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https://www.readbyqxmd.com/read/28328004/red-ml-a-novel-effective-rna-editing-detection-method-based-on-machine-learning
#1
Heng Xiong, Dongbing Liu, Qiye Li, Mengyue Lei, Liqin Xu, Liang Wu, Zongji Wang, Shancheng Ren, Wangsheng Li, Min Xia, Lihua Lu, Haorong Lu, Yong Hou, Shida Zhu, Xin Liu, Yinghao Sun, Jian Wang, Huanming Yang, Kui Wu, Xun Xu, Leo J Lee
Background: With the advancement of second generation sequencing techniques, our ability to detect and quantify RNA editing on a global scale has been vastly improved. As a result, RNA editing is now being studied under a growing number of biological conditions so that its biochemical mechanisms and functional roles can be further understood. However, a major barrier that prevents RNA editing from being a routine RNA-seq analysis, similar to gene expression and splicing analysis for example, is the lack of user-friendly and effective computational tools...
March 2, 2017: GigaScience
https://www.readbyqxmd.com/read/28324725/tailoring-a-compact-and-stable-langmuir-bi-dimensional-pbx-based-layered-perovskite-film-at-the-air-water-interface-and-on-solid-support
#2
Luisa Ariza-Carmona, Gonzalo García-Espejo, María T Martín-Romero, Luis Camacho
The present work studies the stability of Langmuir organic-inorganic superlattice materials thin films consisting of layered perovskite-based films with controlled 2D framework as well as to design experimental conditions for increasing the efficiency of the organic-inorganic perovskite motif by mechanical stimulus. Therefore, a whole covering of the air/water interface by a compact and stable lead-based layered perovskite structure is pursued. A 2D layered perovskite-type hybrid structure of the form [(CH3(CH2)19NH3)2(PbX4)], X=Cl, and Br, in which, two-dimensional sheets stabilized by a inner bilayer of organic monoammonium cation matrix, is mechanically tailored by successive compression-expansion cycles...
March 14, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28315838/germline-proliferation-is-regulated-by-somatic-endocytic-genes-via-jnk-and-bmp-signaling-in-drosophila
#3
Yaning Tang, Qing Geng, Di Chen, Shaowei Zhao, Xian Liu, Zhaohui Wang
Signals derived from the microenvironment contribute greatly to tumorigenesis. The underlying mechanism requires thorough investigation. Here, we use Drosophila testis as a model system to address this question, taking the advantage of the ease to distinguish germline and somatic cells and to track the cell numbers. In an EMS mutagenesis screen, we identified Rab5, a key factor in endocytosis, for its non-autonomous role in germline proliferation. The disruption of Rab5 in somatic cyst cells, which escort the development of germline lineage, induced the over-proliferation of under-differentiated but genetically wild-type germ cells...
March 17, 2017: Genetics
https://www.readbyqxmd.com/read/28290215/genetic-assessment-of-leech-species-from-yak-bos-grunniens-in-the-tract-of-northeast-india
#4
Nilkantha Chatterjee, Bishal Dhar, Debasis Bhattarcharya, Sourabh Deori, Juwar Doley, Joken Bam, Pranab J Das, Asit K Bera, Sitangshu M Deb, Ningthoujam Neelima Devi, Rajesh Paul, Sorokhaibam Malvika, Sankar Kumar Ghosh
Yak is an iconic symbol of Tibet and high altitudes of Northeast India. It is highly cherished for milk, meat, and skin. However, yaks suffer drastic change in milk production, weight loss, etc, when infested by parasites. Among them, infestation by leeches is a serious problem in the Himalayan belt of Northeast India. The parasite feeds on blood externally or from body orifices, like nasopharynx, oral, rectum, etc. But there has been limited data about the leech species infesting the yak in that region because of the difficulties in morphological identification due to plasticity of the body, changes in shape, and surface structure and thus, warrants for the molecular characterization of leech...
March 14, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28289682/stent-grafts-can-convert-unusable-upper-arm-arteriovenous-fistulas-into-a-functioning-hemodialysis-access-a-retrospective-case-series
#5
Charudatta S Bavare, Tiffany K Street, Eric K Peden, Mark G Davies, Joseph J Naoum
INTRODUCTION: Not all newly created arteriovenous fistulas (AVFs) successfully mature and develop into a functioning access for hemodialysis. Percutaneous transluminal angioplasty (PTA) and balloon-assisted maturation (BAM) have been utilized to either treat flow-limiting stenoses or to promote and accelerate maturation. We hypothesized that unusable upper arm AVFs can be rescued by conversion to a functional access using the percutaneous placement of a stent graft (SG). METHODS: Clinical data on 12 patients with an early non-usable upper arm AVF underwent percutaneous revision using SGs...
