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https://www.readbyqxmd.com/read/28214361/identification-of-arabidopsis-genic-and-non-genic-promoters-by-paired-end-sequencing-of-tss-tags
#1
Mutsutomo Tokizawa, Kazutaka Kusunoki, Hiroyuki Koyama, Atsushi Kurotani, Tetsuya Sakurai, Yutaka Suzuki, Tomoaki Sakamoto, Tetsuya Kurata, Yoshiharu Y Yamamoto
Information about transcription start sites (TSSs) provides foundational data for analyses of promoter architecture. In this report, we used paired- and single-end deep sequencing to analyze Arabidopsis TSS tags from several libraries prepared from roots, shoots, flowers, and etiolated seedlings. The clustering of approximately 33 million mapped TSS tags led to the identification of 324,461 promoters that covered 79.7% (21,672/27,206) of protein-coding genes in the Arabidopsis genome. In addition, we identified intragenic, antisense, and Orphan promoters that were not associated with any gene models...
February 18, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28214296/abnormally-high-and-heterogeneous-bone-matrix-mineralization-after-childhood-solid-organ-transplantation-a-complex-pathology-of-low-bone-turnover-and-local-defects-in-mineralization
#2
Nadja Fratzl-Zelman, Helena Valta, Renata C Pereira, Barbara M Misof, Paul Roschger, Hannu Jalanko, Kathrine Wesseling-Perry, Klaus Klaushofer, Outi Mäkitie
Chronic renal, liver and heart failure in children associates with multiple skeletal complications. Increased fracture incidence often persists after transplantation and could be related to alterations in bone material properties. In the present cohort study we evaluated bone mineralization density distribution (BMDD) by quantitative backscattered electron imaging (qBEI) in 23 pediatric solid organ allograft recipients with suspected osteoporosis. We measured BMDD in the entire cross-sectional area of transiliac bone biopsies obtained from kidney (n = 9), liver (n = 9) and heart (n = 5) transplant recipients (aged 7...
February 18, 2017: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/28214189/economic-assessment-of-rotavirus-vaccination-in-saudi-arabia
#3
Amal Y A Al-Aidaroos, Baudouin Standaert, Kinga Meszaros, Atef M Shibl
In the Kingdom of Saudi Arabia (KSA), rotavirus universal mass vaccination has been introduced in 2013, however, there is limited information available on the economic benefit and the epidemiological impact of the programme to date. We used a Markov cohort model to evaluate and compare the economic value of rotavirus vaccination with no vaccination in a birth cohort of 562,428 infants. This lifetime analysis considered the societal perspective. Model input was obtained through consensus of local experts after two rounds of evaluation of the proposed estimates...
February 14, 2017: Journal of Infection and Public Health
https://www.readbyqxmd.com/read/28214103/tracking-the-evolution-and-differences-between-guest-induced-phases-of-ga-mil-53-via-ultra-wideline-69-71-ga-solid-state-nmr-spectroscopy
#4
Yue Zhang, Bryan E G Lucier, Victor V Terskikh, Renlong Zheng, Yining Huang
Ga-MIL-53 is a metal-organic framework (MOF) that exhibits a "breathing effect," in which the pore size and overall MOF topology can be influenced by temperature, pressure, and host-guest interactions. The phase control afforded by this flexible framework renders Ga-MIL-53 a promising material for guest storage and sensing applications. In this work, the structure and behavior of four Ga-MIL-53 phases (as, ht, enp and lt), along with CO2 adsorbed within Ga-MIL-53 at various loading levels, has been investigated using (69/71)Ga solid-state NMR (SSNMR) experiments at 21...
January 31, 2017: Solid State Nuclear Magnetic Resonance
https://www.readbyqxmd.com/read/28214024/long-term-outcomes-of-endolymphatic-sac-shunting-with-local-steroids-for-meniere-s-disease
#5
Cameron C Wick, Nauman F Manzoor, Caileigh McKenna, Maroun T Semaan, Cliff A Megerian
OBJECTIVES: To evaluate the long-term efficacy of endolymphatic sac shunt techniques with and without local steroid administration. STUDY DESIGN: Retrospective case series and patient survey. SETTING: Tertiary university hospital. PATIENTS: Meniere's disease (MD) patients that failed medical therapy and subsequently underwent an endolymphatic sac shunt procedure. All patients had definitive or probable MD and at least 18-months of follow-up...
