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ConsAlign: simultaneous RNA structural aligner based on rich transfer learning and thermodynamic ensemble model of alignment scoring [article]

Masaki Tagashira
2022 bioRxiv   pre-print
We also implemented ConsAlign—a simultaneous RNA structural aligner composed of ConsTrain's learned scoring parameters.  ...  Keeping comparable running time, ConsAlign demonstrated the best alignment prediction quality among current RNA structural aligners.Availability and implementationOur code and our data are freely available  ...  Martin Frith, and their lab members for a year of discussion. We incredibly appreciate valuable comments from Dr. Kengo Sato and Dr. Akito Taneda regarding points to be improved.  ... 
doi:10.1101/2022.04.27.489566 fatcat:2rpexlxrcbhjzlsobgsk7saba4

25th Conference of the European Society for Microcirculation. Budapest, Hungary, August 26–29, 2008

2008 Journal of Vascular Research  
any information storage and retrieval system, without permission in writing from the publisher or, in the case of photocopying, direct payment of a specifi ed fee to the Copyright Clearance Center (see  ...  No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, microcopying, or by  ...  The conversion of DAF-2 to DAF-2T was evaluated in mixtures of 10 µM DAF-2 with NO ranging from 100 to 1200 nM. Sequences of fluorescence images were acquired with a digital camera.  ... 
doi:10.1159/000144991 fatcat:3nbmpjrvyvdrxaimpgurvmgl2i

Society of Nematologists 2011 Meeting: Abstracts: Alphabetically by first author

2011 Journal of nematology  
Our objective was to determine whether co-infection of cotton by Meloidogyne incognita and Rotylenchulus reniformis affects the population level of either nematode compared to infection by each species  ...  A series of split-root trials was conducted; each trial included four treatments and 10 replications in a randomized complete block design.  ...  Five of the endophytes simultaneously demonstrated significant plant growth and health promoting effects in tomato.  ... 
pmid:23431222 pmcid:PMC3547343 fatcat:acgtzmpjengqrhuxtpcnvvmivq

Mapping of the Co-Transcriptomes of UPEC-Infected Macrophages Reveals New Insights into the Molecular Basis of Host-Pathogen Interactions in Human and Mouse

Charalampos Harris Mavromatis
2014
analyses using RNA sequencing.  ...  I developed an effective computational framework that simultaneously separated, annotated, and quantified the mammalian and bacterial transcriptomes.  ...  ACKNOWLEDGEMENTS The authors would like to thank the KAUST Biosciences core Laboratory for the help with the cotranscriptome sequencing. The authors declare no conflict of interest.  ... 
doi:10.25781/kaust-p96tr fatcat:zyod6qp5mnbhfdwaecuhqestjq

Abstracts submitted for the 8th annual conference of the Society for Glycobiology

2003 Glycobiology  
The sequence alignment reveals 60% similiarity between yeast and mouse Stt3p and both proteins are predicted to have 10 to 14 transmembrane segments.  ...  Sequence alignment prediction indicates that domain 5 contains the four key primary amino acid determinants identified as essential for carbohydrate recognition by the CD-MPR and domains 3 and 9 of the  ... 
doi:10.1093/glycob/cwg130 fatcat:24d74tupyvbtreziagois4yjui

Symposium Abstracts

1987 Journal of Psychopharmacology  
Several isolates of B. xylophilus and B. mucronatus in Japan and from some other countries were used for DNA sequencing of the ITS regions in ribosomal DNA.  ...  We hypothesised a route of geographical migration and speciation of these two nematodes by estimating the chronology of speciation.  ...  Analysis of the aligned sequences indicated the presence of 'mosaic' sequences in the 18S gene of P. minor and P. porosus populations and suggested recombination events.  ... 
doi:10.1177/026988118700100110 pmid:22158754 fatcat:bptluh2vevb4ragu2y3dsm3tm4

ABSTRACTS

2016 Journal of nematology  
This specie was used for biosynthesis of silver nanoparticles (AgNPs) as a potential nematicidal agent via reduction of silver nitrate (AgNO 3 ) in cell free protein from P. aeruginosa.  ...  The best results were shown at 200 and 250 mg/ml of AgNPs, with decreases in the numbers of J2 in soil (40, 56%) and inside tomato roots (30, 44%) as well as the gall numbers (46, 68%) and egg masses/g  ...  mature, nitrogen-enriched, with a low C:N relation and with a predominantly bacterial via for organic matter decomposition.  ... 
doi:10.21307/jofnem-2017-038 fatcat:uefdcep5anenxmpagigpw6ma5e

Genetic determinants of rice bran oil quantity and quality: genomic, proteomic and transcriptomic approaches

Gopal Ji Tiwari
2017
The first chapter gives a detailed background about rice grain structure, effect of lipases on lipids in rice and strategies to increase the quantity and quality of oil.  ...  Bioinformatics and expression studies also suggested that Os01g0817700 has two lipase motifs and is also expressed in the bran and embryo of the rice grain.  ...  Günther Daum, Graz University of Technology, Austria, for providing P. pastoris X33 strain for protein induction experiments. We also thank Monash University, Malaysia for research funding.  ... 
doi:10.4225/03/58b8cd153f411 fatcat:ecivzn2b5rgf5mau3yux5szmaa

