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https://www.readbyqxmd.com/read/28645209/genome-wide-mapping-of-in-vivo-er%C3%AE-binding-sites-in-male-mouse-efferent-ductules
#1
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
https://www.readbyqxmd.com/read/28645204/when-homoplasy-is-not-homoplasy-dissecting-trait-evolution-by-contrasting-composite-and-reductive-coding
#2
Alejandro Torres-Montúfar, Thomas Borsch, Helga Ochoterena
The conceptualization and coding of characters is a difficult issue in phylogenetic systematics, no matter which inference method is used when reconstructing phylogenetic trees or if the characters are just mapped onto a specific tree. Complex characters are groups of features that can be divided into simpler hierarchical characters (reductive coding), although the implied hierarchical relational information may change depending on the type of coding (composite vs reductive). Up to now, there is no common agreement to either code characters as complex or simple...
June 22, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28645197/pht%C3%AE-promoted-mobilization-of-non-conjugative-resistance-plasmids-from-enterococcus-faecium-to-enterococcus-faecalis
#3
Laura Di Sante, Gianluca Morroni, Andrea Brenciani, Carla Vignaroli, Alberto Antonelli, Marco Maria D'Andrea, Andrea Di Cesare, Eleonora Giovanetti, Pietro E Varaldo, Gian Maria Rossolini, Francesca Biavasco
Objectives: : To analyse the recombination events associated with conjugal mobilization of two multiresistance plasmids, pRUM 17i48 and pLAG (formerly named pDO1-like), from Enterococcus faecium 17i48 to Enterococcus faecalis JH2-2. Methods: : The plasmids from two E. faecalis transconjugants (JH-4T, tetracycline resistant, and JH-8E, erythromycin resistant) and from the E. faecium donor (also carrying a pHTβ-like conjugative plasmid, named pHTβ 17i48 ) were investigated by several methods, including PCR mapping and sequencing, S1-PFGE followed by Southern blotting and hybridization, and WGS...
June 22, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28645144/increased-alignment-sensitivity-improves-the-usage-of-genome-alignments-for-comparative-gene-annotation
#4
Virag Sharma, Michael Hiller
Genome alignments provide a powerful basis to transfer gene annotations from a well-annotated reference genome to many other aligned genomes. The completeness of these annotations crucially depends on the sensitivity of the underlying genome alignment. Here, we investigated the impact of the genome alignment parameters and found that parameters with a higher sensitivity allow the detection of thousands of novel alignments between orthologous exons that have been missed before. In particular, comparisons between species separated by an evolutionary distance of >0...
June 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28645142/polyphyly-of-arundinoideae-poaceae-and-evolution-of-the-twisted-geniculate-lemma-awn
#5
J K Teisher, M R McKain, B A Schaal, E A Kellogg
Background and Aims: Subfamily Arundinoideae represents one of the last unsolved taxonomic mysteries in the grass family (Poaceae) due to the narrow and remote distributions of many of its 19 morphologically and ecologically heterogeneous genera. Resolving the phylogenetic relationships of these genera could have substantial implications for understanding character evolution in the grasses, for example the twisted geniculate awn - a hygroscopic awn that has been shown to be important in seed germination for some grass species...
June 21, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28645069/controlled-single-bubble-cavitation-collapse-results-in-jet-induced-injury-in-brain-tissue
#6
Saranya Canchi, Karen Kelly, Yu Hong, Michael A King, Ghatu Subhash, Malisa Sarntinoranont
Multiscale damage due to cavitation is considered as a potential mechanism of traumatic brain injury (TBI) associated with explosion. In this study, we employed a TBI relevant hippocampal ex vivo slice model to induce bubble cavitation. Placement of single reproducible seed bubbles allowed control of size, number, and tissue location to visualize and measure deformation parameters. Maximum strain value was measured at 45 µs after bubble collapse, presented with a distinct contour and coincided temporally and spatially with the liquid jet...
June 15, 2017: Journal of the Mechanical Behavior of Biomedical Materials
https://www.readbyqxmd.com/read/28644986/designing-novel-inhibitors-against-histone-acetyltransferase-hat-%C3%A2-gcn5-of-plasmodium-falciparum
#7
Amarjeet Kumar, Krishanu Bhowmick, Kunwar Somesh Vikramdeo, Neelima Mondal, Naidu Subbarao, Suman Kumar Dhar
During active proliferation phase of intra-erythrocytic cycle, the genome of P. falciparum is regulated epigenetically and evolutionary conserved parasite-specific histone proteins are extensively acetylated. The reversible process of lysine acetylation, causing transcriptional activation and its deacetylation, causing transcriptional repression is regulated by balanced activities of HATs and HDACs. They are also known to regulate antigenic variations and gametocytic conversion in P. falciparum. These histone modifying enzymes have been identified as potential targets for development of anitmalarials in literature...
June 10, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28644905/a-realistic-phantom-for-validating-mri-based-synthetic-ct-images-of-the-human-skull
#8
Abraam S Soliman, Levi Burns, Amir Owrangi, Young Lee, William Y Song, Greg Stanisz, Brige P Chugh
PURPOSE: To introduce a new realistic human skull phantom for the validation of synthetic CT images of cortical bone from ultra-short echo-time (UTE) sequences. METHODS AND MATERIALS: A human skull of an adult female was utilized as a realistic representation of skull cortical bone. The skull was stabilized in a special acrylic container and was filled with contrast agents that have T1 and T2 relaxation times similar to human brain. The phantom was MR scanned at 3T with UTE and T2 -weighted sequences, followed by CT...