2017: Frontiers in Surgery
https://www.readbyqxmd.com/read/28288854/irinotecan-induced-bile-acid-malabsorption-is-associated-with-down-regulation-of-ileal-asbt-slc10a2-in-mice
#6
A-Xi Shi, Yan Zhou, Xiao-Yi Zhang, Yan-Shu Zhao, Hong-Yan Qin, Yan-Ping Wang, Xin-An Wu
Irinotecan, (CPT-11), an antitumor agent primarily used for the treatment of solid tumors, has often compromised clinical application due to the inducement of severe delay-onset diarrhea. Bile acid malabsorption (BAM) is widely accepted as the common cause of diarrhea. However, whether CPT-11-induced diarrhea has correlation with BAM is unknown. The aim of this study was to investigate the effect of CPT-11 on the bile acid homeostasis in mice. The mice were administrated with CPT-11 intravenously for four consecutive days...
March 10, 2017: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28286814/trends-of-serum-electrolyte-changes-in-crush-syndrome-patients-of-bam-earthquake-a-cross-sectional-study
#7
Saeed Safari, Mehdi Eshaghzade, Iraj Najafi, Alireza Baratloo, Behrooz Hashemi, Mohammad Mehdi Forouzanfar, Farhad Rahmati
INTRODUCTION: Electrolyte imbalances are very common among crushed earthquake victims but there is not enough data regarding their trend of changes. The present study was designed to evaluate the trend of changes in sodium, calcium, and phosphorus ions among crush syndrome patients. METHODS: In this retrospective cross-sectional study, using the database of Bam earthquake victims, which was developed by Iranian Society of Nephrology following Bam earthquake, Iran, 2003, the 10-day trend of sodium, calcium, and phosphorus ions changes in > 15 years old crush syndrome patients was evaluated...
2017: Emergency (Tehran, Iran)
https://www.readbyqxmd.com/read/28286812/20-day-trend-of-serum-potassium-changes-in-bam-earthquake-victims-with-crush-syndrome-a-cross-sectional-study
#8
Saeed Safari, Iraj Najafi, Mostafa Hosseini, Alireza Baratloo, Mahmoud Yousefifard, Hamidreza Mohammadi
INTRODUCTION: Many of those who survive following an earthquake die in the next phase due to preventable and treatable medical conditions such as hyperkalemia. The present study aimed to evaluate the trend of potassium changes in crush syndrome patients of Bam earthquake. METHODS: In this retrospective cross-sectional study, using the database of Bam earthquake victims, which were developed by Iranian Society of Nephrology following Bam earthquake, Iran, 2003, the 20-day trend of potassium changes in > 15 years old crush syndrome patients was evaluated...
2017: Emergency (Tehran, Iran)
https://www.readbyqxmd.com/read/28283136/temporal-dynamics-of-phlebotomine-sand-flies-population-in-response-to-ambient-temperature-variation-bam-kerman-province-of-iran
#9
Mansour Halimi, Zahra Zarei Cheghabaleki, Mohammad Jafari Modrek, Mahdi Delavari
BACKGROUND: Variations in climate condition may have changed the dynamic of zoonotic cutaneous leishmaniasis (ZCL) and its agents such as sand flies and reservoir in the Bam Kerman the dry region of Iran. OBJECTIVES: In this study we intend to examine the seasonal and interannual dynamics of the phlebotomine mosquito as a function of ambient temperature in Bam, Kerman one of the main leshmaniasis prevalence area in Iran. METHODS: The MODIS land surface temperature product (LST; MODIS/Terra LST/E Monthly L3 Global 0...
September 2016: Annals of Global Health
https://www.readbyqxmd.com/read/28276492/epitaxially-grown-bam-hexaferrite-films-having-uniaxial-axis-in-the-film-plane-for-self-biased-devices
#10
Xiaozhi Zhang, Siqin Meng, Dongsheng Song, Yao Zhang, Zhenxing Yue, Vincent G Harris
Barium hexaferrite (BaM) films with in-plane c-axis orientation are promising and technically important materials for self-biased magnetic microwave devices. In this work, highly oriented BaM films with different thickness and an in-plane easy axis (c-axis) of magnetization were grown on a-plane single-crystal sapphire substrates by direct current magnetron sputtering. A procedure involving seed layers, layer-by-layer annealing was adopted to reduce the substrate-induced strains and allow for the growth of thick (~3...