January 20, 2017: American Journal of Otolaryngology
https://www.readbyqxmd.com/read/28213950/benchmark-performance-of-global-switching-versus-local-switching-for-trajectory-surface-hopping-molecular-dynamic-simulation-cis-trans-azobenzene-photoisomerization
#6
Ling Yue, Le Yu, Chao Xu, Yibo Lei, Yajun Liu, Chaoyuan Zhu
Newly developed global switching algorithm that does not require calculation of nonadiabatic coupling vector reduces computational cost significantly. However, there is a lack of extensive checking its accuracy for this simplest nonadiabatic molecular dynamic method in comparison with conventional Tully's fewest switches. It is very necessary to demonstrate how accurate global switching algorithm is. Extensive comparison between local and global switching on-the-fly trajectory surface hopping molecular dynamics is performed for cis-to-trans (800 sampling trajectories) and trans-to-cis (600 sampling trajectories) azobenzene photoisomerization at the OM2/MRCI level...
February 18, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28213783/high-pten-gene-expression-is-a-negative-prognostic-marker-in-human-primary-breast-cancers-with-preserved-p53-function
#7
Synnøve Yndestad, Eilin Austreid, Stian Knappskog, Ranjan Chrisanthar, Peer Kåre Lilleng, Per Eystein Lønning, Hans Petter Eikesdal
PURPOSE: PTEN is an important tumor suppressor in breast cancer. Here, we examined the prognostic and predictive value of PTEN and PTEN pseudogene (PTENP1) gene expression in patients with locally advanced breast cancer given neoadjuvant chemotherapy. METHODS: The association between pretreatment PTEN and PTENP1 gene expression, response to neoadjuvant chemotherapy, and recurrence-free and disease-specific survival was assessed in 364 patients with locally advanced breast cancer given doxorubicin, 5-fluorouracil/mitomycin, or epirubicin versus paclitaxel in three phase II prospective studies...
February 17, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28213545/antifungal-bacteria-on-woodland-salamander-skin-exhibit-high-taxonomic-diversity-and-geographic-variability
#8
Carly R Muletz-Wolz, Graziella V DiRenzo, Stephanie A Yarwood, Evan H Campbell Grant, Robert C Fleischer, Karen R Lips
Diverse bacteria inhabit amphibian skin, some of which inhibit growth of the fungal pathogen, Batrachochytrium dendrobatidis (Bd). Yet, there has been no systematic survey of anti-Bd bacteria across localities, species and elevations. This is important given geographic and taxonomic variation in amphibian susceptibility to Bd. Our sites were within the Appalachian Mountains where previous sampling indicated low Bd prevalence. We determined the number and identity of anti-Bd bacteria on 61 Plethodon salamanders (37 P...
February 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28213516/rapid-regulation-of-sialidase-activity-in-response-to-neural-activity-and-sialic-acid-removal-during-memory-processing-in-rat-hippocampus
#9
Akira Minami, Yuko Meguro, Sayaka Ishibashi, Ami Ishii, Mako Shiratori, Saki Sai, Yuuki Horii, Hirotaka Shimizu, Hokuto Fukumoto, Sumika Shinba, Risa Taguchi, Tadanobu Takahashi, Tadamune Otsubo, Kiyoshi Ikeda, Takashi Suzuki
Sialidase cleaves sialic acids on the extracellular cell surface as well as inside the cell, and is necessary for normal long-term potentiation (LTP) at MF-CA3 pyramidal cell synapses and for hippocampus-dependent spatial memory. Here, we investigated in detail the role of sialidase in memory processing. Sialidase activity measured with 4MU-Neu5Ac or X-Neu5Ac and FRV LB was increased by high K(+)-induced membrane depolarization. Sialidase activity was also increased by chemical LTP induction with forskolin and activation of BDNF signaling, non-NMDARs or NMDARs...
February 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28213474/a-bayesian-approach-for-analysis-of-whole-genome-bisulphite-sequencing-data-identifies-disease-associated-changes-in-dna-methylation
#10
Owen J L Rackham, Sarah R Langley, Thomas Oates, Eleni Vradi, Nathan Harmston, Prashant K Srivastava, Jacques Behmoaras, Petros Dellaportas, Leonardo Bottolo, Enrico Petretto
DNA methylation is a key epigenetic modification involved in gene regulation whose contribution to disease susceptibility remains to be fully understood. Here, we present a novel Bayesian smoothing approach (called ABBA) to detect differentially methylated regions (DMRs) from whole-genome bisulphite sequencing (WGBS). We also show how this approach can be leveraged to identify disease-associated changes in DNA methylation, suggesting mechanisms through which these alterations might affect disease. From a data modeling perspective, ABBA has the distinctive feature of automatically adapting to different correlation structures in CpG methylation levels across the genome whilst taking into account the distance between CpG sites as a covariate...