June 23, 2017: Medical Physics
https://www.readbyqxmd.com/read/28644903/changes-in-remote-myocardial-tissue-after-acute-myocardial-infarction-and-its-relation-to-cardiac-remodeling-a-cmr-t1-mapping-study
#9
P Stefan Biesbroek, Raquel P Amier, Paul F A Teunissen, Mark B M Hofman, Lourens F H J Robbers, Peter M van de Ven, Aernout M Beek, Albert C van Rossum, Niels van Royen, Robin Nijveldt
OBJECTIVES: To characterize the temporal alterations in native T1 and extracellular volume (ECV) of remote myocardium after acute myocardial infarction (AMI), and to explore their relation to left ventricular (LV) remodeling. METHODS: Forty-two patients with AMI successfully treated with primary PCI underwent cardiovascular magnetic resonance after 4-6 days and 3 months. Cine imaging, late gadolinium enhancement, and T1-mapping (MOLLI) was performed at 1.5T. T1 values were measured in the myocardial tissue opposite of the infarct area...
2017: PloS One
https://www.readbyqxmd.com/read/28644851/comorbidities-in-the-diseasome-are-more-apparent-than-real-what-bayesian-filtering-reveals-about-the-comorbidities-of-depression
#10
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
https://www.readbyqxmd.com/read/28644843/a-high-density-genetic-map-and-qtl-analysis-of-agronomic-traits-in-foxtail-millet-setaria-italica-l-p-beauv-using-rad-seq
#11
Jun Wang, Zhilan Wang, Xiaofen Du, Huiqing Yang, Fang Han, Yuanhuai Han, Feng Yuan, Linyi Zhang, Shuzhong Peng, Erhu Guo
Foxtail millet (Setaria italica), a very important grain crop in China, has become a new model plant for cereal crops and biofuel grasses. Although its reference genome sequence was released recently, quantitative trait loci (QTLs) controlling complex agronomic traits remains limited. The development of massively parallel genotyping methods and next-generation sequencing technologies provides an excellent opportunity for developing single-nucleotide polymorphisms (SNPs) for linkage map construction and QTL analysis of complex quantitative traits...
2017: PloS One
https://www.readbyqxmd.com/read/28644839/genomic-introgression-mapping-of-field-derived-multiple-anthelmintic-resistance-in-teladorsagia-circumcincta
#12
Young-Jun Choi, Stewart A Bisset, Stephen R Doyle, Kymberlie Hallsworth-Pepin, John Martin, Warwick N Grant, Makedonka Mitreva
Preventive chemotherapy has long been practiced against nematode parasites of livestock, leading to widespread drug resistance, and is increasingly being adopted for eradication of human parasitic nematodes even though it is similarly likely to lead to drug resistance. Given that the genetic architecture of resistance is poorly understood for any nematode, we have analyzed multidrug resistant Teladorsagia circumcincta, a major parasite of sheep, as a model for analysis of resistance selection. We introgressed a field-derived multiresistant genotype into a partially inbred susceptible genetic background (through repeated backcrossing and drug selection) and performed genome-wide scans in the backcross progeny and drug-selected F2 populations to identify the major genes responsible for the multidrug resistance...
June 23, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28644810/action-recognition-using-3d-histograms-of-texture-and-a-multi-class-boosting-classifier
#13
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
https://www.readbyqxmd.com/read/28644809/structured-kernel-dictionary-learning-with-correlation-constraint-for-object-recognition
#14
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
https://www.readbyqxmd.com/read/28644804/global-time-delay-estimation-in-ultrasound-elastography
#15
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
https://www.readbyqxmd.com/read/28644644/highly-nuclear-spin-polarized-deuterium-atoms-from-the-uv-photodissociation-of-deuterium-iodide
#16
Dimitris Sofikitis, Pavle Glodic, Greta Koumarianou, Hongyan Jiang, Lykourgos Bougas, Peter C Samartzis, Alexander Andreev, T Peter Rakitzis
We report a novel highly spin-polarized deuterium (SPD) source, via the photodissociation of deuterium iodide at 270 nm. I(^{2}P_{3/2}) photofragments are ionized with m-state selectivity, and their velocity distribution measured via velocity-map slice imaging, from which the D polarization is determined. The process produces ∼100% electronically polarized D at the time of dissociation, which is then converted to ∼60% nuclear D polarization after ∼1.6  ns. These production times for SPD allow collision-limited densities of ∼10^{18}  cm^{-3} and at production rates of ∼10^{21}  s^{-1} which are 10^{6} and 10^{4} times higher than conventional (Stern-Gerlach separation) methods, respectively...
June 9, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28644590/mutyh-associated-polyposis-the-irish-experience
#17
T P McVeigh, M Duff, C Carroll, R O'Shea, L Bradley, M Farrell, D J Gallagher, C Clabby, A J Green
MUTYH is involved in DNA damage repair. Bi-allelic MUTYH mutations predispose to polyposis and gastrointestinal malignancies, distinct genetically from autosomal dominant familial adenomatous polyposis coli. Two common European MUTYH mutations account for 90% of MUTYH-associated polyposis (MAP). We aimed to examine the incidence of MAP in Ireland. A retrospective cohort study was undertaken. Patients undergoing MUTYH testing from 2003-2016 were identified by searching electronic databases using terms "MUTYH" and "MYH"...
December 12, 2016: Irish Medical Journal
https://www.readbyqxmd.com/read/28644563/gas-phase-dissociation-study-of-erythrinian-alkaloids-by-electrospray-ionization-mass-spectrometry-and-computational-methods
#18
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
https://www.readbyqxmd.com/read/28644517/quantitative-insights-into-the-fast-pyrolysis-of-extracted-cellulose-hemicelluloses-and-lignin
#19
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
https://www.readbyqxmd.com/read/28644440/lncrna-sarcc-suppresses-renal-cell-carcinoma-rcc-progression-via-altering-the-androgen-receptor-ar-mirna-143-3p-signals
#20
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
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