March 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28264674/epstein-barr-virus-and-cytomegalovirus-infections-and-their-clinical-relevance-in-egyptian-leukemic-pediatric-patients
#11
Samah Aly Loutfy, Maha A Abo-Shadi, Mohamed Fawzy, Mohamed El-Wakil, Shimaa A Metwally, Manar M Moneer, Nasra F Abdel Fattah, Sara Kassem, Ahmed Elgebaly
BACKGROUND: Epstein-Barr virus (EBV) and human cytomegalovirus (CMV) infections are environmental risk factors affecting the outcome of cancer due to an impairment in the cell-mediated immunity. Therefore, this study aimed to detect the frequency of EBV and CMV DNA and their association with clinical characteristics and outcome of pediatric leukemic patients. METHODS: Samples of 50 immunocompromised pediatric leukemic patients and 30 apparently healthy children were subjected to the amplification of EBV DNA by one version of PCR targeting the Bam H1 W region of the genomic region of EBV, and the amplification of CMV DNA by targeting the CMV UL97 genomic region by a second round PCR...
March 6, 2017: Virology Journal
https://www.readbyqxmd.com/read/28243654/effect-of-chirality-on-monoacylglycerol-ester-monolayer-characteristics-3-monostearoyl-sn-glycerol
#12
D Vollhardt, G Brezesinski
The effect of chirality on the thermodynamic behavior, the morphological features, and the 2D lattice structures of 3-monostearoyl-sn-glycerol monolayers is studied. The present study focusses on the influence of the alkyl chain length on the chiral discrimination. Surface pressure-area (π-A) isotherms, Brewster angle microscopy (BAM), and particularly, grazing incidence X-ray diffraction (GIXD) are the experimental basis of the presented results. The π-A isotherms of the enantiomeric 3-monostearoyl-sn-glycerol monolayers measured between 25 and 38 °C resemble those of the racemic 1-monostearoyl-rac-glycerol monolayers, thus indicating small energetic differences between the enantiomeric and the racemic forms...
February 28, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28241736/bbcanalyzer-a-visual-approach-to-facilitate-variant-calling
#13
Sarah Sandmann, Aniek O de Graaf, Martin Dugas
BACKGROUND: Deriving valid variant calling results from raw next-generation sequencing data is a particularly challenging task, especially with respect to clinical diagnostics and personalized medicine. However, when using classic variant calling software, the user usually obtains nothing more than a list of variants that pass the corresponding caller's internal filters. Any expected mutations (e.g. hotspot mutations), that have not been called by the software, need to be investigated manually...
February 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28239385/hydrogen-peroxide-pretreatment-mitigates-cadmium-induced-oxidative-stress-in-brassica-napus-l-an-intrinsic-study-on-antioxidant-defense-and-glyoxalase-systems
#14
Mirza Hasanuzzaman, Kamrun Nahar, Sarvajeet S Gill, Hesham F Alharby, Bam H N Razafindrabe, Masayuki Fujita
Cadmium (Cd) is considered as one of the most toxic metals for plant growth and development. In the present study, we investigated the role of externally applied hydrogen peroxide (H2O2) in regulating the antioxidant defense and glyoxalase systems in conferring Cd-induced oxidative stress tolerance in rapeseed (Brassica napus L.). Seedlings were pretreated with 50 μM H2O2 for 24 h. These pretreated seedlings as well as non-pretreated seedlings were grown for another 48 h at two concentrations of CdCl(2) (0...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28223520/membrane-integration-of-an-essential-%C3%AE-barrel-protein-prerequires-burial-of-an-extracellular-loop
#15
Joseph S Wzorek, James Lee, David Tomasek, Christine L Hagan, Daniel E Kahne
The Bam complex assembles β-barrel proteins into the outer membrane (OM) of Gram-negative bacteria. These proteins comprise cylindrical β-sheets with long extracellular loops and create pores to allow passage of nutrients and waste products across the membrane. Despite their functional importance, several questions remain about how these proteins are assembled into the OM after their synthesis in the cytoplasm and secretion across the inner membrane. To understand this process better, we studied the assembly of an essential β-barrel substrate for the Bam complex, BamA...