2012 WVAS abstracts

Joseph Horzempa
2016 Proceedings of the West Virginia Academy of Science  
Two small RNA libraries were generated from the pooled RNA isolated from different tissues (leaf, stem, as well as flesh, rind and placenta from the fruits) separately for isogenic diploid and tetraploid  ...  Anaerobic microbial communities are a significant source of bioenergy through the decomposition of organic matter and synthesis of methane and hydrogen.  ... 
doi:10.55632/pwvas.v84i1.148 fatcat:fbc3ctpxing3hen2hmjkbrm77q

High-resolution forensic DNA typing - Construction, optimization, and validation of a human identity panel used with massively parallel sequencing and the development of a web-based genotyping software

Sebastian Ganschow
2020
This class of genetic variation consists of tandem-like repeated elements that are highly variable in both the number of repeat units and the repeat sequence.  ...  Some attractive features of STR sequencing are the increased discrimination power compared to that of electrophoretic sizing and the ability to investigate a wide range of forensic markers in a single  ...  Acknowledgements The authors would like to thank Theresa Groß (Institute of Legal Medicine, University Hospital of Cologne), Céline Pfeifer (Institute of Legal Medicine, University Hospital of Ulm), and  ... 
doi:10.4119/unibi/2948769 fatcat:yuqbrqxfb5fgdbqouore37y3aq

Multiparticle Production in Particle and Nuclear Collisions. II

Tekeshi Kanki, Kisei Kinoshita, Hiroyuki Sumiyoshi, Fujio Takagi
1989 Progress of Theoretical Physics Supplement  
Such a time may be called the lifetime of a bare particle. d. Clustering A pion is often produced via a heavy cluster (or a sequence of clusters) including low-lying resonances such as p and w.  ...  ., daf:',sjdb=l for Ibl<RB (the radius of the nucleus B).  ... 
doi:10.1143/ptps.97b.1 fatcat:nlbhdbmat5gf3dpllgwpvxcl3u

Physiological and pathophysiological regulation of the ryanodine receptor in skeletal muscle

Alisa Umanskaya
2017
This work has broad implications for understanding the underlying mechanisms of skeletal muscle contraction and important disorders that affect human health.  ...  The data presented in this dissertation demonstrate the evolutionarily conserved mechanisms of skeletal muscle ryanodine receptor regulation in the physiological and pathophysiological states.  ...  Numerous important discoveries in neuroscience, development, signal transduction, cell death, aging, and RNA interference (RNA i ) have been made in the relatively short time since Brenner's publication  ... 
doi:10.7916/d8n29vr7 fatcat:jbunrltcv5fy7be3deaae67bra

Final Program, Fortieth Annual Meeting International Neuropsychological Society February 15–18, 2012 Montréal, Québec, Canada

2012 Journal of the International Neuropsychological Society  
In this symposium a panel of neuropsychologists will provide direction and insights towards developing a program of sustained externally funded research.  ...  Didactics will focus on key strategies towards writing competitive grants and the process of NIH study section review.  ...  Following acquisition of informed consent, participants were administered the Cognistat using a face-to-face modality; two weeks later the Cognistat was administered via a RNA modality.  ... 
doi:10.1017/s1355617712000537 fatcat:4p2fkgxxzna3vcf3uxxgac6rsi

Abstracts Presented at the Thirtieth Annual International Neuropsychological Society Conference, February 13???16, 2002 Toronto, Canada

2002 Journal of the International Neuropsychological Society  
scale of functional ability, the Direct Assessment of Functional Status (DAFS; Lowenstein 1992), and a self-report measure of function, the Older Americans Resources and Service Scale (OARS; Duke University  ...  Furthermore, impairment on the DAFS did not significantly predict self-reports of impairment on ADLs (F~10,49! 5 1.876, p 5 .072!  ...  Hebrew reading is based on morphological decomposition of the word into its root and pattern.  ... 
doi:10.1017/s1355617702822019 fatcat:3oxum6t47jhxdkyttu2aqc2mwi

Microscopy at the Frontiers of Science (MFS2019) [article]

Juan De Dios Alché Ramírez, Antonio Jesús Castro López, José Carlos Jiménez-López, Digital.CSIC, Digital.CSIC
2020
EM02161943; and the National Natural Science Foundation of China NFSC-21850410448 and NSFC-21835002.  ...  Acknowledgements The Acknowledgments We acknowledge the support of PPBI-Portuguese Platform of BioImaging: POCI-01-0145-FEDER-022122.  ...  The tail complex shows a tubular conical shape of 293 Å long and 175 Å wide, organized in two 12-fold rings (gp8 and gp11) and a 6-fold nozzle (gp12).  ... 
doi:10.20350/digitalcsic/10868 fatcat:4egxbiipcfbkrgmwazbvxsmx7e
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