6,385 research outputs found
Polypolish: Short-read polishing of long-read bacterial genome assemblies
No full textLong-read-only bacterial genome assemblies usually contain residual errors, most commonly homopolymer-length errors. Short-read polishing tools can use short reads to fix these errors, but most rely on short-read alignment which is unreliable in repeat regions. Errors in such regions are therefore challenging to fix and often remain after short-read polishing. Here we introduce Polypolish, a new short-read polisher which uses all-per-read alignments to repair errors in repeat sequences that other polishers cannot. Polypolish performed well in benchmarking tests using both simulated and real reads, and it almost never introduced errors during polishing. The best results were achieved by using Polypolish in combination with other short-read polishers
Author Co-Citation Analysis (ACA): a powerful tool for representing implicit knowledge of scholar knowledge workers
No full textIn the last decade, knowledge has emerged as one of the most important and valuable organizational assets. Gradually this importance caused to emergence of new discipline entitled ―knowledge management‖. However one of the major challenges of knowledge management is conversion implicit or tacit knowledge to explicit knowledge. Thus Making knowledge visible so that it can be better accessed, discussed, valued or generally managed is a long-standing objective in knowledge management. Accordingly in this paper author co- citation analysis (ACA) will be proposed as an efficient technique of knowledge visualization in academia (Scholar knowledge workers)
Revised diagnostic criteria for Vogt-Koyanagi-Harada disease: report of an international committee on nomenclature
No full textShuffler: A Novel Read Reclaim Scheme for Superblock Management in NAND Flash
No full textInternational audienceSuperblock management is widely used in commercial products of flash memory, in which multiple blocks from different parallel units are organized as a superblock, to provide high-level access parallelism. However, excessive parallelism inadvertently amplifies the negative effects of read reclaim (RR) due to the larger scale of data migrations and space reclamation. This is because a superblock-granularity RR operation must be triggered when any block inside a superblock reaches the RR threshold, even though other blocks are far from the threshold. To improve the RR efficiency for superblock management, this paper proposes a shuffling-based RR scheme for unifying read accesses across all component blocks inside the superblock without any additional space costs. Specifically, it shuffles the blocks of superblock with the granularity of card that consists of multiple data pages in the RR process and ensures no impact on access parallelism after shuffling. As a result, all component blocks may serve a similar number of read requests and approach the RR threshold synchronously. Trace-driven simulation experiments demonstrate that our proposed method can reduce the RR operations and read latency by 14.5 % and 12.9 %, compared with conventional superblock-granularity RR schemes in flash memory, while preserving access parallelism
Analysis of MicroRNA Expression in Embryonic Developmental Toxicity Induced by MC-RR
No full textAs cynobacterial blooms frequently occur in fresh waters throughout the world, microcystins (MCs) have caused serious damage to both wildlife and human health. MCs are known to have developmental toxicity, however, the possible molecular mechanism is largely unknown. This is the first toxicological study to integrate post-transcriptomic, proteomic and bioinformatics analysis to explore molecular mechanisms for developmental toxicity of MCs in zebrafish. After being microinjected directly into embryos, MC-RR dose-dependently decreased survival rates and increased malformation rates of embryos, causing various embryo abnormalities including loss of vascular integrity and hemorrhage. Expressions of 31 microRNAs (miRNAs) and 78 proteins were significantly affected at 72 hours post-fertilisation (hpf). Expressions of miR-430 and miR-125 families were also significantly changed. The altered expressions of miR-31 and miR-126 were likely responsible for the loss of vascular integrity. MC-RR significantly reduced the expressions of a number of proteins involved in energy metabolism, cell division, protein synthesis, cytoskeleton maintenance, response to stress and DNA replication. Bioinformatics analysis shows that several aberrantly expressed miRNAs and proteins (involved in various molecular pathways) were predicted to be potential MC-responsive miRNA-target pairs, and that their aberrant expressions should be the possible molecular mechanisms for the various developmental defects caused by MC-RR