February 17, 2017: Genetics
https://www.readbyqxmd.com/read/28213330/drug-discovery-strategies-in-the-field-of-tumor-energy-metabolism-limitations-by-metabolic-flexibility-and-metabolic-resistance-to-chemotherapy
#11
REVIEW
N D Amoedo, E Obre, R Rossignol
The search for new drugs capable of blocking the metabolic vulnerabilities of human tumors has now entered the clinical evaluation stage, but several projects already failed in phase I or phase II. In particular, very promising in vitro studies could not be translated in vivo at preclinical stage and beyond. This was the case for most glycolysis inhibitors that demonstrated systemic toxicity. A more recent example is the inhibition of glutamine catabolism in lung adenocarcinoma that failed in vivo despite a strong addiction of several cancer cell lines to glutamine in vitro...
February 14, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28213099/polymeric-nanoparticles-loaded-with-dexamethasone-or-%C3%AE-tocopheryl-succinate-to-prevent-cisplatin-induced-ototoxicity
#12
Sergio Martín-Saldaña, Raquel Palao-Suay, María Rosa Aguilar, Rafael Ramírez-Camacho, Julio San Román
: The aim of this work is the development of highly protective agents to be administered locally within the middle ear to avoid cisplatin-induced ototoxicity, which affects to 100% of the clinical patients at ultra-high concentrations (16 mg/kg). The protective agents are based on polymeric nanoparticles loaded with dexamethasone or α-tocopheryl succinate as anti-inflammarory and anti-apoptotic molecules. Dexamethasone and α-tocopheryl succinate are poorly soluble in water and present severe side effects when systemic administered during long periods of time...
February 14, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28213031/antimicrobial-resistance-and-its-association-with-tolerance-to-heavy-metals-in-agriculture-production
#13
REVIEW
Zhongyi Yu, Lynda Gunn, Patrick Wall, Séamus Fanning
Antimicrobial resistance is a recognized public health challenge that since its emergence limits the therapeutic options available to veterinarians and clinicians alike, when treatment is warranted. This development is further compounded by the paucity of new antibiotics. The agri-food industry benefits from the availability of antimicrobial compounds for food-animal production and crop protection. Nonetheless, their improper use can result in the selection for bacteria that are phenotypically resistant to these compounds...
June 2017: Food Microbiology
https://www.readbyqxmd.com/read/28212971/should-countries-set-an-explicit-health-benefits-package-the-case-of-the-english-national-health-service
#14
Peter C Smith, Kalipso Chalkidou
BACKGROUND: A fundamental debate in the transition towards universal health coverage concerns whether to establish an explicit health benefits package to which all citizens are entitled, and the level of detail in which to specify that package. At one extreme, the treatments to be funded, and the circumstances in which patients qualify for the treatment, might be specified in great detail, and be entirely mandatory. This would make clinicians little more than automata, carrying out prescribed practice...
January 2017: Value in Health: the Journal of the International Society for Pharmacoeconomics and Outcomes Research
https://www.readbyqxmd.com/read/28212883/nonlinear-relationship-between-extreme-temperature-and-mortality-in-different-temperature-zones-a-systematic-study-of-122-communities-across-the-mainland-of-china
#15
Chenzhi Wang, Zhao Zhang, Maigeng Zhou, Lingyan Zhang, Peng Yin, Wan Ye, Yi Chen
BACKGROUND: Numerous previous studies have reported that human health risk is extremely sensitive to temperature. Very few studies, however, have characterized the relationship between temperature and mortality in different temperature zones due to the previous conclusions deduced from a regional or administrative division. A research covers different temperature zones was indispensable to have a comprehensive understanding of regional ambient temperature effect on public health. METHODS: Based on the mortality dataset and meteorological variables of 122 communities in China from 2007 to 2012, a distributed lag nonlinear model (DLNM) was utilized to estimate the temperature effect on non-accidental mortality at the community level...
