. Proliferation of existing adult cardiomyocytes (ACM) is a potential source of new cardiomyocytes. Understanding the fundamental biology of ACM proliferation could be of great clinical significance for treating myocardial infarction (MI). We aim to understand the process and regulation of ACM proliferation and its role in new cardiomyocyte formation of post-MI mouse hearts. Methods -β-actin-GFP transgenic mice and fate-mapping Myh6-MerCreMer-tdTomato/lacZ mice were used to trace the fate of ACMs...
June 22, 2017: Circulation
Katherine N Lee, Xiangru Lu, Chau Nguyen, Qingping Feng, Peter Chidiac
Regulator of G protein signalling 2 (RGS2) is known to play a protective role in maladaptive cardiac hypertrophy and heart failure via its ability to inhibit Gq and Gs mediated GPCR signalling. We previously demonstrated that RGS2 can also inhibit protein translation and can thereby attenuate cell growth. This G protein-independent inhibitory effect has been mapped to a 37 amino acid domain (RGS2(eb)) within RGS2 that binds to eukaryotic initiation factor 2B (eIF2B). When expressed in neonatal rat cardiomyocytes, RGS2(eb) attenuates both protein synthesis and hypertrophy induced by Gq- and Gs- activating agents...
June 19, 2017: Journal of Molecular and Cellular Cardiology
Steven A Yamada, Ward H Thompson, Michael D Fayer
Many of water's remarkable properties arise from its tendency to form an intricate and robust hydrogen bond network. Understanding the dynamics that govern this network is fundamental to elucidating the behavior of pure water and water in biological and physical systems. In ultrafast nonlinear infrared experiments, the accessible time scales are limited by water's rapid vibrational relaxation (1.8 ps for dilute HOD in H2O), precluding interrogation of slow hydrogen bond evolution in non-bulk systems. Here, hydrogen bonding dynamics in bulk D2O were studied from the perspective of the much longer lived (36...
June 21, 2017: Journal of Chemical Physics
Heng Huang, Xintao Hu, Yu Zhao, Milad Makkie, Qinglin Dong, Shijie Zhao, Lei Guo, Tianming Liu
Task-based fMRI (tfMRI) has been widely used to study functional brain networks under task performance. Modeling tfMRI data is challenging due to at least two problems: the lack of the ground truth of underlying neural activity and the highly complex intrinsic structure of tfMRI data. To better understand brain networks based on fMRI data, data-driven approaches have been proposed, for instance, Independent Component Analysis (ICA) and Sparse Dictionary Learning (SDL). However, both ICA and SDL only build shallow models, and they are under the strong assumption that original fMRI signal could be linearly decomposed into time series components with their corresponding spatial maps...
June 15, 2017: IEEE Transactions on Medical Imaging
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