March 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28222895/the-epigenetic-regulator-smchd1-in-development-and-disease
#16
REVIEW
Natasha Jansz, Kelan Chen, James M Murphy, Marnie E Blewitt
It has very recently become clear that the epigenetic modifier SMCHD1 has a role in two distinct disorders: facioscapulohumoral muscular dystrophy (FSHD) and Bosma arhinia and micropthalmia (BAMS). In the former there are heterozygous loss-of-function mutations, while both gain- and loss-of-function mutations have been proposed to underlie the latter. These findings have led to much interest in SMCHD1 and how it works at the molecular level. We summarise here current understanding of the mechanism of action of SMCHD1, its role in these diseases, and what has been learnt from study of mouse models null for Smchd1 in the decade since the discovery of SMCHD1...
February 17, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28221928/rapid-identification-of-shiga-toxin-producing-escherichia-coli-o-serogroups-from-fresh-produce-and-raw-milk-enrichment-cultures-by-luminex-bead-based-suspension-array
#17
Julie A Kase, Anna Maounounen-Laasri, Andrew Lin
The U.S. Food and Drug Administration's Bacteriological Analytical Manual (BAM) Chapter 4a describes a Luminex microbead-based suspension array used to screen colonies for 11 clinically relevant Shiga toxin-producing Escherichia coli (STEC) serogroups: O26, O45, O91, O103, O104, O111, O113, O121, O128, O145, and O157. We evaluated the usefulness of this method to identify STEC-positive enrichment samples before agar plating. Twelve E. coli strains were added to three types of fresh produce (bagged baby spinach, alfalfa sprouts, and cilantro) at levels near the detection limit of the test...
September 2016: Journal of Food Protection
https://www.readbyqxmd.com/read/28216659/the-%C3%AE-barrel-assembly-machinery-in-motion
#18
REVIEW
Nicholas Noinaj, James C Gumbart, Susan K Buchanan
In Gram-negative bacteria, the biogenesis of β-barrel outer membrane proteins (OMPs) is mediated by the β-barrel assembly machinery (BAM) complex. During the past decade, structural and functional studies have collectively contributed to advancing our understanding of the structure and function of the BAM complex; however, the exact mechanism that is involved remains elusive. In this Progress article, we discuss recent structural studies that have revealed that the accessory proteins may regulate essential unprecedented conformational changes in the core component BamA during function...
April 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/28212858/refractive-index-and-thickness-determination-in-langmuir-monolayers-of-myelin-lipids
#19
Julio M Pusterla, Antonio A Malfatti-Gasperini, Ximena E Puentes-Martinez, Leide P Cavalcanti, Rafael G Oliveira
Langmuir monolayers at the air/water interface are widely used as biomembrane models and for amphiphilic molecules studies in general. Under controlled intermolecular organization (lateral molecular area), surface pressure, surface potential, reflectivity (R) and other magnitudes can be precisely determined on these planar monomolecular films. However, some physical parameters such as the refractive index of the monolayer (n) still remain elusive. The refractive index is very relevant because (in combination with R) it allows for the determination of the thickness of the film...
February 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28211327/results-from-a-round-robin-test-for-the-ecotoxicological-evaluation-of-construction-products-using-two-leaching-tests-and-an-aquatic-test-battery
#20
Stefan Gartiser, Ines Heisterkamp, Ute Schoknecht, Michael Burkhardt, Monika Ratte, Outi Ilvonen, Frank Brauer, Jan Brückmann, André Dabrunz, Philipp Egeler, Andrea-Maria Eisl, Ute Feiler, Ines Fritz, Sabina König, Herbert Lebertz, Pascal Pandard, Gabriele Pötschke, Dirk Scheerbaum, Frank Schreiber, Přemysl Soldán, Roland Weiß, Reinhilde Weltens
A European round robin test according to ISO 5725-2 was conceptually prepared, realised, and evaluated. The aim was to determine the inter-laboratory variability of the overall process for the ecotoxicological characterization of construction products in eluates and bioassays. To this end, two construction products BAM-G1 (granulate) and HSR-2 (roof sealing sheet), both made of EPDM polymers (rubber), were selected. The granular construction product was eluted in a one stage batch test, the planar product in the Dynamic Surface Leaching test (DSLT)...
May 2017: Chemosphere
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