Adaptive Prediction of RR interval for online MR parameters changes
No full textCardiac MRI sequences are generally synchronized on the R wave of the ECG and the read out is done in the ventricular iastole. Depending to the heart rate (HR) and so on the RR interval, an optimal trigger delay (TD), an acquisition time (AT) (which is a function of MR parameters) and a trigger window (TW) are defined before scanning. For Black Blood acquisition, IR pulses are currently played directly on the R wave to have an inversion time (TI) of the blood on read out. Unfortunately, physiological changes of the RR timing especially during breath hold make all these fixed timings non optimum. Additionally, optimal TI for complete nulling of wash in blood is not always compatible with HR > 85 bpm. Moreover, if acquisition of systolic phase is desired, these IR pulses have to be place before the current R wave in the preceding heart cycle. We propose a prediction of the next RR duration based on previous RR cycles. The prediction of RR interval will be used to adapt MR timing parameters (TD, TW, TI, AT) during scanning and enable black blood images in the systolic phase
The proteomic study on cellular responses of the testes of zebrafish (Danio rerio) exposed to microcystin-RR
No full textMicrocystin-RR (MC-RR) is a commonly encountered cyanotoxin and receives increasing attention due to the risk of its bioaccumulation in aquatic animals like fish. This study investigated the protein profiles of zebrafish (Danio rerio) testes after intraperitoneal injection (i.p.) with 0.5 LD50 (2000 mu g/kg). MC-RR caused a noticeable damage to testicular ultrastructure, showing widened intercellular junction, distention of mitochondria. The testes showed a rapid response of its defense systems to the oxidative stress caused by MC-RR. This is the first to use a proteomic approach to obtain an overview of the effects of MC-RR on the testes of zebrafish. The proteomic results revealed that toxin exposure remarkably altered the abundance of 24 proteins that were involved in cytoskeleton assembly, oxidative stress, glycolysis metabolism, calcium ion binding and other biological functions. In conclusion, MC-RR damaged the testes and was toxic to the reproductive system of male zebrafish mainly through causing oxidative stress.Microcystin-RR (MC-RR) is a commonly encountered cyanotoxin and receives increasing attention due to the risk of its bioaccumulation in aquatic animals like fish. This study investigated the protein profiles of zebrafish (Danio rerio) testes after intraperitoneal injection (i.p.) with 0.5 LD50 (2000 mu g/kg). MC-RR caused a noticeable damage to testicular ultrastructure, showing widened intercellular junction, distention of mitochondria. The testes showed a rapid response of its defense systems to the oxidative stress caused by MC-RR. This is the first to use a proteomic approach to obtain an overview of the effects of MC-RR on the testes of zebrafish. The proteomic results revealed that toxin exposure remarkably altered the abundance of 24 proteins that were involved in cytoskeleton assembly, oxidative stress, glycolysis metabolism, calcium ion binding and other biological functions. In conclusion, MC-RR damaged the testes and was toxic to the reproductive system of male zebrafish mainly through causing oxidative stress
So Tom has turned a poet, what a dear [first line]
No full textstrophicnasame as Box 192 Item 50Cover is duplicated in 192.050.
Music is duplicated in 192.050.Johns Hopkins University, Levy Sheet Music Collection, Box
192, Item 051Thomas M-rr-s, Author of "How They Act in Baltimore." "Mephistophiles K.G.S.
So Tom has turned a poet, what a dear [first line]
No full textstrophicnasame as Box 192 Item 50Cover is duplicated in 192.050.
Music is duplicated in 192.050.Johns Hopkins University, Levy Sheet Music Collection, Box
192, Item 051Thomas M-rr-s, Author of "How They Act in Baltimore." "Mephistophiles K.G.S.
So Tom has turned a poet, what a dear [first line]
No full textstrophicnaCover is duplicated in 192.051.
Music is duplicated in 192.051.Johns Hopkins University, Levy Sheet Music Collection, Box
192, Item 050Thomas M-rr-s, Author of "How They Act in Baltimore." "Mephistophiles K.G.S.
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