February 14, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28212875/genotyping-by-sequencing-provides-the-first-well-resolved-phylogeny-for-coffee-coffea-and-insights-into-the-evolution-of-caffeine-content-in-its-species-gbs-coffee-phylogeny-and-the-evolution-of-caffeine-content
#16
Perla Hamon, Corrinne E Grover, Aaron P Davis, Jean-Jacques Rakotomalala, Nathalie E Raharimalala, Victor A Albert, Hosahalli L Sreenath, Piet Stoffelen, Sharon E Mitchell, Emmanuel Couturon, Serge Hamon, Alexandre de Kochko, Dominique Crouzillat, Michel Rigoreau, Ucu Sumirat, Sélastique Akaffou, Romain Guyot
A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus (Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been limited by low levels of sequence divergence, leading to insufficient topological resolution and statistical support in phylogenetic trees, particularly for the major lineages and for the numerous species occurring in Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesis for coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed, lab-based workflow to integrate short read next-generation sequencing for low numbers of additional samples...
February 14, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28212851/the-high-affinity-phosphodiesterase-pdeh-regulates-development-and-aflatoxin-biosynthesis-in-aspergillus-flavus
#17
Kunlong Yang, Yinghang Liu, Linlin Liang, Zhenguo Li, Qiuping Qin, Xinyi Nie, Shihua Wang
Cyclic AMP signaling controls a range of physiological processes in response to extracellular stimuli in organisms. Among the signaling cascades, cAMP, as a second messenger, is orchestrated by adenylate cyclase(biosynthesis) and cAMP phosphodiesterases (PDEs)(hydrolysis). In this study, we investigated the function of the high-affinity (PdeH) and low-affinity (PdeL) cAMP phosphodiesterase from the carcinogenic aflatoxin producing fungus Aspergillus flavus, and found that instead of PdeL, inactivation of PdeH exhibited a reduction in conidiation and sclerotia formation...
February 14, 2017: Fungal Genetics and Biology: FG & B
https://www.readbyqxmd.com/read/28212703/optimal-shielding-thickness-for-galactic-cosmic-ray-environments
#18
Tony C Slaba, Amir A Bahadori, Brandon D Reddell, Robert C Singleterry, Martha S Clowdsley, Steve R Blattnig
Models have been extensively used in the past to evaluate and develop material optimization and shield design strategies for astronauts exposed to galactic cosmic rays (GCR) on long duration missions. A persistent conclusion from many of these studies was that passive shielding strategies are inefficient at reducing astronaut exposure levels and the mass required to significantly reduce the exposure is infeasible, given launch and associated cost constraints. An important assumption of this paradigm is that adding shielding mass does not substantially increase astronaut exposure levels...
February 2017: Life Sciences in Space Research
https://www.readbyqxmd.com/read/28212642/beyond-cultural-stereotyping-views-on-end-of-life-decision-making-among-religious-and-secular-persons-in-the-usa-germany-and-israel
#19
Mark Schweda, Silke Schicktanz, Aviad Raz, Anita Silvers
BACKGROUND: End-of-life decision making constitutes a major challenge for bioethical deliberation and political governance in modern democracies: On the one hand, it touches upon fundamental convictions about life, death, and the human condition. On the other, it is deeply rooted in religious traditions and historical experiences and thus shows great socio-cultural diversity. The bioethical discussion of such cultural issues oscillates between liberal individualism and cultural stereotyping...
February 17, 2017: BMC Medical Ethics
https://www.readbyqxmd.com/read/28212603/effects-of-renal-denervation-on-cardiac-oxidative-stress-and-local-activity-of-the-sympathetic-nervous-system-and-renin-angiotensin-system-in-acute-myocardial-infracted-dogs
#20
Qiaoli Feng, Chengzhi Lu, Li Wang, Lijun Song, Chao Li, Ravi Chandra Uppada
BACKGROUND: This study sought to evaluate the therapeutic effects of renal denervation (RDN) on acute myocardial infarction (MI) in canines and explore its possible mechanisms of action. METHODS: Eighteen healthy mongrel dogs were randomly assigned to either the control group, the MI group or the MI + RDN group. To assess cardiac function, left ventricular ejection fraction (LVEF), left ventricular end-diastolic dimension (LVEDD), left ventricular end-systolic dimension (LVESD) and fraction shortening (FS) were recorded...
February 17, 2017: BMC Cardiovascular Disorders
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